diff --git a/docs/communities/MSC2_Model_Soil_Consortium.html b/docs/communities/MSC2_Model_Soil_Consortium.html new file mode 100644 index 00000000..f23c7c23 --- /dev/null +++ b/docs/communities/MSC2_Model_Soil_Consortium.html @@ -0,0 +1,1213 @@ + + + + + + Model Soil Consortium-2 (MSC-2) - CommunityMech + + + +
+
+ ← Back to Communities +

Model Soil Consortium-2 (MSC-2)

+
+
+ +
+ +
+
+
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + grassland soil +
+ + ENVO:00001998 + + +
+ + +
+ Source File + MSC2_Model_Soil_Consortium.yaml +
+
+
+ + + +
+

Reduced-complexity model soil consortium assembled from MSC-1 isolates to study community-level chitin decomposition, interspecies interactions, and emergent phenotypes in soil. MSC-2 contains eight bacterial members spanning diverse phyla and was used for isolate genome sequencing, 16S profiling, metatranscriptomics, metabolomics, and KBase-enabled metabolic modeling in the Hofmockel Soil Microbiome SFA context.

+
+ + + + +
+

Taxonomy

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Streptomyces sp. MSC1_001 + + + NCBITaxon:1931 + + + +
+ + CROSS_FEEDER + +
+ + 		N/A
+ Neorhizobium tomejilense MSC1_005 + + + NCBITaxon:2093828 + + + +
+ + CROSS_FEEDER + +
+ + 		N/A
+ Dyadobacter sp. MSC1_007 + + + NCBITaxon:1914288 + + + +
+ + PRIMARY_DEGRADER + +
+ + 		N/A
+ Sphingopyxis sp. MSC1_008 + + + NCBITaxon:1908224 + + + +
+ + CROSS_FEEDER + +
+ + 		N/A
+ Ensifer adhaerens MSC1_011 + + + NCBITaxon:106592 + + + +
+ + PRIMARY_DEGRADER + +
+ + 		N/A
+ Variovorax beijingensis MSC1_012 + + + NCBITaxon:2496117 + + + +
+ + PRIMARY_DEGRADER + + CROSS_FEEDER + +
+ + 		N/A
+ Sinorhizobium meliloti MSC1_014 + + + NCBITaxon:382 + + + +
+ + PRIMARY_DEGRADER + +
+ + 		N/A
+ Rhodococcus sp. MSC1_016 + + + NCBITaxon:1827 + + + +
+ + PRIMARY_DEGRADER + +
+ + 		N/A
+
+ + + +
+

Ecological Interactions

+ + + +
+
+ + Ecological interaction network for Model Soil Consortium-2 (MSC-2) + Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism). + +
+
+ Taxon +
+
+ Cross-feeding +
+
+ Mutualism +
+
+ Syntrophy +
+
+ Competition +
+
+ Commensalism +
+
+
+ + +
+
+

Chitin Breakdown Product Sharing

+ CROSS_FEEDING +
+ + + + + + +

Metabolites: + + chitin + (CHEBI:18246) + +

+ + + + + +
+ Downstream Effects: + +
+ → Community growth on chitin decomposition products +
+ +
+ + + +

Evidence

+
    + +
  • +
    + + PMID:36154140 + + - SUPPORT (IN_VITRO) +
    + +
    "the most abundant members of MSC-2 were not those that were able to metabolize chitin itself, but rather those that were able to take full advantage of interspecies interactions to grow on chitin decomposition products"
    + +
    • + +
+ +
+ +
+
+

Community-Responsive Streptomyces Chitin Phenotype

+ NICHE_PARTITIONING +
+ + +

Source Taxon: Streptomyces sp. MSC1_001

+ + + + + + + + + +
+ Downstream Effects: + +
+ → Distinct functional roles during chitin degradation +
+ +
+ + + +

Evidence

+
    + +
  • +
    + + PMID:36154140 + + - SUPPORT (IN_VITRO) +
    + +
    "Emergent properties of both species and the community were found, including changes in the chitin degradation potential of Streptomyces species and organization of all species into distinct roles in the chitin degradation process."
    + +
    • + +
+ +
+ + +
+ + + +
+

