Cultivation and visualization of a methanogen of the phylum Thermoproteota

Abstract

Methane is the second most abundant climate-active gas and understanding its sources and sinks is a crucial endeavor in microbiology, biogeochemistry, and climate sciences (1,2). For decades, it was thought that methanogenesis, the ability to conserve energy coupled to methane production, was restricted to a taxonomically and metabolically specialized group of archaea, the Euryarchaeota1. The discovery of marker genes for anaerobic alkane cycling in metagenome-assembled genomes obtained from diverse habitats has led to the hypothesis that archaeal lineages outside the Euryarchaeota are involved in methanogenesis (3-6). Here, we cultured Candidatus Methanosuratincola yellowstonensis, a member of the archaeal phylum Thermoproteota, from a terrestrial hot spring. Growth experiments combined with activity assays, stable isotope tracing, and genomic analyses confirmed that this thermophilic archaeon grows via methyl-reducing hydrogenotrophic methanogenesis. Cryo-electron tomography revealed that Ca. M. yellowstonensis cells are archaellated coccoid cells that form intercellular bridges, providing two to three cells with a continuous cytoplasm and S-layer. The wide environmental distribution of Ca. M. yellowstonensis suggests that they might play important and hitherto overlooked roles in carbon cycling within diverse anoxic habitats.

Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring

“…Metagenomic sequencing and phylogenomic analysis confirmed the close relationship of Ca . M. hypatiae to other Mcr-encoding Archaeoglobi and the relatedness of its mcrA to MAGs of the TACK superphylum, some of which have recently been shown to also be methanogens [ 70 , 71 ]. Together, this supports the idea that the capacity for methanogenesis is deeply rooted in the archaea and possibly dates to the last common ancestor of archaea [ 1 , 3 , 7 , 8 , 72 ].…”

Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation ofCa.Methanoglobus hypatiae from a Yellowstone hot spring

“…Metagenomic sequencing and phylogenomic analysis confirmed the close relationship of Ca. M. hypatiae to other Mcr-encoding Archaeoglobi and the relatedness of its mcrA to MAGs of the TACK superphylum, some of which have recently been showed to also be methanogens (56, 57). Together, this supports the idea that the capacity for methanogenesis is deeply rooted in the archaea and possibly dates to the last common ancestor of archaea (1, 3, 7, 8, 58).…”

Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost

“…These 13,290 MAGs were dereplicated at 97% identity using dRep (101) into 1,864 representative MAGs with galah (v0.3.0) (102) using the following parameter set: --precluster-ani 90 --ani 97 --precluster-method finch. Accession information for metagenomic reads is provided in Table S1, and the full database of 13,290 MAGs can be downloaded from https://doi.org/10.5281/zenodo.7596016.…”

“…In contrast to historical paradigms, recent genomic insights have greatly expanded our understanding of the distribution and activity of methylotrophic methanogens, especially in saturated, high-CH4 emitting soils (9)(10)(11)(12)(13)(14)(15)(16)(17). Similarly, biochemical and physiological efforts have expanded the suite of substrates known to be utilized by methylotrophic methanogens (18)(19)(20)(21)(22)(23)(24).…”