Occurrence and expression of genes encoding methyl-compound production in rumen bacteria.

Background: Digestive processes in the rumen lead to the release of methyl-compound, mainly methanol and methylamines, which are used by methyltrophic methanogens to form methane, an important agricultural greenhouse gas. Methylamines are produced from plant phosphatidylcholine degradation, by choline trimethylamine lyase, while methanol comes from demethoxylation of dietary pectins via pectin methylesterase activity. We have screened rumen metagenomic and metatranscriptomic datasets, metagenome assembled genomes, and Hungate1000 genomes to identify organisms producing methyl-compounds and describe the enrichment of methanol-forming and using microbes from sheep rumen contents using pectin and analysis of their genomes via metagenomic assembly. Results: Screens of metagenomic data using the protein domains of choline trimethylamine lyase, and activator protein found good matches only to the Olsenella umbonata and to Caecibacter, while the Hungate1000 genomes set found bacteria within the phyla Actinobacteria, Firmicutes and Proteobacteria. The cutC and cutD genes clustered with structural components of bacterial microcompartment proteins. Prevotella was the dominant genus encoding pectin methyl esterases, with smaller numbers of sequences from other fibre-degrading rumen bacteria. Some large pectin methyl esterases (>2100 aa) were found in Butyrivibrio species. The pectin-utilising, methane-producing consortium was composed of (i) a putative pectin-degrading bacterium (phylum Tenericutes, class Mollicutes), (ii) a galacturonate-using Sphaerochaeta sp. predicted to produce acetate, lactate, and ethanol, and (iii) a methylotrophic methanogen, Methanosphaera sp., with the ability to form methane via a primary ethanol-dependent, hydrogen-independent, methanogenesis pathway. Conclusions: The main bacteria producing methyl-compounds have been identified in ruminants. Their enzymatic activities can now be targeted with the aim of finding ways to reduce the supply of methyl-compound substrates to methanogens, and thereby limit methylotrophic methanogenesis in the rumen.