Associated Datasets

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
DatasetTypeRepositoryAccession
+ MSC-2 isolate genomes + +
BioProject containing the eight isolate genome assemblies used for MSC-2. + + 		GENOMENCBI_BIOPROJECT + + PRJNA788902 + +
+ MSC-2 bacterial isolate genomes (PNNL DataHub) + +
PNNL DataHub record linking the MSC-2 isolate genome assemblies and accessions. + + 		GENOMEOTHER + + 10.25584/PNNLDH/1986536 + +
+ MSC-2 16S growth dataset + +
16S rRNA gene data from MSC-2 growth experiments. + + 		AMPLICON_16SOTHER + + PNNLDH:33231 + +
+ MSC-2 metatranscriptomic dataset + +
Metatranscriptomic data from MSC-2 chitin growth assays. + + 		METATRANSCRIPTOMEOTHER + + PNNLDH:33232 + +
+ MSC-2 primary publication + +
Primary publication describing MSC-2 assembly, multiomics, and community interaction results. + + 		OTHEROTHER + + PMID:36154140 + +
+
+ + + + + + + +
+ + + + + + + + + \ No newline at end of file diff --git a/docs/index.html b/docs/index.html index d055cac5..c5cf78bc 100644 --- a/docs/index.html +++ b/docs/index.html @@ -422,7 +422,7 @@

CommunityMech

- Showing 78 of 78 communities + Showing 79 of 79 communities
@@ -1788,6 +1788,35 @@

MSC-1 Dominant Core

+ +

Model Soil Consortium-2 (MSC-2)

+

Reduced-complexity model soil consortium assembled from MSC-1 isolates to study community-level chitin decomposition, interspecies interactions, and emergent phenotypes in soil. MSC-2 contains eight bacterial members spanning diverse phyla and was used for isolate genome sequencing, 16S profiling, metatranscriptomics, metabolomics, and KBase-enabled metabolic modeling in the Hofmockel Soil Microbiome SFA context.

