Insights into the genomes of archaea mediating the anaerobic oxidation of methane

Abstract

The anaerobic oxidation of methane is a globally significant process which is mediated by consortia of yet uncultivated methanotrophic archaea (ANME) and sulfate-reducing bacteria. In order to gain deeper insights into genome characteristics of the different ANME groups, large-insert genomic libraries were constructed using DNA extracted from a methanotrophic microbial mat growing in the anoxic part of the Black Sea, and from sediments above gas hydrates at the Hydrate Ridge off the coast of Oregon. Analysis of these fosmid libraries with respect to archaeal 16S rRNA gene diversity revealed a single ANME-1b ribotype for the Black Sea libraries, whereas the sequences derived from the Hydrate Ridge library phylogenetically affiliated with the ANME-2a, ANME-2c and ANME-3 group. Genome walking for ANME-1b resulted in a contiguous 155 kb composite genome fragment. The comparison of a set of four genomic fragments belonging to the different ANME groups revealed differences in the rRNA operon structure and the average G+C content, with the ANME-2c contig showing the highest divergence within the set. A detailed analysis of the ANME contigs with respect to genes putatively involved in the anaerobic oxidation of methane led to the identification of: (i) a putative N5,N10-methenyltetrahydromethanopterin cyclohydrolase gene, (ii) a gene cluster supposedly encoding a novel type of heterodisulfide reductase/dehydrogenase complex and (iii) a gene cluster putatively encoding a new type of CO dehydrogenase/acetyl-CoA synthase enzyme complex.

Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics

“…In addition, phylogenetically distinct subgroups of the ANME-2 (a, b, and c) appear to exhibit specific habitat preferences and unique spatial configurations with sulfate-reducing bacteria related to Desulfosarcina (DSS) (16,17), suggesting that the ANME-2 subgroups represent unique ecotypes. Metagenomic sequencing of the microbial community in methane seep sediment has shed light on the physiology and specific mechanism of AOM catalyzed by some of the ANME archaea (18,19). However, details of the metabolic regulation, environmental adaptation, and intracellular communication of these diverse archaea and their bacterial partners are still largely unexplored.…”

A Cysteine-Rich CCG Domain Contains a Novel [4Fe-4S] Cluster Binding Motif As Deduced from Studies with Subunit B of Heterodisulfide Reductase from Methanothermobacter marburgensis

“…Subunits HdrC and HdrB are also conserved in subunit TfrB of thiol:fumarate reductase (TFR) (Figure 1), an anabolic enzyme of methanogens that catalyzes the reduction of fumarate to succinate with CoM-SH plus CoB-SH as electron donors (10). HDR with highly conserved HdrB and HdrC subunits is also encoded by the genomes of uncultivated anaerobic methanotrophic archaea in which the enzyme is thought to catalyze formation of CoM-S-S-CoB from CoM-SH and CoB-SH during anaerobic methane oxidation (11).…”

Discovery of Multiple Modified F 430 Coenzymes in Methanogens and Anaerobic Methanotrophic Archaea Suggests Possible New Roles for F 430 in Nature

“…Solvent A was water with 0.1% formic acid, and solvent B was methanol with 0.1% formic acid. The flow rate was 0.5 ml/min, and gradient elution was employed in the following manner: (time [min], percent solvent B): (0.01, 5), (10,65), and (15,65). Ten microliters of sample was injected.…”

“…The chemically challenging activation of methane by ANME occurs via a reversal of the MCR-catalyzed step in methanogenesis (16). Metagenomic data have shown that ANME possess homologs of MCR as well as most genes normally associated with methanogenic archaea, indicating that these organisms oxidize methane using a pathway which is essentially methanogenesis in reverse (15,17). A modified form of F 430 , F 430 -2 ( Fig.…”

“…The organisms carrying out this difficult biochemical reaction consist of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria found near methane seeps in the ocean, which together convert methane and sulfate to carbonate and hydrogen sulfide (11,12). ANME can be classified into at least three groups which are phylogenetically related to methanogens (13)(14)(15). Group 1 ANME (ANME-1) are likely most closely related to the Methanomicrobiales, while ANME-2 and ANME-3 are affiliated with the Methanosarcinales.…”