The ruminal microbiome associated with methane emissions from ruminant livestock

Abstract

Methane emissions from ruminant livestock contribute significantly to the large environmental footprint of agriculture. The rumen is the principal source of methane, and certain features of the microbiome are associated with low/high methane phenotypes. Despite their primary role in methanogenesis, the abundance of archaea has only a weak correlation with methane emissions from individual animals. The composition of the archaeal community appears to have a stronger effect, with animals harbouring the Methanobrevibacter gottschalkii clade tending to be associated with greater methane emissions. Ciliate protozoa produce abundant H₂, the main substrate for methanogenesis in the rumen, and their removal (defaunation) results in an average 11% lower methane emissions in vivo, but the results are not consistent. Different protozoal genera seem to result in greater methane emissions, though community types (A, AB, B and O) did not differ. Within the bacteria, three different 'ruminotypes' have been identified, two of which predispose animals to have lower methane emissions. The two low-methane ruminotypes are generally characterized by less abundant H₂-producing bacteria. A lower abundance of Proteobacteria and differences in certain Bacteroidetes and anaerobic fungi seem to be associated with high methane emissions. Rumen anaerobic fungi produce abundant H₂ and formate, and their abundance generally corresponds to the level of methane emissions. Thus, microbiome analysis is consistent with known pathways for H₂ production and methanogenesis, but not yet in a predictive manner. The production and utilisation of formate by the ruminal microbiota is poorly understood and may be a source of variability between animals.

Keywords: Archaea; Methane; Microbiome; Rumen.

Fig. 1

Archaea:bacteria relative abundance in relation to methane emissions, preliminary data from the 1000-cow RuminOmics project. Dairy cows on different farms throughout Europe received grass or maize silage:concentrate diets of similar nutrient composition. Feed intake was measured either directly or calculated from faecal long-chain hydrocarbons. Samples of rumen contents were removed by stomach tube and DNA was extracted by the Yu & Morrison method [110]. Abundances were calculated from qPCR of 16S rRNA genes using universal primers for archaea and bacteria

Fig. 2

Relationship between methane emission and rumen protozoa concentration in a meta-analysis of 28 different experiments. The black dashed line represents the average within-experiment relationship. Reproduced from [56] with permission

Fig. 3

Neighbor Joining tree of Prevotella-like OTUs that had a negative (blue dots) or positive (red dots) relation to methane (expressed in terms of g methane/kg DMI) in the 1,000-cow RuminOmics project. Multiple alignment was done using MUSCLE [111]. The Neighbor Joining tree was constructed using p-distance and pairwise-deletion parameters. The tree was resampled 1,000 times and bootstrap values are indicated. The linearized tree was computed using MEGA v5.1 [112] by using most abundant Bacteroidales OTUs to create an “outgroup”