+
+
+ + + + + + + 8 + + ENGINEERED +
+ OTHER +
+ + - + Reduced-complexity model soil consortium assembled from MSC-1 isolates to study + community-level chitin decomposition, interspecies interactions, and emergent + phenotypes in soil. MSC-2 contains eight bacterial members spanning diverse phyla + and was used for isolate genome sequencing, 16S profiling, metatranscriptomics, + metabolomics, and KBase-enabled metabolic modeling in the Hofmockel Soil Microbiome + SFA context. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: >- + Build a reduced, tractable soil consortium for studying how community context + shapes chitin degradation and member success during decomposition. + assembly_strategy: >- + Eight isolates were selected from MSC-1 to include both chitin degraders and + nondegraders while maximizing taxonomic diversity. + inoculation_strategy: Eight individually isolated strains assembled into a defined mixed community. + passaging_regimen: >- + Developed as a reduced-complexity follow-on to the naturally evolved MSC-1 soil + consortium for monoculture and coculture chitin assays. + measurement_endpoints: + - isolate growth on chitin and alternative carbon sources + - 16S rRNA community composition profiling + - metatranscriptomics during community growth on chitin + - community metabolomics during chitin decomposition + notes: >- + The KBase Soil Microbiome SFA page describes MSC-2 as one of the model consortia + used for OMEGGA and ModelSEED2 workflows. + evidence: + - reference: PMID:36154140 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'Chitin was applied to a model soil consortium that we developed, "model soil consortium-2" (MSC-2), consisting of eight members of diverse phyla and including both chitin degraders and nondegraders.' + explanation: Supports the reduced eight-member MSC-2 design and mixed degrader/nondegrader composition. +environment_term: + preferred_term: grassland soil + term: + id: ENVO:00001998 + label: soil + notes: Isolates were derived from IAREC grassland soil in Prosser, Washington. +taxonomy: +- taxon_term: + preferred_term: Streptomyces sp. MSC1_001 + term: + id: NCBITaxon:1931 + label: Streptomyces sp. + strain_designation: + strain_name: MSC1_001 + genome_accession: GCA_023667545.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667545.1 + functional_role: + - CROSS_FEEDER +- taxon_term: + preferred_term: Neorhizobium tomejilense MSC1_005 + term: + id: NCBITaxon:2093828 + label: Neorhizobium tomejilense + strain_designation: + strain_name: MSC1_005 + genome_accession: GCA_023667605.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667605.1 + functional_role: + - CROSS_FEEDER +- taxon_term: + preferred_term: Dyadobacter sp. MSC1_007 + term: + id: NCBITaxon:1914288 + label: Dyadobacter sp. + strain_designation: + strain_name: MSC1_007 + genome_accession: GCA_023667495.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667495.1 + functional_role: + - PRIMARY_DEGRADER +- taxon_term: + preferred_term: Sphingopyxis sp. MSC1_008 + term: + id: NCBITaxon:1908224 + label: Sphingopyxis sp. + strain_designation: + strain_name: MSC1_008 + genome_accession: GCA_023197165.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023197165.1 + functional_role: + - CROSS_FEEDER +- taxon_term: + preferred_term: Ensifer adhaerens MSC1_011 + term: + id: NCBITaxon:106592 + label: Ensifer adhaerens + strain_designation: + strain_name: MSC1_011 + genome_accession: GCA_023667555.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667555.1 + functional_role: + - PRIMARY_DEGRADER +- taxon_term: + preferred_term: Variovorax beijingensis MSC1_012 + term: + id: NCBITaxon:2496117 + label: Variovorax beijingensis + strain_designation: + strain_name: MSC1_012 + genome_accession: GCA_023667525.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667525.1 + functional_role: + - PRIMARY_DEGRADER + - CROSS_FEEDER +- taxon_term: + preferred_term: Sinorhizobium meliloti MSC1_014 + term: + id: NCBITaxon:382 + label: Sinorhizobium meliloti + strain_designation: + strain_name: MSC1_014 + genome_accession: GCA_023197145.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023197145.1 + functional_role: + - PRIMARY_DEGRADER +- taxon_term: + preferred_term: Rhodococcus sp. MSC1_016 + term: + id: NCBITaxon:1827 + label: Rhodococcus + strain_designation: + strain_name: MSC1_016 + genome_accession: GCA_023667485.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667485.1 + functional_role: + - PRIMARY_DEGRADER +associated_datasets: +- name: MSC-2 isolate genomes + dataset_type: GENOME + repository: NCBI_BIOPROJECT + accession: PRJNA788902 + url: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA788902 + description: BioProject containing the eight isolate genome assemblies used for MSC-2. +- name: MSC-2 bacterial isolate genomes (PNNL DataHub) + dataset_type: GENOME + repository: OTHER + accession: 10.25584/PNNLDH/1986536 + url: https://data.pnnl.gov/group/nodes/dataset/33234 + description: PNNL DataHub record linking the MSC-2 isolate genome assemblies and accessions. +- name: MSC-2 16S growth dataset + dataset_type: AMPLICON_16S + repository: OTHER + accession: PNNLDH:33231 + url: https://data.pnnl.gov/group/nodes/dataset/33231 + description: 16S rRNA gene data from MSC-2 growth experiments. +- name: MSC-2 metatranscriptomic dataset + dataset_type: METATRANSCRIPTOME + repository: OTHER + accession: PNNLDH:33232 + url: https://data.pnnl.gov/group/nodes/dataset/33232 + description: Metatranscriptomic data from MSC-2 chitin growth assays. +- name: MSC-2 primary publication + dataset_type: OTHER + repository: OTHER + accession: PMID:36154140 + url: https://pubmed.ncbi.nlm.nih.gov/36154140/ + description: Primary publication describing MSC-2 assembly, multiomics, and community interaction results. +ecological_interactions: +- name: Chitin Breakdown Product Sharing + description: >- + Community growth on chitin is supported by interspecies sharing of decomposition + products, so the most abundant members are not necessarily the taxa that directly + metabolize chitin in monoculture. + interaction_type: CROSS_FEEDING + metabolites: + - preferred_term: chitin + term: + id: CHEBI:18246 + label: chitin + downstream: + - target: Community growth on chitin decomposition products + evidence: + - reference: PMID:36154140 