From 4cdd95dcadaa71e46b7682b6ce8dc6bdc8528da2 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 4 May 2026 10:07:43 -0700 Subject: [PATCH] curate 50 synthetic communities --- ...ic_Denitrification_Disturbance_SynCom.yaml | 74 +++++++++++++++ .../Aerobic_Denitrification_QQ_SynCom.yaml | 73 +++++++++++++++ .../Arabidopsis_Coumarin_Root_SynCom.yaml | 53 +++++++++++ .../Arabidopsis_Phyllosphere_SynCom7.yaml | 57 ++++++++++++ ...dyrhizobium_Straw_Humification_SynCom.yaml | 65 +++++++++++++ .../Banana_Fusarium_Biocontrol_SynCom12.yaml | 74 +++++++++++++++ .../CRC_Fusobacterium_Control_SynCom.yaml | 59 ++++++++++++ ...Cellulose_Methane_Quad_Culture_SynCom.yaml | 86 +++++++++++++++++ .../Desert_Tomato_Salt_Stress_SynCom5.yaml | 57 ++++++++++++ .../GLBRC_Exometabolite_Transwell_SynCom.yaml | 55 +++++++++++ .../Garlic_Pseudomonas_SynCom6.yaml | 53 +++++++++++ .../Honeybee_Core20_Defined_Microbiota.yaml | 58 ++++++++++++ kb/communities/Jala_Maize_PGPB_SynCom.yaml | 81 ++++++++++++++++ .../LBNL_Brachypodium_Drought_SynCom15.yaml | 55 +++++++++++ .../LBNL_Human_Gut_Interaction_SynCom.yaml | 56 +++++++++++ .../LBNL_Switchgrass_Soil_SynCom16.yaml | 58 ++++++++++++ ...ze_Benzoxazinoid_Metabolizing_SynComs.yaml | 54 +++++++++++ .../Maize_Drought_Response_SynCom.yaml | 56 +++++++++++ .../Medicago_Nodule_Biofertilizer_SynCom.yaml | 65 +++++++++++++ ...thane_Oxidation_CrVI_Reduction_SynCom.yaml | 73 +++++++++++++++ ...anthus_REE_Tailings_Nitrogen_SynCom10.yaml | 93 +++++++++++++++++++ ...tiomics_Corn_Straw_Degradation_SynCom.yaml | 56 +++++++++++ ...ycle_Bioflocculation_Model_Consortium.yaml | 57 ++++++++++++ .../Peanut_Seed_Bacterial_CS_SynCom.yaml | 57 ++++++++++++ .../Pepper_Growth_Rhizosphere_SynCom.yaml | 55 +++++++++++ .../Pepper_Phytophthora_SynCom5.yaml | 84 +++++++++++++++++ ...netically_Diverse_Denitrifying_SynCom.yaml | 65 +++++++++++++ .../Populus_Salt_Tolerant_SynComs.yaml | 57 ++++++++++++ ...udomonas_Ecoli_CrossFeeding_Coculture.yaml | 64 +++++++++++++ .../Rice_Acid_Soil_Bioinoculant_SynCom.yaml | 54 +++++++++++ .../Rice_P_Uptake_Intercropping_SynCom4.yaml | 84 +++++++++++++++++ ...wanella_Denitrifying_Richness_SynComs.yaml | 55 +++++++++++ .../SkinCom_Synthetic_Skin_Community.yaml | 55 +++++++++++ ...rophyll_Selected_Biofertilizer_SynCom.yaml | 67 +++++++++++++ ...SynComBac10_Chicken_Intestinal_SynCom.yaml | 59 ++++++++++++ ...nthetic_Periphyton_Freshwater_Biofilm.yaml | 74 +++++++++++++++ .../Teosinte_Maize_Biofertilizer_SynCom7.yaml | 84 +++++++++++++++++ ...Tobacco_Chemotactic_Biocontrol_SynCom.yaml | 64 +++++++++++++ kb/communities/Tomato_Oxylipin_SynCom3.yaml | 74 +++++++++++++++ ...henol_Anaerobic_Bioremediation_SynCom.yaml | 76 +++++++++++++++ .../Urine_Nitrification_SynCom.yaml | 91 ++++++++++++++++++ ...termelon_Rhizosphere_Fusarium_SynCom8.yaml | 66 +++++++++++++ ...heat_Straw_Biogas_Pretreatment_SynCom.yaml | 86 +++++++++++++++++ .../hCom2_Complex_Gut_Microbiome.yaml | 58 ++++++++++++ references_cache/PMID_40904019.md | 72 ++++++++++++++ references_cache/pmid_24743269.txt | 42 +++++++++ references_cache/pmid_25461007.txt | 53 +++++++++++ references_cache/pmid_29152587.txt | 48 ++++++++++ references_cache/pmid_29930200.txt | 50 ++++++++++ references_cache/pmid_31152139.txt | 46 +++++++++ references_cache/pmid_31623889.txt | 56 +++++++++++ references_cache/pmid_32762153.txt | 38 ++++++++ references_cache/pmid_32788711.txt | 47 ++++++++++ references_cache/pmid_34745050.txt | 46 +++++++++ references_cache/pmid_35444261.txt | 56 +++++++++++ references_cache/pmid_35869094.txt | 38 ++++++++ references_cache/pmid_35992653.txt | 54 +++++++++++ references_cache/pmid_36070752.txt | 71 ++++++++++++++ references_cache/pmid_36472419.txt | 60 ++++++++++++ references_cache/pmid_36532452.txt | 48 ++++++++++ references_cache/pmid_36847519.txt | 67 +++++++++++++ references_cache/pmid_37154752.txt | 60 ++++++++++++ references_cache/pmid_37207729.txt | 56 +++++++++++ references_cache/pmid_37275168.txt | 60 ++++++++++++ references_cache/pmid_37299063.txt | 40 ++++++++ references_cache/pmid_37549573.txt | 59 ++++++++++++ references_cache/pmid_37774801.txt | 48 ++++++++++ references_cache/pmid_38277828.txt | 55 +++++++++++ references_cache/pmid_38324131.txt | 22 +++++ references_cache/pmid_38520150.txt | 35 +++++++ references_cache/pmid_38748977.txt | 42 +++++++++ references_cache/pmid_38840214.txt | 60 ++++++++++++ references_cache/pmid_39111313.txt | 58 ++++++++++++ references_cache/pmid_39481489.txt | 58 ++++++++++++ references_cache/pmid_39684532.txt | 47 ++++++++++ references_cache/pmid_39858916.txt | 44 +++++++++ references_cache/pmid_40020349.txt | 63 +++++++++++++ references_cache/pmid_40266232.txt | 44 +++++++++ references_cache/pmid_40270813.txt | 58 ++++++++++++ references_cache/pmid_40433987.txt | 41 ++++++++ references_cache/pmid_40508300.txt | 44 +++++++++ references_cache/pmid_40536564.txt | 46 +++++++++ references_cache/pmid_40670700.txt | 56 +++++++++++ references_cache/pmid_40853002.txt | 51 ++++++++++ references_cache/pmid_40862137.txt | 58 ++++++++++++ references_cache/pmid_41264879.txt | 32 +++++++ references_cache/pmid_41932525.txt | 58 ++++++++++++ references_cache/pmid_42007760.txt | 58 ++++++++++++ 88 files changed, 5142 insertions(+) create mode 100644 kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml create mode 100644 kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml create mode 100644 kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml create mode 100644 kb/communities/Arabidopsis_Phyllosphere_SynCom7.yaml create mode 100644 kb/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.yaml create mode 100644 kb/communities/Banana_Fusarium_Biocontrol_SynCom12.yaml create mode 100644 kb/communities/CRC_Fusobacterium_Control_SynCom.yaml create mode 100644 kb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml create mode 100644 kb/communities/Desert_Tomato_Salt_Stress_SynCom5.yaml create mode 100644 kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml create mode 100644 kb/communities/Garlic_Pseudomonas_SynCom6.yaml create mode 100644 kb/communities/Honeybee_Core20_Defined_Microbiota.yaml create mode 100644 kb/communities/Jala_Maize_PGPB_SynCom.yaml create mode 100644 kb/communities/LBNL_Brachypodium_Drought_SynCom15.yaml create mode 100644 kb/communities/LBNL_Human_Gut_Interaction_SynCom.yaml create mode 100644 kb/communities/LBNL_Switchgrass_Soil_SynCom16.yaml create mode 100644 kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml create mode 100644 kb/communities/Maize_Drought_Response_SynCom.yaml create mode 100644 kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml create mode 100644 kb/communities/Methane_Oxidation_CrVI_Reduction_SynCom.yaml create mode 100644 kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml create mode 100644 kb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml create mode 100644 kb/communities/NCycle_Bioflocculation_Model_Consortium.yaml create mode 100644 kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml create mode 100644 kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml create mode 100644 kb/communities/Pepper_Phytophthora_SynCom5.yaml create mode 100644 kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml create mode 100644 kb/communities/Populus_Salt_Tolerant_SynComs.yaml create mode 100644 kb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml create mode 100644 kb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml create mode 100644 kb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml create mode 100644 kb/communities/Shewanella_Denitrifying_Richness_SynComs.yaml create mode 100644 kb/communities/SkinCom_Synthetic_Skin_Community.yaml create mode 100644 kb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml create mode 100644 kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml create mode 100644 kb/communities/Synthetic_Periphyton_Freshwater_Biofilm.yaml create mode 100644 kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml create mode 100644 kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml create mode 100644 kb/communities/Tomato_Oxylipin_SynCom3.yaml create mode 100644 kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml create mode 100644 kb/communities/Urine_Nitrification_SynCom.yaml create mode 100644 kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml create mode 100644 kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml create mode 100644 kb/communities/hCom2_Complex_Gut_Microbiome.yaml create mode 100644 references_cache/PMID_40904019.md create mode 100644 references_cache/pmid_24743269.txt create mode 100644 references_cache/pmid_25461007.txt create mode 100644 references_cache/pmid_29152587.txt create mode 100644 references_cache/pmid_29930200.txt create mode 100644 references_cache/pmid_31152139.txt create mode 100644 references_cache/pmid_31623889.txt create mode 100644 references_cache/pmid_32762153.txt create mode 100644 references_cache/pmid_32788711.txt create mode 100644 references_cache/pmid_34745050.txt create mode 100644 references_cache/pmid_35444261.txt create mode 100644 references_cache/pmid_35869094.txt create mode 100644 references_cache/pmid_35992653.txt create mode 100644 references_cache/pmid_36070752.txt create mode 100644 references_cache/pmid_36472419.txt create mode 100644 references_cache/pmid_36532452.txt create mode 100644 references_cache/pmid_36847519.txt create mode 100644 references_cache/pmid_37154752.txt create mode 100644 references_cache/pmid_37207729.txt create mode 100644 references_cache/pmid_37275168.txt create mode 100644 references_cache/pmid_37299063.txt create mode 100644 references_cache/pmid_37549573.txt create mode 100644 references_cache/pmid_37774801.txt create mode 100644 references_cache/pmid_38277828.txt create mode 100644 references_cache/pmid_38324131.txt create mode 100644 references_cache/pmid_38520150.txt create mode 100644 references_cache/pmid_38748977.txt create mode 100644 references_cache/pmid_38840214.txt create mode 100644 references_cache/pmid_39111313.txt create mode 100644 references_cache/pmid_39481489.txt create mode 100644 references_cache/pmid_39684532.txt create mode 100644 references_cache/pmid_39858916.txt create mode 100644 references_cache/pmid_40020349.txt create mode 100644 references_cache/pmid_40266232.txt create mode 100644 references_cache/pmid_40270813.txt create mode 100644 references_cache/pmid_40433987.txt create mode 100644 references_cache/pmid_40508300.txt create mode 100644 references_cache/pmid_40536564.txt create mode 100644 references_cache/pmid_40670700.txt create mode 100644 references_cache/pmid_40853002.txt create mode 100644 references_cache/pmid_40862137.txt create mode 100644 references_cache/pmid_41264879.txt create mode 100644 references_cache/pmid_41932525.txt create mode 100644 references_cache/pmid_42007760.txt diff --git a/kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml b/kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml new file mode 100644 index 00000000..1a89c10a --- /dev/null +++ b/kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml @@ -0,0 +1,74 @@ +id: CommunityMech:000116 +name: Aerobic Denitrification Disturbance-Stable SynCom +description: A three-member aerobic denitrification SMC that maintains function under dibutyl phthalate + and levofloxacin disturbances through division of labor. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Resolve how synthetic denitrifying communities maintain functional stability under environmental + disturbances. + assembly_strategy: Pseudomonas aeruginosa N2, Acinetobacter baumannii N1, and Aeromonas hydrophila were + assembled as an aerobic denitrification SMC. + perturbation_design: Dibutyl phthalate and levofloxacin disturbance treatments. + measurement_endpoints: + - denitrification efficiency + - interspecific communication + - energy flux + - electron transfer + - EPS production + evidence: + - &id001 + reference: PMID:40020349 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Understanding how synthetic microbial community (SMC) respond to environmental disturbances + is the key to realizing SMC engineering applications. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Aerobic denitrification synthetic microbial community under pollutant disturbances. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas aeruginosa + term: + id: NCBITaxon:287 + label: Pseudomonas aeruginosa + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Acinetobacter baumannii + term: + id: NCBITaxon:470 + label: Acinetobacter baumannii + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Aeromonas hydrophila + term: + id: NCBITaxon:644 + label: Aeromonas hydrophila + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Disturbance-Stable Division of Labor + description: Members redistribute functional dominance and metabolic pathways to maintain denitrification. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Pseudomonas aeruginosa N2, Acinetobacter baumannii N1, and Aeromonas hydrophila were assembled + as an aerobic denitrification SMC. + description: Dibutyl phthalate and levofloxacin disturbance treatments. + evidence: + - *id001 diff --git a/kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml b/kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml new file mode 100644 index 00000000..e0b9dcb4 --- /dev/null +++ b/kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml @@ -0,0 +1,73 @@ +id: CommunityMech:000115 +name: Aerobic Denitrification Quorum-Quenching SynCom +description: A three-member aerobic denitrification SynCom whose quorum-quenching and AHL-mediated interactions + improve nitrate removal. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Improve aerobic denitrification efficiency by engineering member interactions in a synthetic + microbial community. + assembly_strategy: Acinetobacter baumannii N1, Pseudomonas aeruginosa N2, and Aeromonas hydrophila were + assembled as an SMC. + perturbation_design: Single-culture, co-culture, and three-member SMC denitrification systems were compared. + measurement_endpoints: + - nitrate reduction + - nitrite accumulation + - AHL signaling + - electron transfer + evidence: + - &id001 + reference: PMID:38277828 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: a synthetic microbial community (SMC) composed of denitrifiers Acinetobacter baumannii N1 + (AC), Pseudomonas aeruginosa N2 (PA) and Aeromonas hydrophila (AH) were constructed. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Aerobic denitrification synthetic microbial community for nitrate wastewater removal. +taxonomy: +- taxon_term: + preferred_term: Acinetobacter baumannii + term: + id: NCBITaxon:470 + label: Acinetobacter baumannii + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pseudomonas aeruginosa + term: + id: NCBITaxon:287 + label: Pseudomonas aeruginosa + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Aeromonas hydrophila + term: + id: NCBITaxon:644 + label: Aeromonas hydrophila + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: AHL-Mediated Aerobic Denitrification + description: AHL signaling and quorum quenching coordinate electron transfer and nitrate reduction. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Acinetobacter baumannii N1, Pseudomonas aeruginosa N2, and Aeromonas hydrophila were assembled + as an SMC. + description: Single-culture, co-culture, and three-member SMC denitrification systems were compared. + evidence: + - *id001 diff --git a/kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml b/kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml new file mode 100644 index 00000000..0e7757d6 --- /dev/null +++ b/kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml @@ -0,0 +1,53 @@ +id: CommunityMech:000094 +name: Arabidopsis Coumarin Root SynCom +description: A reduced Arabidopsis root-isolate SynCom used to detect rhizosphere community shifts caused + by phytoalexin, flavonoid, and coumarin exudates. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Determine how Arabidopsis specialized metabolites shape root-associated bacterial community + composition. + assembly_strategy: Reduced synthetic community of Arabidopsis thaliana root-isolated bacteria. + perturbation_design: Plant mutants deficient in secreted phytoalexins, flavonoids, and coumarins. + measurement_endpoints: + - community shifts + - rhizosphere colonization + - metabolite-dependent recruitment + evidence: + - &id001 + reference: PMID:31152139 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: We employed a reduced synthetic community (SynCom) of Arabidopsis thaliana root-isolated + bacteria to detect community shifts that occur in the absence of the secreted small-molecule phytoalexins, + flavonoids, and coumarins. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Arabidopsis root SynCom used to test plant specialized metabolite effects on rhizosphere assembly. +taxonomy: +- taxon_term: + preferred_term: Arabidopsis root-isolated bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Coumarin-Dependent Recruitment + description: Plant exuded specialized metabolites structure which bacteria persist in the rhizosphere. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Reduced synthetic community of Arabidopsis thaliana root-isolated bacteria. + description: Plant mutants deficient in secreted phytoalexins, flavonoids, and coumarins. + evidence: + - *id001 diff --git a/kb/communities/Arabidopsis_Phyllosphere_SynCom7.yaml b/kb/communities/Arabidopsis_Phyllosphere_SynCom7.yaml new file mode 100644 index 00000000..673516b9 --- /dev/null +++ b/kb/communities/Arabidopsis_Phyllosphere_SynCom7.yaml @@ -0,0 +1,57 @@ +id: CommunityMech:000093 +name: Arabidopsis Phyllosphere SynCom7 +description: A seven-strain reduced-complexity Arabidopsis phyllosphere SynCom used to test host genetic + effects on microbiota composition. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Identify Arabidopsis host genetic factors that alter phyllosphere community composition and + abundance. + assembly_strategy: Seven bacterial strains representing abundant phyllosphere phyla were inoculated + onto gnotobiotic Arabidopsis mutants. + perturbation_design: Host mutant panel affecting surface structure, cell wall, defense, secondary metabolism, + and pathogen recognition. + measurement_endpoints: + - community composition + - member abundance + - host genotype effects + evidence: + - &id001 + reference: PMID:24743269 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the model plant Arabidopsis thaliana was used in a gnotobiotic system and inoculated with + a reduced complexity synthetic bacterial community composed of seven strains representing the most + abundant phyla in the phyllosphere. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: phyllosphere + term: + id: ENVO:01001442 + label: phyllosphere + notes: Gnotobiotic Arabidopsis phyllosphere inoculated with a seven-strain bacterial community. +taxonomy: +- taxon_term: + preferred_term: Arabidopsis phyllosphere bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Host-Genotype-Structured Assembly + description: Arabidopsis host genotype shifts the abundance and composition of the phyllosphere SynCom. + interaction_type: NICHE_PARTITIONING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Seven bacterial strains representing abundant phyllosphere phyla were inoculated onto gnotobiotic + Arabidopsis mutants. + description: Host mutant panel affecting surface structure, cell wall, defense, secondary metabolism, + and pathogen recognition. + evidence: + - *id001 diff --git a/kb/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.yaml b/kb/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.yaml new file mode 100644 index 00000000..9b8b4423 --- /dev/null +++ b/kb/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.yaml @@ -0,0 +1,65 @@ +id: CommunityMech:000120 +name: Bacillus-Bradyrhizobium Straw Humification SynCom +description: A two-member Bacillus siamensis and Bradyrhizobium japonicum SynCom that promotes maize straw + humification and soil organic carbon. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: LIGNOCELLULOSE +engineering_design: + objective: Accelerate straw humification and improve soil organic carbon through a functionally stable + SynCom. + assembly_strategy: Keystone taxa from dilution microcosms were assembled as Bacillus siamensis B and + Bradyrhizobium japonicum G. + perturbation_design: Cross-feeding assays, enzyme activity assays, and field straw-return experiments. + measurement_endpoints: + - straw humification + - soil organic carbon + - cellulase activity + - xylanase activity + - nitrogenase activity + evidence: + - &id001 + reference: PMID:41264879 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: From these taxa, we constructed a two-membered SynCom (Bacillus siamensis B and Bradyrhizobium + japonicum G). + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: soil + term: + id: ENVO:00001998 + label: soil + notes: Cropland soil receiving maize straw and two-member SynCom inoculation. +taxonomy: +- taxon_term: + preferred_term: Bacillus siamensis + term: + id: NCBITaxon:1178515 + label: Bacillus siamensis + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Bradyrhizobium japonicum + term: + id: NCBITaxon:375 + label: Bradyrhizobium japonicum + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Straw Humification Cross-Feeding + description: Bacillus and Bradyrhizobium cross-feed to promote straw-degrading enzymes and humification. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Keystone taxa from dilution microcosms were assembled as Bacillus siamensis B and Bradyrhizobium + japonicum G. + description: Cross-feeding assays, enzyme activity assays, and field straw-return experiments. + evidence: + - *id001 diff --git a/kb/communities/Banana_Fusarium_Biocontrol_SynCom12.yaml b/kb/communities/Banana_Fusarium_Biocontrol_SynCom12.yaml new file mode 100644 index 00000000..e0a274dd --- /dev/null +++ b/kb/communities/Banana_Fusarium_Biocontrol_SynCom12.yaml @@ -0,0 +1,74 @@ +id: CommunityMech:000097 +name: Banana Fusarium Wilt Biocontrol SynCom1.2 +description: A three-member banana rhizosphere SynCom designed for biological control of Fusarium oxysporum + f. sp. cubense tropical race 4. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Design a compatible reduced SynCom for biological control of Fusarium wilt of banana. + assembly_strategy: SynCom 1.2 combined Pseudomonas chlororaphis subsp. piscium PS5, Bacillus velezensis + BN8.2, and Trichoderma virens T2C1.4. + perturbation_design: Non-simultaneous soil application was used to reduce cross-inhibition among biocontrol + members. + measurement_endpoints: + - disease incidence + - disease severity + - antagonism against Foc TR4 + - biocontrol trait characterization + evidence: + - &id001 + reference: PMID:35992653 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'SynCom 1.2 was then designed with three isolates: Pseudomonas chlororaphis subsp. piscium + PS5, Bacillus velezensis BN8.2, and Trichoderma virens T2C1.4.' + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Banana rhizosphere-derived biological control SynCom against Fusarium wilt. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas chlororaphis + term: + id: NCBITaxon:587753 + label: Pseudomonas chlororaphis + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Bacillus velezensis + term: + id: NCBITaxon:492670 + label: Bacillus velezensis + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Trichoderma virens + term: + id: NCBITaxon:5547 + label: Trichoderma virens + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Coordinated Pathogen Suppression + description: Bacterial and fungal antagonists suppress Fusarium wilt while avoiding detrimental cross-inhibition. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: SynCom 1.2 combined Pseudomonas chlororaphis subsp. piscium PS5, Bacillus velezensis BN8.2, and + Trichoderma virens T2C1.4. + description: Non-simultaneous soil application was used to reduce cross-inhibition among biocontrol + members. + evidence: + - *id001 diff --git a/kb/communities/CRC_Fusobacterium_Control_SynCom.yaml b/kb/communities/CRC_Fusobacterium_Control_SynCom.yaml new file mode 100644 index 00000000..d1a2aa0c --- /dev/null +++ b/kb/communities/CRC_Fusobacterium_Control_SynCom.yaml @@ -0,0 +1,59 @@ +id: CommunityMech:000128 +name: CRC Fusobacterium Control SynCom +description: A bottom-up designed seven-species synthetic microbial community for ecological control of + Fusobacterium nucleatum-associated colorectal cancer models. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Design a controllable commensal SynCom that suppresses Fusobacterium nucleatum and improves + colorectal cancer model outcomes. + assembly_strategy: Human metagenome and metabolomics data were used with metabolic network reconstruction + to design a seven-species low-competition SynCom. + perturbation_design: The SynCom was tested against Fusobacterium nucleatum in vitro and in an AOM-DSS + mouse colorectal cancer model. + measurement_endpoints: + - Fusobacterium nucleatum inhibition + - in vivo colonization + - tryptophan metabolism + - secondary bile acid conversion + - tumor inhibition + evidence: + - &id001 + reference: PMID:40433987 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: A synthetic microbial community (SynCom) is then designed by metabolic network reconstruction, + and its performance is validated using coculture experiments and an AOM-DSS induced mouse CRC model. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: colorectal gut microbiome + term: + id: UBERON:0001155 + label: colon + notes: Designed commensal SynCom validated in coculture and mouse colorectal cancer models. +taxonomy: +- taxon_term: + preferred_term: seven commensal bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Fusobacterium Ecological Suppression + description: The designed SynCom inhibits F. nucleatum growth and promotes decolonization through ecological + and metabolic control. + interaction_type: COMPETITION + evidence: + - *id001 +environmental_factors: +- name: metabolic network reconstruction design + value: A seven-species SynCom with low competitive interrelationships was designed from human metagenome + and metabolomics data. + description: The SynCom was tested against Fusobacterium nucleatum in vitro and in an AOM-DSS mouse + colorectal cancer model. + evidence: + - *id001 diff --git a/kb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml b/kb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml new file mode 100644 index 00000000..4425efc0 --- /dev/null +++ b/kb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml @@ -0,0 +1,86 @@ +id: CommunityMech:000089 +name: Cellulose-to-Methane Quad-Culture SynCom +description: A four-species anaerobic synthetic community coupling cellulose degradation, sulfate reduction, + and methanogenesis. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: METHANOGENESIS +engineering_design: + objective: Resolve higher-order cross-feeding, competition, and synergy during anaerobic conversion + of cellulose to methane and carbon dioxide. + assembly_strategy: Rational functional-guild assembly of cellulolytic, sulfate-reducing, hydrogenotrophic + methanogenic, and acetoclastic methanogenic members. + perturbation_design: Control cultures were compared with sulfate addition using metaproteomics, metabolite + profiling, and stoichiometric modeling. + measurement_endpoints: + - methane production + - cellulose degradation + - sulfate reduction + - cross-feeding fluxes + evidence: + - &id001 + reference: PMID:36847519 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Here, we constructed a quad-culture consisting of a cellulolytic bacterium (Ruminiclostridium + cellulolyticum), a hydrogenotrophic methanogen (Methanospirillum hungatei), an acetoclastic methanogen + (Methanosaeta concilii), and a sulfate-reducing bacterium (Desulfovibrio vulgaris). + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Anaerobic cellulose-degrading laboratory quad-culture with sulfate perturbation. +taxonomy: +- taxon_term: + preferred_term: Ruminiclostridium cellulolyticum + term: + id: NCBITaxon:1521 + label: Clostridium cellulolyticum + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Methanospirillum hungatei + term: + id: NCBITaxon:323259 + label: Methanospirillum hungatei + functional_role: + - SYNTROPHIC_PARTNER + evidence: + - *id001 +- taxon_term: + preferred_term: Methanosaeta concilii + term: + id: NCBITaxon:2224 + label: Methanosaeta concilii + functional_role: + - SYNTROPHIC_PARTNER + evidence: + - *id001 +- taxon_term: + preferred_term: Desulfovibrio vulgaris + term: + id: NCBITaxon:881 + label: Desulfovibrio vulgaris + functional_role: + - SYNTROPHIC_PARTNER + evidence: + - *id001 +ecological_interactions: +- name: Cellulose Cross-Feeding to Methane + description: Cellulose fermentation products are exchanged with methanogens and sulfate reducers, producing + methane and modulating competition. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Rational functional-guild assembly of cellulolytic, sulfate-reducing, hydrogenotrophic methanogenic, + and acetoclastic methanogenic members. + description: Control cultures were compared with sulfate addition using metaproteomics, metabolite profiling, + and stoichiometric modeling. + evidence: + - *id001 diff --git a/kb/communities/Desert_Tomato_Salt_Stress_SynCom5.yaml b/kb/communities/Desert_Tomato_Salt_Stress_SynCom5.yaml new file mode 100644 index 00000000..f88c4e9a --- /dev/null +++ b/kb/communities/Desert_Tomato_Salt_Stress_SynCom5.yaml @@ -0,0 +1,57 @@ +id: CommunityMech:000096 +name: Desert-Derived Tomato Salt Stress SynCom5 +description: A five-member desert-root bacterial SynCom that protects tomato plants from high salt stress + in non-sterile soil. