Metabolic Capabilities of Microorganisms Involved in and Associated with the Anaerobic Oxidation of Methane

Abstract

In marine sediments the anaerobic oxidation of methane with sulfate as electron acceptor (AOM) is responsible for the removal of a major part of the greenhouse gas methane. AOM is performed by consortia of anaerobic methane-oxidizing archaea (ANME) and their specific partner bacteria. The physiology of these organisms is poorly understood, which is due to their slow growth with doubling times in the order of months and the phylogenetic diversity in natural and in vitro AOM enrichments. Here we study sediment-free long-term AOM enrichments that were cultivated from seep sediments sampled off the Italian Island Elba (20°C; hereon called E20) and from hot vents of the Guaymas Basin, Gulf of California, cultivated at 37°C (G37) or at 50°C (G50). These enrichments were dominated by consortia of ANME-2 archaea and Seep-SRB2 partner bacteria (E20) or by ANME-1, forming consortia with Seep-SRB2 bacteria (G37) or with bacteria of the HotSeep-1 cluster (G50). We investigate lipid membrane compositions as possible factors for the different temperature affinities of the different ANME clades and show autotrophy as characteristic feature for both ANME clades and their partner bacteria. Although in the absence of additional substrates methane formation was not observed, methanogenesis from methylated substrates (methanol and methylamine) could be quickly stimulated in the E20 and the G37 enrichment. Responsible for methanogenesis are archaea from the genus Methanohalophilus and Methanococcoides, which are minor community members during AOM (1–7‰ of archaeal 16S rRNA gene amplicons). In the same two cultures also sulfur disproportionation could be quickly stimulated by addition of zero-valent colloidal sulfur. The isolated partner bacteria are likewise minor community members (1–9‰ of bacterial 16S rRNA gene amplicons), whereas the dominant partner bacteria (Seep-SRB1a, Seep-SRB2, or HotSeep-1) did not grow on elemental sulfur. Our results support a functioning of AOM as syntrophic interaction of obligate methanotrophic archaea that transfer non-molecular reducing equivalents (i.e., via direct interspecies electron transfer) to obligate sulfate-reducing partner bacteria. Additional katabolic processes in these enrichments but also in sulfate methane interfaces are likely performed by minor community members.

Energy Metabolism during Anaerobic Methane Oxidation in ANME Archaea

“…The physiology in that case may be interpreted to operate non-syntrophically, since the amount of energy from sulfate reduction would obviate the need for a syntrophic partner (62). It is not clear how widespread archaeal sulfate reduction with methane is however, since subsequent investigations (108, 109) reported that dominant SRB partner organisms did not grow on elemental sulfur as proposed and microcosm-derived SRB did not have the ability to disproportionate sulfur at the 7:1 stoichiometry of sulfide and sulfate, as previously reported (62). …”

“…In the case of ANME-1-targeted experiments, SRB partners were shown to decouple growth from their archaeal syntrophic partners when H 2 was supplied (108). However, H 2 appears to only decouple in the case of thermophilic consortia and not in their mesophilic relatives, and this may explain why previous studies failed to observe effects with H 2 (60, 66, 67, 109). In the case of de-coupling through an added electron acceptor, a number of soluble electron acceptors have been used to demonstrate that methane oxidation by marine ANME-2 can be de-coupled from bacterial partners (84).…”

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

“…Alternatively, members of ANME−SRB consortia might themselves engage in the production of methane rather than in sulfate-coupled AOM, as previously suggested (51)(52)(53)(54)(55). Recent experiments on the methanogenic potential of ANME-1 and ANME-2 enrichment cultures, however, have not supported this idea (59). A minor amount of methane was detected in our N 2 -containing #3730 and #7136-37 microcosms; however, these levels were similar to concentrations measured as a trace contaminant in the N 2 tank (∼1-10 ppm methane).…”

Reverse Methanogenesis and Respiration in Methanotrophic Archaea

“…In two cases, researchers were successful [23, 100]. In one of these cases, sediment-free long-term AOM enrichments that were dominated by ANME/SRB were incubated with methanogenic substrates.…”

“…In one of these cases, sediment-free long-term AOM enrichments that were dominated by ANME/SRB were incubated with methanogenic substrates. The resulting methanogenic activity most likely came from the enrichment of a minor population of methanogens (up to 7‰ of total archaeal gene tag sequences) that was present in the inoculum [100]. In the second study, methanogenic substrates were added to ANME-1 and ANME-2 dominated microbial mat samples and methanogenesis also occurred [23].…”