A thermophilic, anaerobic, semi-continuously fed methanogenic enrichment microbiome cultivated on mid-season switchgrass at high solids loadings. The community maintained fractional carbohydrate solubilization as solids loading increased from 30 to 150 g/L, with methane and carbon dioxide as the main steady-state products. Metaproteomics identified bacterial carbohydrate-active enzyme strategies and archaeal methanogenesis functions relevant to DOE bioenergy efforts to understand robust lignocellulose deconstruction under industrially relevant process conditions.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Clostridia | NCBITaxon:186801 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
SECONDARY_FERMENTER
|
DOMINANT |
|
|||
| Bacilli | NCBITaxon:91061 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
SECONDARY_FERMENTER
|
ABUNDANT |
|
|||
| Chloroflexota | NCBITaxon:200795 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
SECONDARY_FERMENTER
|
COMMON |
|
|||
| Thermotogota | NCBITaxon:200918 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
SECONDARY_FERMENTER
|
COMMON |
|
|||
| Euryarchaeota — ontology label: Methanobacteriota | NCBITaxon:28890 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
CROSS_FEEDER
|
COMMON |
|
|||
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.
High-Solids Switchgrass Carbohydrate Solubilization
The thermophilic HR1 community maintained fractional carbohydrate solubilization as switchgrass loading increased from 30 to 150 g/L in one sequentially operated reactor. This positive bulk-carbohydrate result does not demonstrate complete lignin mineralization or selectively identify the causal enzyme strategy. Vitamins, medium optimization, mixing and adaptation also changed during operation. LC-MS profiles identify expressed protein groups with annotated CAZyme potential, not direct catalytic activities; the five canonical taxa are a curated subset, not every organism responsible for conversion.
Participating Taxa: Clostridia, Bacilli, Chloroflexota, Thermotogota, Euryarchaeota
Metabolites: cellulose (CHEBI:18246 · MediaIngredientMech · CMMMech), xylan (CHEBI:37166 · MediaIngredientMech · CMMMech)
Biological Processes:
- cellulose catabolic process (GO:0030245 · PathwayMech)
- xylan catabolic process (GO:0045493 · PathwayMech)
PARTIAL - carbohydrate solubilization followed by fermentation can supply carbon and reducing equivalents to methanogenesis, connecting the measured reactor outcomes. The broad trophic model is supported by bulk products and protein profiles, but the hydrogenotrophic contribution and exact donor-to-methanogen flux were not selectively quantified.
Evidence
-
PMID:35790765 - SUPPORT (IN_VITRO)"undiminished fractional carbohydrate solubilization"
-
PMID:35790765 - SUPPORT (COMPUTATIONAL)"specific carbohydrate-active enzyme classes"
Fraction-Associated CAZyme Protein Profiles
Chloroflexi-assigned CAZyme proteins were more prevalent in the planktonic-cell fraction, whereas Thermotogae-assigned proteins were more represented in supernatant and substrate-bound fractions. These positive metaproteomic profiles motivated the authors' functional-niche interpretation. Centrifugation-enriched fractions and protein adsorption do not directly locate every living organism, establish competitive niche partitioning, or demonstrate a Chloroflexota-to-Thermotogota interaction.
Participating Taxa: Chloroflexota, Thermotogota
Metabolites: cellulose (CHEBI:18246 · MediaIngredientMech · CMMMech), xylan (CHEBI:37166 · MediaIngredientMech · CMMMech)
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
PARTIAL - fraction-associated CAZyme proteins could contribute complementary hydrolysis functions that maintain carbohydrate solubilization. Protein abundance and localization profiles support this interpretation, not selective perturbation establishing that spatial partitioning causes the maintained phenotype.
Evidence
-
PMID:35790765 - SUPPORT (COMPUTATIONAL)"CAZymes from the phylum Chloroflexi were more prevalent in the PC fraction while enzymes from the phylum Thermotogae were more represented in the SNT and SB fractions"
-
PMID:35790765 - SUPPORT (COMPUTATIONAL)"each sample was split into three fractions: supernatant (SNT), planktonic cells (PC), and substrate-bound (SB)"
Methane Production and Inferred Hydrogenotrophic Route
Methane and carbon dioxide were measured reactor products. The higher abundance and diversity of proteins assigned to hydrogenotrophic rather than acetoclastic pathways suggest a major hydrogenotrophic route, but do not quantify its fraction of methane production or exclude other routes. Steady-state hydrogen and volatile fatty acids below detection do not mean absent turnover. The canonical archaeal group represents inferred methanogenic capacity, not the complete community or an experimentally resolved partner pair.
Participating Taxa: Euryarchaeota
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech), dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech)
Biological Processes:
- methanogenesis (GO:0015948 · PathwayMech)
Evidence
-
PMID:35790765 - SUPPORT (IN_VITRO)"The main products observed were methane"
-
PMID:35790765 - PARTIAL (COMPUTATIONAL)"both the aggregate abundance and diversity (protein count) of those mapping the hydrogenotrophic pathway markedly exceeded that of the acetoclastic pathway"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
High-solids microbiome MassIVE metaproteomics dataset
Raw mass spectra for the metaproteomics study of the high-solids switchgrass microbiome. |
METAPROTEOMICS | OTHER | MSV000088319 |
|
High-solids microbiome ProteomeXchange dataset
ProteomeXchange record for the metaproteomics data from the high-solids switchgrass microbiome. |
METAPROTEOMICS | OTHER | PXD029582 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which enzymes and metabolic routes maintain conversion at high solids?
One sequential HR1 reactor supports positive conversion and gas outcomes but does not isolate solids loading from vitamin, medium, mixing or adaptation changes. Metaproteomic replicates are not independent replicate reactors, and the sequence database was derived from lower-solids metagenomes. Selective enzyme perturbations, catalytic assays and route-resolved flux would test both existing arrows. AA6 enrichment motivated an oxidative/Fenton accessibility hypothesis, but ROS, iron cycling and lignin-depolymerization flux were not directly established in the inspected study; no new oxidative branch is asserted. The authors' proposed syntrophic acetate oxidation likewise remains unresolved. Canonical broad taxa are incomplete and are not a newly grounded strain roster. Cache abstract-only metadata coexists with an appended primary full body, which was read. Non-graph metadata is preserved, not recertified.
Attaches to: ecological_interactions#High-Solids Switchgrass Carbohydrate Solubilization, ecological_interactions#Fraction-Associated CAZyme Protein Profiles, ecological_interactions#Methane Production and Inferred Hydrogenotrophic Route
External Resources
| Name | Repository | Resource ID |
|---|---|---|
|
Exact-system primary publication - high-solids switchgrass microbiome
Primary ORNL/NREL-associated publication reporting metaproteomics of the anaerobic thermophilic switchgrass microbiome at increasing solids loading. |
OTHER | PMID:35790765 |
|
||
|
Nature Communications full-text article
Open-access article with methods, data availability, and supplementary metaproteomics tables. |
OTHER | doi:10.1038/s41467-022-31433-x |
|
MassIVE dataset DOI
Dataset DOI for raw metaproteomics mass spectra. |
OTHER | doi:10.25345/C5H85T |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Switchgrass solids loading | 30 to 150 | g/L |
|
||
| Anaerobic thermophilic operation | anaerobic thermophilic enrichment | N/A |
|
||
| High-solids enzyme response | increased AA6, beta-glucosidase, xylosidase, debranching, and pectin-acting enzyme abundance | N/A |
|
||
Growth Media
Cross-Mech Suite Links
Explore related entities across the CultureBotAI X-Mech knowledge bases: