In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic Archaea were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic Methanococcoides burtonii relatives and several new autotrophic Methanogenium lineages, confirming the cooccurrence of Methanosarcinales and Methanomicrobiales methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
In cold seep ecosystems, sediments are colonized by various dense microbial and sometimes macrofaunal populations, forming a mosaic of patchy habitats on the seafloor (1, 2). The metabolism of these organisms, based on chemosynthesis, is mainly fueled by seep fluids, rich in reduced compounds and hydrocarbons, such as methane (3). Most of the methane is consumed microbiologically by anaerobic and aerobic methanotrophic communities before reaching the water column, forming an efficient biofilter (4). In marine sediments and typically in cold seep ecosystems, methanogenesis driven by archaeal communities accumulates large amounts of methane, which can be trapped in gas hydrates. Microbial populations involved in methane production (methanogens) are phylogenetically affiliated with 7 orders within the phylum Euryarchaeota, which comprises the Methanosarcinales, Methanocellales, Methanomicrobiales, Methanococcales, Methanopyrales, Methanobacteriales (5), and the recently described Methanoplasmatales (6), also known as Methanomassiliicoccales (7). Furthermore, deeply branching uncharacterized orders have been recently detected (8). Enrichment cultures from methane-rich environments, such as marine sediments, mangroves, animal guts, or wastewater bioreactors, previously showed that methanogens could use different substrates for methane production under anaerobic conditions (9-18). In marine sediments, methylated compounds (e.g., methylamine, dimethylamine, trimethylamine [TMA], methanol, dimethylaminesulfate, and dimethylsulfide), volatile fatty acids (formate and acetate), bicarbonate, and, more recently, choline and glycine betaine (19,20) have been identified as primary carbon substrates for methanogenesis. These compounds can be metabolized through three different specifi...