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Engineer a simplified desert microbiome SynCom that confers abiotic salt-stress resilience + to tomato. + assembly_strategy: Five bacterial strains originating from the root of Indigofera argentea were assembled + into a SynCom. + perturbation_design: High salt stress in natural non-sterile soil substrate. + measurement_endpoints: + - tomato salt-stress resilience + - SynCom strain penetrance + - salt-stress gene expression + - ion accumulation + evidence: + - &id001 + reference: PMID:35444261 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Here we show that a SynCom of five bacterial strains, originating from the root of the desert + plant Indigofera argentea, protected tomato plants growing in a non-sterile substrate against a + high salt stress. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Five bacterial strains from desert plant roots applied to tomato in non-sterile substrate. +taxonomy: +- taxon_term: + preferred_term: desert root bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Desert Microbiome Salt Protection + description: Desert root isolates improve tomato salt-stress tolerance in a natural soil microbiome + context. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Five bacterial strains originating from the root of Indigofera argentea were assembled into a + SynCom. + description: High salt stress in natural non-sterile soil substrate. + evidence: + - *id001 diff --git a/kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml b/kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml new file mode 100644 index 00000000..24abd30e --- /dev/null +++ b/kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml @@ -0,0 +1,55 @@ +id: CommunityMech:000091 +name: GLBRC Exometabolite Transwell SynCom System +description: A synthetic community assay system for probing chemically mediated microbial interactions + through shared exometabolites. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOTECHNOLOGY +engineering_design: + objective: Interrogate exometabolite interactions among physically separated microbial populations. + assembly_strategy: Synthetic community members are cultured in a filter plate system that separates + cells while allowing chemical exchange through shared medium. + perturbation_design: Shared-reservoir chemical interactions are assayed using sensitive mass spectrometry. + measurement_endpoints: + - exometabolite profiles + - member growth + - productivity + - gene regulation + evidence: + - &id001 + reference: PMID:29152587 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we describe a straightforward synthetic community system that can be used to interrogate + exometabolite interactions among microorganisms. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Filter plate Transwell synthetic community system for exometabolite-mediated microbial interactions. +taxonomy: +- taxon_term: + preferred_term: exometabolite-interacting bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Exometabolite-Mediated Interaction + description: Community members interact chemically through small molecules, extracellular enzymes, and + antibiotics in shared medium. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Synthetic community members are cultured in a filter plate system that separates cells while + allowing chemical exchange through shared medium. + description: Shared-reservoir chemical interactions are assayed using sensitive mass spectrometry. + evidence: + - *id001 diff --git a/kb/communities/Garlic_Pseudomonas_SynCom6.yaml b/kb/communities/Garlic_Pseudomonas_SynCom6.yaml new file mode 100644 index 00000000..3cb6ecc7 --- /dev/null +++ b/kb/communities/Garlic_Pseudomonas_SynCom6.yaml @@ -0,0 +1,53 @@ +id: CommunityMech:000095 +name: Garlic Rhizosphere Pseudomonas SynCom6 +description: A six-strain Pseudomonas SynCom selected from garlic rhizosphere microbiome data for plant + growth promotion. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Use top-down rhizosphere microbiome analysis to identify and apply plant growth-promoting + Pseudomonas strains. + assembly_strategy: Six Pseudomonas strains isolated from garlic rhizosphere were combined into a SynCom. + perturbation_design: Garlic growth periods, soil types, and agricultural practices informed candidate + selection. + measurement_endpoints: + - plant growth promotion + - PGPR enrichment + - rhizosphere community structure + evidence: + - &id001 + reference: PMID:32762153 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: SynCom with six Pseudomonas strains isolated from the garlic rhizosphere were constructed, + which showed that they have the ability to promote plant growth. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Six Pseudomonas strains isolated from the garlic rhizosphere. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas sp. + term: + id: NCBITaxon:306 + label: Pseudomonas sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Pseudomonas-Mediated Growth Promotion + description: Pseudomonas strains selected from garlic rhizosphere promote host plant growth. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Six Pseudomonas strains isolated from garlic rhizosphere were combined into a SynCom. + description: Garlic growth periods, soil types, and agricultural practices informed candidate selection. + evidence: + - *id001 diff --git a/kb/communities/Honeybee_Core20_Defined_Microbiota.yaml b/kb/communities/Honeybee_Core20_Defined_Microbiota.yaml new file mode 100644 index 00000000..9926419d --- /dev/null +++ b/kb/communities/Honeybee_Core20_Defined_Microbiota.yaml @@ -0,0 +1,58 @@ +id: CommunityMech:000124 +name: Honeybee Core-20 Defined Microbiota +description: A stably transmitted 20-strain synthetic gut microbiota from honeybee intestine that primes + host immunity and reduces Hafnia alvei prevalence. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Test whether a defined honeybee gut community can stably colonize and protect the host against + pathogen prevalence. + assembly_strategy: Twenty strains isolated from honeybee intestine were selected using phylogeny analysis + to create the Core-20 community. + perturbation_design: Honeybees were colonized through passages and challenged in the context of Hafnia + alvei inhibition. + measurement_endpoints: + - immune gene expression + - Hafnia alvei prevalence + - stable gut colonization + - carbohydrate-utilization functions + evidence: + - &id001 + reference: PMID:36532452 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: we assembled a defined microbial community based on phylogeny analysis, the 'Core-20' community, + consisting of 20 strains isolated from the honeybee intestine. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: honeybee intestine + term: + id: UBERON:0000160 + label: intestine + notes: Defined microbial community isolated from the honeybee gut. +taxonomy: +- taxon_term: + preferred_term: honeybee gut bacterial Core-20 members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Immune-Mediated Pathogen Protection + description: The defined Core-20 community primes host immune gene expression and reduces Hafnia alvei + prevalence. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: stably transmitted defined microbiota + value: The Core-20 community was passaged through honeybee guts and evaluated for stable colonization + and immune effects. + description: Honeybees were colonized through passages and challenged in the context of Hafnia alvei + inhibition. + evidence: + - *id001 diff --git a/kb/communities/Jala_Maize_PGPB_SynCom.yaml b/kb/communities/Jala_Maize_PGPB_SynCom.yaml new file mode 100644 index 00000000..1a355c7a --- /dev/null +++ b/kb/communities/Jala_Maize_PGPB_SynCom.yaml @@ -0,0 +1,81 @@ +id: CommunityMech:000099 +name: Jala Maize PGPB SynCom +description: Synthetic microbial communities assembled from plant growth-promoting bacteria of the Jala + maize landrace to improve Zea mays growth and yield. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Promote maize growth and yield using PGPB SynComs from native maize landrace isolates. + assembly_strategy: Multiple SynComs were assembled from PGPB with growth promotion, biocontrol, and + induced systemic resistance traits. + perturbation_design: Gnotobiotic, greenhouse, and open-field maize experiments. + measurement_endpoints: + - root length + - shoot length + - greenhouse growth + - field yield + evidence: + - &id001 + reference: PMID:37275168 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: synthetic microbial communities (SynCom) were assembled with a set of PGPB isolated from + the Jala maize landrace + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Plant growth-promoting bacteria isolated from Jala maize landrace. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas protegens + term: + id: NCBITaxon:380021 + label: Pseudomonas protegens + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pantoea ananatis + term: + id: NCBITaxon:553 + label: Pantoea ananatis + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Klebsiella variicola + term: + id: NCBITaxon:244366 + label: Klebsiella variicola + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Burkholderia sp. + term: + id: NCBITaxon:32008 + label: Burkholderia + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Maize Growth Promotion + description: PGPB members contribute growth-promotion, biocontrol, and induced systemic resistance traits. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Multiple SynComs were assembled from PGPB with growth promotion, biocontrol, and induced systemic + resistance traits. + description: Gnotobiotic, greenhouse, and open-field maize experiments. + evidence: + - *id001 diff --git a/kb/communities/LBNL_Brachypodium_Drought_SynCom15.yaml b/kb/communities/LBNL_Brachypodium_Drought_SynCom15.yaml new file mode 100644 index 00000000..fbbc4d74 --- /dev/null +++ b/kb/communities/LBNL_Brachypodium_Drought_SynCom15.yaml @@ -0,0 +1,55 @@ +id: CommunityMech:000088 +name: LBNL Brachypodium Drought SynCom15 +description: A stable 15-member Brachypodium rhizosphere SynCom constructed with network and cultivation-guided + methods to promote drought resilience. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Construct a stable trait-informed bacterial SynCom that improves Brachypodium performance + under drought stress. + assembly_strategy: Network analysis and cultivation-guided selection of 15 rhizobiome strains spanning + five bacterial phyla. + perturbation_design: Drought stress and in vitro versus in planta stability testing. + measurement_endpoints: + - SynCom stability + - plant recovery from drought + - root-tip colonization + - plant growth-promoting traits + evidence: + - &id001 + reference: PMID:40862137 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Here, we present a systematic approach using a combination of network analysis and cultivation-guided + methods to construct a 15-member SynCom from the rhizobiome of Brachypodium distachyon. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Fifteen-member Brachypodium distachyon rhizobiome SynCom tested under drought stress. +taxonomy: +- taxon_term: + preferred_term: Brachypodium rhizobiome bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Drought Resilience Promotion + description: SynCom members encode and express plant growth-promoting traits linked to drought recovery. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Network analysis and cultivation-guided selection of 15 rhizobiome strains spanning five bacterial + phyla. + description: Drought stress and in vitro versus in planta stability testing. + evidence: + - *id001 diff --git a/kb/communities/LBNL_Human_Gut_Interaction_SynCom.yaml b/kb/communities/LBNL_Human_Gut_Interaction_SynCom.yaml new file mode 100644 index 00000000..286c2cba --- /dev/null +++ b/kb/communities/LBNL_Human_Gut_Interaction_SynCom.yaml @@ -0,0 +1,56 @@ +id: CommunityMech:000122 +name: LBNL Human Gut Interaction SynCom +description: A diverse synthetic human gut microbiome community used with model-guided time-series experiments + to infer pairwise ecological interactions and metabolic drivers of coexistence. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Infer ecological interaction structure and metabolic design principles in a synthetic human + gut microbiome community. + assembly_strategy: Defined human gut species were assembled into lower-order and higher-order consortia + for time-resolved community measurements. + perturbation_design: Initial species proportions and lower-order community combinations were varied + to predict higher-dimensional dynamics. + measurement_endpoints: + - time-resolved abundance dynamics + - ecological interaction network + - extracellular metabolites + - coexistence stability + evidence: + - &id001 + reference: PMID:29930200 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This method was employed to decipher microbial interactions in a diverse human gut microbiome + synthetic community. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: human gut microbiome + term: + id: UBERON:0001007 + label: digestive system + notes: Synthetic human-associated intestinal community studied in vitro. +taxonomy: +- taxon_term: + preferred_term: human gut bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Pairwise Gut Community Interactions + description: Pairwise positive and negative interactions structure multi-species community dynamics. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: model-guided synthetic community design + value: Lower-order assemblages were used to predict higher-dimensional human gut SynCom dynamics. + description: Initial species proportions and lower-order community combinations were varied to predict + higher-dimensional dynamics. + evidence: + - *id001 diff --git a/kb/communities/LBNL_Switchgrass_Soil_SynCom16.yaml b/kb/communities/LBNL_Switchgrass_Soil_SynCom16.yaml new file mode 100644 index 00000000..cbeda077 --- /dev/null +++ b/kb/communities/LBNL_Switchgrass_Soil_SynCom16.yaml @@ -0,0 +1,58 @@ +id: CommunityMech:000087 +name: LBNL Switchgrass Soil SynCom16 +description: A 16-member synthetic soil community from switchgrass-associated soil, optimized for reproducible + in vitro and EcoFAB plant-microbe experiments. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Provide a reproducible, tunable model soil SynCom for plant-soil microbe interaction studies. + assembly_strategy: Bottom-up assembly of 16 culturable soil microorganisms commonly found in plant rhizospheres, + with tuned inoculum ratios and cryopreservation. + perturbation_design: Low-nutrient media, starting composition ratios, cryopreservation, and EcoFAB plant + colonization were evaluated. + measurement_endpoints: + - community alpha diversity + - replicate reproducibility + - cryopreservation recovery + - EcoFAB colonization + evidence: + - &id001 + reference: PMID:36472419 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the + rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, + has been developed and optimized for in vitro experiments. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: soil + term: + id: ENVO:00001998 + label: soil + notes: Sixteen soil microorganisms isolated from soil surrounding switchgrass were optimized as a reproducible + rhizosphere SynCom. +taxonomy: +- taxon_term: + preferred_term: soil bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Reproducible Rhizosphere Assembly + description: Defined members reproducibly assemble under low-nutrient and EcoFAB conditions. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Bottom-up assembly of 16 culturable soil microorganisms commonly found in plant rhizospheres, + with tuned inoculum ratios and cryopreservation. + description: Low-nutrient media, starting composition ratios, cryopreservation, and EcoFAB plant colonization + were evaluated. + evidence: + - *id001 diff --git a/kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml b/kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml new file mode 100644 index 00000000..be0ff630 --- /dev/null +++ b/kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml @@ -0,0 +1,54 @@ +id: CommunityMech:000101 +name: Maize Benzoxazinoid-Metabolizing SynComs +description: Two maize root bacterial SynComs sharing six common strains and differing in a seventh benzoxazinoid-metabolizing + member. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Test how individual benzoxazinoid tolerance and metabolism traits combine at community scale. + assembly_strategy: Two seven-strain synthetic communities of maize root bacteria with shared core strains + and alternate benzoxazinoid-metabolizing capacity. + perturbation_design: In vitro exposure to MBOA, a maize benzoxazinoid breakdown product. + measurement_endpoints: + - benzoxazinoid metabolization + - community composition + - strain interactions + evidence: + - &id001 + reference: PMID:40853002 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we designed two synthetic communities of maize root bacteria that share six common strains + and differ in their ability to metabolize benzoxazinoids based on the seventh strain. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Maize root bacterial synthetic communities exposed to benzoxazinoid exudates. +taxonomy: +- taxon_term: + preferred_term: maize root bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Benzoxazinoid-Mediated Niche Partitioning + description: Community members differ in benzoxazinoid tolerance and metabolism, redirecting metabolite + fate. + interaction_type: NICHE_PARTITIONING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Two seven-strain synthetic communities of maize root bacteria with shared core strains and alternate + benzoxazinoid-metabolizing capacity. + description: In vitro exposure to MBOA, a maize benzoxazinoid breakdown product. + evidence: + - *id001 diff --git a/kb/communities/Maize_Drought_Response_SynCom.yaml b/kb/communities/Maize_Drought_Response_SynCom.yaml new file mode 100644 index 00000000..e58d0cd1 --- /dev/null +++ b/kb/communities/Maize_Drought_Response_SynCom.yaml @@ -0,0 +1,56 @@ +id: CommunityMech:000103 +name: Maize Drought Response SynCom +description: A plant-beneficial bacterial SynCom that modulates physiology and drought response of commercial + maize hybrids. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Quantify how bacterial SynCom inoculation changes maize physiology, resilience, and productivity + under drought. + assembly_strategy: Synthetic community of plant-beneficial bacteria applied to three commercial maize + hybrids. + perturbation_design: Drought stress and rehydration tracked with real-time non-invasive phenotyping. + measurement_endpoints: + - yield loss + - leaf temperature + - turgor loss + - sap flow + - SynCom colonization + evidence: + - &id001 + reference: PMID:34745050 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we used a non-invasive real-time phenotyping platform in a one-to-one (plant-sensors) set + up to investigate the impact of a synthetic community (SynCom) harboring plant-beneficial bacteria + on the physiology and response of three commercial maize hybrids to drought stress (DS). + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Plant-beneficial bacterial SynCom applied to maize under drought stress. +taxonomy: +- taxon_term: + preferred_term: plant-beneficial maize bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Maize Drought Physiology Modulation + description: SynCom inoculation modulates maize water-use physiology and drought recovery. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Synthetic community of plant-beneficial bacteria applied to three commercial maize hybrids. + description: Drought stress and rehydration tracked with real-time non-invasive phenotyping. + evidence: + - *id001 diff --git a/kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml b/kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml new file mode 100644 index 00000000..44022e8e --- /dev/null +++ b/kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml @@ -0,0 +1,65 @@ +id: CommunityMech:000108 +name: Medicago Nodule Biofertilizer SynCom +description: A four-strain nodule synthetic bacterial community with Ensifer and Pseudomonas members for + Medicago sativa biofertilization under abiotic stress. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Promote alfalfa growth and nodulation in degraded estuarine soils under metal, salinity, + drought, and heat stress. + assembly_strategy: Two Ensifer and two Pseudomonas strains isolated from Medicago nodules were assembled + as a SynCom. + perturbation_design: Metal contamination, salinity, drought, and high temperature in estuarine soils. + measurement_endpoints: + - plant growth + - nodulation + - PGP trait maintenance + - abiotic stress tolerance + evidence: + - &id001 + reference: PMID:37299063 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This work was aimed to determine the potential of a nodule synthetic bacterial community + (SynCom), including two Ensifer sp. and two Pseudomonas sp. strains isolated from Medicago spp. + nodules, to promote M. sativa growth and nodulation in degraded estuarine soils under several abiotic + stresses + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: soil + term: + id: ENVO:00001998 + label: soil + notes: Estuarine soils inoculated with Medicago nodule-derived bacteria. +taxonomy: +- taxon_term: + preferred_term: Ensifer sp. + term: + id: NCBITaxon:106591 + label: Ensifer + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pseudomonas sp. + term: + id: NCBITaxon:306 + label: Pseudomonas sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Legume Nodule Biofertilization + description: Nodule endophytes support growth and nodulation under abiotic stress. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Two Ensifer and two Pseudomonas strains isolated from Medicago nodules were assembled as a SynCom. + description: Metal contamination, salinity, drought, and high temperature in estuarine soils. + evidence: + - *id001 diff --git a/kb/communities/Methane_Oxidation_CrVI_Reduction_SynCom.yaml b/kb/communities/Methane_Oxidation_CrVI_Reduction_SynCom.yaml new file mode 100644 index 00000000..53d689b3 --- /dev/null +++ b/kb/communities/Methane_Oxidation_CrVI_Reduction_SynCom.yaml @@ -0,0 +1,73 @@ +id: CommunityMech:000121 +name: Methane Oxidation-Cr(VI) Reduction SynCom +description: A methane-oxidizing synthetic microbial community coupling Cr(VI) reduction to division of + labor and extracellular electron transfer. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Reveal division of labor in methane oxidation coupled to chromium reduction. + assembly_strategy: SynCom was constructed by controlling methane concentration and chromium load, enriching + Methylocystis with Hyphomicrobium and Thiobacillus partners. + perturbation_design: Methane concentration, chromium load, and methane oxidation inhibition. + measurement_endpoints: + - Cr(VI) removal load + - methane oxidation + - extracellular electron transfer + - multi-omics protein expression + evidence: + - &id001 + reference: PMID:41932525 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: In this study, a synthetic microbial community (SynCom) was constructed by controlling methane + concentration and chromium load. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Hypoxic methane-fed synthetic microbial community for chromium reduction. +taxonomy: +- taxon_term: + preferred_term: Methylocystis sp. + term: + id: NCBITaxon:133 + label: Methylocystis + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Hyphomicrobium sp. + term: + id: NCBITaxon:82 + label: Hyphomicrobium + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Thiobacillus sp. + term: + id: NCBITaxon:919 + label: Thiobacillus + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Methane-Driven Chromium Reduction + description: Methanotrophs and partner genera couple methane oxidation with Cr(VI) reduction through + extracellular electron transfer. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: SynCom was constructed by controlling methane concentration and chromium load, enriching Methylocystis + with Hyphomicrobium and Thiobacillus partners. + description: Methane concentration, chromium load, and methane oxidation inhibition. + evidence: + - *id001 diff --git a/kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml b/kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml new file mode 100644 index 00000000..16a25554 --- /dev/null +++ b/kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml @@ -0,0 +1,93 @@ +id: CommunityMech:000111 +name: Miscanthus REE Tailings Nitrogen SynCom10 +description: A ten-strain Miscanthus root-derived SynCom with nitrification and denitrification capabilities + for ammonia nitrogen removal in rare earth mine tailings. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Convert pollutant ammonia nitrogen into plant nutrients and enhance phytoremediation in REE + mine tailings. + assembly_strategy: Ten bacterial strains from Miscanthus floridulus roots representing Burkholderia, + Paraburkholderia, Curtobacterium, Leifsonia, and Sinomonas. + perturbation_design: Live versus dead SynCom inoculation, with and without Miscanthus plants in tailing + soil. + measurement_endpoints: + - ammonia nitrogen reduction + - shoot biomass + - root biomass + - nitrogen-cycle strain enrichment + evidence: + - &id001 + reference: PMID:39481489 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This SynCom, consisting of 10 bacterial strains, included species of the genera Burkholderia + (5) Paraburkholderia (1), Curtobacterium (1), Leifsonia (1) and Sinomonas (2). + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: contaminated soil + term: + id: ENVO:00002874 + label: contaminated soil + notes: Ionic rare earth mine tailing soil with high ammonia nitrogen. +taxonomy: +- taxon_term: + preferred_term: Burkholderia sp. + term: + id: NCBITaxon:32008 + label: Burkholderia + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Paraburkholderia sp. + term: + id: NCBITaxon:1822464 + label: Paraburkholderia + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Curtobacterium sp. + term: + id: NCBITaxon:2034 + label: Curtobacterium + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Leifsonia sp. + term: + id: NCBITaxon:2025 + label: Leifsonia + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Sinomonas sp. + term: + id: NCBITaxon:37927 + label: Sinomonas + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Nitrogen Transformation in REE Tailings + description: Root-derived bacteria couple nitrification, denitrification, and plant growth promotion + to remove ammonia nitrogen. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Ten bacterial strains from Miscanthus floridulus roots representing Burkholderia, Paraburkholderia, + Curtobacterium, Leifsonia, and Sinomonas. + description: Live versus dead SynCom inoculation, with and without Miscanthus plants in tailing soil. + evidence: + - *id001 diff --git a/kb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml b/kb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml new file mode 100644 index 00000000..6146201f --- /dev/null +++ b/kb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml @@ -0,0 +1,56 @@ +id: CommunityMech:000119 +name: Multiomics Corn Straw Degradation SynCom +description: A core synthetic microbial community designed by multiomics linkage technology to degrade + corn straw lignocellulose. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: LIGNOCELLULOSE +engineering_design: + objective: Construct a functionally targeted SynCom for efficient lignocellulose degradation. + assembly_strategy: Species analysis and functional predictions across ecosystems were coupled to construct + a core synthetic microbial community. + perturbation_design: Solid-state fermentation optimization for inoculum level, nitrogen source ratio, + and fermentation time. + measurement_endpoints: + - cellulose degradation + - hemicellulose degradation + - lignin degradation + - proteomic enzyme profiles + evidence: + - &id001 + reference: PMID:37774801 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The synthetic microbial community was employed to degrade corn straw via solid-state fermentation. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Solid-state corn straw fermentation with an eight-strain lignocellulose-degrading SynCom. +taxonomy: +- taxon_term: + preferred_term: lignocellulose-degrading bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +ecological_interactions: +- name: Corn Straw Lignocellulose Degradation + description: A multi-strain community partitions enzymatic roles for cellulose, hemicellulose, and lignin + conversion. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Species analysis and functional predictions across ecosystems were coupled to construct a core + synthetic microbial community. + description: Solid-state fermentation optimization for inoculum level, nitrogen source ratio, and fermentation + time. + evidence: + - *id001 diff --git a/kb/communities/NCycle_Bioflocculation_Model_Consortium.yaml b/kb/communities/NCycle_Bioflocculation_Model_Consortium.yaml new file mode 100644 index 00000000..7d72eafe --- /dev/null +++ b/kb/communities/NCycle_Bioflocculation_Model_Consortium.yaml @@ -0,0 +1,57 @@ +id: CommunityMech:000126 +name: N-Cycle Bioflocculation Model Consortium +description: A reduced-complexity N-cycle model consortium of nitrifiers and denitrifiers used to study + bioflocculation mechanisms in biological wastewater treatment. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOTECHNOLOGY +engineering_design: + objective: Build a reduced-complexity living model of activated sludge flocculation. + assembly_strategy: Nitrifying bacteria were entrapped to form microcolonies and then released with denitrifier + flocs to form macroclusters. + perturbation_design: Oxic/anoxic sequencing batch reactor cycles and alginate entrapment were used to + control aggregation. + measurement_endpoints: + - microcolony formation + - macrocluster formation + - bioflocculation + - FISH aggregation readouts + evidence: + - &id001 + reference: PMID:40536564 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: We show that it is feasible to exploit a model (N-cycle) consortium with reduced complexity + to fundamentally study bioflocculation. