Description and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov

Abstract

The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.

Fig 1. Correlation between the concentration of free ammonia and the abundance of the 16S rRNA phylotype of J.3.6.1-F.2.7.3^T in anaerobic digesters of twelve different full-scale biogas plants.

The size of the digesters is represented by the corresponding size of the filled circles, and the location of the biogas plant is indicated by numbers. The main substrate fed and the temperature regime are indicated by colors. The best correlation of the measured values was obtained with logarithmic regression. The formula of the trend line and the coefficient of determination (R²) of the model are given in the graph. The data used were previously published by Campanaro et al. [53].

Fig 2. Phylogenomic tree based on concatenated amino acid sequences of 122 conserved archaeal proteins showing the placement of the strain J.3.6.1-F.2.7.3^T within the order Methanomicrobiales.

The tree was reconstructed under the maximum-likelihood criterion with the model LG+F+I+G4 of protein evolution and ultrafast bootstrap analysis with a maximum of 1,000 iterations. The genome of Methanocella paludicola (AP011532, not shown) was used as an outgroup. The names of the representative strains of each species are listed in S1 Table. Accession numbers are given in parenthesis. Only bootstrap support values above 80% are shown at the respective nodes. Background shading with different colors is used to delineate clades at the family level. The scale bar indicates the expected number of substitutions per site.

Fig 3. Morphology of cells of the isolate J.3.6.1-F.2.7.3^T.

(A) Phase contrast micrograph of a culture in the stationary phase showing several single cells and a long filament containing partially lysed cells; (B) negative contrast transmission electron micrograph of the end of a whole cell with a bundle of polar archaella (large arrow), the spacing of the striation on the sheath surface is marked with small arrowheads (see also the inset with an enlarged section); (C) negative contrast transmission electron micrograph of a thin section showing the cell spacer (large arrow) and the multilayered spacer plugs (arrowheads).

Fig 4. Venn diagram depicting the intersections of sets of predicted proteins of M. hungatei JF-1^T, M. hungatei GP1 and the novel isolate J.3.6.1-F.2.7.3^T.

The corresponding protein sets and their overlaps were calculated with the Roary software tool [87], which is included in the IPGA package, using the default settings. Total numbers are in parentheses. Diagram generated using the area-proportional Venn diagram plotter from BioInforRX (https://bioinforx.com/apps/venn.php).

Fig 5. Conserved cluster of genes present in the genome of isolate J.3.6.1-F.2.7.3^T and related Methanospirillum strains with the ability to utilize 2-propanol.

The locus tags are given for the first and last gene of the region found in the genome of J.3.6.1-F.2.7.3^T. The region marked with square brackets is also conserved in M. hungatei JF-1^T. Genes and the corresponding enzymes involved in key steps of methanogenesis are highlighted in color: red, formylmethanofuran dehydrogenase (FmdABCDFG); orange, heterodisulfide reductase (HdrABC); purple, carbonic anhydrase (Can); blue, electron-transfer subunit of F₄₂₀-nonreducing hydrogenases (MvhD) and membrane-bound H₂-evolving [NiFe]-hydrogenase (HyfBCEFGI); green, F₄₂₀-dependent formate dehydrogenase (FdhAB) and formate transporter (FdhC). Abbreviations: CoB, coenzyme B; CoM, coenzyme M; F₄₂₀, coenzyme F₄₂₀; Fd, ferredoxin; MF, methanofuran.

Fig 6. Proposed pathway for the utilization of 2-propanol in Methanospirillum strains.

The reactants of the metabolic pathway are shown in blue and the reaction products in red. Numbers in circles indicate involved enzymes: 1, F₄₂₀-dependent secondary alcohol dehydrogenase (Adf); 2, F₄₂₀-dependent formate dehydrogenase (Fdh); 3; heterodisulfide reductase, bifurcating (Hdr); 4, formyl-MF dehydrogenase (Fmd); 5, formyl-MF:H₄MPT formyltransferase (Ftr); 6, methenyl-H₄MPT cyclohydrolase (Mch); 7, methylene-H₄MPT dehydrogenase (Mtd); 8, methylene-H₄MPT reductase (Mer); 9, methyl-H₄MPT:CoM methyltransferase (Mtr); 10, methyl-CoM reductase (Mcr). Abbreviations: CoB, coenzyme B; CoM, coenzyme M; F₄₂₀, coenzyme F₄₂₀; Fd, ferredoxin; H₄MPT, tetrahydromethanopterin; MF, methanofuran.