Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane

Abstract

Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.

Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria

“…The same picture is for AAI: 90.4%, 80.4%, and 72.3%, respectively. The MAG of ANME-3 microorganism is closely related to MAG from the Karabetova Gora mud volcano, which was described in detail in our previous work [ 5 ].…”

“…Dissimilatory iron reduction was experimentally shown for representatives of the family Desulfobulbaceae and the genera Desulfuromonas and Deferrisoma , [ 51 , 52 , 53 ]. It is assumed that the ANME-2 also have the ability to reduce Fe(III) [ 5 , 6 ]. If the Fe-AOM in our enrichment cultures proceeds with the participation of a syntrophic bacterial partner, the most likely candidate for this role is the uncultured Desulfobulbaceae, which is constantly present in all enrichments.…”

“…The presence of multiheme c-type cytochromes (MHCs) has been reported for ANME-1, ANME-2, and ANME-3 [ 5 , 57 , 66 ]. Among the members of Ca.…”

“…Marine biotopes—cold methane seeps, sulfate-methane transition zones of sediments, water columns, and hydrotherms have been studied in the most detail [ 1 , 2 ]. In terrestrial ecosystems, ANME have been detected in mud volcanoes, freshwater sediments, and oilfield waters [ 1 , 3 , 4 , 5 ].…”

The first cultivated representatives of the actinobacterial lineage OPB41 isolated from subsurface environments constitute a novel order Anaerosomatales

“…TMV fluids generate local physicochemical gradients that allow the proliferation of microorganisms with various metabolic patterns ( Khomyakova et al, 2020 ; Slobodkina et al, 2020 ; Frolova et al, 2021 ). Representatives of the phylum Actinomycetota are not a major component of TMV’s microbial communities, where methane-oxidizing and sulfur-metabolizing prokaryotes usually predominate ( Wang et al, 2014 ; Lin et al, 2018 ; Mardanov et al, 2020 ; Merkel et al, 2021 ; Tu et al, 2022 ). However, in several TMVs the relative abundance of Actinomycetota reaches 12–15% ( Yang et al, 2012 ; Khomyakova et al, 2022 ).…”