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: activated sludge floc model + term: + id: ENVO:00002046 + label: sludge + notes: Model consortium designed to emulate aggregation in biological wastewater treatment. +taxonomy: +- taxon_term: + preferred_term: N-cycle bacterial consortium members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Nitrifier-Denitrifier Aggregate Formation + description: Nitrifier microcolonies and denitrifier flocs formed larger aggregate structures under + reactor cycling. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: oxic/anoxic sequencing batch reactor cycling + value: Oxic/anoxic cycles and alginate entrapment were used to produce nitrifier microcolonies and mixed + aggregates. + description: Oxic/anoxic sequencing batch reactor cycles and alginate entrapment were used to control + aggregation. + evidence: + - *id001 diff --git a/kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml b/kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml new file mode 100644 index 00000000..a2f07ea8 --- /dev/null +++ b/kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml @@ -0,0 +1,57 @@ +id: CommunityMech:000102 +name: Peanut Seed Bacterial CS SynCom +description: A combined peanut seed-borne bacterial synthetic community that suppresses Aspergillus flavus + and Fusarium oxysporum while promoting seedling growth. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Construct conserved, growth-promoting, and combined peanut seed bacterial SynComs for pathogen + resistance. + assembly_strategy: Synthetic communities were derived from 16S profiling, strain isolation, and plant + growth promotion indicators. + perturbation_design: Peanut seed and seedling pathogen challenges with Aspergillus flavus and Fusarium + oxysporum. + measurement_endpoints: + - root rot resistance + - aflatoxin suppression + - defense enzyme activity + - seedling growth + evidence: + - &id001 + reference: PMID:38520150 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Potentially conserved microbial synthetic communities (C), growth-promoting synthetic communities + (S), and combined synthetic communities (CS) of peanut seeds were constructed after 16S rRNA Illumina + sequencing, strain isolation, and measurement of plant growth promotion indicators. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Seed-borne peanut bacterial SynComs tested against seed and root fungal pathogens. +taxonomy: +- taxon_term: + preferred_term: peanut seed bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Seed-Borne Fungal Suppression + description: Seed-borne bacterial consortia suppress fungal invasion and stimulate host defense. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Synthetic communities were derived from 16S profiling, strain isolation, and plant growth promotion + indicators. + description: Peanut seed and seedling pathogen challenges with Aspergillus flavus and Fusarium oxysporum. + evidence: + - *id001 diff --git a/kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml b/kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml new file mode 100644 index 00000000..cc740a98 --- /dev/null +++ b/kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml @@ -0,0 +1,55 @@ +id: CommunityMech:000104 +name: Pepper Growth Rhizosphere SynCom +description: A pepper seedling SynCom treatment that enhances growth and root morphology by modulating + rhizosphere microbial communities. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Determine how SynCom inoculation at seedling stage enhances pepper growth and rhizosphere + microbiome structure. + assembly_strategy: Synthetic microbial community applied during pepper seedling establishment. + perturbation_design: SynCom inoculated versus uninoculated pepper seedlings. + measurement_endpoints: + - shoot height + - root vigor + - root length + - rhizosphere microbial diversity + - key taxa abundance + evidence: + - &id001 + reference: PMID:39858916 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper + growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Pepper seedling rhizosphere SynCom inoculation system. +taxonomy: +- taxon_term: + preferred_term: pepper rhizosphere SynCom bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Pepper Rhizosphere Growth Promotion + description: SynCom inoculation enriches growth-associated rhizosphere taxa and improves pepper root + traits. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Synthetic microbial community applied during pepper seedling establishment. + description: SynCom inoculated versus uninoculated pepper seedlings. + evidence: + - *id001 diff --git a/kb/communities/Pepper_Phytophthora_SynCom5.yaml b/kb/communities/Pepper_Phytophthora_SynCom5.yaml new file mode 100644 index 00000000..2505eb12 --- /dev/null +++ b/kb/communities/Pepper_Phytophthora_SynCom5.yaml @@ -0,0 +1,84 @@ +id: CommunityMech:000105 +name: Pepper Phytophthora-Resistance SynCom5 +description: A five-isolate pepper rhizosphere SynCom that reduces Phytophthora capsici disease severity + and enhances pepper growth. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Evaluate a five-member bacterial SynCom for improving pepper resilience against Phytophthora + capsici. + assembly_strategy: Bacillus, Flavobacterium, Cytobacillus, Streptomyces, and Pseudomonas isolates from + healthy pepper rhizosphere. + perturbation_design: Pepper plants challenged with P. capsici after SynCom application. + measurement_endpoints: + - disease severity + - plant growth + - phosphate solubilization + - IAA production + - siderophore synthesis + evidence: + - &id001 + reference: PMID:40508300 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: We then applied this 5-isolate synthetic microbial community (SynCom) to Capsicum annuum + to evaluate its efficacy in improving pepper resilience against P. capsici. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Five-isolate pepper rhizosphere SynCom tested against Phytophthora capsici. +taxonomy: +- taxon_term: + preferred_term: Bacillus sp. + term: + id: NCBITaxon:1386 + label: Bacillus + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Flavobacterium sp. + term: + id: NCBITaxon:237 + label: Flavobacterium + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Streptomyces sp. + term: + id: NCBITaxon:1931 + label: Streptomyces sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pseudomonas sp. + term: + id: NCBITaxon:306 + label: Pseudomonas sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Phytophthora Suppression + description: Rhizosphere isolates combine antagonism and plant growth-promoting traits to suppress pathogen + damage. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Bacillus, Flavobacterium, Cytobacillus, Streptomyces, and Pseudomonas isolates from healthy pepper + rhizosphere. + description: Pepper plants challenged with P. capsici after SynCom application. + evidence: + - *id001 diff --git a/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml b/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml new file mode 100644 index 00000000..45656a32 --- /dev/null +++ b/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml @@ -0,0 +1,65 @@ +id: CommunityMech:000113 +name: Phylogenetically Diverse Denitrifying SynCom +description: Closely related and distantly related synthetic denitrifying communities used to test how + phylogenetic diversity affects denitrification and stability. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Determine whether phylogenetic diversity improves denitrification function and temporal stability. + assembly_strategy: Closely related communities used Shewanella strains; distantly related communities + used constituents from different genera. + perturbation_design: Experimental evolution for 200 generations. + measurement_endpoints: + - denitrification rate + - productivity + - temporal stability + - complementarity + evidence: + - &id001 + reference: PMID:37207729 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'we selected denitrifiers based on their phylogenetic distance to construct two groups of + synthetic denitrifying communities: one closely related (CR) group with all strains from the genus + Shewanella and the other distantly related (DR) group with all constituents from different genera.' + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Synthetic denitrifying communities experimentally evolved under laboratory conditions. +taxonomy: +- taxon_term: + preferred_term: Shewanella sp. + term: + id: NCBITaxon:22 + label: Shewanella + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Paracoccus denitrificans + term: + id: NCBITaxon:266 + label: Paracoccus denitrificans + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Phylogenetic Complementarity in Denitrification + description: Distantly related denitrifiers improve function and stability through complementarity and + asynchronous fluctuations. + interaction_type: NICHE_PARTITIONING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Closely related communities used Shewanella strains; distantly related communities used constituents + from different genera. + description: Experimental evolution for 200 generations. + evidence: + - *id001 diff --git a/kb/communities/Populus_Salt_Tolerant_SynComs.yaml b/kb/communities/Populus_Salt_Tolerant_SynComs.yaml new file mode 100644 index 00000000..060a7a6c --- /dev/null +++ b/kb/communities/Populus_Salt_Tolerant_SynComs.yaml @@ -0,0 +1,57 @@ +id: CommunityMech:000090 +name: Populus Salt-Tolerant Rhizosphere SynComs +description: Function-driven Populus rhizosphere SynComs selected from high-salt soil to improve salt + resistance in hybrid poplar. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Tailor simplified salt-tolerant SynComs that confer salt stress resistance to Populus. + assembly_strategy: Isolate-select-construct workflow from 512 high-salt rhizosphere isolates, with nine + growth-promoting salt-tolerant strains selected. + perturbation_design: High-salinity plant stress assays comparing multiple SynCom formulations. + measurement_endpoints: + - salt-stress growth + - oxidative stress markers + - osmolyte adjustment + - ion balance + evidence: + - &id001 + reference: PMID:40904019 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This study aimed to establish a framework (isolate-select-construct) for tailoring simplified + salt-tolerant synthetic microbial communities (SynComs) and explore how they confer salt stress + resistance to the plant. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Synthetic communities selected from high-salt Populus euphratica rhizosphere soil and tested + on hybrid poplar. +taxonomy: +- taxon_term: + preferred_term: Populus salt-tolerant rhizosphere bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Salt Stress Protection + description: Selected rhizosphere bacteria improve plant salt tolerance through oxidative stress, osmolyte, + and ion-balance mechanisms. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Isolate-select-construct workflow from 512 high-salt rhizosphere isolates, with nine growth-promoting + salt-tolerant strains selected. + description: High-salinity plant stress assays comparing multiple SynCom formulations. + evidence: + - *id001 diff --git a/kb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml b/kb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml new file mode 100644 index 00000000..2bac3beb --- /dev/null +++ b/kb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml @@ -0,0 +1,64 @@ +id: CommunityMech:000092 +name: Rhodopseudomonas-E. coli Cross-Feeding Coculture +description: A reciprocal cross-feeding coculture pairing N2-fixing Rhodopseudomonas palustris with fermentative + Escherichia coli. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOTECHNOLOGY +engineering_design: + objective: Test whether nutrient uptake adaptation can drive emergence of reciprocal cross-feeding. + assembly_strategy: Two-member coculture based on nitrogen transfer from R. palustris and carbon-rich + fermentation product transfer from E. coli. + perturbation_design: Wild-type and engineered cross-feeding contexts were compared during coculture + evolution. + measurement_endpoints: + - ammonium uptake + - fermentation product exchange + - recipient adaptation + - coculture growth + evidence: + - &id001 + reference: PMID:32788711 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Previously we engineered a cross-feeding coculture between N2-fixing Rhodopseudomonas palustris + and fermentative Escherichia coli. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Engineered and evolved two-member cross-feeding coculture. +taxonomy: +- taxon_term: + preferred_term: Rhodopseudomonas palustris + term: + id: NCBITaxon:1076 + label: Rhodopseudomonas palustris + functional_role: + - PRIMARY_PRODUCER + evidence: + - *id001 +- taxon_term: + preferred_term: Escherichia coli + term: + id: NCBITaxon:562 + label: Escherichia coli + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Reciprocal Carbon-Nitrogen Cross-Feeding + description: R. palustris supplies ammonium while E. coli supplies fermentation products. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Two-member coculture based on nitrogen transfer from R. palustris and carbon-rich fermentation + product transfer from E. coli. + description: Wild-type and engineered cross-feeding contexts were compared during coculture evolution. + evidence: + - *id001 diff --git a/kb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml b/kb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml new file mode 100644 index 00000000..7c4a1b74 --- /dev/null +++ b/kb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml @@ -0,0 +1,54 @@ +id: CommunityMech:000109 +name: Rice Acid Soil Bioinoculant SynCom +description: A customized rhizosphere-competent bacterial SynCom used as a bioinoculant to improve rice + production in acid soils. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Overcome acid soil and aluminum toxicity constraints in rice using selected rhizosphere-competent + bacteria. + assembly_strategy: Carefully selected rhizosphere-competent bacterial strains composed the rice bioinoculant + SynCom. + perturbation_design: Acid soil and aluminum toxicity stress. + measurement_endpoints: + - rice growth + - rice yield + - soil acidity resistance + - aluminum toxicity resistance + evidence: + - &id001 + reference: PMID:38324131 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: A customised synthetic microbial community (SynCom) composed of carefully selected rhizosphere-competent + bacterial strains improved rice growth, yield and resistance to soil acidity and Al toxicity. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: contaminated soil + term: + id: ENVO:00002874 + label: contaminated soil + notes: Acid soil with aluminum toxicity constraints for rice production. +taxonomy: +- taxon_term: + preferred_term: rice rhizosphere-competent bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Rice Acid-Soil Stress Mitigation + description: Rhizosphere competent bacteria improve rice growth and yield under acid soil stress. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Carefully selected rhizosphere-competent bacterial strains composed the rice bioinoculant SynCom. + description: Acid soil and aluminum toxicity stress. + evidence: + - *id001 diff --git a/kb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml b/kb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml new file mode 100644 index 00000000..bbf260f2 --- /dev/null +++ b/kb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml @@ -0,0 +1,84 @@ +id: CommunityMech:000110 +name: Rice Phosphorus Uptake Intercropping SynCom4 +description: A four-strain rice rhizosphere SynCom from intercropping systems that enhances biomass and + phosphorus uptake. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Harness intercropping-associated bacteria to improve rice phosphorus acquisition. + assembly_strategy: Variovorax paradoxus, Novosphingobium subterraneum, Hydrogenophaga pseudoflava, and + Acidovorax sp. were assembled into a bacterial SynCom. + perturbation_design: Pot experiments testing rice growth and phosphorus uptake after SynCom inoculation. + measurement_endpoints: + - biomass + - phosphorus uptake + - soil available phosphorus + - root morphology + - phosphate transporter expression + evidence: + - &id001 + reference: PMID:39684532 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: A bacterial synthetic community (SynCom) composed of four bacterial strains (Variovorax paradoxus, + Novosphingobium subterraneum, Hydrogenophaga pseudoflava, Acidovorax sp.) significantly enhanced + the biomass and P uptake of potted rice plants. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Rice rhizosphere SynCom isolated from rice-soybean intercropping systems. +taxonomy: +- taxon_term: + preferred_term: Variovorax paradoxus + term: + id: NCBITaxon:34073 + label: Variovorax paradoxus + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Novosphingobium subterraneum + term: + id: NCBITaxon:48935 + label: Novosphingobium subterraneum + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Hydrogenophaga pseudoflava + term: + id: NCBITaxon:47421 + label: Hydrogenophaga pseudoflava + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Acidovorax sp. + term: + id: NCBITaxon:12916 + label: Acidovorax + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Phosphorus Acquisition Promotion + description: SynCom members increase soil available phosphorus and support root-to-shoot phosphorus + transport. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Variovorax paradoxus, Novosphingobium subterraneum, Hydrogenophaga pseudoflava, and Acidovorax + sp. were assembled into a bacterial SynCom. + description: Pot experiments testing rice growth and phosphorus uptake after SynCom inoculation. + evidence: + - *id001 diff --git a/kb/communities/Shewanella_Denitrifying_Richness_SynComs.yaml b/kb/communities/Shewanella_Denitrifying_Richness_SynComs.yaml new file mode 100644 index 00000000..b1c30137 --- /dev/null +++ b/kb/communities/Shewanella_Denitrifying_Richness_SynComs.yaml @@ -0,0 +1,55 @@ +id: CommunityMech:000114 +name: Shewanella Denitrifying Richness SynComs +description: A panel of synthetic denitrifying communities assembled from 12 Shewanella denitrifiers with + richness spanning one to twelve species. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Measure biodiversity-ecosystem functioning relationships during microbial experimental evolution. + assembly_strategy: Random selection from a 12-member Shewanella denitrifier candidate pool to create + richness-gradient communities. + perturbation_design: Approximately 180 days of experimental evolution with 60 transfers. + measurement_endpoints: + - productivity + - denitrification rate + - community richness + - evolutionary change + evidence: + - &id001 + reference: PMID:37154752 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) + with a richness gradient spanning 1 to 12 species + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Synthetic denitrifying communities with Shewanella richness gradient. +taxonomy: +- taxon_term: + preferred_term: Shewanella denitrifiers + term: + id: NCBITaxon:22 + label: Shewanella + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Richness-Dependent Denitrification + description: Shewanella richness gradients produce dynamic biodiversity-function relationships during + evolution. + interaction_type: NICHE_PARTITIONING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Random selection from a 12-member Shewanella denitrifier candidate pool to create richness-gradient + communities. + description: Approximately 180 days of experimental evolution with 60 transfers. + evidence: + - *id001 diff --git a/kb/communities/SkinCom_Synthetic_Skin_Community.yaml b/kb/communities/SkinCom_Synthetic_Skin_Community.yaml new file mode 100644 index 00000000..f5809d41 --- /dev/null +++ b/kb/communities/SkinCom_Synthetic_Skin_Community.yaml @@ -0,0 +1,55 @@ +id: CommunityMech:000125 +name: SkinCom Synthetic Skin Community +description: A standardized synthetic skin microbial community for reproducible in vitro and in vivo studies + of skin-associated microbe-metabolite interactions. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Create a reproducible microbial component for experimental human skin microbiome models. + assembly_strategy: Aerobic and anaerobic skin-associated bacteria were assembled into the SkinCom standardized + community. + perturbation_design: SkinCom was tested with common cosmetic chemicals in vitro and on dorsal skin of + mice in vivo. + measurement_endpoints: + - community reproducibility + - DNA and RNA recovery + - chemical response agreement + - microbe-metabolite interactions + evidence: + - &id001 + reference: PMID:39111313 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: SkinCom represents a valuable, standardized tool for investigating microbe-metabolite interactions + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: skin-associated microbial habitat + term: + id: UBERON:0002097 + label: skin of body + notes: Synthetic community applied to skin and skin-like experimental systems. +taxonomy: +- taxon_term: + preferred_term: skin bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Skin Microbe-Metabolite Response + description: The standardized SkinCom enables reproducible assays of microbial responses to skin-relevant + chemicals. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: standardized skin model conditions + value: SkinCom was evaluated in vitro and after application to dorsal skin of mice. + description: SkinCom was tested with common cosmetic chemicals in vitro and on dorsal skin of mice in + vivo. + evidence: + - *id001 diff --git a/kb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml b/kb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml new file mode 100644 index 00000000..c4a061b2 --- /dev/null +++ b/kb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml @@ -0,0 +1,67 @@ +id: CommunityMech:000129 +name: Soybean Chlorophyll-Selected Biofertilizer SynCom +description: A plant-guided soybean rhizosphere SynCom selected through iterative chlorophyll-based microbiome + engineering to improve nodulation and biomass in soil. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Develop a multi-member soybean biofertilizer SynCom using host-mediated microbiome engineering. + assembly_strategy: A starting consortium of Bradyrhizobium spp. and non-rhizobial soil isolates was + recurrently selected using leaf chlorophyll content. + perturbation_design: Eight consecutive gnotobiotic selection rounds were followed by evaluation in non-sterile + soil. + measurement_endpoints: + - leaf chlorophyll content + - rhizosphere community composition + - nodule number + - plant biomass + - nitrogen transformation potential + evidence: + - &id001 + reference: PMID:42007760 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: a synthetic microbial community (SynCom) was developed through a host-mediated microbiome + engineering approach guided by leaf chlorophyll content as a rapid, non-destructive plant trait. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: soybean rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Soybean-associated rhizosphere community selected under gnotobiotic and non-sterile soil conditions. +taxonomy: +- taxon_term: + preferred_term: soybean rhizosphere bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Bradyrhizobium + term: + id: NCBITaxon:374 + label: Bradyrhizobium + functional_role: + - PRIMARY_PRODUCER + evidence: + - *id001 +ecological_interactions: +- name: Plant-Guided Beneficial Rhizosphere Assembly + description: Recurrent host-mediated selection favored nodulating Bradyrhizobium and associated beneficial + rhizosphere taxa. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: chlorophyll-guided recurrent selection + value: Rhizosphere communities from superior soybean performers were pooled and propagated across selection + rounds. + description: Eight consecutive gnotobiotic selection rounds were followed by evaluation in non-sterile + soil. + evidence: + - *id001 diff --git a/kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml b/kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml new file mode 100644 index 00000000..dc939959 --- /dev/null +++ b/kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml @@ -0,0 +1,59 @@ +id: CommunityMech:000127 +name: SynComBac10 Chicken Intestinal SynCom +description: A 10-member synthetic chicken intestinal community that promotes gut homeostasis and anti-Salmonella + immunity through segmented filamentous bacteria establishment. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Manipulate chicken gut microbiota development and anti-infection immunity with a designed + microbial consortium. + assembly_strategy: Ten intestinal bacterial members were selected to recapitulate adult chicken intestinal + phylogenetic diversity and functional capability. + perturbation_design: Early-life exposure and Salmonella infection challenge were used to test gut maturation + and immune resistance. + measurement_endpoints: + - growth performance + - epithelial barrier maturation + - segmented filamentous bacteria colonization + - Th17 immune response + - Salmonella resistance + evidence: + - &id001 + reference: PMID:40266232 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: we constructed a 10-member synthetic microbial community (SynComBac10) that recapitulated + the phylogenetic diversity and functional capability of adult chicken intestinal microbiota. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: chicken intestine + term: + id: UBERON:0000160 + label: intestine + notes: Designed chicken intestinal microbiota used in early-life exposure experiments. +taxonomy: +- taxon_term: + preferred_term: chicken intestinal SynComBac10 members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: SynCom-Stimulated SFB Cross-Feeding + description: SynComBac10-derived metabolites likely facilitate early establishment of segmented filamentous + bacteria. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: early-life gut SynCom exposure + value: Chickens were exposed early in life to SynComBac10 and evaluated for gut maturation and Salmonella + resistance. + description: Early-life exposure and Salmonella infection challenge were used to test gut maturation + and immune resistance. + evidence: + - *id001 diff --git a/kb/communities/Synthetic_Periphyton_Freshwater_Biofilm.yaml b/kb/communities/Synthetic_Periphyton_Freshwater_Biofilm.yaml new file mode 100644 index 00000000..1a51b3fb --- /dev/null +++ b/kb/communities/Synthetic_Periphyton_Freshwater_Biofilm.yaml @@ -0,0 +1,74 @@ +id: CommunityMech:000130 +name: Synthetic Periphyton Freshwater Biofilm +description: A 26-member phototrophic synthetic periphyton biofilm used as a reproducible freshwater model + system for species dynamics and stressor response. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: PHYTOPLANKTON +engineering_design: + objective: Create a controlled synthetic periphyton model for manipulating freshwater phototrophic biofilm + species dynamics. + assembly_strategy: Twenty-six phototrophic species including diatoms, green algae, and cyanobacteria + were inoculated in successional sequence onto glass slides. + perturbation_design: Temperature increase and herbicide stressors were applied singly and in combination. + measurement_endpoints: + - species-level abundance dynamics + - community reproducibility + - biofilm function + - 3D spatial structure + - stressor response + evidence: + - &id001 + reference: PMID:35869094 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we rationally developed a workflow to construct a synthetic community by co-culturing 26 + phototrophic species (i.e., diatoms, green algae, and cyanobacteria) + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: freshwater periphyton biofilm + term: + id: ENVO:01001242 + label: freshwater environment + notes: Synthetic periphytic biofilm grown on glass slides under controlled conditions. +taxonomy: +- taxon_term: + preferred_term: diatoms + term: + id: NCBITaxon:2836 + label: Bacillariophyta + functional_role: + - PRIMARY_PRODUCER + evidence: + - *id001 +- taxon_term: + preferred_term: green algae + term: + id: NCBITaxon:3041 + label: Chlorophyta + functional_role: + - PRIMARY_PRODUCER + evidence: + - *id001 +- taxon_term: + preferred_term: cyanobacteria + term: + id: NCBITaxon:1117 + label: Cyanobacteria + functional_role: + - PRIMARY_PRODUCER + evidence: + - *id001 +ecological_interactions: +- name: Successional Periphyton Biofilm Assembly + description: Phototrophic species assemble into a diverse, stable, reproducible biofilm with trackable + species dynamics. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: successional inoculation on glass slides + value: Phototrophic species were inoculated sequentially to construct a synthetic periphytic biofilm. + description: Temperature increase and herbicide stressors were applied singly and in combination. + evidence: + - *id001 diff --git a/kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml b/kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml new file mode 100644 index 00000000..8d0cfe57 --- /dev/null +++ b/kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml @@ -0,0 +1,84 @@ +id: CommunityMech:000100 +name: Teosinte-Derived Maize Biofertilizer SynCom7 +description: A seven-strain teosinte-derived bacterial SynCom tested as a maize biofertilizer under conventional + and precision fertilization strategies. