The rumen microbial metagenome associated with high methane production in cattle

Abstract

BackgroundMethane represents 16 % of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 % of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high- and low-methane-emitting cattle phenotypes.MethodsFour pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes databasefor functional analysis.ResultsDeep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5× more numerous (P = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; P = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed 100 % identity with a publicly available protein sequence.ConclusionsThe abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals, a finding useful for genetic screening purposes. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis, as similarly postulated for Australian macropods. Large numbers of predicted protein sequences differed between high- and low-methane-emitting cattle. Ninety-nine percent were unknown, indicating a fertile area for future exploitation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2032-0) contains supplementary material, which is available to authorized users.

Invited review: Large-scale indirect measurements for enteric methane emissions in dairy cattle: A review of proxies and their potential for use in management and breeding decisions

“…The relationship between rumen methanogen abundance and methanogenesis is less clear when changes in enteric CH 4 emissions are modulated by diet or are a consequence of selecting phenotypes related to feed efficiency or MeY. Whereas in some reports, significant positive relationships were identified (Aguinaga Casañas et al, 2015;Arndt et al, 2015;Sun et al, 2015;Wallace et al, 2015), in many others, the concentration of methanogens was unrelated to methanogenesis (e.g., Morgavi et al, 2012;Kittelmann et al, 2014;Shi et al, 2014;Bouchard et al, 2015). Bouchard et al (2015) even reported a reduction in methanogens without a significant decrease in MeP for steers fed sainfoin silage.…”

“…Some methodological and experimental differences might explain some of these apparent contradictions, such as the type of gene target and primers used for nucleic acid amplification. Effects are seen most clearly when the difference in MeP between groups of animals is large; for example, Wallace et al (2015) used treatments that generated a 1.9-fold difference in CH 4 emissions. Roehe et al (2016) observed that the ranking of sire groups for CH 4 emissions measured with respiration chambers was the same as that for ranking on archaea:bacteria ratio, providing further evidence that host control of archaeal abundance contributes to genetic variation in CH 4 emissions, at least in some circumstances.…”

Global beef cattle methane emissions: yield prediction by cluster and meta-analyses

“…No strong associations were found between the most abundant rumen bacteria and archaea (~3% of microbes that are mostly autotrophic methanogens). However, Wallace et al (2015) reported that the abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis.…”

Functional and comparative studies of members of the genus Methanosphaera, and their adaptations to the gut environment

“…spp. in the "high" emitters (Wallace et al, 2015). Such findings suggest that gaseous hydrogen formation by the microbiota can affect both the ecology and quantity of methanogenic archaea .…”

“…in the "high" emitters, while changes in the bacterial population favouring the succinate-producers like Succinivibrionaceae were found in the "low" emitting animals. Furthermore, these variations in metagenomic data between the "high" and "low" emitters have been proposed as biomarkers for animal selection and breeding strategies that seek to reduce methane emissions and/or improve feed efficiency (Wallace et al, 2015). Indeed, it would seem that the alterations in methanogen profiles observed among animals stratified by their methane emissions involves genotype x environment interactions that affect rumen fermentation and gaseous hydrogen formation .…”