Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates
Year: 2021
Type: article
Abstract: Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid-forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2-fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal-methanogen physical associations and fungal cell wall development and remodeling.
Source: Biotechnology for Biofuels
Institutions: University of California, Santa Barbara, Lawrence Berkeley National Laboratory, Joint Genome Institute, Colorado State University, King Abdulaziz University, Technical University of Denmark, Centre National de la Recherche Scientifique, Aix-Marseille Université, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Architecture et Fonction des Macromolécules Biologiques, University of California, Berkeley, Joint BioEnergy Institute
Language: English
Field: Energy
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $2,790
Funders: National Science Foundation, U.S. Department of Energy, Camille and Henry Dreyfus Foundation, Joint Genome Institute, Directorate for Biological Sciences, Office of Science, U.S. Army, University of California, Santa Barbara, Materials Research Science and Engineering Center, Harvard University, Division of Materials Research, California NanoSystems Institute, Army Research Office, Institute for Collaborative Biotechnologies
Awards: G1035847006, G1095314820, G1242324316, G1286236842, G1306973634, G1314494723, G1863003419, G2279853913, G2627137527, CAREER: Designing Synthetic Anaerobic Consortia for Bioproduction, G2758699378, G2790100486, G3010040163, G3051274983, G3083819904, G3437827786, G3650945766, G3769941588, G419881185, G42916606, G4501827968, Center of Excellence for Materials Research and Innovation at UCSB, ENGINEERING ANAEROBIC GUT FUNGI FOR LIGNOCELLULOSE BREAKDOWN, G4796240486, G498139845, G503935606, MRI-R2: Acquisition of a high performance central computing facility at UCSB, G5326108313, G582811279, G608057831, G6395071522, G6652958823, G6839228936, G7039353146, G7205239661, G7452299184, G7498246471, ENGINEERING ANAEROBIC GUT FUNGI FOR LIGNOCELLULOSE BREAKDOWN, G8067201233, G834277795, G8415477955, G960073642, G969889393
OpenAlex ID: W4200547201