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Modulate maize microbiome composition, growth, yield, and soil functionality using teosinte-associated + bacteria. + assembly_strategy: Seven bacterial strains from teosinte-associated microbes were formulated as a SynCom. + perturbation_design: Conventional fertilization, drone-assisted precision delivery, and SynCom biofertilization + were compared. + measurement_endpoints: + - maize plant performance + - soil bacterial community shifts + - soil fungal community shifts + - beneficial taxa abundance + evidence: + - &id001 + reference: PMID:40270813 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'This SynCom consisted of seven bacterial strains: Serratia nematodiphila EDR2, Klebsiella + variicola EChLG19, Bacillus thuringiensis EML22, Pantoea agglomerans EMH25, Bacillus thuringiensis + EBG39, Serratia marcescens EPLG52, and Bacillus tropicus EPP72.' + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Seven teosinte-associated bacteria applied as maize biofertilizer. +taxonomy: +- taxon_term: + preferred_term: Serratia sp. + term: + id: NCBITaxon:613 + label: Serratia + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Klebsiella variicola + term: + id: NCBITaxon:244366 + label: Klebsiella variicola + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Bacillus thuringiensis + term: + id: NCBITaxon:1428 + label: Bacillus thuringiensis + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pantoea agglomerans + term: + id: NCBITaxon:549 + label: Pantoea agglomerans + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Teosinte-Maize Biofertilization + description: Teosinte-associated SynCom members reshape maize-associated microbial communities and enrich + beneficial taxa. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Seven bacterial strains from teosinte-associated microbes were formulated as a SynCom. + description: Conventional fertilization, drone-assisted precision delivery, and SynCom biofertilization + were compared. + evidence: + - *id001 diff --git a/kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml b/kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml new file mode 100644 index 00000000..0a8b7f85 --- /dev/null +++ b/kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml @@ -0,0 +1,64 @@ +id: CommunityMech:000106 +name: Tobacco Chemotactic Biocontrol SynCom +description: A chemotactic three-member SynCom in bioorganic fertilizer for suppressing Ralstonia solanacearum + in tobacco fields. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Construct a chemotactic SynCom with compatibility, antagonism, and chemotaxis traits for + bacterial wilt control. + assembly_strategy: Two Pseudomonas strains and one Bacillus strain selected from healthy tobacco rhizosphere + isolates. + perturbation_design: Bioorganic fertilizer formulation plus growth-promoting metabolites including vitamin + C, propionic acid, and esculetin. + measurement_endpoints: + - Ralstonia suppression + - tobacco yield + - chemotaxis marker presence + - rhizosphere community enrichment + evidence: + - &id001 + reference: PMID:40670700 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we constructed a chemotactic SynCom comprising two Pseudomonas strains and one Bacillus strain. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Chemotactic tobacco rhizosphere SynCom delivered in bioorganic fertilizer. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas sp. + term: + id: NCBITaxon:306 + label: Pseudomonas sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Bacillus sp. + term: + id: NCBITaxon:1386 + label: Bacillus + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Chemotactic Bacterial Wilt Suppression + description: Chemotactic SynCom members colonize the rhizosphere and suppress Ralstonia invasion. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Two Pseudomonas strains and one Bacillus strain selected from healthy tobacco rhizosphere isolates. + description: Bioorganic fertilizer formulation plus growth-promoting metabolites including vitamin C, + propionic acid, and esculetin. + evidence: + - *id001 diff --git a/kb/communities/Tomato_Oxylipin_SynCom3.yaml b/kb/communities/Tomato_Oxylipin_SynCom3.yaml new file mode 100644 index 00000000..a2f6ce80 --- /dev/null +++ b/kb/communities/Tomato_Oxylipin_SynCom3.yaml @@ -0,0 +1,74 @@ +id: CommunityMech:000107 +name: Tomato Oxylipin-Protective SynCom3 +description: A three-species simplified tomato rhizosphere SynCom that steers oxylipin pathways and protects + against Botrytis cinerea. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Use pathogen-induced and stably colonizing rhizosphere bacteria to intensify plant defense + oxylipin pathways. + assembly_strategy: A 38-species community was simplified to Asticcacaulis, Arachidicoccus, and Phenylobacterium + representatives. + perturbation_design: Botrytis cinerea foliar infection and tomato oxylipin pathway perturbation. + measurement_endpoints: + - gray mold protection + - biofilm formation + - defense response triggering + - divinyl ether production + evidence: + - &id001 + reference: PMID:37549573 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Through the analysis of the rhizosphere bacterial community, we established a synthetic community + harboring 8 phytopathogen-inducible and 30 stably-colonizing bacteria species. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Tomato rhizosphere SynCom simplified from phytopathogen-inducible and stably colonizing bacteria. +taxonomy: +- taxon_term: + preferred_term: Asticcacaulis sp. + term: + id: NCBITaxon:76890 + label: Asticcacaulis + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Arachidicoccus sp. + term: + id: NCBITaxon:1499392 + label: Arachidicoccus + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Phenylobacterium sp. + term: + id: NCBITaxon:28448 + label: Phenylobacterium + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Oxylipin-Mediated Disease Resistance + description: Inducible and stable colonizers synergize to trigger host defense and biofilm-mediated + protection. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: A 38-species community was simplified to Asticcacaulis, Arachidicoccus, and Phenylobacterium + representatives. + description: Botrytis cinerea foliar infection and tomato oxylipin pathway perturbation. + evidence: + - *id001 diff --git a/kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml b/kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml new file mode 100644 index 00000000..48f2f8ec --- /dev/null +++ b/kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml @@ -0,0 +1,76 @@ +id: CommunityMech:000112 +name: Tribromophenol Anaerobic Bioremediation SynCom +description: A synthetic anaerobic community with Clostridium, Dehalobacter, and Desulfatiglans functions + for 2,4,6-tribromophenol mineralization. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Mineralize 2,4,6-tribromophenol to carbon dioxide through coordinated reductive debromination, + fermentation, and phenol degradation. + assembly_strategy: Dehalobacter phylotype FTH1, Clostridium strain Ma13, and Desulfatiglans parachlorophenolica + strain DS were combined functionally. + perturbation_design: Optimization of glucose, sulfate, and inoculum density under anaerobic conditions. + measurement_endpoints: + - tribromophenol mineralization + - phenol degradation + - debromination + - carbon dioxide production + evidence: + - &id001 + reference: PMID:25461007 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Anaerobic mineralization of 2,4,6-tribromophenol (2,4,6-TBP) was achieved by a synthetic + anaerobe community comprising a highly enriched culture of Dehalobacter sp. phylotype FTH1 acting + as a reductive debrominator; Clostridium sp. strain Ma13 acting as a hydrogen supplier via glucose + fermentation; and a novel 4-chlorophenol-degrading anaerobe, Desulfatiglans parachlorophenolica + strain DS. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Anaerobic laboratory consortium for halogenated aromatic mineralization. +taxonomy: +- taxon_term: + preferred_term: Dehalobacter sp. + term: + id: NCBITaxon:55552 + label: Dehalobacter + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Clostridium sp. + term: + id: NCBITaxon:1485 + label: Clostridium + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Desulfatiglans parachlorophenolica + term: + id: NCBITaxon:1121382 + label: Desulfatiglans parachlorophenolica + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Anaerobic Halophenol Mineralization + description: Debromination, hydrogen supply, and phenol degradation are partitioned among members. + interaction_type: SYNTROPHY + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Dehalobacter phylotype FTH1, Clostridium strain Ma13, and Desulfatiglans parachlorophenolica + strain DS were combined functionally. + description: Optimization of glucose, sulfate, and inoculum density under anaerobic conditions. + evidence: + - *id001 diff --git a/kb/communities/Urine_Nitrification_SynCom.yaml b/kb/communities/Urine_Nitrification_SynCom.yaml new file mode 100644 index 00000000..6ed513b1 --- /dev/null +++ b/kb/communities/Urine_Nitrification_SynCom.yaml @@ -0,0 +1,91 @@ +id: CommunityMech:000117 +name: Urine Nitrification Synthetic Microbial Community +description: A five-member synthetic microbial community containing nitrifiers and ureolytic heterotrophs + for urine nitrification. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOTECHNOLOGY +engineering_design: + objective: Convert urine nitrogen to nitrate fertilizer while managing salinity and organic compounds. + assembly_strategy: Nitrosomonas europaea, Nitrobacter winogradskyi, Pseudomonas fluorescens, Acidovorax + delafieldii, and Delftia acidovorans were compiled. + perturbation_design: Salt adaptation and urine feeding in nitrification reactors. + measurement_endpoints: + - ammonium removal + - nitrate production + - salt adaptation + - organic removal + evidence: + - &id001 + reference: PMID:31623889 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: In this study, a synthetic microbial community containing an AOB (Nitrosomonas europaea), + NOB (Nitrobacter winogradskyi), and three ureolytic heterotrophs (Pseudomonas fluorescens, Acidovorax + delafieldii, and Delftia acidovorans) was compiled and evaluated for these challenges. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Synthetic and real urine nitrification reactors. +taxonomy: +- taxon_term: + preferred_term: Nitrosomonas europaea + term: + id: NCBITaxon:915 + label: Nitrosomonas europaea + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Nitrobacter winogradskyi + term: + id: NCBITaxon:913 + label: Nitrobacter winogradskyi + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pseudomonas fluorescens + term: + id: NCBITaxon:294 + label: Pseudomonas fluorescens + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Acidovorax delafieldii + term: + id: NCBITaxon:80867 + label: Acidovorax delafieldii + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Delftia acidovorans + term: + id: NCBITaxon:80866 + label: Delftia acidovorans + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Nitrifier-Heterotroph Urine Conversion + description: Ureolytic heterotrophs and nitrifiers cooperate to convert urine nitrogen to nitrate. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Nitrosomonas europaea, Nitrobacter winogradskyi, Pseudomonas fluorescens, Acidovorax delafieldii, + and Delftia acidovorans were compiled. + description: Salt adaptation and urine feeding in nitrification reactors. + evidence: + - *id001 diff --git a/kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml b/kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml new file mode 100644 index 00000000..b1e444cf --- /dev/null +++ b/kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml @@ -0,0 +1,66 @@ +id: CommunityMech:000098 +name: Watermelon Rhizosphere Fusarium-Protective SynCom8 +description: A simplified eight-member watermelon rhizosphere SynCom derived from an initial 16-member + grafted-watermelon core community. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Use synergistic rhizosphere bacteria to protect watermelon against Fusarium oxysporum and + promote growth. + assembly_strategy: Initial 16 core bacterial strains from grafted watermelon rhizosphere were refined + to eight synergistic bacteria centered on Pseudomonas. + perturbation_design: Ungrafted watermelon grown in non-sterile soil under soil-borne disease pressure. + measurement_endpoints: + - plant growth + - disease resistance + - Pseudomonas abundance + - biofilm-forming pathways + evidence: + - &id001 + reference: PMID:38840214 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Here, we constructed a synthetic community (SynCom) of 16 core bacterial strains obtained + from the rhizosphere of grafted watermelon plants. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Grafted watermelon rhizosphere-derived SynCom protecting ungrafted watermelon in non-sterile + soil. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas sp. + term: + id: NCBITaxon:306 + label: Pseudomonas sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: watermelon rhizosphere bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Synergistic Watermelon Disease Suppression + description: Pseudomonas and partner bacteria act synergistically to improve plant growth and disease + resistance. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Initial 16 core bacterial strains from grafted watermelon rhizosphere were refined to eight synergistic + bacteria centered on Pseudomonas. + description: Ungrafted watermelon grown in non-sterile soil under soil-borne disease pressure. + evidence: + - *id001 diff --git a/kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml b/kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml new file mode 100644 index 00000000..02686c92 --- /dev/null +++ b/kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml @@ -0,0 +1,86 @@ +id: CommunityMech:000118 +name: Wheat Straw Biogas Pretreatment SynCom +description: A four-member bacterial-fungal synthetic microbial community that produces enzymes for wheat + straw pretreatment and enhanced biogas production. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: LIGNOCELLULOSE +engineering_design: + objective: Improve lignocellulose degradation and biogas production from wheat straw. + assembly_strategy: Core microorganisms with lignocellulose-degrading abilities were screened from straw + and forest environments and combined. + perturbation_design: Synthetic microbial community enzyme pretreatment compared with commercial enzyme + pretreatments. + measurement_endpoints: + - cellulose degradation + - hemicellulose degradation + - lignin degradation + - cumulative biogas production + evidence: + - &id001 + reference: PMID:38748977 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'Herein, a metagenomic approach was used to screen core microorganisms (Bacillus subtilis, + Acinetobacter johnsonii, Trichoderma viride, and Aspergillus niger) possessing lignocellulose-degrading + abilities among samples from three environments: pile retting wheat straw (WS), WS returned to soil, + and forest soil.' + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Synthetic microbial community for enzyme production and wheat straw pretreatment before anaerobic + digestion. +taxonomy: +- taxon_term: + preferred_term: Bacillus subtilis + term: + id: NCBITaxon:1423 + label: Bacillus subtilis + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Acinetobacter johnsonii + term: + id: NCBITaxon:40214 + label: Acinetobacter johnsonii + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Trichoderma viride + term: + id: NCBITaxon:5544 + label: Trichoderma viride + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Aspergillus niger + term: + id: NCBITaxon:5061 + label: Aspergillus niger + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +ecological_interactions: +- name: Lignocellulose Enzyme Pretreatment + description: Bacterial and fungal enzyme producers jointly degrade wheat straw polymers before anaerobic + digestion. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Core microorganisms with lignocellulose-degrading abilities were screened from straw and forest + environments and combined. + description: Synthetic microbial community enzyme pretreatment compared with commercial enzyme pretreatments. + evidence: + - *id001 diff --git a/kb/communities/hCom2_Complex_Gut_Microbiome.yaml b/kb/communities/hCom2_Complex_Gut_Microbiome.yaml new file mode 100644 index 00000000..804a564b --- /dev/null +++ b/kb/communities/hCom2_Complex_Gut_Microbiome.yaml @@ -0,0 +1,58 @@ +id: CommunityMech:000123 +name: hCom2 Complex Gut Microbiome +description: A complex defined human gut microbiome assembled from hCom1 and iteratively augmented after + fecal challenge to improve stability and colonization resistance in gnotobiotic mice. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Construct a defined but complex gut microbiome that models human gut community functions + in vivo. + assembly_strategy: A 104-species hCom1 community was challenged with fecal microbiota in germ-free mice + and augmented with engrafting species to yield hCom2. + perturbation_design: Fecal challenge and pathogenic Escherichia coli challenge were used to test stability + and colonization resistance. + measurement_endpoints: + - engraftment + - community stability + - colonization resistance + - host phenotypes + evidence: + - &id001 + reference: PMID:36070752 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: We identified new species that engrafted following fecal challenge and added them to hCom1, + yielding hCom2. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: human gut + term: + id: UBERON:0001007 + label: digestive system + notes: Defined human gut microbiome used in gnotobiotic mouse experiments. +taxonomy: +- taxon_term: + preferred_term: defined human gut bacterial members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Gut Niche Filling and Colonization Resistance + description: Iterative niche filling improved stability to fecal challenge and resistance to pathogenic + Escherichia coli. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: gnotobiotic fecal challenge + value: Germ-free mice colonized with hCom1 were challenged with a human fecal sample to identify additional + engrafting species. + description: Fecal challenge and pathogenic Escherichia coli challenge were used to test stability and + colonization resistance. + evidence: + - *id001 diff --git a/references_cache/PMID_40904019.md b/references_cache/PMID_40904019.md new file mode 100644 index 00000000..e0b531c2 --- /dev/null +++ b/references_cache/PMID_40904019.md @@ -0,0 +1,72 @@ +--- +reference_id: PMID:40904019 +title: Rhizosphere Microbes From Populus euphratica Conferred Salt Stress Resistance to Populus alba × Populus glandulosa. +authors: +- Li L +- Cheng K +- Du Y +- Zhang Y +- Zhou Y +- Jin Y +- He X +journal: Plant Cell Environ +year: '2025' +doi: 10.1111/pce.70160 +keywords: +- "Populus/microbiology, physiology" +- Rhizosphere +- Salt Stress +- Soil Microbiology +- Salt Tolerance +- Plant Roots/microbiology +- Microbiota/physiology +- Salt-Tolerant Plants +content_type: abstract_only +--- + +# Rhizosphere Microbes From Populus euphratica Conferred Salt Stress Resistance to Populus alba × Populus glandulosa. +**Authors:** Li L, Cheng K, Du Y, Zhang Y, Zhou Y, Jin Y, He X +**Journal:** Plant Cell Environ (2025) +**DOI:** [10.1111/pce.70160](https://doi.org/10.1111/pce.70160) + +## Content + +1. Plant Cell Environ. 2025 Dec;48(12):8743-8755. doi: 10.1111/pce.70160. Epub +2025 Sep 3. + +Rhizosphere Microbes From Populus euphratica Conferred Salt Stress Resistance to +Populus alba × Populus glandulosa. + +Li L(1)(2), Cheng K(2), Du Y(2), Zhang Y(2), Zhou Y(2), Jin Y(2), He X(1)(2). + +Author information: +(1)State Key Laboratory of Efficient Production of Forest Resources, Beijing +Forestry University, Beijing, China. +(2)College of Biological Sciences and Technology, Beijing Forestry University, +Beijing, China. + +The rhizosphere microbiomes of halophytes are crucial for plant adaptation to +high-salinity soil conditions, but how to harness rhizosphere microbes to confer +salt stress resistance to plants remains obscure. This study aimed to establish +a framework (isolate-select-construct) for tailoring simplified salt-tolerant +synthetic microbial communities (SynComs) and explore how they confer salt +stress resistance to the plant. First, a total of 512 strains were isolated from +the high-salt rhizosphere soil of Populus euphratica through high-throughput +cultivation. Among these, nine strains were further selected for their +salt-tolerant and growth-promoting abilities, with three isolates identified as +key microbes, including hub microbes, keystone taxa and biomarkers. Guided by a +function-driven strategy, we constructed five distinct SynComs, with SynCom5, +SynCom7 and SynCom9 showing the most significant improvement in the growth of +hybrid Poplar 84K (Populus alba × Populus glandulosa). Mechanistic +investigations revealed that these SynComs can increase resistance to salt +stress by directly reducing oxidative stress, adjusting osmolytes and balancing +ions. Additionally, these SynComs were observed to recruit specific +root-associated bacterial consortia that enhance the adaptability of poplar to +salt stress. Overall, this study lays the groundwork for designing SynComs that +promote plant growth and offers insights into harnessing specific microbial +communities to boost plants' salt resistance. + +© 2025 John Wiley & Sons Ltd. + +DOI: 10.1111/pce.70160 +PMID: 40904019 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_24743269.txt b/references_cache/pmid_24743269.txt new file mode 100644 index 00000000..4f6505b2 --- /dev/null +++ b/references_cache/pmid_24743269.txt @@ -0,0 +1,42 @@ +1. PLoS Genet. 2014 Apr 17;10(4):e1004283. doi: 10.1371/journal.pgen.1004283. +eCollection 2014 Apr. + +A synthetic community approach reveals plant genotypes affecting the +phyllosphere microbiota. + +Bodenhausen N(1), Bortfeld-Miller M(1), Ackermann M(2), Vorholt JA(1). + +Author information: +(1)Institute of Microbiology, ETH Zurich, Zurich, Switzerland. +(2)Department of Environmental Sciences, ETH Zurich, Zurich, Switzerland; +Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland. + +The identity of plant host genetic factors controlling the composition of the +plant microbiota and the extent to which plant genes affect associated microbial +populations is currently unknown. Here, we use a candidate gene approach to +investigate host effects on the phyllosphere community composition and +abundance. To reduce the environmental factors that might mask genetic factors, +the model plant Arabidopsis thaliana was used in a gnotobiotic system and +inoculated with a reduced complexity synthetic bacterial community composed of +seven strains representing the most abundant phyla in the phyllosphere. From a +panel of 55 plant mutants with alterations in the surface structure, cell wall, +defense signaling, secondary metabolism, and pathogen recognition, a small +number of single host mutations displayed an altered microbiota composition +and/or abundance. Host alleles that resulted in the strongest perturbation of +the microbiota relative to the wild-type were lacs2 and pec1. These mutants +affect cuticle formation and led to changes in community composition and an +increased bacterial abundance relative to the wild-type plants, suggesting that +different bacteria can benefit from a modified cuticle to different extents. +Moreover, we identified ein2, which is involved in ethylene signaling, as a host +factor modulating the community's composition. Finally, we found that different +Arabidopsis accessions exhibited different communities, indicating that plant +host genetic factors shape the associated microbiota, thus harboring significant +potential for the identification of novel plant factors affecting the microbiota +of the communities. + +DOI: 10.1371/journal.pgen.1004283 +PMCID: PMC3990490 +PMID: 24743269 [Indexed for MEDLINE] + +Conflict of interest statement: The authors have declared that no competing +interests exist. \ No newline at end of file diff --git a/references_cache/pmid_25461007.txt b/references_cache/pmid_25461007.txt new file mode 100644 index 00000000..6ed4e1c9 --- /dev/null +++ b/references_cache/pmid_25461007.txt @@ -0,0 +1,53 @@ +1. Bioresour Technol. 2015 Jan;176:225-32. doi: 10.1016/j.biortech.2014.10.097. +Epub 2014 Oct 25. + +Anaerobic mineralization of 2,4,6-tribromophenol to CO2 by a synthetic microbial +community comprising Clostridium, Dehalobacter, and Desulfatiglans. + +Li Z(1), Yoshida N(2), Wang A(3), Nan J(4), Liang B(5), Zhang C(6), Zhang D(7), +Suzuki D(6), Zhou X(8), Xiao Z(7), Katayama A(9). + +Author information: +(1)State Key Laboratory of Urban Water Resources and Environment, Harbin +Institute of Technology (SKLUWRE, HIT), Harbin 150090, China; EcoTopia Science +Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan. +(2)Center for Fostering Young and Innovative Researchers, Nagoya Institute of +Technology, Syowa, Nagoya 466-8555, Japan. +(3)State Key Laboratory of Urban Water Resources and Environment, Harbin +Institute of Technology (SKLUWRE, HIT), Harbin 150090, China; Key Laboratory of +Environmental Biotechnology, Research Center for Eco-Environmental Sciences, +Chinese Academy of Sciences, Beijing 100085, China. +(4)State Key Laboratory of Urban Water Resources and Environment, Harbin +Institute of Technology (SKLUWRE, HIT), Harbin 150090, China. +(5)Key Laboratory of Environmental Biotechnology, Research Center for +Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. +(6)EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, +Japan. +(7)Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, +Japan. +(8)Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8601, +Japan. +(9)EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, +Japan; Graduate School of Engineering, Nagoya University, Chikusa, Nagoya +464-8603, Japan; Graduate School of Environmental Studies, Nagoya University, +Nagoya 464-8601, Japan. Electronic address: a-katayama@esi.nagoya-u.ac.jp. + +Anaerobic mineralization of 2,4,6-tribromophenol (2,4,6-TBP) was achieved by a +synthetic anaerobe community comprising a highly enriched culture of +Dehalobacter sp. phylotype FTH1 acting as a reductive debrominator; Clostridium +sp. strain Ma13 acting as a hydrogen supplier via glucose fermentation; and a +novel 4-chlorophenol-degrading anaerobe, Desulfatiglans parachlorophenolica +strain DS. 2,4,6-TBP was debrominated to phenol by the combined action of Ma13 +and FTH1, then mineralized into CO2 by sequential introduction of DS, confirmed +using [ring-(14)C(U)] phenol. The optimum concentrations of glucose, SO4(2-), +and inoculum densities were 0.5 or 2.5mM, 1.0 or 2.5mM, and the densities +equivalent to 10(4)copiesmL(-1) of the 16S rRNA genes, respectively. This +resulted in the complete mineralization of 23μM 2,4,6-TBP within 35days +(0.58μmolL(-1)d(-1)). Thus, using a synthetic microbial community of isolates or +highly enriched cultures would be an efficient, optimizable, low-cost strategy +for anaerobic bioremediation of halogenated aromatics. + +Copyright © 2014 Elsevier Ltd. All rights reserved. + +DOI: 10.1016/j.biortech.2014.10.097 +PMID: 25461007 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_29152587.txt b/references_cache/pmid_29152587.txt new file mode 100644 index 00000000..e304613d --- /dev/null +++ b/references_cache/pmid_29152587.txt @@ -0,0 +1,48 @@ +1. mSystems. 2017 Nov 14;2(6):e00129-17. doi: 10.1128/mSystems.00129-17. +eCollection 2017 Nov-Dec. + +A Synthetic Community System for Probing Microbial Interactions Driven by +Exometabolites. + +Chodkowski JL(1), Shade A(1)(2). + +Author information: +(1)Department of Microbiology and Molecular Genetics, Michigan State University, +East Lansing, Michigan, USA. +(2)Department of Plant, Soil and Microbial Sciences, Program in Ecology, +Evolutionary Biology, and Behavior, The DOE Great Lakes Bioenergy Center, and +The Plant Resilience Institute, Michigan State University, East Lansing, +Michigan, USA. + +Though most microorganisms live within a community, we have modest knowledge +about microbial interactions and their implications for community properties and +ecosystem functions. To advance understanding of microbial interactions, we +describe a straightforward synthetic community system that can be used to +interrogate exometabolite interactions among microorganisms. The filter plate +system (also known as the Transwell system) physically separates microbial +populations, but allows for chemical interactions via a shared medium reservoir. +Exometabolites, including small molecules, extracellular enzymes, and +antibiotics, are assayed from the reservoir using sensitive mass spectrometry. +Community member outcomes, such as growth, productivity, and gene regulation, +can be determined using flow cytometry, biomass measurements, and transcript +analyses, respectively. The synthetic community design allows for determination +of the consequences of microbiome diversity for emergent community properties +and for functional changes over time or after perturbation. Because it is +versatile, scalable, and accessible, this synthetic community system has the +potential to practically advance knowledge of microbial interactions that occur +within both natural and artificial communities. IMPORTANCE Understanding +microbial interactions is a fundamental objective in microbiology and ecology. +The synthetic community system described here can set into motion a range of +research to investigate how the diversity of a microbiome and interactions among +its members impact its function, where function can be measured as +exometabolites. The system allows for community exometabolite profiling to be +coupled with genome mining, transcript analysis, and measurements of member +productivity and population size. It can also facilitate discovery of natural +products that are only produced within microbial consortia. Thus, this synthetic +community system has utility to address fundamental questions about a diversity +of possible microbial interactions that occur in both natural and engineered +ecosystems. + +DOI: 10.1128/mSystems.00129-17 +PMCID: PMC5686522 +PMID: 29152587 \ No newline at end of file diff --git a/references_cache/pmid_29930200.txt b/references_cache/pmid_29930200.txt new file mode 100644 index 00000000..b89fd473 --- /dev/null +++ b/references_cache/pmid_29930200.txt @@ -0,0 +1,50 @@ +1. Mol Syst Biol. 2018 Jun 21;14(6):e8157. doi: 10.15252/msb.20178157. + +Deciphering microbial interactions in synthetic human gut microbiome +communities. + +Venturelli OS(1), Carr AC(2), Fisher G(2), Hsu RH(3), Lau R(2), Bowen BP(2), +Hromada S(4), Northen T(2), Arkin AP(2)(3)(5)(6). + +Author information: +(1)Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA +venturelli@wisc.edu. +(2)Environmental Genomics and Systems Biology, Lawrence Berkeley National +Laboratory, Berkeley, CA, USA. +(3)California Institute for Quantitative Biosciences, University of California +Berkeley, Berkeley, CA, USA. +(4)Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, +USA. +(5)Department of Bioengineering, University of California Berkeley, Berkeley, +CA, USA. +(6)Energy Biosciences Institute, University of California Berkeley, Berkeley, +CA, USA. + +Comment in + Mol Syst Biol. 2018 Jun 21;14(6):e8425. doi: 10.15252/msb.20188425. + Nat Methods. 