Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. Strain Z is the type strain of this species. It was isolated from surface sediments of Tar Pit Lake at the La Brea Tar Pits in Los Angeles [1]. Most of the other described members of this family have been isolated from anaerobic digesters or waste water [2]. The genus covers organisms with a wide temperature range. One psychrotolerant strain was isolated from a Russian pond polluted with paper mill waste water [3], while other strains were found in heated sediment at a hydrothermal vent site [4]. Methanocorpusculum species may be common in subsurface environments as they were the most prominent genus found in a coal bed in Indiana [5] and in shale in northern Michigan [6].

Methanogens have been divided into two groups known as Class I and Class II based on phylogeny [7]. Class I includes the orders Methanococcales, Methanobacteriales, and Methanopyrales, which use H₂/CO₂ or formate as substrates for methanogenesis, although some can also use alcohols as electron donors. Class II includes the orders Methanosarcinales and Methanomicrobiales. Some of the Methanosarcinales are capable of using various methyl compounds as substrates for methanogenesis including acetate, methylamines, and methanol, but Methanomicrobiales are restricted to the same substrates as the Class I methanogens [2]. Therefore, Methanomicrobiales are phylogenetically closer to Methanosarcinales but physiologically more similar to Class I methanogens, making them an interesting target for genome sequencing. In a 2006 Community Sequencing Program (CSP) project, we proposed sequencing two members of the order Methanomicrobiales: M. labreanum and Methanoculleus marisnigri. Previously only one genome was available from this order, that of Methanospirillum hungatei. Methanocorpusculum labreanum and Methanoculleus marisnigri are phylogenetically distant from each other and from Methanospirillum hungatei (Figure 1), and they represent the three families within the order Methanomicrobiales. We report here the sequence and annotation of M. labreanum type strain Z.

Figure 1 Phylogenetic tree of 16S rRNA of selected Methanomicrobiales showing the distance between the three organisms for which complete genomes are available – Methanospirillum hungatei, Methanocorpusculum labreanum, and Methanoculleus marisnigri. The tree uses sequences aligned within the Ribosomal Database Project (RDP), and the tree was constructed with the RDP Tree Builder [8]. Methanosarcina barkeri was used as the outgroup. The numbers indicate bootstrap values based on 100 replicates.

Methanocorpusculum labreanum Z was isolated from surface sediments at the La Brea Tar Pits [1]. A polypropylene bottle was filled with half surface sediment and half lake water. In an anaerobic chamber the contents of the bottle were mixed to suspend the sediment, and 0.5 ml of the slurry was added to 5 ml enrichment medium. The enrichment medium contained sodium formate, trypticase peptone, and salts. The gas phase was H₂/CO₂ at a ratio of 4:1 and a pressure of 152 kPa. The physiological characteristics of M. labreanum were described as follows [1]. The cells were coccoid with a diameter of 0.4-2.0 μm. They were irregular in shape under some growth conditions, such as higher salt or with added acetate. Motility was not observed and flagella were not observed. Growth was observed on H₂/CO₂ or formate, but not with acetate, propionate, methanol, trimethylamine, or ethanol. Growth was observed in a narrow window of pH, from 6.5 to 7.5, with pH 7.0 as the optimal value. Growth was observed between 25 and 40°C, with an optimum at 37°C. M. labreanum can tolerate a wide range of salt concentration, from 0 to 30 g/L NaCl. Acetate was stimulatory at lower salt concentrations. Trypticase peptone, yeast extract, or cysteine was required for growth. The features of M. labreanum Z are presented in Table 1.

The genome sequence of M. labreanum Z shows some similarities to Class I methanogens and some to Methanosarcinales but also has some unique features. In common with Class I methanogens, M. labreanum uses a partial reductive TCA cycle to synthesize 2-oxoglutarate, and it has the Eha membrane-bound hydrogenase. Similar to Methanosarcinales, M. labreanum has the Ech membrane-bound hydrogenase. A unique feature of M. labreanum and the other Methanomicrobiales is the presence of anti- and anti-anti-sigma factors, which is surprising as Archaea do not use sigma factors. Phylogenetic analysis of methanogenesis and cofactor biosynthesis enzymes suggest that Methanomicrobiales form a group distinct from other methanogens, and therefore methanogens can be split in to three classes [12]. Surprisingly M. labreanum lacks the F₄₂₀-nonreducing hydrogenase, which has been proposed to couple Coenzyme M-Coenzyme B heterodisulfide reduction and ferredoxin reduction for the first step of methanogenesis in the cytoplasm of Methanomicrobiales [21]. In place of this hydrogenase, M. labreanum may use the membrane-bound hydrogenase Mbh or energy-converting hydrogenase Ech to couple heterodisulfide reduction to a transmembrane ion gradient [12].