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Coniochaeta-Sphingobacterium-Citrobacter Wheat Straw Consortium

Community ID CommunityMech:000195
Ecological State ENGINEERED
Environment wheat-straw laboratory culture
ENVO:01001405

A three-member bacterial-fungal synthetic consortium cultivated on wheat straw to study division of labor during lignocellulose degradation. The community combines the fungus Coniochaeta sp. 2T2.1 with the bacterium originally reported as Sphingobacterium multivorum w15 and later proposed as Sphingobacterium paramultivorum w15, plus Citrobacter freundii so4. The system is relevant to DOE bioenergy because it links a Joint Genome Institute fungal genome resource to transcriptomic and metatranscriptomic evidence for cellulose, xylan, hemicellulose, lignin-modification, detoxification, and vitamin B2-associated functions in a model lignocellulose-degrading consortium.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Coniochaeta sp. 2T2.1 NCBITaxon:1571157
PRIMARY_DEGRADER
COMMON
  • PMID:31769802 - SUPPORT (IN_VITRO)
    "Coniochaeta sp. strain 2T2.1"
  • PMID:36991472 - SUPPORT (COMPUTATIONAL)
    "strongly involved in cellulose and xylan"
Sphingobacterium multivorum w15 NCBITaxon:2886510
PRIMARY_DEGRADER CROSS_FEEDER
COMMON
  • PMID:31769802 - SUPPORT (IN_VITRO)
    "Sphingobacterium multivorum w15"
  • PMID:34683378 - SUPPORT (COMPUTATIONAL)
    "members of the novel species, coined Sphingobacterium paramultivorum"
Citrobacter freundii so4 NCBITaxon:546
SECONDARY_FERMENTER CROSS_FEEDER
COMMON
  • PMID:31769802 - SUPPORT (IN_VITRO)
    "Citrobacter freundii so4"
  • PMID:36991472 - SUPPORT (COMPUTATIONAL)
    "detoxification-related proteins"

Ecological Interactions

Ecological interaction network for Coniochaeta-Sphingobacterium-Citrobacter Wheat Straw Consortium 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
Niche partitioning
Colonization facilitation
Strain competition
Predation

Fungal Cellulose-Xylan-Lignin Modification Role

NICHE_PARTITIONING

Source Taxon: Coniochaeta sp. 2T2.1

Metabolites: cellulose (CHEBI:18246), xylan (CHEBI:37686), lignin (CHEBI:6457)

Biological Processes:

Evidence

  • PMID:31769802 - SUPPORT (COMPUTATIONAL)
    "carbohydrate-active enzymes indicated an onset of (hemi)cellulose degradation"
  • PMID:36991472 - SUPPORT (COMPUTATIONAL)
    "lignin modification processes"

Bacterial Hemicellulose And Oligosaccharide Partitioning

NICHE_PARTITIONING

Source Taxon: Sphingobacterium multivorum w15

Target Taxon: Citrobacter freundii so4

Metabolites: xylan (CHEBI:37686), riboflavin (CHEBI:17015)

Biological Processes:

Evidence

  • PMID:36991472 - SUPPORT (COMPUTATIONAL)
    "S. paramultivorum w15 is involved in the degradation of mainly hemicellulose"
  • PMID:36991472 - SUPPORT (COMPUTATIONAL)
    "C. freundii so4 in the degradation of oligosaccharides or sugar dimers"

Inter-Kingdom Interaction And Amensalism Signal

COMPETITION

Source Taxon: Sphingobacterium multivorum w15

Target Taxon: Coniochaeta sp. 2T2.1

Biological Processes:

  • biological process involved in interspecies interaction between organisms (GO:0044419)

Evidence

  • PMID:31769802 - SUPPORT (COMPUTATIONAL)
    "inter-kingdom interactions (e.g. amensalism)"
  • PMID:31769802 - SUPPORT (IN_VITRO)
    "lower degradation percentages within the microbial consortium"

Associated Datasets

Dataset Type Repository Accession
Tripartite consortium metatranscriptome BioProject
SRA BioProject for the tripartite consortium metatranscriptome data from the two-shaking-speed study. 		METATRANSCRIPTOME NCBI_BIOPROJECT PRJNA870051
Coniochaeta sp. 2T2.1 JGI genome project
JGI/MycoCosm genome resource for the Coniochaeta sp. 2T2.1 fungal member. 		GENOME OTHER JGI Project 1019910
Sphingobacterium w15 genome assembly
Draft genome assembly for the w15 bacterial member originally reported as S. multivorum. 		GENOME OTHER PHGV01000000
Citrobacter freundii so4 genome assembly
Draft genome assembly for the C. freundii so4 bacterial member. 		GENOME OTHER PHGU01000000

External Resources

Name Repository Resource ID
Exact-system primary publication - Coniochaeta eco-enzymological role
Primary publication reporting Coniochaeta sp. 2T2.1 transcriptomics in monoculture and in the exact tripartite wheat-straw consortium with Sphingobacterium w15 and C. freundii so4. 		OTHER PMID:31769802
  • PMID:31769802 - SUPPORT (IN_VITRO)
    "synthetic microbial consortium with Sphingobacterium multivorum w15 and Citrobacter freundii so4"
Exact-system metatranscriptomic publication - shaking-speed perturbation
Later publication using the same exact consortium composition and updated w15 taxonomy to compare metatranscriptomes at 180 and 60 rpm. 		OTHER PMID:36991472
  • PMID:36991472 - SUPPORT (IN_VITRO)
    "Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1"
w15 taxonomy publication
Taxonomic analysis proposing that the strain originally assigned to S. multivorum w15 should be named Sphingobacterium paramultivorum. 		OTHER PMID:34683378
  • PMID:34683378 - SUPPORT (COMPUTATIONAL)
    "Strain w15 was originally assigned to the species Sphingobacterium multivorum"
JGI publication page
DOE JGI publication page for the FEMS Microbiology Ecology exact-system paper. 		OTHER doi:10.1093/femsec/fiz186

Environmental Factors

Factor Value Unit
Wheat straw substrate wheat straw N/A
  • PMID:31769802 - SUPPORT (IN_VITRO)
    "wheat straw-driven cultures"
  • PMID:36991472 - SUPPORT (IN_VITRO)
    "lignocellulose-degrading activities"
Shaking speed 180 and 60 rpm
  • PMID:36991472 - SUPPORT (IN_VITRO)
    "two shaking speeds (180 and 60 rpm)"
Sampling time points 1, 5, and 13 days
  • PMID:36991472 - SUPPORT (IN_VITRO)
    "three time points (1, 5 and 13 days)"

Growth Media

Wheat straw-driven lignocellulose consortium culture

Composition

Component Concentration Unit CHEBI
wheat straw N/A N/A N/A
cellulose N/A N/A CHEBI:18246
xylan N/A N/A CHEBI:37686
lignin N/A N/A CHEBI:6457

Preparation notes: The curated publications support wheat straw-driven cultures and shaking-speed perturbations; this record does not assert the full salts or trace-component medium recipe.

Evidence

PMID:31769802

"wheat straw-driven cultures"

PMID:36991472

"growth at two shaking speeds"