Abstract
Methanobrevibacter millerae SM9 was isolated from the rumen of a sheep maintained on a fresh forage diet, and its genome has been sequenced to provide information on the phylogenetic diversity of rumen methanogens with a view to developing technologies for methane mitigation. It is the first rumen isolate from the Methanobrevibacter gottschalkii clade to have its genome sequence completed. The 2.54 Mb SM9 chromosome has an average G + C content of 31.8 %, encodes 2269 protein-coding genes, and harbors a single prophage. The overall gene content is comparable to that of Methanobrevibacter ruminantium M1 and the type strain of M. millerae (ZA-10T) suggesting that the basic metabolism of these two hydrogenotrophic rumen methanogen species is similar. However, M. millerae has a larger complement of genes involved in methanogenesis including genes for methyl coenzyme M reductase II (mrtAGDB) which are not found in M1. Unusual features of the M. millerae genomes include the presence of a tannase gene which shows high sequence similarity with the tannase from Lactobacillus plantarum, and large non-ribosomal peptide synthase genes. The M. millerae sequences indicate that methane mitigation strategies based on the M. ruminantium M1 genome sequence are also likely to be applicable to members of the M. gottschalkii clade.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-016-0171-9) contains supplementary material, which is available to authorized users.
Highlights
Ruminant livestock such as cattle and sheep produce methane as a product of enteric fermentation and ruminant-derived methane accounts for almost 30 % of New Zealand’s anthropogenic greenhouse gas emissions
Methane is produced by methanogenic archaea, and sequencing of 16S rRNA gene amplicons has shown that members of the orders Methanobacteriales and Methanomassiliicoccales are the dominant methanogens in the rumens of farmed New Zealand ruminants [1, 2]
We have previously used the genome sequence of the type strain of M. ruminantium to identify methane mitigation targets [4] and here we present the genome sequence of M. millerae SM9, a rumen representative of the M. gottschalkii clade
Summary
Ruminant livestock such as cattle and sheep produce methane as a product of enteric fermentation and ruminant-derived methane accounts for almost 30 % of New Zealand’s anthropogenic greenhouse gas emissions. Genome project history Methanobrevibacter millerae SM9 was selected for genome sequencing on the basis of its phylogenetic position relative to other methanogens belonging to the family Methanobacteriaceae, and falls within the M. gottschalkii clade of rumen methanogens. A total of 169 additional reactions were used to close gaps and to improve the quality of the genome sequence to ensure correct assembly and to resolve any remaining baseconflicts. Assignment of protein function to ORFs was performed manually using results from the following sources; BLASTP [18] to both a non-redundant protein database provided by the National Centre for Biotechnology Information [20] and Clusters of Orthologous Groups database [21]. The genomes of M. millerae SM9 and M. ruminantium M1 do not show significant synteny (Fig. 4b), their gene contents are comparable suggesting that the basic metabolism of these two hydrogenotrophic rumen methanogen species is similar. M. millerae SM9 has the same set of methanogenesis genes as M. ruminantium M1, and has several genes not found in M1 including an additional gene cluster containing the methyl coenzyme M reductase II (mrtAGDB) genes together with a second copy of F420-dependent methylenetetrahydromethanopterin dehydrogenase (mtd), and a second set of
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