Diverse hydrogen production and consumption pathways influence methane production in ruminants

Abstract

Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H2), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H2 metabolism. Two-thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyse H2 production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g., Ruminococcus) accounted for half of all hydrogenase transcripts. Various H2 uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate and nitrite reduction (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis-related transcripts predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared with pure culture. We conclude that H2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognised. There is evidence that alternative hydrogenotrophs, including acetogenic and respiratory bacteria, can prosper in the rumen and effectively compete with methanogens for H2. These findings may help to inform ongoing strategies to mitigate methane emissions by increasing flux through alternative H2 uptake pathways, including through animal selection, dietary supplementation and methanogenesis inhibitors.

Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions

“…Dihydrogen has a central role in the flows of [H] in the rumen. Genes encoding hydrogenases are widespread in the genomes of rumen bacteria and archaea, highlighting that an important proportion of [H] is transferred and incorporated between cells as H 2 (Greening et al, 2019). This agrees with the historical finding by Hungate (1967) of H 2 being the main [H] donor for CH 4 formation in rumen fermentation.…”

“…the Hungate culture collection and others. Furthermore, confurcating hydrogenases were the most abundant hydrogenase transcripts in sheep rumens, which shows the importance of this relatively recently discovered e − transfer mechanism in rumen fermentation (Greening et al, 2019). The rumen bacterium Ruminococcus albus, for example, can produce H 2 from NADH in confurcation with the oxidation of Fd red 2− (Zheng et al, 2014).…”

“…The rumen bacterium Ruminococcus albus, for example, can produce H 2 from NADH in confurcation with the oxidation of Fd red 2− (Zheng et al, 2014). Greening et al (2019) found that the expression in R. albus of an 8-gene cluster encoding for an alcohol and aldehyde dehydrogenase involved in the production of ethanol, a ferredoxin H 2 -evolving hydrogenase, and a sensory hydrogenase, were sharply decreased in co-culture with the H 2 -utilizer Wolinella succinogenes in comparison to the mono-culture. In the co-culture, NADH was re-oxidized only through confurcation with Fd red 2− , as NADH was not utilized as reductant for ethanol production.…”

Metabolic flexibility allows generalist bacteria to become dominant in a frequently disturbed ecosystem

“…In addition, we searched ORFs from the 135 MAGs retrieved from this study and 12 MAGs that were previously reported 38 . These genes are involved in sulfur cycling (AsrA, FCC, Sqr, DsrA, Sor, SoxB), nitrogen cycling (AmoA, HzsA, NifH, NarG, NapA, NirS, NirK, NrfA, NosZ, NxrA, NorB), iron cycling (Cyc2, OmcB), reductive dehalogenation (RdhA), photosynthesis (PsaA, PsbA, energy-converting microbial rhodopsin), methane cycling (McrA, MmoA, PmoA), hydrogen cycling (large subunit of NiFe-, FeFe-, and Fe-hydrogenases), carbon monoxide oxidation (CoxL), succinate oxidation (SdhA), fumarate reduction (FrdA), and acetogenesis (AcsB) 71–73 Results were further filtered based on an identity threshold of 50%, except for group 4 NiFe-hydrogenases, FeFe-hydrogenases, CoxL, AmoA, and NxrA (all 60%), PsaA (80%), and PsbA (70%). Subgroup classification of reads was based on the closest match to the sequences in databases.…”

Thermogenic hydrocarbons fuel a redox stratified subseafloor microbiome in deep sea cold seep sediments

“…After removal of short sequences, they were further manually curated using BLASTp against NCBI-based nr protein sequences by checking top hits to relevant genes. For identification of McrA and DsrA, protein sequences were screened against local protein databases 79 using BLASTp (cutoffs: evalue 1e-20 + pident 30% + qcovs 70%). McrA and DsrA protein sequences were cross-checked against MetaErg annotations and phylogenetic analyses, while hydrogenases were confirmed and classified using the HydDB tool 52 .…”