The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments

Abstract

Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLP(T) was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.

Figure 1

Scanning electron micrograph of cells of Mhp. mahii strain SLP^T. Bar = 2 μm.

Figure 2

16S rRNA-based phylogenetic tree showing the position of Mhp. mahii relative to the other type strains within the order Methanosarcinales. The tree was inferred from 1341 aligned characters [25, 32] of the 16S rRNA gene sequence under the maximum likelihood criterion [26] and rooted with representatives of the Methanocellaceae. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from bootstrap replicates [28] if larger than 60%. Lineages with type strain-genome sequencing projects registered in GOLD [10] are shown in blue, published genomes in bold.

Figure 3

Maximum likelihood (ML) phylogenetic tree inferred from the 2344-gene supermatrix. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from ML (left) and maximum parsimony (MP; right) bootstrapping. The tree was rooted with the Haloterrigena turkmenica genome [19] included in the sample. The topology of the single best MP tree was identical to the one depicted here except for the unsupported branch connecting Methanosphaerula palustris and Methanospirillum hungatei.

Figure 4

(a) Graphical circular map of the genome. From outside to the center: genes on forward strand (color by COG categories), genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, and other RNAs black), GC content, GC skew. (b) Color code for COG categories.

Figure 5

Proposed pathway of methanogenesis in Mhp. mahii. Numbers in circles indicate involved enzymes: (1), methyltransferase system; (2), methyl-CoM reductase; (3), methyl-H₄MPT:HS-CoM methyltransferase; (4), methylene-H₄MPT reductase; (5), methylene-H₄MPT dehydrogenase; (6), methenyl-H₄MPT cyclohydrolase; (7), formyl-MF:H₄MPT formyltransferase; (8), formyl-MF dehydrogenase; (9), acetyl-CoA synthase/CO dehydrogenase. Abbreviations: Fd_red, reduced ferredoxin; Fd_ox, oxidized ferredoxin; MF, methanofuran; H₄MPT, tetrahydromethanopterin; F₄₂₀H₂, reduced coenzyme  F₄₂₀; F₄₂₀, oxidized coenzyme F₄₂₀; CoA-SH, coenzyme A; CoM-SH, coenzyme M; CoB-SH, coenzyme B; CoM-S-S-CoB, heterodisulfide of CoM and CoB.

Figure 6

Comparison of proposed energy conserving electron-transfer routes in (a) freshwater-inhabiting and (b) saltwater-adapted members of the family Methanosarcinaceae. The proposed models of the energy metabolism are mainly based on the results of gene deletion and expression analyses in the species Msc. barkeri [54], Msc. mazei [55] and Msc. acetivorans [42, 56, 57]. The postulated coupling ion for ATP-synthesis is shown in blue (H⁺) or red (Na⁺). Enzyme complexes and reactions that are thought to bypass the main route of electron transfer are shown in grey. The shown electron bifurcation at the HdrABC complex is based on a proposal of Buan and Metcalf [58]. A membrane-bound sodium-translocating Mtr complex that could participate in the utilization of a chemiosmotic gradient was omitted from the figure for simplicity reasons. Abbreviations for electron transfer complexes and cofactors are explained in the text and Table 3.