2018 Aug;15(8):572. doi: 10.1038/s41592-018-0094-z. + +The ecological forces that govern the assembly and stability of the human gut +microbiota remain unresolved. We developed a generalizable model-guided +framework to predict higher-dimensional consortia from time-resolved +measurements of lower-order assemblages. This method was employed to decipher +microbial interactions in a diverse human gut microbiome synthetic community. We +show that pairwise interactions are major drivers of multi-species community +dynamics, as opposed to higher-order interactions. The inferred ecological +network exhibits a high proportion of negative and frequent positive +interactions. Ecological drivers and responsive recipient species were +discovered in the network. Our model demonstrated that a prevalent positive and +negative interaction topology enables robust coexistence by implementing a +negative feedback loop that balances disparities in monospecies fitness levels. +We show that negative interactions could generate history-dependent responses of +initial species proportions that frequently do not originate from bistability. +Measurements of extracellular metabolites illuminated the metabolic capabilities +of monospecies and potential molecular basis of microbial interactions. In sum, +these methods defined the ecological roles of major human-associated intestinal +species and illuminated design principles of microbial communities. + +© 2018 The Authors. Published under the terms of the CC BY 4.0 license. + +DOI: 10.15252/msb.20178157 +PMCID: PMC6011841 +PMID: 29930200 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_31152139.txt b/references_cache/pmid_31152139.txt new file mode 100644 index 00000000..ccd05040 --- /dev/null +++ b/references_cache/pmid_31152139.txt @@ -0,0 +1,46 @@ +1. Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12558-12565. doi: +10.1073/pnas.1820691116. Epub 2019 May 31. + +Plant-derived coumarins shape the composition of an Arabidopsis synthetic root +microbiome. + +Voges MJEEE(1)(2), Bai Y(3), Schulze-Lefert P(3)(4), Sattely ES(5)(6). + +Author information: +(1)Department of Chemical Engineering, Stanford University, Stanford, CA 94305. +(2)Department of Bioengineering, Stanford University, Stanford, CA 94305. +(3)Department of Plant Microbe Interactions, Max Planck Institute for Plant +Breeding Research, 50829 Cologne, Germany. +(4)Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant +Breeding Research, 50829 Cologne, Germany. +(5)Department of Chemical Engineering, Stanford University, Stanford, CA 94305; +sattely@stanford.edu. +(6)Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305. + +The factors that contribute to the composition of the root microbiome and, in +turn, affect plant fitness are not well understood. Recent work has highlighted +a major contribution of the soil inoculum in determining the composition of the +root microbiome. However, plants are known to conditionally exude a diverse +array of unique secondary metabolites, that vary among species and environmental +conditions and can interact with the surrounding biota. Here, we explore the +role of specialized metabolites in dictating which bacteria reside in the +rhizosphere. We employed a reduced synthetic community (SynCom) of Arabidopsis +thaliana root-isolated bacteria to detect community shifts that occur in the +absence of the secreted small-molecule phytoalexins, flavonoids, and coumarins. +We find that lack of coumarin biosynthesis in f6'h1 mutant plant lines causes a +shift in the root microbial community specifically under iron deficiency. We +demonstrate a potential role for iron-mobilizing coumarins in sculpting the A. +thaliana root bacterial community by inhibiting the proliferation of a +relatively abundant Pseudomonas species via a redox-mediated mechanism. This +work establishes a systematic approach enabling elucidation of specific +mechanisms by which plant-derived molecules mediate microbial community +composition. Our findings expand on the function of conditionally exuded +specialized metabolites and suggest avenues to effectively engineer the +rhizosphere with the aim of improving crop growth in iron-limited alkaline +soils, which make up a third of the world's arable soils. + +DOI: 10.1073/pnas.1820691116 +PMCID: PMC6589675 +PMID: 31152139 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_31623889.txt b/references_cache/pmid_31623889.txt new file mode 100644 index 00000000..a74a0282 --- /dev/null +++ b/references_cache/pmid_31623889.txt @@ -0,0 +1,56 @@ +1. Syst Appl Microbiol. 2019 Nov;42(6):126021. doi: 10.1016/j.syapm.2019.126021. +Epub 2019 Sep 23. + +Urine nitrification with a synthetic microbial community. + +Christiaens MER(1), De Paepe J(2), Ilgrande C(1), De Vrieze J(1), Barys J(2), +Teirlinck P(1), Meerbergen K(3), Lievens B(4), Boon N(1), Clauwaert P(1), +Vlaeminck SE(5). + +Author information: +(1)Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure +Links 653, 9000 Gent, Belgium. +(2)Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure +Links 653, 9000 Gent, Belgium; Department of Chemical, Biological and +Environmental Engineering, School of Engineering, Universitat Autònoma de +Barcelona, Bellaterra 08193 Barcelona, Spain. +(3)Laboratory for Process Microbial Ecology and Bioinspirational Management +(PME&BIM), Technology Cluster Bioengineering Technology (CBeT), Campus De Nayer +Sint-Katelijne-Waver, KU Leuven, Jan De Nayerlaan 5, 2860 Sint-Katelijne-Waver, +Belgium; Technology Cluster Materials Technology, Campus Groep T, KU Leuven, +Andreas Vesaliusstraat 13 - Bus 2600, 3000 Leuven, Belgium. +(4)Laboratory for Process Microbial Ecology and Bioinspirational Management +(PME&BIM), Technology Cluster Bioengineering Technology (CBeT), Campus De Nayer +Sint-Katelijne-Waver, KU Leuven, Jan De Nayerlaan 5, 2860 Sint-Katelijne-Waver, +Belgium. +(5)Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure +Links 653, 9000 Gent, Belgium; Research Group of Sustainable Energy, Air, and +Water Technology, Department of Bioscience Engineering, University of Antwerp, +Groenenborgerlaan 171, 2020 Antwerpen, Belgium. Electronic address: +siegfried.vlaeminck@uantwerpen.be. + +During long-term extra-terrestrial missions, food is limited and waste is +generated. By recycling valuable nutrients from this waste via regenerative life +support systems, food can be produced in space. Astronauts' urine can, for +instance, be nitrified by micro-organisms into a liquid nitrate fertilizer for +plant growth in space. Due to stringent conditions in space, microbial +communities need to be be defined (gnotobiotic); therefore, synthetic rather +than mixed microbial communities are preferred. For urine nitrification, +synthetic communities face challenges, such as from salinity, ureolysis, and +organics. In this study, a synthetic microbial community containing an AOB +(Nitrosomonas europaea), NOB (Nitrobacter winogradskyi), and three ureolytic +heterotrophs (Pseudomonas fluorescens, Acidovorax delafieldii, and Delftia +acidovorans) was compiled and evaluated for these challenges. In reactor 1, salt +adaptation of the ammonium-fed AOB and NOB co-culture was possible up to +45mScm-1, which resembled undiluted nitrified urine, while maintaining a +44±10mgNH4+-NL-1d-1 removal rate. In reactor 2, the nitrifiers and ureolytic +heterotrophs were fed with urine and achieved a 15±6mg NO3--NL-1d-1 production +rate for 1% and 10% synthetic and fresh real urine, respectively. Batch activity +tests with this community using fresh real urine even reached 29±3mgNL-1d-1. +Organics removal in the reactor (69±15%) should be optimized to generate a +nitrate fertilizer for future space applications. + +Copyright © 2019 Elsevier GmbH. All rights reserved. + +DOI: 10.1016/j.syapm.2019.126021 +PMID: 31623889 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_32762153.txt b/references_cache/pmid_32762153.txt new file mode 100644 index 00000000..b0af9d32 --- /dev/null +++ b/references_cache/pmid_32762153.txt @@ -0,0 +1,38 @@ +1. Microb Biotechnol. 2021 Mar;14(2):488-502. doi: 10.1111/1751-7915.13640. Epub +2020 Aug 6. + +Synthetic community with six Pseudomonas strains screened from garlic +rhizosphere microbiome promotes plant growth. + +Zhuang L(1), Li Y(1), Wang Z(1), Yu Y(1), Zhang N(1), Yang C(1), Zeng Q(1), Wang +Q(1). + +Author information: +(1)Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green +Management, College of Plant Protection, China Agricultural University, Beijing, +100193, China. + +The rhizosphere microbiome plays an important role in the growth and health of +many plants, particularly for plant growth-promoting rhizobacteria (PGPR). +Although the use of PGPR could improve plant production, real-world applications +are still held back by low-efficiency methods of finding and using PGPR. In this +study, the structure of bacterial and fungal rhizosphere communities of Jinxiang +garlic under different growth periods (resume growth, bolting and maturation), +soil types (loam, sandy loam and sandy soil) and agricultural practices (with +and without microbial products) were explored by using amplicon sequencing. +High-efficiency top-down approaches based on high-throughput technology and +synthetic community (SynCom) approaches were used to find PGPR in garlic +rhizosphere and improve plant production. Our findings indicated that +Pseudomonas was a key PGPR in the rhizosphere of garlic. Furthermore, SynCom +with six Pseudomonas strains isolated from the garlic rhizosphere were +constructed, which showed that they have the ability to promote plant growth. + +© 2020 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd +and Society for Applied Microbiology. + +DOI: 10.1111/1751-7915.13640 +PMCID: PMC7936309 +PMID: 32762153 [Indexed for MEDLINE] + +Conflict of interest statement: None of the authors have any conflict of +interest. \ No newline at end of file diff --git a/references_cache/pmid_32788711.txt b/references_cache/pmid_32788711.txt new file mode 100644 index 00000000..37738642 --- /dev/null +++ b/references_cache/pmid_32788711.txt @@ -0,0 +1,47 @@ +1. ISME J. 2020 Nov;14(11):2816-2828. doi: 10.1038/s41396-020-00737-5. Epub 2020 +Aug 12. + +Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between +bacteria in a synthetic community. + +Fritts RK(1), Bird JT(2), Behringer MG(3), Lipzen A(4), Martin J(4), Lynch M(3), +McKinlay JB(5). + +Author information: +(1)Department of Biology, Indiana University, Bloomington, IN, 47405, USA. +(2)Department of Biochemistry and Molecular Biology, University of Arkansas for +Medical Sciences, Little Rock, AR, 72205, USA. +(3)School of Life Sciences, Biodesign Center for Mechanisms of Evolution, +Arizona State University, Tempe, AZ, 85281, USA. +(4)Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. +(5)Department of Biology, Indiana University, Bloomington, IN, 47405, USA. +jmckinla@indiana.edu. + +Interactive microbial communities are ubiquitous, influencing biogeochemical +cycles and host health. One widespread interaction is nutrient exchange, or +cross-feeding, wherein metabolites are transferred between microbes. Some +cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are +communally valuable and impose a cost on the producer. The mechanisms that +enforce cross-feeding of communally valuable metabolites are not fully +understood. Previously we engineered a cross-feeding coculture between N2-fixing +Rhodopseudomonas palustris and fermentative Escherichia coli. Engineered R. +palustris excretes essential nitrogen as NH4+ to E. coli, while E. coli excretes +essential carbon as fermentation products to R. palustris. Here, we sought to +determine whether a reciprocal cross-feeding relationship would evolve +spontaneously in cocultures with wild-type R. palustris, which is not known to +excrete NH4+. Indeed, we observed the emergence of NH4+ cross-feeding, but +driven by adaptation of E. coli alone. A missense mutation in E. coli NtrC, a +regulator of nitrogen scavenging, resulted in constitutive activation of an NH4+ +transporter. This activity likely allowed E. coli to subsist on the small amount +of leaked NH4+ and better reciprocate through elevated excretion of fermentation +products from a larger E. coli population. Our results indicate that enhanced +nutrient uptake by recipients, rather than increased excretion by producers, is +an underappreciated yet possibly prevalent mechanism by which cross-feeding can +emerge. + +DOI: 10.1038/s41396-020-00737-5 +PMCID: PMC7784955 +PMID: 32788711 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare that they have no conflict +of interest. \ No newline at end of file diff --git a/references_cache/pmid_34745050.txt b/references_cache/pmid_34745050.txt new file mode 100644 index 00000000..0391c1ee --- /dev/null +++ b/references_cache/pmid_34745050.txt @@ -0,0 +1,46 @@ +1. Front Microbiol. 2021 Oct 21;12:747541. doi: 10.3389/fmicb.2021.747541. +eCollection 2021. + +Modulating Drought Stress Response of Maize by a Synthetic Bacterial Community. + +Armanhi JSL(1)(2), de Souza RSC(1)(2), Biazotti BB(1)(2)(3), Yassitepe +JECT(2)(4), Arruda P(1)(2)(3). + +Author information: +(1)Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de +Campinas (UNICAMP), Campinas, Brazil. +(2)Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de +Campinas (UNICAMP), Campinas, Brazil. +(3)Departamento de Genética e Evolução, Instituto de Biologia, Universidade +Estadual de Campinas (UNICAMP), Campinas, Brazil. +(4)Embrapa Informática Agropecuária, Campinas, Brazil. + +Plant perception and responses to environmental stresses are known to encompass +a complex set of mechanisms in which the microbiome is involved. Knowledge about +plant physiological responses is therefore critical for understanding the +contribution of the microbiome to plant resilience. However, as plant growth is +a dynamic process, a major hurdle is to find appropriate tools to effectively +measure temporal variations of different plant physiological parameters. Here, +we used a non-invasive real-time phenotyping platform in a one-to-one +(plant-sensors) set up to investigate the impact of a synthetic community +(SynCom) harboring plant-beneficial bacteria on the physiology and response of +three commercial maize hybrids to drought stress (DS). SynCom inoculation +significantly reduced yield loss and modulated vital physiological traits. +SynCom-inoculated plants displayed lower leaf temperature, reduced turgor loss +under severe DS and a faster recovery upon rehydration, likely as a result of +sap flow modulation and better water usage. Microbiome profiling revealed that +SynCom bacterial members were able to robustly colonize mature plants and +recruit soil/seed-borne beneficial microbes. The high-resolution temporal data +allowed us to record instant plant responses to daily environmental +fluctuations, thus revealing the impact of the microbiome in modulating maize +physiology, resilience to drought, and crop productivity. + +Copyright © 2021 Armanhi, de Souza, Biazotti, Yassitepe and Arruda. + +DOI: 10.3389/fmicb.2021.747541 +PMCID: PMC8566980 +PMID: 34745050 + +Conflict of interest statement: The authors declare that the research was +conducted in the absence of any commercial or financial relationships that could +be construed as a potential conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_35444261.txt b/references_cache/pmid_35444261.txt new file mode 100644 index 00000000..5ad0d03b --- /dev/null +++ b/references_cache/pmid_35444261.txt @@ -0,0 +1,56 @@ +1. ISME J. 2022 Aug;16(8):1907-1920. doi: 10.1038/s41396-022-01238-3. Epub 2022 +Apr 20. + +Synthetic bacterial community derived from a desert rhizosphere confers salt +stress resilience to tomato in the presence of a soil microbiome. + +Schmitz L(#)(1), Yan Z(#)(1), Schneijderberg M(1), de Roij M(1), Pijnenburg +R(1), Zheng Q(1), Franken C(1), Dechesne A(2), Trindade LM(2), van Velzen R(3), +Bisseling T(1), Geurts R(4), Cheng X(5)(6). + +Author information: +(1)Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, +Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, +Wageningen, The Netherlands. +(2)Laboratory of Plant Breeding, Plant Sciences Group, Wageningen University & +Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. +(3)Biosystematics, Plant Sciences Group, Wageningen University & Research, +Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. +(4)Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, +Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, +Wageningen, The Netherlands. rene.geurts@wur.nl. +(5)Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, +Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, +Wageningen, The Netherlands. xu.cheng@wur.nl. +(6)Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome +Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics +Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, +China. xu.cheng@wur.nl. +(#)Contributed equally + +The root bacterial microbiome is important for the general health of the plant. +Additionally, it can enhance tolerance to abiotic stresses, exemplified by plant +species found in extreme ecological niches like deserts. These complex +microbe-plant interactions can be simplified by constructing synthetic bacterial +communities or SynComs from the root microbiome. Furthermore, SynComs can be +applied as biocontrol agents to protect crops against abiotic stresses such as +high salinity. However, there is little knowledge on the design of a SynCom that +offers a consistent protection against salt stress for plants growing in a +natural and, therefore, non-sterile soil which is more realistic to an +agricultural setting. Here we show that a SynCom of five bacterial strains, +originating from the root of the desert plant Indigofera argentea, protected +tomato plants growing in a non-sterile substrate against a high salt stress. +This phenotype correlated with the differential expression of salt stress +related genes and ion accumulation in tomato. Quantification of the SynCom +strains indicated a low penetrance into the natural soil used as the non-sterile +substrate. Our results demonstrate how a desert microbiome could be engineered +into a simplified SynCom that protected tomato plants growing in a natural soil +against an abiotic stress. + +© 2022. The Author(s). + +DOI: 10.1038/s41396-022-01238-3 +PMCID: PMC9296610 +PMID: 35444261 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no competing interests. \ No newline at end of file diff --git a/references_cache/pmid_35869094.txt b/references_cache/pmid_35869094.txt new file mode 100644 index 00000000..a552fb79 --- /dev/null +++ b/references_cache/pmid_35869094.txt @@ -0,0 +1,38 @@ +7. NPJ Biofilms Microbiomes. 2022 Jul 22;8(1):61. doi: +10.1038/s41522-022-00322-y. + +Synthetic periphyton as a model system to understand species dynamics in complex +microbial freshwater communities. + +Lamprecht O(1), Wagner B(1), Derlon N(1), Tlili A(2). + +Author information: +(1)Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, +Switzerland. +(2)Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, +Switzerland. ahmed.tlili@eawag.ch. + +Phototrophic biofilms, also known as periphyton, are microbial freshwater +communities that drive crucial ecological processes in streams and lakes. +Gaining a deep mechanistic understanding of the biological processes occurring +in natural periphyton remains challenging due to the high complexity and +variability of such communities. To address this challenge, we rationally +developed a workflow to construct a synthetic community by co-culturing 26 +phototrophic species (i.e., diatoms, green algae, and cyanobacteria) that were +inoculated in a successional sequence to create a periphytic biofilm on glass +slides. We show that this community is diverse, stable, and highly reproducible +in terms of microbial composition, function, and 3D spatial structure of the +biofilm. We also demonstrate the ability to monitor microbial dynamics at the +single species level during periphyton development and how their abundances are +impacted by stressors such as increased temperature and a herbicide, singly and +in combination. Overall, such a synthetic periphyton, grown under controlled +conditions, can be used as a model system for theory testing through targeted +manipulation. + +© 2022. The Author(s). + +DOI: 10.1038/s41522-022-00322-y +PMCID: PMC9307524 +PMID: 35869094 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no competing interests. diff --git a/references_cache/pmid_35992653.txt b/references_cache/pmid_35992653.txt new file mode 100644 index 00000000..370dae46 --- /dev/null +++ b/references_cache/pmid_35992653.txt @@ -0,0 +1,54 @@ +1. Front Microbiol. 2022 Aug 5;13:967885. doi: 10.3389/fmicb.2022.967885. +eCollection 2022. + +Designing a synthetic microbial community devoted to biological control: The +case study of Fusarium wilt of banana. + +Prigigallo MI(1), Gómez-Lama Cabanás C(2), Mercado-Blanco J(2), Bubici G(1). + +Author information: +(1)Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale +delle Ricerche, Bari, Italy. +(2)Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, +Agencia Estatal Consejo Superior de Investigaciones Científicas, Córdoba, Spain. + +Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 (TR4) is threatening +banana production because of its increasing spread. Biological control +approaches have been widely studied and constitute interesting complementary +measures to integrated disease management strategies. They have been based +mainly on the use of single biological control agents (BCAs). In this study, we +moved a step forward by designing a synthetic microbial community (SynCom) for +the control of Fusarium wilt of banana (FWB). Ninety-six isolates of Pseudomonas +spp., Bacillus spp., Streptomyces spp., and Trichoderma spp. were obtained from +the banana rhizosphere and selected in vitro for the antagonism against Foc TR4. +In pot experiments, a large community such as SynCom 1.0 (44 isolates with +moderate to high antagonistic activity) or a small one such as SynCom 1.1 (seven +highly effective isolates) provided similar disease control (35% symptom +severity reduction). An in vitro study of the interactions among SynCom 1.1 +isolates and between them and Foc revealed that beneficial microorganisms not +only antagonized the pathogen but also some of the SynCom constituents. +Furthermore, Foc defended itself by antagonizing the beneficial microbes. We +also demonstrated that fusaric acid, known as one of the secondary metabolites +of Fusarium species, might be involved in such an interaction. With this +knowledge, SynCom 1.2 was then designed with three isolates: Pseudomonas +chlororaphis subsp. piscium PS5, Bacillus velezensis BN8.2, and Trichoderma +virens T2C1.4. A non-simultaneous soil application of these isolates (to +diminish cross-inhibition) delayed FWB progress over time, with significant +reductions in incidence and severity. SynCom 1.2 also performed better than two +commercial BCAs, BioPak® and T-Gro. Eventually, SynCom 1.2 isolates were +characterized for several biocontrol traits and their genome was sequenced. Our +data showed that assembling a SynCom for biocontrol is not an easy task. The +mere mixtures of antagonists (e.g., SynCom 1.0 and 1.1) might provide effective +biocontrol, but an accurate investigation of the interactions among beneficial +microorganisms is needed to improve the results (e.g., SynCom 1.2). SynCom 1.2 +is a valuable tool to be further developed for the biological control of FWB. + +Copyright © 2022 Prigigallo, Gómez-Lama Cabanás, Mercado-Blanco and Bubici. + +DOI: 10.3389/fmicb.2022.967885 +PMCID: PMC9389584 +PMID: 35992653 + +Conflict of interest statement: The authors declare that the research was +conducted in the absence of any commercial or financial relationships that could +be construed as a potential conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_36070752.txt b/references_cache/pmid_36070752.txt new file mode 100644 index 00000000..c2b7c2e2 --- /dev/null +++ b/references_cache/pmid_36070752.txt @@ -0,0 +1,71 @@ +1. Cell. 2022 Sep 15;185(19):3617-3636.e19. doi: 10.1016/j.cell.2022.08.003. Epub + 2022 Sep 6. + +Design, construction, and in vivo augmentation of a complex gut microbiome. + +Cheng AG(1), Ho PY(2), Aranda-Díaz A(2), Jain S(3), Yu FB(4), Meng X(4), Wang +M(5), Iakiviak M(6), Nagashima K(6), Zhao A(6), Murugkar P(7), Patil A(6), +Atabakhsh K(6), Weakley A(4), Yan J(3), Brumbaugh AR(6), Higginbottom S(6), +Dimas A(6), Shiver AL(2), Deutschbauer A(8), Neff N(3), Sonnenburg JL(9), Huang +KC(10), Fischbach MA(11). + +Author information: +(1)Department of Gastroenterology & Hepatology, Stanford School of Medicine, +Stanford, CA 94305, USA. Electronic address: alicec2@stanford.edu. +(2)Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. +(3)Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. +(4)Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, +Stanford University, Stanford, CA 94305, USA. +(5)Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; +Department of Microbiology and Immunology, Stanford University School of +Medicine, Stanford University, Stanford, CA 94305, USA. +(6)Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; +ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of +Microbiology and Immunology, Stanford University School of Medicine, Stanford +University, Stanford, CA 94305, USA. +(7)ChEM-H Institute, Stanford University, Stanford, CA 94305, USA. +(8)Environmental Genomics and Systems Biology Division, Lawrence Berkeley +National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial +Biology, University of California, Berkeley, Berkeley, CA 94720, USA. +(9)Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of +Microbiology and Immunology, Stanford University School of Medicine, Stanford +University, Stanford, CA 94305, USA. +(10)Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; +Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford +University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, +Stanford University School of Medicine, Stanford University, Stanford, CA 94305, +USA. Electronic address: kchuang@stanford.edu. +(11)Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; +Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford +University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, +Stanford University School of Medicine, Stanford University, Stanford, CA 94305, +USA. Electronic address: fischbach@fischbachgroup.org. + +Efforts to model the human gut microbiome in mice have led to important insights +into the mechanisms of host-microbe interactions. However, the model communities +studied to date have been defined or complex, but not both, limiting their +utility. Here, we construct and characterize in vitro a defined community of 104 +bacterial species composed of the most common taxa from the human gut microbiota +(hCom1). We then used an iterative experimental process to fill open niches: +germ-free mice were colonized with hCom1 and then challenged with a human fecal +sample. We identified new species that engrafted following fecal challenge and +added them to hCom1, yielding hCom2. In gnotobiotic mice, hCom2 exhibited +increased stability to fecal challenge and robust colonization resistance +against pathogenic Escherichia coli. Mice colonized by either hCom2 or a human +fecal community are phenotypically similar, suggesting that this consortium will +enable a mechanistic interrogation of species and genes on microbiome-associated +phenotypes. + +Copyright © 2022 Elsevier Inc. All rights reserved. + +DOI: 10.1016/j.cell.2022.08.003 +PMCID: PMC9691261 +PMID: 36070752 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of interests Stanford University and +the Chan Zuckerberg Biohub have patents pending for microbiome technologies on +which the authors are co-inventors. M.A.F. is a co-founder and director of +Federation Bio and Kelonia, a co-founder of Revolution Medicines, and a member +of the scientific advisory boards of NGM Bio and Zymergen. A.G.C. and K.N. have +been paid consultants to Federation Bio. A.R.B. has been an employee of +Federation Bio. \ No newline at end of file diff --git a/references_cache/pmid_36472419.txt b/references_cache/pmid_36472419.txt new file mode 100644 index 00000000..58328e44 --- /dev/null +++ b/references_cache/pmid_36472419.txt @@ -0,0 +1,60 @@ +1. mSystems. 