Phylogenetic analysis of methanogens from the bovine rumen

Abstract

Background: Interest in methanogens from ruminants has resulted from the role of methane in global warming and from the fact that cattle typically lose 6 % of ingested energy as methane. Several species of methanogens have been isolated from ruminants. However they are difficult to culture, few have been consistently found in high numbers, and it is likely that major species of rumen methanogens are yet to be identified.

Results: Total DNA from clarified bovine rumen fluid was amplified using primers specific for Archaeal 16S rRNA gene sequences (rDNA). Phylogenetic analysis of 41 rDNA sequences identified three clusters of methanogens. The largest cluster contained two distinct subclusters with rDNA sequences similar to Methanobrevibacter ruminantium 16S rDNA. A second cluster contained sequences related to 16S rDNA from Methanosphaera stadtmanae, an organism not previously described in the rumen. The third cluster contained rDNA sequences that may form a novel group of rumen methanogens.

Conclusions: The current set of 16S rRNA hybridization probes targeting methanogenic Archaea does not cover the phylogenetic diversity present in the rumen and possibly other gastro-intestinal tract environments. New probes and quantitative PCR assays are needed to determine the distribution of the newly identified methanogen clusters in rumen microbial communities.

Figure 1

Unrooted phylogenetic tree constructed using a neighbor-joining method. The clones from this study are labeled ARC## and are shown in relation to related species and clones. Brackets indicate clusters UNI (unknown methanogens), Mbr (Methanobrevibacter ruminantium related clones), and Mss (Methanosphaera stadtmanae related clones). Bootstrap values greater than 70% for 1000 trees are shown at major branch points. Halobacterium halobium was used as the out-group. The bar represents a sequence divergence of 10 %.