MSC-1 Dominant Core - CommunityMech

Community ID CommunityMech:000042

Ecological State STABLE

Environment arid grassland soil
ENVO:00001998

A naturally evolved dominant core subset of the Model Soil Consortium-1 (MSC-1) containing 13 bacterial species from arid grassland soil. This stable consortium was enriched through serial dilution and passaging on chitin as the primary carbon source. The core members include representatives from Actinobacteria, Bacteroidetes, and Proteobacteria, with key species including Rhodococcus sp., Dyadobacter sp., Taibaiella sp., Bosea sp., and Streptomyces sp. The consortium exhibits cooperative chitin degradation and nitrogen mineralization functions essential for soil carbon and nitrogen cycling.

Taxonomy

Taxon	Ontology ID	Functional Roles	Abundance
Rhodococcus sp.	NCBITaxon:1827	PRIMARY_DEGRADER	DOMINANT
PMID:32983014 - SUPPORT (IN_VITRO) "Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa"
Streptomyces sp.	NCBITaxon:1931	PRIMARY_DEGRADER	DOMINANT
PMID:32983014 - SUPPORT (IN_VITRO) "Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation"
Dyadobacter sp.	NCBITaxon:1914288	PRIMARY_DEGRADER	DOMINANT
PMID:32983014 - SUPPORT (IN_VITRO) "Samples were collected from an arid grassland soil and microbial communities (consisting mainly of bacterial species) were enriched on agar plates containing chitin as the main carbon source"
Taibaiella sp.	NCBITaxon:1869185	SYNTROPHIC_PARTNER	COMMON
PMID:32983014 - SUPPORT (IN_VITRO) "Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation"
Bosea sp.	NCBITaxon:85413	SYNTROPHIC_PARTNER	COMMON
PMID:32983014 - SUPPORT (IN_VITRO) "Samples were collected from an arid grassland soil and microbial communities (consisting mainly of bacterial species) were enriched on agar plates containing chitin as the main carbon source"
Neorhizobium sp.	NCBITaxon:1911909	SYNTROPHIC_PARTNER	COMMON
PMID:32983014 - SUPPORT (IN_VITRO) "Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa"
Sphingopyxis sp.	NCBITaxon:1908224	SYNTROPHIC_PARTNER	COMMON
PMID:32983014 - SUPPORT (IN_VITRO) "Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation"
Ensifer sp.	NCBITaxon:1872086	SYNTROPHIC_PARTNER	COMMON
PMID:32983014 - SUPPORT (IN_VITRO) "Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation"
Variovorax sp.	NCBITaxon:1871043	SYNTROPHIC_PARTNER	COMMON
PMID:32983014 - SUPPORT (IN_VITRO) "Here, we reduced this complexity by developing model soil microbial consortia that are simpler and more amenable to experimental analysis but still represent important microbial functions of the native soil ecosystem"
Sinorhizobium sp.	NCBITaxon:42445	SYNTROPHIC_PARTNER	COMMON
PMID:32983014 - SUPPORT (IN_VITRO) "Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation"
Mycobacterium sp.	NCBITaxon:1785	SYNTROPHIC_PARTNER	COMMON
PMID:32983014 - SUPPORT (IN_VITRO) "Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa"
Actinobacteria bacterium	NCBITaxon:201174	SYNTROPHIC_PARTNER	RARE
PMID:32983014 - SUPPORT (IN_VITRO) "Several soil consortia were derived that had tractable richness (30-50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia"
Bacteroidetes bacterium	NCBITaxon:976	SYNTROPHIC_PARTNER	RARE
PMID:32983014 - SUPPORT (IN_VITRO) "Several soil consortia were derived that had tractable richness (30-50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Chitin Polymer Degradation

SYNTROPHY

Source Taxon: Rhodococcus sp.

Target Taxon: Streptomyces sp.

Metabolites: chitin (CHEBI:18246), chitooligosaccharide (CHEBI:142816)

Biological Processes:

chitin catabolic process (GO:0006032)
chitinase activity (GO:0004568)

Downstream Effects:

→ N-Acetylglucosamine Processing

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation"

N-Acetylglucosamine Processing

SYNTROPHY

Source Taxon: Dyadobacter sp.

Target Taxon: Mycobacterium sp.

Metabolites: N-acetyl-D-glucosamine (CHEBI:28009), D-glucosamine (CHEBI:15767)

Biological Processes:

glucosamine catabolic process (GO:0006046)
carbohydrate metabolic process (GO:0005975)

Downstream Effects:

→ Nitrogen Mineralization

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa"

Nitrogen Mineralization

SYNTROPHY

Source Taxon: Mycobacterium sp.

Target Taxon: Neorhizobium sp.

Metabolites: ammonium (CHEBI:28938), organic nitrogen compound (CHEBI:35352)

Biological Processes:

nitrogen cycle metabolic process (GO:0071941)
cellular amino acid metabolic process (GO:0006520)

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation"

Syntrophic Partnership with Taibaiella

SYNTROPHY

Source Taxon: Rhodococcus sp.

Target Taxon: Taibaiella sp.

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation"

Syntrophic Partnership with Bosea

SYNTROPHY

Source Taxon: Mycobacterium sp.

Target Taxon: Bosea sp.

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa"

Syntrophic Partnership with Sphingopyxis

SYNTROPHY

Source Taxon: Streptomyces sp.

Target Taxon: Sphingopyxis sp.

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation"

Syntrophic Partnership with Ensifer

SYNTROPHY

Source Taxon: Neorhizobium sp.

Target Taxon: Ensifer sp.

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa"

Syntrophic Partnership with Variovorax

SYNTROPHY

Source Taxon: Rhodococcus sp.

Target Taxon: Variovorax sp.

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation"

Syntrophic Partnership with Sinorhizobium

SYNTROPHY

Source Taxon: Mycobacterium sp.

Target Taxon: Sinorhizobium sp.

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa"

Syntrophic Partnership with Actinobacteria

SYNTROPHY

Source Taxon: Streptomyces sp.

Target Taxon: Actinobacteria bacterium

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Several soil consortia were derived that had tractable richness (30-50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia"

Syntrophic Partnership with Bacteroidetes

SYNTROPHY

Source Taxon: Dyadobacter sp.

Target Taxon: Bacteroidetes bacterium

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32983014 - SUPPORT (IN_VITRO)

"Several soil consortia were derived that had tractable richness (30-50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia"

Environmental Factors

Factor	Value	Unit
Source environment	arid grassland soil	N/A
Primary substrate	chitin	N/A
Environmental conditions	arid conditions	N/A
Community complexity	reduced complexity model	N/A
Functional redundancy	genomic redundancy	N/A
Storage stability	cryopreservation	N/A