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 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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COMMON |
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| Sphingobacterium multivorum w15 — ontology label: Sphingobacterium paramultivorum | NCBITaxon:2886510 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
CROSS_FEEDER
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COMMON |
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| Citrobacter freundii so4 — ontology label: Citrobacter freundii | NCBITaxon:546 · TaxonMech · TraitMech |
SECONDARY_FERMENTER
CROSS_FEEDER
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COMMON |
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Ecological Interactions
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
Fungal Lignocellulose-Associated Transcript Profile
Coniochaeta sp. 2T2.1 expresses genes annotated for cellulose and xylan degradation and lignin modification. The 2023 study measures transcript profiles across 60 and 180 rpm and days 1, 5 and 13. These data support inferred fungal capacity, not directly measured enzyme activity, transferred products or a demonstrated reduction of competition through niche partitioning.
Source Taxon: Coniochaeta sp. 2T2.1
Metabolites: cellulose (CHEBI:18246 · MediaIngredientMech · CMMMech), xylan (CHEBI:37166 · MediaIngredientMech · CMMMech), lignin (CHEBI:6457 · MediaIngredientMech · CMMMech)
Biological Processes:
- cellulose catabolic process (GO:0030245 · PathwayMech)
- xylan catabolic process (GO:0045493 · PathwayMech)
PARTIAL - expression of fungal lignocellulose-associated genes is consistent with a contribution to measured wheat-straw loss. Protein activity, partner-resolved flux and selective enzyme perturbations are needed to assign the fungal share or show that transcript differences mediate the shaking-speed effect.
Evidence
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PMID:31769802 - PARTIAL (COMPUTATIONAL)"carbohydrate-active enzymes indicated an onset of (hemi)cellulose degradation"
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PMID:36991472 - PARTIAL (COMPUTATIONAL)"lignin modification processes"
Bacterial Carbohydrate And Support Transcript Profiles
Transcript profiles support proposed roles for w15 in hemicellulose use and so4 in oligosaccharide or sugar-dimer use and stress responses. PARTIAL - these are functional hypotheses, not demonstrated w15-to-so4 transfer or reduced competition. RibE is encoded by all three members, the medium supplies riboflavin, and so4 ribE expression increases late at 60 rpm; exclusive w15 vitamin B2 donation is not established.
Participating Taxa: Sphingobacterium multivorum w15, Citrobacter freundii so4
Metabolites: xylan (CHEBI:37166 · MediaIngredientMech · CMMMech), riboflavin (CHEBI:17015 · MediaIngredientMech · CMMMech)
Biological Processes:
- xylan catabolic process (GO:0045493 · PathwayMech)
- riboflavin biosynthetic process (GO:0009231 · PathwayMech)
PARTIAL - the inferred bacterial carbohydrate and support functions could contribute to whole-consortium wheat-straw loss. Transcript patterns and observed growth support this contribution, but do not selectively establish enzyme activity, detoxification, exchanged-carbon flux or the bacterial share of degradation.
Evidence
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PMID:36991472 - PARTIAL (COMPUTATIONAL)"S. paramultivorum w15 is involved in the degradation of mainly hemicellulose"
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PMID:36991472 - PARTIAL (COMPUTATIONAL)"C. freundii so4 in the degradation of oligosaccharides or sugar dimers"
Bacterial-Pair-Associated Fungal Response
The 2020 abstract reports altered fungal transcripts and lower degradation in the tripartite consortium than with Coniochaeta alone under its tested conditions. The bacterial pair, not isolated w15, was compared with the fungal monoculture. Amensalism is suggested, not established reciprocal competitive harm. The 2023 shaking-speed comparison shows condition-dependent transcript and growth patterns, so inhibition must not be generalized to every culture condition.
Participating Taxa: Coniochaeta sp. 2T2.1, Sphingobacterium multivorum w15, Citrobacter freundii so4
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:31769802 - PARTIAL (COMPUTATIONAL)"inter-kingdom interactions (e.g. amensalism)"
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PMID:31769802 - SUPPORT (IN_VITRO)"lower degradation percentages within the microbial consortium"
Community Wheat-Straw Degradation
The tripartite consortium lost more wheat-straw mass after 13 days at 60 rpm (27.1 +/- 2.4%) than at 180 rpm (16.2 +/- 1.7%) in the 2023 experiment. This supports a culture-condition effect on community degradation, not selectively demonstrated enzyme synergism or universal improvement over fungal monoculture. Functional roles, detoxification and vitamin exchange remain proposed contributors.
Participating Taxa: Coniochaeta sp. 2T2.1, Sphingobacterium multivorum w15, Citrobacter freundii so4
Metabolites: cellulose (CHEBI:18246 · MediaIngredientMech · CMMMech), xylan (CHEBI:37166 · MediaIngredientMech · CMMMech), riboflavin (CHEBI:17015 · MediaIngredientMech · CMMMech)
Biological Processes:
- cellulose catabolic process (GO:0030245 · PathwayMech)
- xylan catabolic process (GO:0045493 · PathwayMech)
Evidence
-
PMID:36991472 - PARTIAL (COMPUTATIONAL)"The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite 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. |
METATRANSCRIPTOMICS | NCBI_BIOPROJECT | PRJNA870051 |
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Coniochaeta sp. 2T2.1 JGI genome project
JGI/MycoCosm genome resource for the Coniochaeta sp. 2T2.1 fungal member. |
GENOMICS | OTHER | JGI Project 1019910 |
|
Sphingobacterium w15 genome assembly
Draft genome assembly for the w15 bacterial member originally reported as S. multivorum. |
GENOMICS | OTHER | PHGV01000000 |
|
Citrobacter freundii so4 genome assembly
Draft genome assembly for the C. freundii so4 bacterial member. |
GENOMICS | OTHER | PHGU01000000 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which partner functions mediate the condition-dependent wheat-straw degradation?
The 2023 primary body reports mass loss, growth and transcript differences under two shaking speeds, with vitamin-supplemented medium. Selective partner/enzyme perturbations and flux measurements are needed to test inferred carbohydrate roles, detoxification or vitamin transfer. The 2020 abstract reports a bacterial-pair comparison, not a w15-only effect; its full Methods and Results were inaccessible. Do not infer reciprocal harm, exclusive donation or universal synergy from these observations.
Attaches to: ecological_interactions#Fungal Lignocellulose-Associated Transcript Profile, ecological_interactions#Bacterial Carbohydrate And Support Transcript Profiles, ecological_interactions#Bacterial-Pair-Associated Fungal Response, ecological_interactions#Community Wheat-Straw Degradation
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 |
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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 |
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w15 taxonomy publication
Taxonomic analysis proposing that the strain originally assigned to S. multivorum w15 should be named Sphingobacterium paramultivorum. |
OTHER | PMID:34683378 |
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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 |
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| Shaking speed | 180 and 60 | rpm |
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| Sampling time points | 1, 5, and 13 | days |
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Growth Media
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