Phylogenetic and genomic analysis ofMethanomassiliicoccalesin wetlands and animal intestinal tracts reveals clade-specific habitat preferences

Abstract

Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems.

Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens

“…This supports recent metagenomic studies, which showed that besides gut and rumen environments (6,13,14), Methanomassiliicoccales also occur ubiquitously in marine and terrestrial anaerobic environments (10,15,82,83). Similarly to the case for WOR, 16S rRNA gene sequences of Methanomassiliicoccales were not reported for the investigated sites, likely due to a mismatch of commonly used primers against hitherto-undetected clades (22), while other uncultured Thermoplasmata were detected (84).…”

“…1). In fact, members of the "environmental clade" of Methanomassiliicoccales were previously assigned to TMEG (15). Although Methanomassiliicoccales were not specifically described in WOR sediments, which is likely due to the low coverage of commonly used primers for Methanomassiliicoccales, closely related clades such as MBG-D and TMEG were abundant in these samples (35,80).…”

“…Of these, the Methanomassiliicoccales have only recently been described, representing the seventh order of methanogens (6,7,9). These Euryarchaeota have been detected based on gene biomarker analyses in diverse environments such as lakes, soils, and marine sediments but are particularly abundant in the digestive tracts of ruminants (10)(11)(12)(13)(14)(15). A single pure culture, Methanomassiliicoccus luminyensis, as well as a few enrichment cultures, have been obtained, all of which reduce methanol or methylamines with H 2 as the electron donor (6,(16)(17)(18)(19)(20).…”

Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle

“…In the meantime, we identified two archaeal taxa, Methanomassiliicoccales and Methanobrevibacter ruminantium, as the most active methanogens in the rumen of steers fed a barley diet. Methanomassiliicoccales utilize methanol and methylamines as major energy and carbon sources to produce methane (19,36), while Methanobrevibacter ruminantium produces CH 4 by utilizing CO 2 , formate, and H 2 as substrates (3,37). Their high abundances suggest that the methyl compound conversion route and the CO 2 reduction route are the major methanogenesis pathways in the rumen of beef steers fed a barley-based diet.…”

Characterization of the Microbial Communities in Rumen Fluid Inoculated Reactors for the Biogas Digestion of Wheat Straw

“…In rumen, the aceticlastic pathway was not important with low numbers of Methanosarcina retrieved [13,14]. Recent years, methylotrophic Methanomassiliicocales, which was one of the most important methanogens populations [15,16], was found to be abundant in some rumens [17].…”