2022 Dec 20;7(6):e0095122. doi: 10.1128/msystems.00951-22. Epub 2022 + Dec 6. + +A Reproducible and Tunable Synthetic Soil Microbial Community Provides New +Insights into Microbial Ecology. + +Coker J(1), Zhalnina K(2), Marotz C(1), Thiruppathy D(3), Tjuanta M(3), D'Elia +G(3), Hailu R(3), Mahosky T(3), Rowan M(3), Northen TR(2)(4), Zengler +K(1)(3)(5). + +Author information: +(1)Department of Pediatrics, University of California, San Diego, La Jolla, +California, USA. +(2)Environmental Genomics and Systems Biology Division, Berkeley Lab, Berkeley, +California, USA. +(3)Department of Bioengineering, University of California, San Diego, La Jolla, +California, USA. +(4)The DOE Joint Genome Institute, Berkeley Lab, Berkeley, California, USA. +(5)Center for Microbiome Innovation, University of California, San Diego, La +Jolla, California, USA. + +Microbial soil communities form commensal relationships with plants to promote +the growth of both parties. The optimization of plant-microbe interactions to +advance sustainable agriculture is an important field in agricultural research. +However, investigation in this field is hindered by a lack of model microbial +community systems and efficient approaches for building these communities. Two +key challenges in developing standardized model communities are maintaining +community diversity over time and storing/resuscitating these communities after +cryopreservation, especially considering the different growth rates of +organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms +commonly found in the rhizosphere of diverse plant species, isolated from soil +surrounding a single switchgrass plant, has been developed and optimized for in +vitro experiments. The model soil community grows reproducibly between +replicates and experiments, with a high community α-diversity being achieved +through growth in low-nutrient media and through the adjustment of the starting +composition ratios for the growth of individual organisms. The community can +additionally be cryopreserved with glycerol, allowing for easy replication and +dissemination of this in vitro system. Furthermore, the SynCom also grows +reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the +application of this community to an existing in vitro plant-microbe system. +EcoFABs allow reproducible research in model plant systems, offering the precise +control of environmental conditions and the easy measurement of plant microbe +metrics. Our results demonstrate the generation of a stable and diverse +microbial SynCom for the rhizosphere that can be used with EcoFAB devices and +can be shared between research groups for maximum reproducibility. IMPORTANCE +Microbes associate with plants in distinct soil communities to the benefit of +both the soil microbes and the plants. Interactions between plants and these +microbes can improve plant growth and health and are therefore a field of study +in sustainable agricultural research. In this study, a model community of 16 +soil bacteria has been developed to further the reproducible study of plant-soil +microbe interactions. The preservation of the microbial community has been +optimized for dissemination to other research settings. Overall, this work will +advance soil microbe research through the optimization of a robust, reproducible +model community. + +DOI: 10.1128/msystems.00951-22 +PMCID: PMC9765266 +PMID: 36472419 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_36532452.txt b/references_cache/pmid_36532452.txt new file mode 100644 index 00000000..2d7f5957 --- /dev/null +++ b/references_cache/pmid_36532452.txt @@ -0,0 +1,48 @@ +1. Front Microbiol. 2022 Dec 1;13:1074153. doi: 10.3389/fmicb.2022.1074153. +eCollection 2022. + +Stably transmitted defined microbial community in honeybees preserves Hafnia +alvei inhibition by regulating the immune system. + +Wang J(1), Lang H(1), Zhang W(2), Zhai Y(3)(4), Zheng L(3)(4), Chen H(3)(4), Liu +Y(3)(4), Zheng H(1). + +Author information: +(1)College of Food Science and Nutritional Engineering, China Agricultural +University, Beijing, China. +(2)Faculty of Agriculture and Food, Kunming University of Science and +Technology, Kunming, China. +(3)Shandong Academy of Agricultural Sciences, Institute of Plant Protection, +Jinan, China. +(4)Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural +Affairs, Jinan, China. + +The gut microbiota of honeybees is highly diverse at the strain level and +essential to the proper function and development of the host. Interactions +between the host and its gut microbiota, such as specific microbes regulating +the innate immune system, protect the host against pathogen infections. However, +little is known about the capacity of these strains deposited in one colony to +inhibit pathogens. In this study, we assembled a defined microbial community +based on phylogeny analysis, the 'Core-20' community, consisting of 20 strains +isolated from the honeybee intestine. The Core-20 community could trigger the +upregulation of immune gene expressions and reduce Hafnia alvei prevalence, +indicating immune priming underlies the microbial protective effect. Functions +related to carbohydrate utilization and the phosphoenolpyruvate-dependent sugar +phosphotransferase system (PTS systems) are represented in genomic analysis of +the defined community, which might be involved in manipulating immune responses. +Additionally, we found that the defined Core-20 community is able to colonize +the honeybee gut stably through passages. In conclusion, our findings highlight +that the synthetic gut microbiota could offer protection by regulating the host +immune system, suggesting that the strain collection can yield insights into +host-microbiota interactions and provide solutions to protect honeybees from +pathogen infections. + +Copyright © 2022 Wang, Lang, Zhang, Zhai, Zheng, Chen, Liu and Zheng. + +DOI: 10.3389/fmicb.2022.1074153 +PMCID: PMC9751035 +PMID: 36532452 + +Conflict of interest statement: The authors declare that the research was +conducted in the absence of any commercial or financial relationships that could +be construed as a potential conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_36847519.txt b/references_cache/pmid_36847519.txt new file mode 100644 index 00000000..a16c8cff --- /dev/null +++ b/references_cache/pmid_36847519.txt @@ -0,0 +1,67 @@ +1. mBio. 2023 Apr 25;14(2):e0318922. doi: 10.1128/mbio.03189-22. Epub 2023 Feb +27. + +Cross-Feedings, Competition, and Positive and Negative Synergies in a +Four-Species Synthetic Community for Anaerobic Degradation of Cellulose to +Methane. + +Wang D(1), Hunt KA(2), Candry P(2), Tao X(1)(3), Wofford NQ(1), Zhou +J(1)(3)(4)(5)(6), McInerney MJ(1), Stahl DA(2), Tanner RS(1), Zhou A(1)(3), +Winkler M(2), Pan C(1)(6). + +Author information: +(1)Department of Microbiology and Plant Biology, University of Oklahoma, Norman, +Oklahoma, USA. +(2)Department of Civil and Environmental Engineering, University of Washington, +Seattle, Washington, USA. +(3)Institute for Environmental Genomics, University of Oklahoma, Norman, +Oklahoma, USA. +(4)School of Civil Engineering and Environmental Sciences, University of +Oklahoma, Norman, Oklahoma, USA. +(5)Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, +Berkeley, California, USA. +(6)School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA. + +Complex interactions exist among microorganisms in a community to carry out +ecological processes and adapt to changing environments. Here, we constructed a +quad-culture consisting of a cellulolytic bacterium (Ruminiclostridium +cellulolyticum), a hydrogenotrophic methanogen (Methanospirillum hungatei), an +acetoclastic methanogen (Methanosaeta concilii), and a sulfate-reducing +bacterium (Desulfovibrio vulgaris). The four microorganisms in the quad-culture +cooperated via cross-feeding to produce methane using cellulose as the only +carbon source and electron donor. The community metabolism of the quad-culture +was compared with those of the R. cellulolyticum-containing tri-cultures, +bi-cultures, and mono-culture. Methane production was higher in the quad-culture +than the sum of the increases in the tri-cultures, which was attributed to a +positive synergy of four species. In contrast, cellulose degradation by the +quad-culture was lower than the additive effects of the tri-cultures which +represented a negative synergy. The community metabolism of the quad-culture was +compared between a control condition and a treatment condition with sulfate +addition using metaproteomics and metabolic profiling. Sulfate addition enhanced +sulfate reduction and decreased methane and CO2 productions. The cross-feeding +fluxes in the quad-culture in the two conditions were modeled using a community +stoichiometric model. Sulfate addition strengthened metabolic handoffs from R. +cellulolyticum to M. concilii and D. vulgaris and intensified substrate +competition between M. hungatei and D. vulgaris. Overall, this study uncovered +emergent properties of higher-order microbial interactions using a four-species +synthetic community. IMPORTANCE A synthetic community was designed using four +microbial species that together performed distinct key metabolic processes in +the anaerobic degradation of cellulose to methane and CO2. The microorganisms +exhibited expected interactions, such as cross-feeding of acetate from a +cellulolytic bacterium to an acetoclastic methanogen and competition of H2 +between a sulfate reducing bacterium and a hydrogenotrophic methanogen. This +validated our rational design of the interactions between microorganisms based +on their metabolic roles. More interestingly, we also found positive and +negative synergies as emergent properties of high-order microbial interactions +among three or more microorganisms in cocultures. These microbial interactions +can be quantitatively measured by adding and removing specific members. A +community stoichiometric model was constructed to represent the fluxes in the +community metabolic network. This study paved the way toward a more predictive +understanding of the impact of environmental perturbations on microbial +interactions sustaining geochemically significant processes in natural systems. + +DOI: 10.1128/mbio.03189-22 +PMCID: PMC10128006 +PMID: 36847519 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_37154752.txt b/references_cache/pmid_37154752.txt new file mode 100644 index 00000000..91f526ae --- /dev/null +++ b/references_cache/pmid_37154752.txt @@ -0,0 +1,60 @@ +1. Microbiol Spectr. 2023 Jun 15;11(3):e0452822. doi: 10.1128/spectrum.04528-22. +Epub 2023 May 8. + +Synthetic Denitrifying Communities Reveal a Positive and Dynamic +Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution. + +Wu B(1), Guan X(1), Deng T(1), Yang X(1), Li J(2), Zhou M(1), Wang C(1), Wang +S(1), Yan Q(1), Shu L(1), He Q(3), He Z(1)(2). + +Author information: +(1)Environmental Microbiomics Research Center, School of Environmental Science +and Engineering, Southern Marine Science and Engineering Guangdong Laboratory +(Zhuhai), Sun Yat-sen University, Guangzhou, China. +(2)College of Agronomy, Hunan Agricultural University, Changsha, China. +(3)Department of Civil and Environmental Engineering, The University of +Tennessee, Knoxville, Tennessee, USA. + +Biodiversity is vital for ecosystem functions and services, and many studies +have reported positive, negative, or neutral biodiversity-ecosystem functioning +(BEF) relationships in plant and animal systems. However, if the BEF +relationship exists and how it evolves remains elusive in microbial systems. +Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying +communities (SDCs) with a richness gradient spanning 1 to 12 species, which were +subjected to approximately 180 days (with 60 transfers) of experimental +evolution with generational changes in community functions continuously tracked. +A significant positive correlation was observed between community richness and +functions, represented by productivity (biomass) and denitrification rate, +however, such a positive correlation was transient, only significant in earlier +days (0 to 60) during the evolution experiment (180 days). Also, we found that +community functions generally increased throughout the evolution experiment. +Furthermore, microbial community functions with lower richness exhibited greater +increases than those with higher richness. Biodiversity effect analysis revealed +positive BEF relationships largely attributable to complementary effects, which +were more pronounced in communities with lower richness than those with higher +richness. This study is one of the first studies that advances our understanding +of BEF relationships and their evolutionary mechanisms in microbial systems, +highlighting the crucial role of evolution in predicting the BEF relationship in +microbial systems. IMPORTANCE Despite the consensus that biodiversity supports +ecosystem functioning, not all experimental models of macro-organisms support +this notion with positive, negative, or neutral biodiversity-ecosystem +functioning (BEF) relationships reported. The fast-growing, metabolically +versatile, and easy manipulation nature of microbial communities allows us to +explore well the BEF relationship and further interrogate if the BEF +relationship remains constant during long-term community evolution. Here, we +constructed multiple synthetic denitrifying communities (SDCs) by randomly +selecting species from a candidate pool of 12 Shewanella denitrifiers. These +SDCs differ in species richness, spanning 1 to 12 species, and were monitored +continuously for community functional shifts during approximately 180-day +parallel cultivation. We demonstrated that the BEF relationship was dynamic with +initially (day 0 to 60) greater productivity and denitrification among SDCs of +higher richness. However, such pattern was reversed thereafter with greater +productivity and denitrification increments in lower-richness SDCs, likely due +to a greater accumulation of beneficial mutations during the experimental +evolution. + +DOI: 10.1128/spectrum.04528-22 +PMCID: PMC10269844 +PMID: 37154752 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_37207729.txt b/references_cache/pmid_37207729.txt new file mode 100644 index 00000000..82ed88da --- /dev/null +++ b/references_cache/pmid_37207729.txt @@ -0,0 +1,56 @@ +1. Environ Res. 2023 Aug 15;231(Pt 2):116184. doi: 10.1016/j.envres.2023.116184. +Epub 2023 May 18. + +Synthetic phylogenetically diverse communities promote denitrification and +stability. + +Zhou M(1), Guan X(1), Deng T(1), Hu R(1), Qian L(1), Yang X(1), Wu B(1), Li +J(2), He Q(3), Shu L(1), Yan Q(4), He Z(5). + +Author information: +(1)Environmental Microbiomics Research Center, School of Environmental Science +and Engineering, Southern Marine Science and Engineering Guangdong Laboratory +(Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, +Guangzhou, 510006, China. +(2)College of Agronomy, Hunan Agricultural University, Changsha, 410128, China. +(3)Department of Civil and Environmental Engineering, The University of +Tennessee, Knoxville, TN, 37996, USA. +(4)Environmental Microbiomics Research Center, School of Environmental Science +and Engineering, Southern Marine Science and Engineering Guangdong Laboratory +(Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, +Guangzhou, 510006, China. Electronic address: yanqingyun@sml-zhuhai.cn. +(5)Environmental Microbiomics Research Center, School of Environmental Science +and Engineering, Southern Marine Science and Engineering Guangdong Laboratory +(Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, +Guangzhou, 510006, China; College of Agronomy, Hunan Agricultural University, +Changsha, 410128, China. Electronic address: hezhili@sml-zhuhai.cn. + +Denitrification is an important process of the global nitrogen cycle as some of +its intermediates are environmentally important or related to global warming. +However, how the phylogenetic diversity of denitrifying communities affects +their denitrification rates and temporal stability remains unclear. Here we +selected denitrifiers based on their phylogenetic distance to construct two +groups of synthetic denitrifying communities: one closely related (CR) group +with all strains from the genus Shewanella and the other distantly related (DR) +group with all constituents from different genera. All synthetic denitrifying +communities (SDCs) were experimentally evolved for 200 generations. The results +showed that high phylogenetic diversity followed by experimental evolution +promoted the function and stability of synthetic denitrifying communities. +Specifically, the productivity and denitrification rates were significantly +(P < 0.05) higher with Paracocus denitrificans as the dominant species (since +the 50th generation) in the DR community than those in the CR community. The DR +community also showed significantly (t = 7.119, df = 10, P < 0.001) higher +stability through overyielding and asynchrony of species fluctuations, and +showed more complementarity than the CR group during the experimental evolution. +This study has important implications for applying synthetic communities to +remediate environmental problems and mitigate greenhouse gas emissions. + +Copyright © 2023 Elsevier Inc. All rights reserved. + +DOI: 10.1016/j.envres.2023.116184 +PMID: 37207729 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_37275168.txt b/references_cache/pmid_37275168.txt new file mode 100644 index 00000000..01477337 --- /dev/null +++ b/references_cache/pmid_37275168.txt @@ -0,0 +1,60 @@ +1. Front Microbiol. 2023 May 19;14:1167839. doi: 10.3389/fmicb.2023.1167839. +eCollection 2023. + +Promotion of the growth and yield of Zea mays by synthetic microbial communities +from Jala maize. + +De la Vega-Camarillo E(1), Sotelo-Aguilar J(1), Rios-Galicia B(1), +Mercado-Flores Y(2), Arteaga-Garibay R(3), Villa-Tanaca L(1), +Hernández-Rodríguez C(1). + +Author information: +(1)Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de +Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico +Nacional, Ciudad de México, Mexico. +(2)Laboratorio de Aprovechamiento Integral de Recursos Bióticos, Universidad +Politécnica de Pachuca, Hidalgo, Mexico. +(3)Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos +Genéticos, INIFAP, Jalisco, Mexico. + +Plant growth-promoting bacteria (PGPB) are a source of nutrient supply, +stimulate plant growth, and even act in the biocontrol of phytopathogens. +However, these phenotypic traits have rarely been explored in culturable +bacteria from native maize landraces. In this study, synthetic microbial +communities (SynCom) were assembled with a set of PGPB isolated from the Jala +maize landrace, some of them with additional abilities for the biocontrol of +phytopathogenic fungi and the stimulation of plant-induced systemic resistance +(ISR). Three SynCom were designed considering the phenotypic traits of bacterial +strains, including Achromobacter xylosoxidans Z2K8, Burkholderia sp. Z1AL11, +Klebsiella variicola R3J3HD7, Kosakonia pseudosacchari Z2WD1, Pantoea ananatis +E2HD8, Pantoea sp. E2AD2, Phytobacter diazotrophicus Z2WL1, Pseudomonas +protegens E1BL2, and P. protegens E2HL9. Plant growth promotion in gnotobiotic +and greenhouse seedlings assays was performed with Conejo landrace; meanwhile, +open field tests were carried out on hybrid CPL9105W maize. In all experimental +models, a significant promotion of plant growth was observed. In gnotobiotic +assays, the roots and shoot length of the maize seedlings increased 4.2 and 3.0 +times, respectively, compared to the untreated control. Similarly, the sizes and +weights of the roots and shoots of the plants increased significantly in the +greenhouse assays. In the open field assay performed with hybrid CPL9105W maize, +the yield increased from 11 tons/ha for the control to 16 tons/ha inoculated +with SynCom 3. In addition, the incidence of rust fungal infections decreased +significantly from 12.5% in the control to 8% in the treatment with SynCom 3. +All SynCom designs promoted the growth of maize in all assays. However, SynCom 3 +formulated with A. xylosoxidans Z2K8, Burkholderia sp. Z1AL11, K. variicola +R3J3HD7, P. ananatis E2HD8, P. diazotrophicus Z2WL1, and P. protegens E1BL2 +displayed the best results for promoting plant growth, their yield, and the +inhibition of fungal rust. This study demonstrated the biotechnological +eco-friendly plant growth-promoting potential of SynCom assemblies with +culturable bacteria from native maize landraces for more sustainable and +economic agriculture. + +Copyright © 2023 De la Vega-Camarillo, Sotelo-Aguilar, Rios-Galicia, +Mercado-Flores, Arteaga-Garibay, Villa-Tanaca and Hernández-Rodríguez. + +DOI: 10.3389/fmicb.2023.1167839 +PMCID: PMC10235630 +PMID: 37275168 + +Conflict of interest statement: The authors declare that the research was +conducted in the absence of any commercial or financial relationships that could +be construed as a potential conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_37299063.txt b/references_cache/pmid_37299063.txt new file mode 100644 index 00000000..9525a13f --- /dev/null +++ b/references_cache/pmid_37299063.txt @@ -0,0 +1,40 @@ +1. Plants (Basel). 2023 May 24;12(11):2083. doi: 10.3390/plants12112083. + +Nodule Synthetic Bacterial Community as Legume Biofertilizer under Abiotic +Stress in Estuarine Soils. + +Flores-Duarte NJ(1), Navarro-Torre S(1), Mateos-Naranjo E(2), Redondo-Gómez +S(2), Pajuelo E(1), Rodríguez-Llorente ID(1). + +Author information: +(1)Departamento de Microbiología y Parasitología, Universidad de Sevilla, 41012 +Seville, Spain. +(2)Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, 41012 +Seville, Spain. + +Estuaries are ecologically important ecosystems particularly affected by climate +change and human activities. Our interest is focused on the use of legumes to +fight against the degradation of estuarine soils and loss of fertility under +adverse conditions. This work was aimed to determine the potential of a nodule +synthetic bacterial community (SynCom), including two Ensifer sp. and two +Pseudomonas sp. strains isolated from Medicago spp. nodules, to promote M. +sativa growth and nodulation in degraded estuarine soils under several abiotic +stresses, including high metal contamination, salinity, drought and high +temperature. These plant growth promoting (PGP) endophytes were able to maintain +and even increase their PGP properties in the presence of metals. Inoculation +with the SynCom in pots containing soil enhanced plant growth parameters (from +3- to 12-fold increase in dry weight), nodulation (from 1.5- to 3-fold increase +in nodules number), photosynthesis and nitrogen content (up to 4-fold under +metal stress) under all the controlled conditions tested. The increase in plant +antioxidant enzymatic activities seems to be a common and important mechanism of +plant protection induced by the SynCom under abiotic stress conditions. The +SynCom increased M. sativa metals accumulation in roots, with low levels of +metals translocation to shoots. Results indicated that the SynCom used in this +work is an appropriate ecological and safe tool to improve Medicago growth and +adaptation to degraded estuarine soils under climate change conditions. + +DOI: 10.3390/plants12112083 +PMCID: PMC10255395 +PMID: 37299063 + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_37549573.txt b/references_cache/pmid_37549573.txt new file mode 100644 index 00000000..a595f654 --- /dev/null +++ b/references_cache/pmid_37549573.txt @@ -0,0 +1,59 @@ +1. Plant Physiol Biochem. 2023 Sep;202:107941. doi: 10.1016/j.plaphy.2023.107941. + Epub 2023 Aug 5. + +A simplified synthetic rhizosphere bacterial community steers plant oxylipin +pathways for preventing foliar phytopathogens. + +Huang J(1), Zhu L(2), Lu X(1), Cui F(3), Wang J(1), Zhou C(4). + +Author information: +(1)Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural +Affairs, Anhui Science and Technology University, Chuzhou 233100, China. +(2)Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural +Affairs, Anhui Science and Technology University, Chuzhou 233100, China; School +of Life Science and Technology, Tongji University, Shanghai 200092, China. +(3)Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural +Affairs, Anhui Science and Technology University, Chuzhou 233100, China. +Electronic address: cuif@ahstu.edu.cn. +(4)Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural +Affairs, Anhui Science and Technology University, Chuzhou 233100, China; Jiangsu +Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative +Innovation Center of Solid Organic Wastes, Educational Ministry Engineering +Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing +210095, China. Electronic address: zhoucheng@njau.edu.cn. + +Rhizosphere-enriched microbes induced by foliar phytopathogen infection can be +assembled into a functional community to enhance plant defense mechanisms. +However, the functions of stably-colonizing rhizosphere microbiota are rarely +investigated. In this study, Botrytis cinerea infection changed rhizosphere +bacterial communities in tomato plants. The phytopathogen-infected plants +recruited specific rhizosphere bacterial taxa, while several bacterial taxa +stably colonized the rhizosphere, regardless of phytopathogen infection. Through +the analysis of the rhizosphere bacterial community, we established a synthetic +community harboring 8 phytopathogen-inducible and 30 stably-colonizing bacteria +species. Furthermore, the 38-species community was simplified into a +three-species community, consisting of one phytopathogen-inducible +(Asticcacaulis sp.) and two stably-colonizing species (Arachidicoccus sp. And +Phenylobacterium sp.). The simplified community provided a durable protection +for the host plants by synergistic effects, with the phytopathogen-inducible +species triggering plant defense responses and the stably-colonizing species +promoting biofilm formation. The simplified community exhibited similar +protective effects as the 38-species community. Moreover, the activation of +oxylipin pathways in the phytopathogen-infected leaves was significantly +intensified by the simplified community. However, the inhibited biosynthesis of +antimicrobial divinyl ethers, including colneleic and colnelenic acid, fully +abolished the community-induced plant disease resistance. In contrast, +transgenic plants overexpressing SlLOX5 and SlDES1, with higher levels of +divinyl ethers, displayed stronger resistance against B. cinerea compared to +wild-type plants. Collectively, these findings provided insights into the +utilization of the simplified community for preventing gray mold disease. + +Copyright © 2023 Elsevier Masson SAS. All rights reserved. + +DOI: 10.1016/j.plaphy.2023.107941 +PMID: 37549573 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_37774801.txt b/references_cache/pmid_37774801.txt new file mode 100644 index 00000000..1de49022 --- /dev/null +++ b/references_cache/pmid_37774801.txt @@ -0,0 +1,48 @@ +1. Bioresour Technol. 