Abstract
Methanobrevibacter sp. AbM4 was originally isolated from the abomasal contents of a sheep and was chosen as a representative of the Methanobrevibacter wolinii clade for genome sequencing. The AbM4 genome is smaller than that of the rumen methanogen M. ruminantium M1 (2.0 Mb versus 2.93 Mb), encodes fewer open reading frames (ORFs) (1,671 versus 2,217) and has a lower G+C percentage (29% versus 33%). Overall, the composition of the AbM4 genome is very similar to that of M1 suggesting that the methanogenesis pathway and central metabolism of these strains are highly similar, and both organisms are likely to be amenable to inhibition by small molecule inhibitors and vaccine-based methane mitigation technologies targeting these conserved features. The main differences compared to M1 are that AbM4 has a complete coenzyme M biosynthesis pathway and does not contain a prophage or non-ribosomal peptide synthase genes. However, AbM4 has a large CRISPR region and several type I and type II restriction-modification system components. Unusually, DNA-directed RNA polymerase B′ and B′′ subunits of AbM4 are joined, a feature only previously observed in some thermophilic archaea. AbM4 has a much reduced complement of genes encoding adhesin-like proteins which suggests it occupies a ruminal niche different from that of M1.
Highlights
Methane formed in the ruminant fore-stomach is a significant source of greenhouse gas emissions for countries that are reliant on ruminant-based agriculture
Molecular surveys of ruminants have shown that small subunit ribosomal RNA gene sequences affiliated with species of the genus Methanobrevibacter predominate in most rumen microbiomes, on average making up almost two thirds of the rumen archaea [1]
Sequences are mainly associated with M. gottschalkii (33.6%) and M. ruminantium (27.3%), and with M. wolinii (0.1%), M. smithii (0.1%) and other Methanobrevibacter spp. (0.5%)
Summary
Methane formed in the ruminant fore-stomach (reticulo-rumen) is a significant source of greenhouse gas emissions for countries that are reliant on ruminant-based agriculture. Genome sequencing has improved our knowledge of the processes that methanogens contribute to rumen function and is already providing information directly applicable to methane mitigation strategies based on vaccine and small-molecule inhibitor approaches [2,3]. Mitigation technologies for methane emissions from ruminants should target features that are conserved across all rumen methanogens, and be specific for methanogens so that the remaining rumen microbes can continue their normal digestive functions. Targeting ruminal methanogens using vaccine and small molecule inhibitor approaches needs to take into account the phylogenetic diversity covering the different groups of methanogens within the rumen and capture the inter-species diversity within a genus. Our group is sequencing the genomes of cultured representatives of rumen methanogens [4] to define their conserved features as targets and to understand
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