Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes

Abstract

Anaerobic gut fungi are biomass degraders that form syntrophic associations with other microbes in their native rumen environment. Here, RNA-Seq was used to track and quantify carbohydrate active enzyme (CAZyme) transcription in a synthetic consortium composed of the anaerobic fungus Anaeromyces robustus with methanogen Methanobacterium bryantii. Approximately 5% of total A. robustus genes were differentially regulated in co-culture with M. bryantii relative to cultivation of A. robustus alone. We found that 105 CAZymes (12% of the total predicted CAZymes of A. robustus) were upregulated while 29 were downregulated. Upregulated genes encode putative proteins with a wide array of cellulolytic, xylanolytic, and carbohydrate transport activities; 75% were fused to fungal dockerin domains, associated with a carbohydrate binding module, or both. Collectively, this analysis suggests that co-culture of A. robustus with M. bryantii remodels the transcriptional landscape of CAZymes and associated metabolic pathways in the fungus to aid in lignocellulose breakdown.

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Acknowledgements

The authors are grateful for funding support from the National Science Foundation (Directorate for Biological Sciences, Grant no. MCB-1553721), the Institute for Collaborative Biotechnologies through Grants W911NF-09-0001 and W911NF-19-D-0001 from the U.S. Army Research Office, and the Camille Dreyfus Teacher-Scholar Awards Program. CLS is also supported by a National Science Foundation Graduate Research Fellowship Program under Grant no. 1650114. We thank Dr. Jennifer Smith, manager of the Biological Nanostructures Laboratory within the California NanoSystems Institute, supported by the University of California, Santa Barbara and the University of California, Office of the President. The authors acknowledge support from the Center for Scientific Computing from the CNSI, MRL: an NSF MRSEC (DMR-1121053) and NSF CNS-0960316.

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Correspondence to Michelle A. O’Malley.

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Swift, C.L., Brown, J.L., Seppälä, S. et al. Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes. J Ind Microbiol Biotechnol 46, 1427–1433 (2019). https://doi.org/10.1007/s10295-019-02188-0

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Keywords

  • Anaerobic fungi
  • Methanogens
  • Consortia
  • Transcriptomics
  • CAZymes