2023 Dec;389:129799. doi: 10.1016/j.biortech.2023.129799. +Epub 2023 Sep 27. + +Construction of a synthetic microbial community based on multiomics linkage +technology and analysis of the mechanism of lignocellulose degradation. + +Chen J(1), Cai Y(1), Wang Z(1), Xu Z(1), Li J(1), Ma X(1), Zhuang W(2), Liu +D(2), Wang S(3), Song A(4), Xu J(1), Ying H(2). + +Author information: +(1)School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, +Zhengzhou 450001, China. +(2)School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, +Zhengzhou 450001, China; National Engineering Technique Research Center for +Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, +College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech +University, Nanjing 210009, China. +(3)School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, +Zhengzhou 450001, China. Electronic address: shileiwang@zzu.edu.cn. +(4)College of Life Science, Henan Agricultural University, 218 Ping An Avenue, +Zhengdong New District, Zhengzhou 450002, China. + +The efficient degradation of lignocellulose is a bottleneck for its integrated +utilization. This research performed species analysis and made functional +predictions in various ecosystems using multiomics coupling to construct a core +synthetic microbial community with efficient lignocellulose degradation +function. The synthetic microbial community was employed to degrade corn straw +via solid-state fermentation. The degradation mechanisms were resolved using +proteomics. The optimum culture conditions included 10% inoculum level (w/v), 4% +nitrogen source ratio and a fermentation time of 23 d. Under these conditions, +the degradation rates of cellulose, hemicellulose, and lignin were 34.91%, +45.94%, and 23.34%, respectively. Proteomic analysis revealed that lignin +1,4-β-xylanase, β-xylosidase and endo-1,4-β-xylanase were closely related to +lignocellulose degradation. The metabolic pathways involved in lignocellulose +degradation and the functional roles of eight strains were obtained. The +synthesis of a microbial community via multiomics linkage technology can +effectively decompose lignocellulose, which is useful for their further +utilization. + +Copyright © 2023 Elsevier Ltd. All rights reserved. + +DOI: 10.1016/j.biortech.2023.129799 +PMID: 37774801 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of Competing Interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_38277828.txt b/references_cache/pmid_38277828.txt new file mode 100644 index 00000000..6730c60a --- /dev/null +++ b/references_cache/pmid_38277828.txt @@ -0,0 +1,55 @@ +1. Water Res. 2024 Mar 1;251:121162. doi: 10.1016/j.watres.2024.121162. Epub 2024 + Jan 18. + +Deciphering the potential role of quorum quenching in efficient aerobic +denitrification driven by a synthetic microbial community. + +He Y(1), Yun H(2), Peng L(1), Ji J(1), Wang W(1), Li X(3). + +Author information: +(1)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou 730000, China. +(2)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou 730000, China; Gansu Key Laboratory of Biomonitoring and +Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou +University, Tianshui South Road #222, Lanzhou 730000, China. Electronic address: +yunh@lzu.edu.cn. +(3)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou 730000, China; Gansu Key Laboratory of Biomonitoring and +Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou +University, Tianshui South Road #222, Lanzhou 730000, China. Electronic address: +xkli@lzu.edu.cn. + +Low efficiency is one of the main challenges for the application of aerobic +denitrification technology in wastewater treatment. To improve denitrification +efficiency, a synthetic microbial community (SMC) composed of denitrifiers +Acinetobacter baumannii N1 (AC), Pseudomonas aeruginosa N2 (PA) and Aeromonas +hydrophila (AH) were constructed. The nitrate (NO3--N) reduction efficiency of +the SMC reached 97 % with little nitrite (NO2--N) accumulation, compared to the +single-culture systems and co-culture systems. In the SMC, AH proved to mainly +contribute to NO3--N reduction with the assistance of AC, while PA exerted +NO2--N reduction. AC and AH secreted N-hexanoyl-DL-homoserine lactone (C6-HSL) +to promote the electron transfer from the quinone pool to nitrate reductase. The +declined N-(3-oxododecanoyl)-L-homoserine lactone (3OC12-HSL), resulting from +quorum quenching (QQ) by AH, stimulated the excretion of pyocyanin, which could +improve the electron transfer from complex III to downstream denitrifying +enzymes for NO2--N reduction. In addition, C6-HSL mainly secreted by PA led to +the up-regulation of TCA cycle-related genes and provided sufficient energy +(such as NADH and ATP) for aerobic denitrification. In conclusion, members of +the SMC achieved efficient denitrification through the interactions between QQ, +electron transfer, and energy metabolism induced by N-acyl-homoserine lactones +(AHLs). This study provided a theoretical basis for the engineering application +of synthetic microbiome to remove nitrate wastewater. + +Copyright © 2024. Published by Elsevier Ltd. + +DOI: 10.1016/j.watres.2024.121162 +PMID: 38277828 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_38324131.txt b/references_cache/pmid_38324131.txt new file mode 100644 index 00000000..7f961b98 --- /dev/null +++ b/references_cache/pmid_38324131.txt @@ -0,0 +1,22 @@ +1. Sci China Life Sci. 2024 May;67(5):1085-1086. doi: 10.1007/s11427-024-2533-2. +Epub 2024 Feb 2. + +A synthetic microbial community used as a bioinoculant can overcome rice +production constraints in acid soils. + +O'Callaghan M(1), Shi S(2). + +Author information: +(1)Resilient Agriculture Group, AgResearch, Lincoln, Christcurch, 8140, New +Zealand. maureen.ocallaghan@agresearch.co.nz. +(2)Resilient Agriculture Group, AgResearch, Lincoln, Christcurch, 8140, New +Zealand. + +A customised synthetic microbial community (SynCom) composed of carefully +selected rhizosphere-competent bacterial strains improved rice growth, yield and +resistance to soil acidity and Al toxicity. + +© 2024. Science China Press. + +DOI: 10.1007/s11427-024-2533-2 +PMID: 38324131 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_38520150.txt b/references_cache/pmid_38520150.txt new file mode 100644 index 00000000..cd7e18fa --- /dev/null +++ b/references_cache/pmid_38520150.txt @@ -0,0 +1,35 @@ +1. J Appl Microbiol. 2024 Apr 1;135(4):lxae073. doi: 10.1093/jambio/lxae073. + +Seed-borne bacterial synthetic community resists seed pathogenic fungi and +promotes plant growth. + +Luo DL(1), Huang SY(1), Ma CY(1), Zhang XY(1), Sun K(1), Zhang W(1), Dai CC(1). + +Author information: +(1)Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu +Engineering and Technology and Research Center for Industrialization of +Microbial Resources, College of Life Sciences, Nanjing Normal University, +Nanjing, Jiangsu 210023, China. + +AIMS: In this study, the control effects of synthetic microbial communities +composed of peanut seed bacteria against seed aflatoxin contamination caused by +Aspergillus flavus and root rot by Fusarium oxysporum were evaluated. +METHODS AND RESULTS: Potentially conserved microbial synthetic communities (C), +growth-promoting synthetic communities (S), and combined synthetic communities +(CS) of peanut seeds were constructed after 16S rRNA Illumina sequencing, strain +isolation, and measurement of plant growth promotion indicators. Three synthetic +communities showed resistance to root rot and CS had the best effect after +inoculating into peanut seedlings. This was achieved by increased defense enzyme +activity and activated salicylic acid (SA)-related, systematically induced +resistance in peanuts. In addition, CS also inhibited the reproduction of A. +flavus on peanut seeds and the production of aflatoxin. These effects are +related to bacterial degradation of toxins and destruction of mycelia. +CONCLUSIONS: Inoculation with a synthetic community composed of seed bacteria +can help host peanuts resist the invasion of seeds by A. flavus and seedlings by +F. oxysporum and promote the growth of peanut seedlings. + +© The Author(s) 2024. Published by Oxford University Press on behalf of Applied +Microbiology International. + +DOI: 10.1093/jambio/lxae073 +PMID: 38520150 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_38748977.txt b/references_cache/pmid_38748977.txt new file mode 100644 index 00000000..6c5094d4 --- /dev/null +++ b/references_cache/pmid_38748977.txt @@ -0,0 +1,42 @@ +1. Environ Sci Technol. 2024 May 28;58(21):9446-9455. doi: +10.1021/acs.est.4c02789. Epub 2024 May 15. + +Construction of a Synthetic Microbial Community for Enzymatic Pretreatment of +Wheat Straw for Biogas Production via Anaerobic Digestion. + +Chen J(1), Cai Y(1)(2), Wang Z(1), Wang S(2), Li J(1), Song C(2), Zhuang +W(1)(3), Liu D(1)(3), Wang S(1), Song A(4), Xu J(1), Ying H(1)(3). + +Author information: +(1)School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, +Zhengzhou 450001, China. +(2)Luzhou LaoJiao Co., Ltd, Luzhou 646000, China. +(3)National Engineering Technique Research Center for Biotechnology, State Key +Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology +and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China. +(4)College of Life Science, Henan Agricultural University, 218 Ping An Avenue, +Zhengdong New District, Zhengzhou 450002, China. + +Biological pretreatment is a viable method for enhancing biogas production from +straw crops, with the improvement in lignocellulose degradation efficiency being +a crucial factor in this process. Herein, a metagenomic approach was used to +screen core microorganisms (Bacillus subtilis, Acinetobacter johnsonii, +Trichoderma viride, and Aspergillus niger) possessing lignocellulose-degrading +abilities among samples from three environments: pile retting wheat straw (WS), +WS returned to soil, and forest soil. Subsequently, synthetic microbial +communities were constructed for fermentation-enzyme production. The crude +enzyme solution obtained was used to pretreat WS and was compared with two +commercial enzymes. The synthetic microbial community enzyme-producing +pretreatment (SMCEP) yielded the highest enzymatic digestion efficacy for WS, +yielding cellulose, hemicellulose, and lignin degradation rates of 39.85, 36.99, +and 19.21%, respectively. Furthermore, pretreatment of WS with an enzyme +solution, followed by anaerobic digestion achieved satisfactory results. SMCEP +displayed the highest cumulative biogas production at 801.16 mL/g TS, which was +38.79% higher than that observed for WS, 22.15% higher than that of solid-state +commercial enzyme pretreatment and 25.41% higher than that of liquid commercial +enzyme pretreatment. These results indicate that enzyme-pretreated WS can +significantly enhance biogas production. This study represents a solution to the +environmental burden and energy use of crop residues. + +DOI: 10.1021/acs.est.4c02789 +PMID: 38748977 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_38840214.txt b/references_cache/pmid_38840214.txt new file mode 100644 index 00000000..f89486dc --- /dev/null +++ b/references_cache/pmid_38840214.txt @@ -0,0 +1,60 @@ +1. Microbiome. 2024 Jun 5;12(1):101. doi: 10.1186/s40168-024-01814-z. + +Synthetic community derived from grafted watermelon rhizosphere provides +protection for ungrafted watermelon against Fusarium oxysporum via microbial +synergistic effects. + +Qiao Y(1), Wang Z(1), Sun H(1), Guo H(1), Song Y(2), Zhang H(1), Ruan Y(1), Xu +Q(1)(3), Huang Q(1), Shen Q(1), Ling N(4)(5). + +Author information: +(1)Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab +for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, +210095, China. +(2)Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht +University, Padualaan 8, Utrecht, 3584 CH, the Netherlands. +(3)Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement +and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and +Technology, Lanzhou University, Lanzhou, 730020, China. +(4)Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab +for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, +210095, China. nling@njau.edu.cn. +(5)Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement +and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and +Technology, Lanzhou University, Lanzhou, 730020, China. nling@njau.edu.cn. + +BACKGROUND: Plant microbiota contributes to plant growth and health, including +enhancing plant resistance to various diseases. Despite remarkable progress in +understanding diseases resistance in plants, the precise role of rhizosphere +microbiota in enhancing watermelon resistance against soil-borne diseases +remains unclear. Here, we constructed a synthetic community (SynCom) of 16 core +bacterial strains obtained from the rhizosphere of grafted watermelon plants. We +further simplified SynCom and investigated the role of bacteria with synergistic +interactions in promoting plant growth through a simple synthetic community. +RESULTS: Our results demonstrated that the SynCom significantly enhanced the +growth and disease resistance of ungrafted watermelon grown in non-sterile soil. +Furthermore, analysis of the amplicon and metagenome data revealed the pivotal +role of Pseudomonas in enhancing plant health, as evidenced by a significant +increase in the relative abundance and biofilm-forming pathways of Pseudomonas +post-SynCom inoculation. Based on in vitro co-culture experiments and bacterial +metabolomic analysis, we selected Pseudomonas along with seven other members of +the SynCom that exhibited synergistic effects with Pseudomonas. It enabled us to +further refine the initially constructed SynCom into a simplified SynCom +comprising the eight selected bacterial species. Notably, the plant-promoting +effects of simplified SynCom were similar to those of the initial SynCom. +Furthermore, the simplified SynCom protected plants through synergistic effects +of bacteria. +CONCLUSIONS: Our findings suggest that the SynCom proliferate in the rhizosphere +and mitigate soil-borne diseases through microbial synergistic interactions, +highlighting the potential of synergistic effects between microorganisms in +enhancing plant health. This study provides a novel insight into using the +functional SynCom as a promising solution for sustainable agriculture. Video +Abstract. + +© 2024. The Author(s). + +DOI: 10.1186/s40168-024-01814-z +PMCID: PMC11151650 +PMID: 38840214 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no competing interests. \ No newline at end of file diff --git a/references_cache/pmid_39111313.txt b/references_cache/pmid_39111313.txt new file mode 100644 index 00000000..dda2a7eb --- /dev/null +++ b/references_cache/pmid_39111313.txt @@ -0,0 +1,58 @@ +1. Cell Rep Methods. 2024 Aug 19;4(8):100832. doi: 10.1016/j.crmeth.2024.100832. +Epub 2024 Aug 6. + +SkinCom, a synthetic skin microbial community, enables reproducible +investigations of the human skin microbiome. + +Lekbua A(1), Thiruppathy D(2), Coker J(3), Weng Y(4), Askarian F(3), Kousha +A(3), Marotz C(3), Hauw A(3), Nizet V(5), Zengler K(6). + +Author information: +(1)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA; School of +Biological Sciences, University of California, San Diego, La Jolla, CA 92093, +USA. +(2)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA; Department of +Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA. +(3)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA. +(4)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and +Systems Biology Program, University of California, San Diego, La Jolla, CA +92093, USA. +(5)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA; Glycobiology +Research and Training Center, University of California, San Diego, La Jolla, CA +92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of +California, San Diego, La Jolla, CA 92093, USA. +(6)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA; Department of +Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; +Center for Microbiome Innovation, University of California, San Diego, La Jolla, +CA 92093, USA; Program in Materials Science and Engineering, University of +California, San Diego, La Jolla, CA 92093, USA. Electronic address: +kzengler@ucsd.edu. + +Existing models of the human skin have aided our understanding of skin health +and disease. However, they currently lack a microbial component, despite +microbes' demonstrated connections to various skin diseases. Here, we present a +robust, standardized model of the skin microbial community (SkinCom) to support +in vitro and in vivo investigations. Our methods lead to the formation of an +accurate, reproducible, and diverse community of aerobic and anaerobic bacteria. +Subsequent testing of SkinCom on the dorsal skin of mice allowed for DNA and RNA +recovery from both the applied SkinCom and the dorsal skin, highlighting its +practicality for in vivo studies and -omics analyses. Furthermore, 66% of the +responses to common cosmetic chemicals in vitro were in agreement with a human +trial. Therefore, SkinCom represents a valuable, standardized tool for +investigating microbe-metabolite interactions and facilitates the experimental +design of in vivo studies targeting host-microbe relationships. + +Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved. + +DOI: 10.1016/j.crmeth.2024.100832 +PMCID: PMC11384088 +PMID: 39111313 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of interests The authors declare no +competing interests. \ No newline at end of file diff --git a/references_cache/pmid_39481489.txt b/references_cache/pmid_39481489.txt new file mode 100644 index 00000000..990d5998 --- /dev/null +++ b/references_cache/pmid_39481489.txt @@ -0,0 +1,58 @@ +1. Chemosphere. 2024 Nov;367:143650. doi: 10.1016/j.chemosphere.2024.143650. Epub + 2024 Nov 1. + +A synthetic bacterial community engineered from Miscanthus floridulus roots +enhances ammonia nitrogen removal in ionic rare earth mine tailings. + +Zhaoyu K(1), Ye J(1), Pei K(1), He Y(1), Wang B(1), Huang S(1), Cai Q(1), Liu +Y(1), Ge G(2), Wu L(3). + +Author information: +(1)School of Life Science, Key Laboratory of Poyang Lake Environment and +Resource Utilization, Ministry of Education, Nanchang University, Nanchang, +330022, China. +(2)School of Life Science, Key Laboratory of Poyang Lake Environment and +Resource Utilization, Ministry of Education, Nanchang University, Nanchang, +330022, China. Electronic address: gge@ncu.edu.cn. +(3)School of Life Science, Key Laboratory of Poyang Lake Environment and +Resource Utilization, Ministry of Education, Nanchang University, Nanchang, +330022, China. Electronic address: ncusk724@hotmail.com. + +Ammonium sulfate, as the primary leaching agent, has caused significant nitrogen +pollution in rare earth elements (REEs) mining areas. Phytoremediation is a +promising remediation method, relying on the synergistic relationships between +plants and their root-associated microbiome. Nevertheless, harnessing the +microbiome to accelerate nitrogen transformation and absorption by plants is +challenging. Here, we investigated the composition, activities and culturable +fraction of the root bacterial microbiome of the pioneer plant Miscanthus +floridulus grown in a REEs tailing soil containing a high ammonia nitrogen (AN) +concentration at 344.35 mg kg-1. Based on this, we constructed a simplified +synthetic microbial community (SynCom) derived from the roots of M. floridulus, +possessing nitrification and denitrification capabilities, to help REEs mine +plants efficiently convert pollutant AN into nutrients, thereby enhancing plant +growth and AN removal. This SynCom, consisting of 10 bacterial strains, included +species of the genera Burkholderia (5) Paraburkholderia (1), Curtobacterium (1), +Leifsonia (1) and Sinomonas (2). As a result, this SynCom alone achieved a +significant reduction of 24.8% in AN content in tailing soil. When the SynCom +inoculated with plants, the reduction in AN was even more significant (32.6%), +surpassing the reduction achieved solely by plants (25.5%). Moreover, live +SynCom inoculation significantly increased shoot and root biomass by 39.8% and +49.7%, respectively, compared to dead SynCom inoculation. These results indicate +that the reduction in AN can be attributed to the SynCom's nitrification and +denitrification capabilities, as well as its ability to enhance plant nitrogen +absorption by stimulating their growth. Notably, seven nitrifying and +denitrifying strains of the SynCom are particularly enriched, suggesting that +plant roots selectively recruit nitrogen cycle-related bacteria to accelerate +nitrogen transformation and absorption. These results provide a practical +solution for harnessing the synergistic relationships between plants and their +root microbiome in environmental remediation efforts. + +Copyright © 2024 Elsevier Ltd. All rights reserved. + +DOI: 10.1016/j.chemosphere.2024.143650 +PMID: 39481489 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_39684532.txt b/references_cache/pmid_39684532.txt new file mode 100644 index 00000000..52ee27dc --- /dev/null +++ b/references_cache/pmid_39684532.txt @@ -0,0 +1,47 @@ +1. Int J Mol Sci. 2024 Nov 28;25(23):12819. doi: 10.3390/ijms252312819. + +Synthetic Microbial Community Isolated from Intercropping System Enhances P +Uptake in Rice. + +Ma H(1), Zhang H(1), Zheng C(2), Liu Z(1), Wang J(3)(4), Tian P(1), Wu Z(1), +Zhang H(5). + +Author information: +(1)Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China. +(2)ISPA, INRAE, F-33140 Villenave d'Ornon, France. +(3)State Key Laboratory of Vegetation and Environmental Change, Institute of +Botany, Chinese Academy of Sciences, Beijing 100093, China. +(4)China National Botanical Garden, Beijing 100093, China. +(5)Institute of Soil and Water Resources and Environmental Science, College of +Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of +Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, +China. + +Changes in root traits and rhizosphere microbiome are important ways to optimize +plant phosphorus (P) efficiency and promote multifunctionality in intercropping. +However, whether and how synthetic microbial communities isolated from +polyculture systems can facilitate plant growth and P uptake are still largely +unknown. A field experiment was first carried out to assess the rice yield and P +uptake in the rice/soybean intercropping systems, and a synthetic microbial +community (SynCom) isolated from intercropped rice was then constructed to +elucidate the potential mechanisms of growth-promoting effects on rice growth +and P uptake in a series of pot experiments. Our results showed that the yield +and P uptake of intercropped rice were lower than those of rice grown in +monoculture. However, bacterial networks in the rice rhizosphere were more +stable in polyculture, exhibiting more hub nodes and greater modularity compared +to the rice monoculture. A bacterial synthetic community (SynCom) composed of +four bacterial strains (Variovorax paradoxus, Novosphingobium subterraneum, +Hydrogenophaga pseudoflava, Acidovorax sp.) significantly enhanced the biomass +and P uptake of potted rice plants. These growth-promoting effects are +underpinned by multiple pathways, including the direct activation of soil +available P, increased root surface area and root tip number, reduced root +diameter, and promotion of root-to-shoot P translocation through up-regulation +of Pi transporter genes (OsPht1;1, OsPht1;2, OsPht1;4, OsPht1;6). This study +highlights the potential of harnessing synthetic microbial communities to +enhance nutrient acquisition and improve crop production. + +DOI: 10.3390/ijms252312819 +PMCID: PMC11641191 +PMID: 39684532 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflicts of interest. \ No newline at end of file diff --git a/references_cache/pmid_39858916.txt b/references_cache/pmid_39858916.txt new file mode 100644 index 00000000..318a8c73 --- /dev/null +++ b/references_cache/pmid_39858916.txt @@ -0,0 +1,44 @@ +1. Microorganisms. 2025 Jan 13;13(1):148. doi: 10.3390/microorganisms13010148. + +Synthetic Microbial Communities Enhance Pepper Growth and Root Morphology by +Regulating Rhizosphere Microbial Communities. + +You T(1)(2)(3), Liu Q(2)(3), Chen M(1)(2)(3), Tang S(2), Ou L(1), Li D(2)(3). + +Author information: +(1)College of Horticulture, Hunan Agricultural University, Changsha 410125, +China. +(2)Hunan Provincial Key Laboratory of Agroecological Engineering, Key Laboratory +of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical +Agriculture, Chinese Academy of Sciences, Changsha 410125, China. +(3)Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang +Observation and Research Station for Karst Ecosystems, Chinese Academy of +Sciences, Huanjiang 547100, China. + +Synthetic microbial community (SynCom) application is efficient in promoting +crop yield and soil health. However, few studies have been conducted to enhance +pepper growth via modulating rhizosphere microbial communities by SynCom +application. This study aimed to investigate how SynCom inoculation at the +seedling stage impacts pepper growth by modulating the rhizosphere microbiome +using high-throughput sequencing technology. SynCom inoculation significantly +increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll +content, leaf number, root vigor, root tips, total root length, and +root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, +27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the +control. The Chao index of the rhizosphere microbial community and Bray-Curtis +dissimilarity of the fungal community significantly increased, while Bray-Curtis +dissimilarity of the bacterial community significantly decreased by SynCom +inoculation. The abundances of key taxa such as Scedosporium, Sordariomycetes, +Pseudarthrobacter, norankSBR1031, and norankA4b significantly increased with +SynCom inoculation, and positively correlated with indices of pepper growth. Our +findings suggest that SynCom inoculation can effectively enhance pepper growth +and regulate root morphology by regulating rhizosphere microbial communities and +increasing key taxa abundance like Sordariomycetes and Pseudarthrobacter, +thereby benefiting nutrient acquisition, resistance improvement, and pathogen +resistance of crops to ensure sustainability. + +DOI: 10.3390/microorganisms13010148 +PMCID: PMC11767384 +PMID: 39858916 + +Conflict of interest statement: The authors declare no conflicts of interest. \ No newline at end of file diff --git a/references_cache/pmid_40020349.txt b/references_cache/pmid_40020349.txt new file mode 100644 index 00000000..79cdffce --- /dev/null +++ b/references_cache/pmid_40020349.txt @@ -0,0 +1,63 @@ +1. Water Res. 2025 Jun 1;277:123270. doi: 10.1016/j.watres.2025.123270. Epub 2025 + Feb 10. + +Synthetic microbial community maintains the functional stability of aerobic +denitrification under environmental disturbances: Insight into the mechanism of +interspecific division of labor. + +He Y(1), Yun H(2), Peng L(1), Wang W(1), Xu T(1), Zhang W(1), Li X(3). + +Author information: +(1)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou, 730000, China. +(2)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou, 730000, China; Gansu Key Laboratory of Biomonitoring and +Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou +University, Tianshui South Road #222, Lanzhou, 730000, China. Electronic +address: yunh@lzu.edu.cn. +(3)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou, 730000, China; Gansu Key Laboratory of Biomonitoring and +Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou +University, Tianshui South Road #222, Lanzhou, 730000, China. Electronic +address: xkli@lzu.edu.cn. + +Understanding how synthetic microbial community (SMC) respond to environmental +disturbances is the key to realizing SMC engineering applications. Here, dibutyl +phthalate (DBP) and levofloxacin (LOFX) were used as environmental disturbances +to study their effects on the aerobic denitrification functional stability of +SMC composed of Pseudomonas aeruginosa N2 (PA), Acinetobacter baumannii N1(AC) +and Aeromonas hydrophila (AH). The results showed that aerobic denitrification +efficiency could be maintained at about 93 % under DBP or LOFX disturbance, and +interspecific communication was mainly carried out through +N-butyryl-L-homoserine lactone (C4-HSL) and N-(3-oxododecanoyl)-L-homoserine +lactone (3OC12-HSL), correspondingly. DBP and LOFX induced the acceleration of +tricarboxylic acid (TCA) cycle, which facilitated the energy flux and +extracellular polymeric substances (EPS) production, thereby allowing SMC to +adapt to disturbances. Under DBP disturbance, DBP stimulated +phenazine-1-carboxylic acid production to accelerate electron transfer from the +quinone pool to complex III, resulting in an increase in electron transfer +activity. Up-regulation of complex I, complex III and heme synthesis genes under +LOFX disturbance led to enhanced denitrification enzymes expression and electron +transfer efficiency. SMC re-regulated different metabolic pathways to build +metabolic networks to maintain normal metabolic activity under different +disturbances. Overall, SMC maintained functional stability through the labor +division in modulation of interspecific communication, formation of defensive +barriers, promotion of energy flux, directional transfer of electron flux, and +reconstruction of metabolic networks. DBP stimulated AH and PA to occupy +functional dominance, while LOFX induced AC and PA to play a major role. The +understanding of the stability mechanism under different environmental +disturbances provides valuable guidance for stability maintenance and +engineering applications of SMC. + +Copyright © 2025. Published by Elsevier Ltd. + +DOI: 10.1016/j.watres.2025.123270 +PMID: 40020349 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_40266232.txt b/references_cache/pmid_40266232.txt new file mode 100644 index 00000000..67143b1b --- /dev/null +++ b/references_cache/pmid_40266232.txt @@ -0,0 +1,44 @@ +1. ISME J. 2025 Jan 2;19(1):wraf076. doi: 10.1093/ismejo/wraf076. + +Synthetic microbial community improves chicken intestinal homeostasis and +provokes anti-Salmonella immunity mediated by segmented filamentous bacteria. + +Zhang M(1), Shi S(1), Feng Y(1), Zhang F(1), Xiao Y(1), Li X(1), Pan X(2), Feng +Y(1), Liu D(1), Guo Y(1), Hu Y(1). + +Author information: +(1)State Key Laboratory of Animal Nutrition and Feeding, College of Animal +Science and Technology, China Agricultural University, Haidian District, Beijing +100193, China. +(2)Department of Microbiology, Beijing General Station of Animal Husbandry, +Chaoyang District, Beijing 100107, China. + +Applying synthetic microbial communities to manipulate the gut microbiota is a +promising manner for reshaping the chicken gut microbial community. However, it +remains elusive the role of a designed microbial community in chicken +physiological metabolism and immune responses. In this study, we constructed a +10-member synthetic microbial community (SynComBac10) that recapitulated the +phylogenetic diversity and functional capability of adult chicken intestinal +microbiota. We found that early-life SynComBac10 exposure significantly enhanced +chicken growth performance and facilitated the maturation of both the intestinal +epithelial barrier function and the gut microbiota. Additionally, SynComBac10 +promoted the pre-colonization and growth of segmented filamentous bacteria +(SFB), which in turn induced Th17 cell-mediated immune responses, thereby +conferring resistance to Salmonella infection. Through metagenomic sequencing, +we assembled the genomes of two distinct species of SFB from the chicken gut +microbiota, which displayed common metabolic deficiencies with SFB of other host +origins. In silico analyses indicated that the SynComBac10-stimulated early +establishment of SFB in the chicken intestine was likely through +SynComBac10-derived metabolite cross-feeding. Our study demonstrated the pivotal +role of a designed microbial consortium in promoting chicken gut homeostasis and +anti-infection immunity, providing a new avenue for engineering chicken gut +microbiota. + +© The Author(s) 2025. Published by Oxford University Press on behalf of the +International Society for Microbial Ecology. + +DOI: 10.1093/ismejo/wraf076 +PMCID: PMC12527353 +PMID: 40266232 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no competing interests. diff --git a/references_cache/pmid_40270813.txt b/references_cache/pmid_40270813.txt new file mode 100644 index 00000000..b8c1640e --- /dev/null +++ b/references_cache/pmid_40270813.txt @@ -0,0 +1,58 @@ +1. Front Microbiol. 