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the most abundant members of MSC-2 were not those that were able to metabolize chitin itself, but rather those that were able to take full advantage of interspecies interactions to grow on chitin decomposition products + explanation: Supports cross-feeding and shared access to products released during community chitin degradation. +- name: Community-Responsive Streptomyces Chitin Phenotype + description: >- + Streptomyces exhibits a community-responsive chitin phenotype, and MSC-2 organizes + members into distinct functional roles during decomposition. + interaction_type: NICHE_PARTITIONING + source_taxon: + preferred_term: Streptomyces sp. MSC1_001 + term: + id: NCBITaxon:1931 + label: Streptomyces sp. + downstream: + - target: Distinct functional roles during chitin degradation + evidence: + - reference: PMID:36154140 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Emergent properties of both species and the community were found, including changes in the chitin degradation potential of Streptomyces species and organization of all species into distinct roles in the chitin degradation process. + explanation: Supports that Streptomyces behavior and community roles depend on the surrounding MSC-2 membership. +external_resources: +- name: KBase Soil Microbiome SFA collaboration page + repository: KBASE + resource_id: hofmockel-sfa + url: https://www.kbase.us/research/hofmockel-sfa/ + description: KBase Soil Microbiome SFA page describing OMEGGA and MSC-2 use in ModelSEED2 workflows. diff --git a/references_cache/PMID_36154140.md b/references_cache/PMID_36154140.md new file mode 100644 index 00000000..45edffba --- /dev/null +++ b/references_cache/PMID_36154140.md @@ -0,0 +1,96 @@ +--- +reference_id: PMID:36154140 +title: Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes. +authors: +- McClure R +- Farris Y +- Danczak R +- Nelson W +- Song HS +- Kessell A +- Lee JY +- Couvillion S +- Henry C +- Jansson JK +- Hofmockel KS +journal: mSystems +year: '2022' +doi: 10.1128/msystems.00372-22 +keywords: +- Chitin/metabolism +- Soil/chemistry +- Microbiota/genetics +- Carbon +- Nitrogen/metabolism +content_type: abstract_only +--- + +# Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes. +**Authors:** McClure R, Farris Y, Danczak R, Nelson W, Song HS, Kessell A, Lee JY, Couvillion S, Henry C, Jansson JK, Hofmockel KS +**Journal:** mSystems (2022) +**DOI:** [10.1128/msystems.00372-22](https://doi.org/10.1128/msystems.00372-22) + +## Content + +1. mSystems. 2022 Oct 26;7(5):e0037222. doi: 10.1128/msystems.00372-22. Epub 2022 + Sep 26. + +Interaction Networks Are Driven by Community-Responsive Phenotypes in a +Chitin-Degrading Consortium of Soil Microbes. + +McClure R(1), Farris Y(1), Danczak R(1), Nelson W(1), Song HS(2)(3), Kessell +A(2), Lee JY(1), Couvillion S(1), Henry C(4), Jansson JK(1), Hofmockel KS(1)(5). + +Author information: +(1)Biological Sciences Division, Pacific Northwest National +Laboratorygrid.451303.0, Richland, Washington, USA. +(2)Department of Biological Systems Engineering, University of Nebraska-Lincoln, +Lincoln, Nebraska, USA. +(3)Department of Food Science and Technology, Nebraska Food for Health Center, +University of Nebraska-Lincoln, Lincoln, Nebraska, USA. +(4)Data Science and Learning Division, Argonne National Laboratory, Lemont, +Illinois, USA. +(5)Department of Agronomy, Iowa State University, Ames, Iowa, USA. + +Soil microorganisms provide key ecological functions that often rely on +metabolic interactions between individual populations of the soil microbiome. To +better understand these interactions and community processes, we used chitin, a +major carbon and nitrogen source in soil, as a test substrate to investigate +microbial interactions during its decomposition. Chitin was applied to a model +soil consortium that we developed, "model soil consortium-2" (MSC-2), consisting +of eight members of diverse phyla and including both chitin degraders and +nondegraders. A multiomics approach revealed how MSC-2 community-level processes +during chitin decomposition differ from monocultures of the constituent species. +Emergent properties of both species and the community were found, including +changes in the chitin degradation potential of Streptomyces species and +organization of all species into distinct roles in the chitin degradation +process. The members of MSC-2 were further evaluated via metatranscriptomics and +community metabolomics. Intriguingly, the most abundant members of MSC-2 were +not those that were able to metabolize chitin itself, but rather those that were +able to take full advantage of interspecies interactions to grow on chitin +decomposition products. Using a model soil consortium greatly increased our +knowledge of how carbon is decomposed and metabolized in a community setting, +showing that niche size, rather than species metabolic capacity, can drive +success and that certain species become active carbon degraders only in the +context of their surrounding community. These conclusions fill important +knowledge gaps that are key to our understanding of community interactions that +support carbon and nitrogen cycling in soil. IMPORTANCE The soil microbiome +performs many functions that are key to ecology, agriculture, and nutrient +cycling. However, because of the complexity of this ecosystem we do not know the +molecular details of the interactions between microbial species that lead to +these important functions. Here, we use a representative but simplified model +community of bacteria to understand the details of these interactions. We show +that certain species act as primary degraders of carbon sources and that the +most successful species are likely those that can take the most advantage of +breakdown products, not necessarily the primary degraders. We also show that a +species phenotype, including whether it is a primary degrader or not, is driven +in large part by the membership of the community it resides in. These +conclusions are critical to a better understanding of the soil microbial +interaction network and how these interactions drive central soil microbiome +functions. + +DOI: 10.1128/msystems.00372-22 +PMCID: PMC9599572 +PMID: 36154140 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file