Methanotrophy below pH 1 by a new Verrucomicrobia species

Abstract

Mud volcanoes, mudpots and fumaroles are remarkable geological features characterized by the emission of gas, water and/or semi-liquid mud matrices with significant methane fluxes to the atmosphere (10(-1) to 10(3) t y(-1)). Environmental conditions in these areas vary from ambient temperature and neutral pH to high temperatures and low pH. Although there are strong indications for biological methane consumption in mud volcanoes, no methanotrophic bacteria are known that would thrive in the hostile conditions of fumaroles (temperatures up to 70 degrees C and pH down to 1.8). The first step in aerobic methane oxidation is performed by a soluble or membrane-bound methane mono-oxygenase. Here we report that pmoA (encoding the beta-subunit of membrane-bound methane mono-oxygenase) clone libraries, made by using DNA extracted from the Solfatara volcano mudpot and surrounding bare soil near the fumaroles, showed clusters of novel and distant pmoA genes. After methanotrophic enrichment at 50 degrees C and pH 2.0 the most distant cluster, sharing less than 50% identity with any other described pmoA gene, was represented in the culture. Finally we isolated an acidiphilic methanotrophic bacterium Acidimethylosilex fumarolicum SolV belonging to the Planctomycetes/Verrucomicrobia/Chlamydiae superphylum, 'outside' the subphyla of the Alpha- and Gammaproteobacteria containing the established methanotrophs. This bacterium grows under oxygen limitation on methane as the sole source of energy, down to pH 0.8--far below the pH optimum of any previously described methanotroph. A. fumarolicum SolV has three different pmoA genes, with two that are very similar to sequences retrieved from the mudpot. Highly homologous environmental 16S rRNA gene sequences from Yellowstone Park show that this new type of methanotrophic bacteria may be a common inhabitant of extreme environments. This is the first time that a representative of the widely distributed Verrucomicrobia phylum, of which most members remain uncultivated, is coupled to a geochemically relevant reaction.

Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington

“…These results suggest that these organisms may be involved in metabolism of methane in the site, either directly or indirectly. Indeed, methanotrophic Verrucomicrobiales have been described recently from acidic environments (Dunfield et al 2007;Pol et al, 2007;Islam et al, 2008) and our data suggest the existence of methanotrophic Verrucomicrobiales in freshwater lakes.…”

Hydrocarbon monooxygenase in Mycobacterium: recombinant expression of a member of the ammonia monooxygenase superfamily

“…However, when structures of pMMO were solved, two metal sites were revealed (Lieberman and Rosenzweig, 2005;Hakemian and Rosenzweig, 2007) and recently the PmoB site was confirmed as having methane hydroxylase activity when the PmoB subunit of the M. capsulatus pMMO was expressed in soluble form in E. coli (Balasubramanian et al, 2010). However, a paradox remains since the ligands for the PmoB site are not conserved across all methanotrophs (Dunfield et al, 2007;Pol et al, 2007), and this experiment does not explain the canonical membrane association of CuMMOs. The availability of a recombinant expression system for the holoenzyme creates new opportunities to probe the nature of the metal centers in this enzyme family.…”

Active methylotrophs in the sediments of Lonar Lake, a saline and alkaline ecosystem formed by meteor impact

“…One of them showed maximum identity to the 16S rRNA gene of an uncultured Verrucomicrobium clone obtained from alkaline Mono Lake (Humayoun et al, unpublished). This sequence did not, however, cluster with that of thermo-acidophilic Verrucomicrobia methanotrophs (Dunfield et al, 2007;Pol et al, 2007;Islam et al, 2008) (Figure 3).…”

“…Methanotrophs are a specialized group of methylotrophs that use methane as the sole carbon and energy source. These are distributed among Gammaproteobacteria (type I methanotrophs), Alphaproteobacteria (type II methanotrophs) (reviewed in Trotsenko and Murrell, 2008), filamentous methane oxidizers (Stoecker et al, 2006;Vigliotta et al, 2007) and Verrucomicrobia (Dunfield et al, 2007;Pol et al, 2007;Islam et al, 2008). Methanotrophs oxidize methane to methanol by the enzyme methane monooxygenase (MMO), present either as the particulate form (pMMO) in all characterized methanotrophs (except in the genus Methylocella (Dedysh et al, 2000)) or as the soluble form (sMMO) in some methanotrophs (Trotsenko and Murrell, 2008).…”