Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen

Abstract

Methane generated during enteric fermentation in ruminant livestock species is a major contributor to global anthropogenic greenhouse gas emissions. A period of moderate feed restriction followed by ad libitum access to feed is widely applied in cattle management to exploit the animal's compensatory growth potential and reduce feed costs. In the present study, we utilised microbial RNA from rumen digesta samples to assess the phylogenetic diversity of transcriptionally active methanogens from feed-restricted and non-restricted animals. To determine the contribution of different rumen methanogens to methanogenesis during dietary restriction of cattle, we conducted high-throughput mcrA cDNA amplicon sequencing on an Illumina MiSeq and analysed both the abundance and phylogenetic origin of different mcrA cDNA sequences. When compared to their unrestricted contemporaries, in feed-restricted animals, the methanogenic activity, based on mcrA transcript abundance, of Methanobrevibacter gottschalkii clade increased while the methanogenic activity of the Methanobrevibacter ruminantium clade and members of the Methanomassiliicoccaceae family decreased. This study shows that the quantity of feed consumed can evoke large effects on the composition of methanogenically active species in the rumen of cattle. These data potentially have major implications for targeted CH₄ mitigation approaches such as anti-methanogen vaccines and/or tailored dietary management.

Figure 1

The evolutionary history which approximately identifies the phylogeny of clustered sequences was inferred using the Maximum Parsimony method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. Branches with less than 30% support were collapsed. The MP tree was obtained using the Subtree-Pruning-Regrafting (SPR) algorithm with search level 1 in which the initial trees were obtained by the random addition of sequences (10 replicates). All positions with less than 85% site coverage were eliminated. There were a total of 157 positions in the final dataset. The 4 numbers in red separated by a “;” after each cluster represent the average representation of this cluster in R, A, RA and AA groups respectively.

Figure 2

nMDS plot indicating similarity of metabolically active methanogens between treatments. Distance between samples, based on similarity of cluster composition (similarity 97%) of each sample calculated using Bray-curtis similarity index and plotted using non-metric multidimensional scaling (nMDS). Each point represents a different sample plotted according to their cluster conformation and abundance (stress value = 0.1). A greater distance between two points infers a lower similarity between them, whereas samples composed of similar MCRA clusters will group closer together.

Figure 3

Principal coordinate analysis (PCoA) of the relative abundances of clusters. PCoA was used to compare variation of relative cluster abundances within the liquid rumen samples from treatment A, AA, R and RA.

Figure 4

Dendrogram of Bray-Curtis similarity of MCRA clusters in treatment groups; A, AA, R and RA.

Figure 5

Square root transformed relative abundance heat map (white = absence, dark blue = high) of MCRA clusters in treatment groups; A, AA, R and RA.