Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome.
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 H2and 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.IMPORTANCEThe 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 lowin situlevels 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.
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
J A
JA
Frank
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
M Ø
MØ
Arntzen
Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, Uppsala, Sweden.
L
L
Sun
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
L H
LH
Hagen
Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
A C
AC
McHardy
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
S J
SJ
Horn
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
V G H
VG
Eijsink
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway; Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, Uppsala, Sweden.
A
A
Schnürer
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
P B
PB
Pope
anaerobic digestion; biogas; metagenomics; metaproteomics; syntrophic acetate oxidation