Abstract
Previous shotgun metagenomic analyses of ruminal digesta identified some microbial information that might be useful as biomarkers to select cattle that emit less methane (CH4), which is a potent greenhouse gas. It is known that methane production (g/kgDMI) and to an extent the microbial community is heritable and therefore biomarkers can offer a method of selecting cattle for low methane emitting phenotypes. In this study a wider range of Bos Taurus cattle, varying in breed and diet, was investigated to determine microbial communities and genetic markers associated with high/low CH4 emissions. Digesta samples were taken from 50 beef cattle, comprising four cattle breeds, receiving two basal diets containing different proportions of concentrate and also including feed additives (nitrate or lipid), that may influence methane emissions. A combination of partial least square analysis and network analysis enabled the identification of the most significant and robust biomarkers of CH4 emissions (VIP > 0.8) across diets and breeds when comparing all potential biomarkers together. Genes associated with the hydrogenotrophic methanogenesis pathway converting carbon dioxide to methane, provided the dominant biomarkers of CH4 emissions and methanogens were the microbial populations most closely correlated with CH4 emissions and identified by metagenomics. Moreover, these genes grouped together as confirmed by network analysis for each independent experiment and when combined. Finally, the genes involved in the methane synthesis pathway explained a higher proportion of variation in CH4 emissions by PLS analysis compared to phylogenetic parameters or functional genes. These results confirmed the reproducibility of the analysis and the advantage to use these genes as robust biomarkers of CH4 emissions. Volatile fatty acid concentrations and ratios were significantly correlated with CH4, but these factors were not identified as robust enough for predictive purposes. Moreover, the methanotrophic Methylomonas genus was found to be negatively correlated with CH4. Finally, this study confirmed the importance of using robust and applicable biomarkers from the microbiome as a proxy of CH4 emissions across diverse production systems and environments.
Highlights
Recent metagenomic analyses have highlighted the exciting opportunity that rumen microbial biomarkers of methane (CH4) emissions could enable the selection by breeding of cattle which emit less CH4 and may lower agricultural greenhouse gas (GHG) emissions. Ross et al (2013) highlighted that this approach may surpass current prediction accuracies that are based on the host genome, especially for traits that are difficult to measure and largely influenced by the gut microbiome
The aim of this study was (i) to evaluate the effect of two basal diets, and additives on the rumen microbiome of a selection of four beef livestock breeds and to identify robust biomarkers of CH4 emissions associated with the microbiome or microbial activities, (ii) the identification of robust biomarkers of CH4 emissions associated with data from the microbial community composition, the relative abundance of microbial populations, the relative abundance of genes within the microbiome or volatile fatty acids (VFA) concentrations, all data collected from three independent experiments, and (iii) the comparison of these biomarkers to identify those highly correlated with CH4 emissions across diverse breeds and diets and the evaluation of the possibility of implementing a breeding strategy using these microbial biomarkers from the rumen microbiome
CH4 emissions were higher in animals fed the forage compared to concentrate basal diet (P < 0.001)
Summary
Recent metagenomic analyses have highlighted the exciting opportunity that rumen microbial biomarkers of methane (CH4) emissions could enable the selection by breeding of cattle which emit less CH4 and may lower agricultural greenhouse gas (GHG) emissions. Ross et al (2013) highlighted that this approach may surpass current prediction accuracies that are based on the host genome, especially for traits that are difficult to measure and largely influenced by the gut microbiome. Methane has a large impact on global warming, being 28-fold more potent as a GHG than carbon dioxide (CO2) (IPCC, 2014) It is one of the main anthropogenic sources (IPCC, 2014) and ruminants are major producers of CH4, accounting for 37% of total GHG from agriculture in the UK (Cottle et al, 2011). Higher abundance of bacteria populations involved in propionate metabolism is associated with reduced methane emissions compared to acetate metabolism because more H2 is utilized per mole VFA reducing availability for methane production (Janssen, 2010; Wanapat et al, 2015) Methanotrophic populations within both archaea and bacteria are known to metabolize methane as a carbon and energy source but the impact of such populations in the rumen seems likely to be minor (Parmar et al, 2015; Wallace et al, 2015)
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