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Research article - Peer-reviewed, 2016

Novel syntrophic populations dominate an ammonia-tolerant methanogenic microbiome

Frank, J. A.; Arntzen, M. O.; Sun, L.; Hagen, L. H.; McHardy, A. C.; Horn, S. J.; Eijsink, V. G. H.; Schnurer, A.; Pope, P. B.

Abstract

Biogas reactors operating with protein-rich substrates have high methane potential and industrial value; however, they are highly susceptible to process failure because of the accumulation of ammonia. High ammonia levels cause a decline in acetate-utilizing methanogens and instead promote the conversion of acetate via a two-step mechanism involving syntrophic acetate oxidation (SAO) to H-2 and CO2, followed by hydrogenotrophic methanogenesis. Despite the key role of syntrophic acetate-oxidizing bacteria (SAOB), only a few culturable representatives have been characterized. Here we show that the microbiome of a commercial, ammonia-tolerant biogas reactor harbors a deeply branched, uncultured phylotype (unFirm_1) accounting for approximately 5% of the 16S rRNA gene inventory and sharing 88% 16S rRNA gene identity with its closest characterized relative. Reconstructed genome and quantitative metaproteomic analyses imply unFirm_1's metabolic dominance and SAO capabilities, whereby the key enzymes required for acetate oxidation are among the most highly detected in the reactor microbiome. While culturable SAOB were identified in genomic analyses of the reactor, their limited proteomic representation suggests that unFirm_1 plays an important role in channeling acetate toward methane. Notably, unFirm_1-like populations were found in other high-ammonia biogas installations, conjecturing a broader importance for this novel clade of SAOB in anaerobic fermentations.IMPORTANCE The microbial production of methane or "biogas" is an attractive renewable energy technology that can recycle organic waste into biofuel. Biogas reactors operating with protein-rich substrates such as household municipal or agricultural wastes have significant industrial and societal value; however, they are highly unstable and frequently collapse due to the accumulation of ammonia. We report the discovery of a novel uncultured phylotype (unFirm_1) that is highly detectable in metaproteomic data generated from an ammonia-tolerant commercial reactor. Importantly, unFirm_1 is proposed to perform a key metabolic step in biogas microbiomes, whereby it syntrophically oxidizes acetate to hydrogen and carbon dioxide, which methanogens then covert to methane. Only very few culturable syntrophic acetate-oxidizing bacteria have been described, and all were detected at low in situ levels compared to unFirm_1. Broader comparisons produced the hypothesis that unFirm_1 is a key mediator toward the successful long-term stable operation of biogas production using protein-rich substrates.

Keywords

anaerobic digestion; biogas; metagenomics; metaproteomics; syntrophic acetate oxidation

Published in

mSystems
2016, volume: 1, number: 5, article number: UNSP e00092-16

Authors' information

Frank, J. A.
Norwegian University of Life Sciences (NMBU)
Arntzen, M. Ø.
Norwegian University of Life Sciences (NMBU)
Swedish University of Agricultural Sciences, Department of Microbiology
Hagen, L. H.
Norwegian University of Life Sciences (NMBU)
McHardy, A. C.
Helmholtz Centre for Infection Research
Horn, Svein Jarle
Norwegian University of Life Sciences (NMBU)
Eijsink, Vincent G. H.
Norwegian University of Life Sciences (NMBU)
Norwegian University of Life Sciences (NMBU)
Swedish University of Agricultural Sciences, Department of Microbiology
Pope, Phillip B.
Norwegian University of Life Sciences (NMBU)

Sustainable Development Goals

SDG7 Affordable and clean energy
SDG12 Ensure sustainable consumption and production patterns

UKÄ Subject classification

Microbiology
Bioinformatics and Systems Biology
Bioenergy

Publication Identifiers

DOI: https://doi.org/10.1128/mSystems.00092-16

URI (permanent link to this page)

https://res.slu.se/id/publ/81272