Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

Abstract

The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.

Sulfide toxicity as key control on anaerobic oxidation of methane in eutrophic coastal sediments

“…MAG 11 ANME-2 had several genes encoding multiheme c-type cytochromes (Figure 3) including S-layer proteins, lowly expressed in Fe-AOM-performing ANME-2d (Cai et al, 2018), and OmcZ-like proteins recently suggested as the ANME mechanism for extracellular electron transfer (Chadwick et al, 2022), which could be used for electron transfer to a sulfate-reducing partner or to metal oxides. Multiheme c-type cytochromes identified in ANME might be targets of sulfite toxicity (Liu, Beer, & Whitman, 2012).…”

“…This is particularly relevant for relatively shallow coastal sites, such as Site 7 in the Stockholm Archipelago. Genes encoding F 420 -dependent sulfite reductases have been found in ANME-1, ANME-2 and ANME-3 genomes (Chadwick et al, 2022), suggesting that sulfide-driven sulfite toxicity may be a commonly encountered environmental pressure by ANME and, therefore, a widespread control on AOM activity.…”

“…Methanomarinus sp. nov. 1 (Chadwick et al, 2022) (Supplemental Figure 3). MAG 011 was 98.4% complete and 2% contaminated and had potential for a full reverse methanogenesis pathway, as well as acetate production or assimilation via an acetyl-CoA synthase (acss) gene (Figure 5).…”

“…ANME-2a were enriched in Fe-AOM incubations with sediments of the North Sea (Aromokeye et al, 2020) and their 16S rRNA gene-based abundance correlated to methane and iron concentrations in sediments of the Bothnian Sea (Rasigraf et al, 2019). Moreover, ANME-2a, 2b, 2c, 2d and ANME-3 genomes have genes predicted to encode multiheme c-type cytochromes potentially implicated in extracellular electron transfer and iron reduction (Chadwick et al, 2022), suggesting that multiple ANME groups might perform metal-AOM.…”

“…Phylogenetically, ANME form three major clades: ANME-1, ANME-2, and ANME-3, recently assigned a putative nomenclature at family and genus level (Chadwick et al, 2022), to which we refer in this section. ANME-1, in the order Methanophagales, comprises the family Methanophagaceae with at least 6 genera, and are present in a broad range of temperatures, from 2 to 100°C (S. Bhattarai, Cassarini, & Lens, 2019).…”