New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments

Abstract

Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus ‘Methanomassiliicoccus armoricus MXMAG1’. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades (‘free-living’/non-host-associated environmental clade and ‘host-associated’/digestive clade) allowed us to explore the putative physiological traits of Candidatus ‘M. armoricus MXMAG1’. As expected, Ca. ‘Methanomassiliicoccus armoricus MXMAG1’ had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the ‘free-living’ clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.

Ancestral archaea expanded the genetic code with pyrrolysine

“…However, it is reasonable to assume that these organisms do not encode PylSn given that (1) a PylSn gene was not found in the available genome sequence and (2) molecular phylogeny (described later) shows that the PylSc proteins in these organisms are very similar to those from confirmed ΔPylSn organisms. As previously described, the majority of ΔPylSn enzymes (15 of 21 sequences) belong to the Methanomassiliicoccales, an order of methanogenic archaea associated with animal digestive tracts ( 9 , 15 , 16 , 36 ). In addition to the Methanomassiliicoccales, which belong to the phylum Ca.…”

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom

“…This contrasts with many non-host environments (e.g. sediments, peat bogs), where hydrogenotrophic methyl-reducing methanogens constitute a minor fraction of the overall methanogenic community 38 , 87 . It also reinforces the hypothesis that the gut environment is particularly propitious for this kind of methanogenesis, which could have led to the transition from methylotrophic (methyl-dismutation) and CO 2 -reducing methanogenesis to methyl-reducing methanogenesis in Methanimicrococcus and Methanosphaera , respectively 36 .…”

Factors shaping the abundance and diversity of archaea in the animal gut

“…This contrasts with many non-host environments (e.g. sediments, peat bog), where hydrogenotrophic methyl-reducing methanogens constitute a minor fraction of the overall methanogens 39,85 . It also reinforces the hypothesis that the gut environment is particularly propitious for this kind of methanogenesis, which could have led to the transition from methylotrophic and CO -reducing methanogenesis to methyl-reducing methanogenesis in Methanimicrococcus and Methanosphaera, respectively 35 .…”