Abstract
BackgroundDigestive processes in the rumen lead to the release of methyl-compounds, 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 the Hungate1000 genomes to identify organisms capable of producing methyl-compounds. We also describe the enrichment of pectin-degrading and methane-forming microbes from sheep rumen contents and the analysis of their genomes via metagenomic assembly.ResultsScreens of metagenomic data using the protein domains of choline trimethylamine lyase (CutC), and activator protein (CutD) found good matches only to Olsenella umbonata and to Caecibacter, while the Hungate1000 genomes and metagenome assembled genomes from the cattle rumen found bacteria within the phyla Actinobacteria, Firmicutes and Proteobacteria. The cutC and cutD genes clustered with genes that encode structural components of bacterial microcompartment proteins. Prevotella was the dominant genus encoding pectin methyl esterases, with smaller numbers of sequences identified from other fibre-degrading rumen bacteria. Some large pectin methyl esterases (> 2100 aa) were found to be encoded in Butyrivibrio genomes. 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.ConclusionsThe main bacteria that produce 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.
Highlights
Digestive processes in the rumen lead to the release of methyl-compounds, mainly methanol and methylamines, which are used by methyltrophic methanogens to form methane, an important agricultural greenhouse gas
Analyses against the combined assembly of metagenome and metatranscriptome reads derived from rumen contents of sheep selected for differences in CH4 yield (11,801,660 ORFs) [26] revealed good matches for both Choline trimethylamine lyase (CutC) and Choline trimethylamine lyase activator protein (CutD) from Olsenella umbonata (Actinobacteria, Coriobacteriaceae, two hits) and Caecibacter (Firmicutes, Veillonellaceae, one hit), but to no other organisms. (Figure 1a, Additional file 1: Table S1A = CutC MG&MT sheet)
The ability to form methanol from methoxylated pectin via pectin methyl esterases (PMEs) activity is widespread among rumen bacteria, but is most prevalent among members of the genus Prevotella
Summary
Digestive processes in the rumen lead to the release of methyl-compounds, 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. Methane (CH4) is an important greenhouse gas (GHG) accounting for ~ 14% of total global GHG emissions [1]. As a consequence of the digestive processes in the rumen, by-products of fibre degradation and fermentation end-products, including hydrogen (H2), carbon dioxide (CO2), methanol, methylamines, and methylsulphides, are formed but not used by the host animal. Hydrogenotrophic and methylotrophic methanogens in the rumen are able to remove these end products by reducing them to CH4, which is eructated from the animal leading to atmospheric emissions of CH4 [3]. Hydrogenotrophic rumen methanogens mainly belong to the genus Methanobrevibacter, while the core rumen methylotrophic methanogens are from the genus Methanosphaera and the order Methanomassiliicoccales [3]
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