2025 Apr 9;16:1534327. doi: 10.3389/fmicb.2025.1534327. +eCollection 2025. + +Teosinte-derived SynCom and precision biofertilization modulate the maize +microbiome, enhancing growth, yield, and soil functionality in a Mexican field. + +Hernández-García JA(1), Bernal JS(2), Antony-Babu S(3), Villa-Tanaca L(1), +Hernández-Rodríguez C(1), De-la-Vega-Camarillo E(1)(2)(3). + +Author information: +(1)Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de +Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico +Nacional, Ciudad de México, México. +(2)Department of Entomology, Texas A&M University, College Station, TX, United +States. +(3)Department of Plant Pathology and Microbiology, Texas A&M University, College +Station, TX, United States. + +Modern agriculture faces the challenge of optimizing fertilization practices +while maintaining soil resilience and microbial diversity, both critical for +sustainable crop production. We evaluated the effects of multiple fertilization +strategies on soil microbial communities and plant performance, comparing +conventional methods (urea-based and phosphorus fertilizers applied manually or +via drone-assisted precision delivery) with biofertilization using a synthetic +microbial consortium (SynCom) derived from teosinte-associated microbes. This +SynCom consisted of seven bacterial strains: Serratia nematodiphila EDR2, +Klebsiella variicola EChLG19, Bacillus thuringiensis EML22, Pantoea agglomerans +EMH25, Bacillus thuringiensis EBG39, Serratia marcescens EPLG52, and Bacillus +tropicus EPP72. High-throughput sequencing revealed significant shifts in +bacterial and fungal communities across treatments. Untreated soils showed +limited diversity, dominated by Enterobacteriaceae (>70%). Conventional +fertilization gradually reduced Enterobacteriaceae while increasing Pseudomonas +and Lysinibacillus populations. Drone-assisted conventional fertilization +notably enhanced Acinetobacter and Rhizobiales growth. Biofertilization +treatments produced the most pronounced shifts, reducing Enterobacteriaceae +below 50% while significantly increasing beneficial taxa like Bacillus, Pantoea, +and Serratia. Network analysis demonstrated that microbial interaction +complexity increased across treatments, with Bacillus emerging as a keystone +species. Drone-assisted biofertilization fostered particularly intricate +microbial networks, enhancing synergistic relationships involved in nutrient +cycling and biocontrol, though maintaining the stability of these complex +interactions requires careful monitoring. Our findings provide key insights into +how precision biofertilization with teosinte-derived microbial consortia can +sustainably reshape the maize microbiome, improving crop performance and soil +resilience. + +Copyright © 2025 Hernández-García, Bernal, Antony-Babu, Villa-Tanaca, +Hernández-Rodríguez and De-la-Vega-Camarillo. + +DOI: 10.3389/fmicb.2025.1534327 +PMCID: PMC12015678 +PMID: 40270813 + +Conflict of interest statement: The authors declare that the research was +conducted without any commercial or financial relationships that could be +construed as a potential conflict of interest. The author(s) declared that they +were an editorial board member of Frontiers, at the time of submission. This had +no impact on the peer review process and the final decision. \ No newline at end of file diff --git a/references_cache/pmid_40433987.txt b/references_cache/pmid_40433987.txt new file mode 100644 index 00000000..b4c39f9c --- /dev/null +++ b/references_cache/pmid_40433987.txt @@ -0,0 +1,41 @@ +2. Adv Sci (Weinh). 2025 Aug;12(31):e14232. doi: 10.1002/advs.202414232. Epub +2025 May 28. + +Tailoring a Functional Synthetic Microbial Community Alleviates Fusobacterium +nucleatum-infected Colorectal Cancer via Ecological Control. + +Zhou Z(1), Yang M(1), Fang H(1), Zhang B(1), Ma Y(1), Li Y(1), Liu Y(1), Cheng +Z(1), Zhao Y(1), Si Z(1), Zhu H(1), Chen P(1). + +Author information: +(1)School of Pharmacy, Lanzhou University, No. 199 Donggang West Road, Lanzhou, +Gansu, 730000, P. R. China. + +Polymorphic microbiomes play important roles in colorectal cancer (CRC) +occurrence and development. In particular, Fusobacterium nucleatum (F. +nucleatum) is prevalent in patients with CRC, and eliminating it is beneficial +for treatment. Here, multiple metagenomic sequencing cohorts are combined with +multiomics to analyze the microbiome and related functional alterations. +Furthermore, local human metagenome and metabolomics are used to discover +commensal consortia. A synthetic microbial community (SynCom) is then designed +by metabolic network reconstruction, and its performance is validated using +coculture experiments and an AOM-DSS induced mouse CRC model. The sequencing +result shows that F. nucleatum is more abundant in both the feces and tumor +tissues of CRC patients. It causes alterations through various pathways, +including microbial dysbiosis, lipid metabolism, amino acid metabolism, and bile +acid metabolism disorders. The designed SynCom contains seven species with low +competition interrelationship. Furthermore, the SynCom successfully inhibits F. +nucleatum growth in vitro and achieves colonization in vivo. Additionally, it +promotes F. nucleatum decolonization, and enhances tryptophan metabolism and +secondary bile acid conversion, leading to reduced lipid accumulation, decreased +inflammatory reaction, and enhanced tumor inhibition effect. Overall, the +bottom-up designed SynCom is a controllable and promising approach for treating +F. nucleatum-positive CRC. + +© 2025 The Author(s). Advanced Science published by Wiley‐VCH GmbH. + +DOI: 10.1002/advs.202414232 +PMCID: PMC12376641 +PMID: 40433987 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflicts of interest. diff --git a/references_cache/pmid_40508300.txt b/references_cache/pmid_40508300.txt new file mode 100644 index 00000000..efb60aa5 --- /dev/null +++ b/references_cache/pmid_40508300.txt @@ -0,0 +1,44 @@ +1. Plants (Basel). 2025 May 26;14(11):1625. doi: 10.3390/plants14111625. + +Application of a Synthetic Microbial Community to Enhance Pepper Resistance +Against Phytophthora capsici. + +Bashizi TF(1), Kim MJ(2), Lim K(1), Lee G(1), Tagele SB(3), Shin JH(1). + +Author information: +(1)Department of Applied Biosciences, Kyungpook National University, Daegu +41566, Republic of Korea. +(2)NGS Core Facility, Kyungpook National University, Daegu 41566, Republic of +Korea. +(3)Department of Microbiology and Plant Pathology, University of California +Riverside, Riverside, CA 92507, USA. + +Pepper (Capsicum annuum) production faces significant challenges from soil-borne +pathogens, particularly Phytophthora capsici, which induces root rot and +damping-off diseases. Management of this pathogen remains challenging owing to +the scarcity of resistant cultivars and the ineffectiveness of chemical control +methods. A single strain has been used to prevent pathogenic disease, and this +approach limits the exploration of consortia comprising different genera. In +this study, we isolated five bacterial strains (Bacillus sp. T3, Flavobacterium +anhuiense T4, Cytobacillus firmus T8, Streptomyces roseicoloratus T14, and +Pseudomonas frederiksbergensis A6) from the rhizosphere of healthy pepper +plants. We then applied this 5-isolate synthetic microbial community (SynCom) to +Capsicum annuum to evaluate its efficacy in improving pepper resilience against +P. capsici. The SynCom members exhibited phosphate solubilization, +indole-3-acetic acid production, catalase activity, siderophore synthesis, and +strong antagonism against P. capsici. The SynCom reduced disease severity and +enhanced the growth of pepper plants. Furthermore, the beneficial genera such as +Bacillus, Fusicolla, and Trichoderma, significantly increased in the rhizosphere +of pepper after the application of the SynCom. Microbial functional prediction +analysis revealed that these microbial shifts were associated with nitrogen +cycling and pathogen suppression. Our SynCom approach demonstrates the +effectiveness of microbial consortia in promoting the growth of +pathogen-infected plants by reprogramming the microbial community in the +rhizosphere. + +DOI: 10.3390/plants14111625 +PMCID: PMC12157186 +PMID: 40508300 + +Conflict of interest statement: The authors have no conflict of interest to +declare. \ No newline at end of file diff --git a/references_cache/pmid_40536564.txt b/references_cache/pmid_40536564.txt new file mode 100644 index 00000000..623365a8 --- /dev/null +++ b/references_cache/pmid_40536564.txt @@ -0,0 +1,46 @@ +1. Appl Microbiol Biotechnol. 2025 Jun 19;109(1):149. doi: +10.1007/s00253-025-13522-1. + +Establishing a co-culture aggregate of N-cycle bacteria to elucidate +flocculation in biological wastewater treatment. + +Parret L(1), Simoens K(1), Horemans B(1)(2), De Vrieze J(3)(4), Smets I(5). + +Author information: +(1)Department of Chemical Engineering, Bio- & Chemical Reactor Engineering and +Safety (CREaS), KU Leuven, Celestijnenlaan 200F box 2424, B-3001, Leuven, +Belgium. +(2)Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, +B-3001, Leuven, Belgium. +(3)Centre for Microbial Ecology and Technology (CMET), Ghent University, Frieda +Saeysstraat 1, B-9052, Gent, Belgium. +(4)Centre for Advanced Process Technology for Urban Resource Recovery (CAPTURE), +Frieda Saeysstraat 1, B-9052, Gent, Belgium. +(5)Department of Chemical Engineering, Bio- & Chemical Reactor Engineering and +Safety (CREaS), KU Leuven, Celestijnenlaan 200F box 2424, B-3001, Leuven, +Belgium. ilse.smets@kuleuven.be. + +Biological flocculation is a complex phenomenon that is often treated as a black +box. As a result, flocculation problems are usually remediated without knowledge +of the exact causes. We show that it is feasible to exploit a model (N-cycle) +consortium with reduced complexity to fundamentally study bioflocculation. +Strong nitrifier microcolonies were formed during oxic/anoxic cycles in +sequencing batch reactors, using alginate entrapment as a cell retention system. +After the release of these aggregates into suspension, macroclusters with flocs +of the denitrifier were observed. These results suggest that a living model of a +full-scale activated sludge floc can be built through the use of this bottom-up +approach. By eliminating shifts in the microbial community, the applied +experimental conditions have a more direct effect on the observations. Key +Points  ∙  Studying flocculation with a model consortium is feasible  ∙  +Alginate entrapment leads to strong microcolony formation of nitrifiers  ∙  FISH +by itself is not suitable to study aggregation of a coculture. + +© 2025. The Author(s). + +DOI: 10.1007/s00253-025-13522-1 +PMCID: PMC12178987 +PMID: 40536564 [Indexed for MEDLINE] + +Conflict of interest statement: Declarations. Conflict of interest: The authors +declare no competing interests. Ethical approval: This article does not contain +any studies with human participants or animals performed by any of the authors. \ No newline at end of file diff --git a/references_cache/pmid_40670700.txt b/references_cache/pmid_40670700.txt new file mode 100644 index 00000000..55b09334 --- /dev/null +++ b/references_cache/pmid_40670700.txt @@ -0,0 +1,56 @@ +1. Appl Microbiol Biotechnol. 2025 Jul 16;109(1):168. doi: +10.1007/s00253-025-13547-6. + +Development of a chemotactic SynCom bioorganic fertilizer for biocontrol of +bacterial wilt in tobacco fields. + +Liu Y(#)(1), Zhang W(#)(2), Guo L(2), Li H(1), Zhu J(1), Li X(3), Zhang X(2), +Yang X(2), Xu Y(2), Shen Q(2), Yang T(4), Wei Z(2). + +Author information: +(1)Guizhou Academy of Tobacco Science, Guiyang, 550081, China. +(2)Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of +Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center for +Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving +fertilizers, Nanjing Agricultural University, Nanjing, 210095, China. +(3)Guizhou Tobacco Corporation of CNTC, Guiyang, 550003, China. +newcool1361214@163.com. +(4)Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of +Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center for +Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving +fertilizers, Nanjing Agricultural University, Nanjing, 210095, China. +tjyang@njau.edu.cn. +(#)Contributed equally + +Bacterial wilt caused by Ralstonia solanacearum is one of the most severe plant +diseases all over the world. Currently, many scientists are using SynCom +(synthetic microbial community) to control this disease. However, designing of +highly efficient SynCom remains challenging. In this study, we isolated 372 +bacteria with different morphologies from the rhizosphere soil of healthy +tobacco plants in a diseased field. Based on the antagonistic activity, +compatibility, and presence of cheA gene, a marker gene of chemotaxis, we +constructed a chemotactic SynCom comprising two Pseudomonas strains and one +Bacillus strain. In vitro experiments revealed that vitamin C, propionic acid, +and esculetin significantly promoted the growth and antagonistic ability of +chemotactic SynCom strains. Next, we optimized the proportion of organic +fertilizer to support the growth of the SynCom strains. The application of the +bioorganic fertilizer containing chemotactic SynCom can protect diseased tobacco +field from R. solanacearum invasion and enhance yields. Finally, rhizosphere +bacterial community analysis showed that phyla Bacillota and Chloroflexiota were +significantly enriched. This study highlights the potential of chemotactic +SynCom for effective biocontrol, offering a new approach for managing bacterial +wilt and enhancing crop yields. KEY POINTS: • The bioorganic fertilizer +containing chemotactic SynCom suppresses R. solanacearum and boosts tobacco +yields. • Root exudate-selected prebiotics enhance the antagonistic effects of +SynCom against pathogens. • SynCom bioorganic fertilizer regulates the +rhizosphere microbiome, enriching beneficial bacterial phyla. + +© 2025. The Author(s). + +DOI: 10.1007/s00253-025-13547-6 +PMCID: PMC12267373 +PMID: 40670700 [Indexed for MEDLINE] + +Conflict of interest statement: Declarations. Ethical approval: This article +contains no studies with human participants or animals performed by any authors. +Competing interests: The authors declare no competing interests. \ No newline at end of file diff --git a/references_cache/pmid_40853002.txt b/references_cache/pmid_40853002.txt new file mode 100644 index 00000000..7d5e0b4c --- /dev/null +++ b/references_cache/pmid_40853002.txt @@ -0,0 +1,51 @@ +1. mSphere. 2025 Sep 30;10(9):e0015925. doi: 10.1128/msphere.00159-25. Epub 2025 +Aug 25. + +Synthetic communities of maize root bacteria interact and redirect benzoxazinoid +metabolization. + +Thoenen L(1)(2), Pestalozzi C(2), Zuest T(1)(3), Kreuzer M(4), Mateo P(1), +Karasawa M(2), Deslandes G(1), Robert CA(1), Bruggmann R(4), Erb M(1), Schlaeppi +K(1)(2). + +Author information: +(1)Institute of Plant Sciences, University of Bern, Bern, Switzerland. +(2)Department of Environmental Sciences, University of Basel, Basel, +Switzerland. +(3)Department of Systematic and Evolutionary Botany, University of Zurich, +Zurich, Switzerland. +(4)Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland. + +Plant roots are colonized by diverse microbial communities. These communities +are shaped by root exudates, including plant-specialized metabolites. +Benzoxazinoids are such secreted compounds of maize. Individual microbes differ +in their ability to tolerate and metabolize antimicrobial benzoxazinoids. To +investigate how these traits combine in a community, we designed two synthetic +communities of maize root bacteria that share six common strains and differ in +their ability to metabolize benzoxazinoids based on the seventh strain. We +exposed both communities to the benzoxazinoid MBOA +(6-methoxybenzoxazolin-2(3H)-one) in vitro and found that the metabolizing +community did not degrade MBOA to its aminophenoxazinone, as observed for +individual strains, but, as a community, they formed the corresponding +acetamide. MBOA shaped the differential compositions of both communities and +increased the fraction of MBOA-tolerant strains. The benzoxazinoid-metabolizing +community showed a higher tolerance to MBOA and was able to utilize MBOA as +their sole carbon source for growth. Hence, bacterial interaction results in +alternative benzoxazinoid metabolization and increases community performance in +the presence of these antimicrobial compounds. Future work is needed to uncover +the genetics of this metabolic interaction and ecological consequences for the +bacterial community and the host plant.IMPORTANCEWe investigated how maize root +bacteria-alone or in community-tolerate and metabolize antimicrobial compounds +of their host plant. We found that the capacity to metabolize such a compound +impacts bacterial community size and structure and, most importantly, benefits +community fitness. We also found that interacting bacteria redirected the +metabolization of the antimicrobial compound to an alternative degradation +pathway. Our work highlights the need to study the teamwork of microbes to +uncover their community traits to ultimately understand the ecological +consequences for the bacterial community and eventually the host plant. + +DOI: 10.1128/msphere.00159-25 +PMCID: PMC12483121 +PMID: 40853002 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_40862137.txt b/references_cache/pmid_40862137.txt new file mode 100644 index 00000000..9777f4e4 --- /dev/null +++ b/references_cache/pmid_40862137.txt @@ -0,0 +1,58 @@ +1. Front Microbiol. 2025 Aug 11;16:1649750. doi: 10.3389/fmicb.2025.1649750. +eCollection 2025. + +A stable 15-member bacterial SynCom promotes Brachypodium growth under drought +stress. + +Yadav A(#)(1), Chen M(#)(1), Acharya SM(1), Kim G(2), Yang Y(1), Zhao TZ(1), +Tsang E(1), Chakraborty R(1). + +Author information: +(1)Climate and Ecosystem Sciences Division, Earth & Environmental Sciences Area, +Lawrence Berkeley National Laboratory, Berkeley, CA, United States. +(2)Department of Molecular and Cell Biology, University of California Berkeley, +Berkeley, CA, United States. +(#)Contributed equally + +INTRODUCTION: Rhizosphere microbiomes are known to drive soil nutrient cycling +and influence plant fitness during adverse environmental conditions. +Field-derived robust Synthetic Communities (SynComs) of microbes mimicking the +diversity of rhizosphere microbiomes can greatly advance a deeper understanding +of such processes. However, assembling stable, genetically tractable, +reproducible, and scalable SynComs remains challenging. +METHODS: Here, we present a systematic approach using a combination of network +analysis and cultivation-guided methods to construct a 15-member SynCom from the +rhizobiome of Brachypodium distachyon. This SynCom incorporates diverse strains +from five bacterial phyla. Genomic analysis of the individual strains was +performed to reveal encoded plant growth-promoting traits, including genes for +the synthesis of osmoprotectants (trehalose and betaine) and Na+/K+ +transporters, and some predicted traits were validated by laboratory phenotypic +assays. +RESULTS: The SynCom demonstrates strong stability both in vitro and in planta. +Most strains encoded multiple plant growth-promoting functions, and several of +these were confirmed experimentally. The presence of osmoprotectant and ion +transporter genes likely contributed to the observed resilience of Brachypodium +to drought stress, where plants amended with the SynCom recovered better than +those without. We further observed preferential colonization of SynCom strains +around root tips under stress, likely due to active interactions between plant +root metabolites and bacteria. +DISCUSSION: Our results demonstrate that trait-informed construction of +synthetic communities can yield stable, functionally diverse consortia that +enhance plant resilience under drought. Preferential colonization near root tips +points to active, localized plant-microbe signaling as a component of +stress-responsive recruitment. This stable SynCom provides a scalable platform +for probing mechanisms of plant-microbe interaction and for developing +microbiome-based strategies to improve soil and crop performance in variable +environments. + +Copyright © 2025 Yadav, Chen, Acharya, Kim, Yang, Zhao, Tsang and Chakraborty. + +DOI: 10.3389/fmicb.2025.1649750 +PMCID: PMC12375656 +PMID: 40862137 + +Conflict of interest statement: The authors declare that the research was +conducted in the absence of any commercial or financial relationships that could +be construed as a potential conflict of interest. The author(s) declared that +they were an editorial board member of Frontiers, at the time of submission. +This had no impact on the peer review process and the final decision. \ No newline at end of file diff --git a/references_cache/pmid_41264879.txt b/references_cache/pmid_41264879.txt new file mode 100644 index 00000000..d2b9a424 --- /dev/null +++ b/references_cache/pmid_41264879.txt @@ -0,0 +1,32 @@ +1. Environ Sci Technol. 2025 Dec 9;59(48):25960-25972. doi: +10.1021/acs.est.5c07865. Epub 2025 Nov 20. + +Synthetic Microbial Community Promotes Straw Humification and Improves Soil +Organic Carbon in Cropland. + +Wang X(1), Wang L(1), Han X(1), Wang L(1), Zhang Y(1). + +Author information: +(1)School of Resources and Environment, Northeast Agricultural University, +Harbin 150030, China. + +Straw return is considered an effective approach to increase soil organic carbon +(SOC) and improve soil multifunctionality (SMF), yet the relatively low +humification rate under field conditions limits these benefits. The application +of synthetic microbial communities (SynComs) represents a promising strategy for +promoting straw humification. Nevertheless, challenges remain in designing +functionally stable SynComs for straw humification. Here, by combining +progressive dilution-microcosm cultivation with co-occurrence network and +functional analyses, we identified keystone taxa that promoted maize straw +humification in the microcosm. From these taxa, we constructed a two-membered +SynCom (Bacillus siamensis B and Bradyrhizobium japonicum G). By cross-feeding, +SynCom members enable each other to grow, increase the activities of key enzymes +(carboxymethyl cellulase, xylanase, lignin peroxidase, and nitrogenase), and +thereby promote maize straw humification. Field experiments further demonstrated +that SynCom inoculation enhanced the in vivo turnover pathway of the microbial +carbon pump, thereby promoting straw humification and improving SOC. Overall, we +provide a systematic approach for identifying and applying keystone taxa to +construct SynComs that promote maize straw humification and improve SOC. + +DOI: 10.1021/acs.est.5c07865 +PMID: 41264879 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_41932525.txt b/references_cache/pmid_41932525.txt new file mode 100644 index 00000000..668c155b --- /dev/null +++ b/references_cache/pmid_41932525.txt @@ -0,0 +1,58 @@ +1. Bioresour Technol. 2026 Jul;451:134546. doi: 10.1016/j.biortech.2026.134546. +Epub 2026 Apr 1. + +Synthetic microbial community drive methane oxidation coupled to Cr(VI) +reduction via division of labor and extracellular electron transfer. + +Liu Q(1), Wei S(1), Li Y(2), Yu X(1), Zhang Z(1), Li J(3). + +Author information: +(1)College of Resources and Environmental Engineering, Key Laboratory of Karst +Georesources and Environment, Ministry of Education, Guizhou University, Guiyang +550025, China. +(2)College of Resources and Environmental Engineering, Key Laboratory of Karst +Georesources and Environment, Ministry of Education, Guizhou University, Guiyang +550025, China; Guizhou Karst Environmental Ecosystems Observation and Research +Station, Ministry of Education, Guiyang 550025, China; Guizhou Provincial Key +Laboratory for Prevention and Control of Emerging Contaminants, Guiyang 550025, +China. Electronic address: ycli3@gzu.edu.cn. +(3)College of Resources and Environmental Engineering, Key Laboratory of Karst +Georesources and Environment, Ministry of Education, Guizhou University, Guiyang +550025, China; Guizhou Karst Environmental Ecosystems Observation and Research +Station, Ministry of Education, Guiyang 550025, China; Guizhou Provincial Key +Laboratory for Prevention and Control of Emerging Contaminants, Guiyang 550025, +China. + +While methane oxidation coupled to Cr(VI) reduction has been widely +investigated, the functional specialization and division of labor within +microbial consortia remain insufficiently understood. In this study, a synthetic +microbial community (SynCom) was constructed by controlling methane +concentration and chromium load. The maximum Cr(VI) removal load of this system +reached 20.63 mg/L/d. The metagenomic assembly genome analysis showed that under +hypoxic conditions, Methylocystis (6.30%) was the core microorganism driving +methane oxidation. It achieved extracellular electron transfer (EET) through +multiheme c-type cytochromes and conductive pili, or jointly with dominant +genera such as Hyphomicrobium and Thiobacillus, to couple methane oxidation with +Cr(VI) reduction. Integrated multi-omics revealed significant enrichment of +differentially expressed proteins involved in quorum sensing and methane +metabolism, along with elevated expression of ABC transporter substrate-binding +protein and porin. The primary metabolites included N-Methyl-L-Proline, +L-Histidine, and Hypaphorin, with L-Glutamine serving as a central node +connecting the highest number of pathways in the metabolic network. The +inhibition experiments confirmed that inhibiting the methane oxidation would +directly reduce the efficiency of Cr(VI) reduction. This study revealed the +microbial division of labor and the microscopic process of EET driven by aerobic +methanotrophs under hypoxic conditions, and expanded its application potential +in bioremediation from the perspective of SynCom. It could be a scientific +foundation for pollution control technologies of methane-based biotransformation +and utilization. + +Copyright © 2026. Published by Elsevier Ltd. + +DOI: 10.1016/j.biortech.2026.134546 +PMID: 41932525 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_42007760.txt b/references_cache/pmid_42007760.txt new file mode 100644 index 00000000..53324958 --- /dev/null +++ b/references_cache/pmid_42007760.txt @@ -0,0 +1,58 @@ +3. Appl Environ Microbiol. 2026 Apr 20:e0254825. doi: 10.1128/aem.02548-25. +Online ahead of print. + +A synthetic microbial community for soybean biofertilization designed via +chlorophyll-based iterative selection. + +Brignoli D(1)(2), Colla D(1), Frickel-Critto E(3), Castells CB(3), Pérez-Giménez +J(1), Lodeiro AR(1)(2). + +Author information: +(1)Instituto de Biotecnología y Biología Molecular (IBBM)-Facultad de Ciencias +Exactas, Universidad Nacional de La Plata (UNLP) y CCT-La Plata, CONICET, La +Plata, Argentina. +(2)Cátedra de Genética-Facultad de Ciencias Agrarias y Forestales, Universidad +Nacional de La Plata (UNLP), La Plata, Argentina. +(3)Laboratorio de Investigación y Desarrollo de Métodos Analíticos, Universidad +Nacional de La Plata (UNLP) y CIC-PBA, La Plata, Argentina. + +Improving the effectiveness of microbial inoculants for soybean is essential to +enhance biological nitrogen fixation and reduce fertilizer dependence; however, +inoculated Bradyrhizobium strains frequently display inconsistent field +performance. Inoculation is usually carried out with single-strain formulations, +overlooking the possible influence of the native soil microbiota on nodulation +success. This limitation may be addressed by formulating inoculants with +consortia that include selected members of the soil microbiota. To this end, a +synthetic microbial community (SynCom) was developed through a host-mediated +microbiome engineering approach guided by leaf chlorophyll content as a rapid, +non-destructive plant trait. The experiment was initiated by inoculating soybean +plants with a consortium of 9 Bradyrhizobium spp. and 14 non-rhizobial soil +isolates. Across eight consecutive selection rounds under gnotobiotic +conditions, rhizosphere communities associated with superior plant performance +were pooled and propagated. Recurrent selection induced significant shifts in +community composition, consistently favoring Bradyrhizobium diazoefficiens as +the dominant nodulating member and enriching taxa from Pseudomonadales, +Burkholderiales, and Sphingomonadales. Sequencing-based profiling and network +analysis suggested the emergence of a cohesive and functionally enriched +community, with increased potential for nitrogen transformations and organic +matter turnover. When evaluated in non-sterile soil, the SynCom derived from the +sixth selection round increased nodule number and biomass relative to an +uninoculated control and a commercial inoculant strain. These results suggest +that plant-guided selection can steer rhizosphere community assembly toward +beneficial configurations and support the development of improved soybean +bioinoculants.IMPORTANCESoybean [Glycine max (L.) Merr.] is a major global crop +characterized by high seed protein content, which demands elevated nitrogen +assimilation. To meet this demand, the crop can utilize atmospheric nitrogen +through the process of biological nitrogen fixation in symbiosis with +Bradyrhizobium bacteria, thus mitigating soil nitrogen depletion. Although +Bradyrhizobium-based inoculants are applied at sowing, their interplay with +other members of the rhizosphere microbiota remains poorly understood. It is +well documented that plants and rhizosphere microbiota interact to shape plant +growth and soil productivity. Therefore, this work evaluated the inoculation of +soybean with a synthetic microbial consortium as a strategy to develop +new-generation inoculants. These bioinputs are designed to harness +plant-soil-microbe interactions to improve soybean productivity while preserving +soil properties. + +DOI: 10.1128/aem.02548-25 +PMID: 42007760