Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA

• DOI: 10.1128/msystems.00314-24
• Publication Date: 2024-06-28T12:45:52Z
• Authors: Anna N. Rasmussen; Bradley B. Tolar; John R. Bargar; Kristin Boye; Christopher A. Fr...
• Keywords: Acetogenesis; Candidatus

ABSTRACT We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling—particularly methane-cycling—microorganisms in montane riparian floodplain sediments. generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- 150-cm depth below the sediment surface capturing transition between oxic, unsaturated sediments anoxic, saturated Slate River (SR) (Crested Butte, CO, USA). recovered of putative methanogens, methanotrophs, methylotrophs ( n = 57). Methanogens, found only deep, anoxic depths at SR, originate three different clades Methanoregulaceae , Methanotrichaceae Methanomassiliicoccales ), each with a methanogenesis pathway; methanotrophic within Archaea Candidatus Methanoperedens) uncultured bacteria Ca . Binatia) oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens exceptionally abundant (~1,400× coverage, >50% abundance MAG library) one sample that also contained aceticlastic indicating potential C1/methane-cycling hotspot. Methylomirabilis SR encode pathways methylotrophy but do harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports clade genus is methanotrophic. The genetic was widespread, over 10% 19% encoding methanol dehydrogenase substrate-specific methyltransferase, respectively. Thermoplasmata archaea Gimiplasmatales (UBA10834) contain may allow anaerobic methylotrophic acetogenesis. Overall, reveal production consumption system robust methylotrophy. IMPORTANCE cycling carbon by microorganisms subsurface environments particular relevance face global climate change. Riparian high organic can be degraded into C1 compounds such as methane, methanol, methylamines, fate which depends on microbial metabolisms present well hydrological conditions availability oxygen. In study, we 1,000 river are capable producing consuming other compounds, highlighting both without sample, hotspot system.