Pseudodesulfovibrio alkaliphilus, sp. nov., an alkaliphilic sulfate-reducing bacterium isolated from a terrestrial mud volcano

Diversity, Methane Oxidation Activity, and Metabolic Potential of Microbial Communities in Terrestrial Mud Volcanos of the Taman Peninsula

Microbial communities of terrestrial mud volcanoes are involved in aerobic and anaerobic methane oxidation, but the biological mechanisms of these processes are still understudied. We have investigated the taxonomic composition, rates of methane oxidation, and metabolic potential of microbial communities in five mud volcanoes of the Taman Peninsula, Russia. Methane oxidation rates measured by the radiotracer technique varied from 2.0 to 460 nmol CH4 cm-3 day-1 in different mud samples. This is the first measurement of high activity of microbial methane oxidation in terrestrial mud volcanos. 16S rRNA gene amplicon sequencing has shown that Bacteria accounted for 65-99% of prokaryotic diversity in all samples. The most abundant phyla were Pseudomonadota, Desulfobacterota, and Halobacterota. A total of 32 prokaryotic genera, which include methanotrophs, sulfur or iron reducers, and facultative anaerobes with broad metabolic capabilities, were detected in relative abundance >5%. The most highly represented genus of aerobic methanotrophs was Methyloprofundus reaching 36%. The most numerous group of anaerobic methanotrophs was ANME-2a-b (Ca. Methanocomedenaceae), identified in 60% of the samples and attaining relative abundance of 54%. The analysis of the metagenome-assembled genomes of a community with high methane oxidation rate indicates the importance of CO2 fixation, Fe(III) and nitrate reduction, and sulfide oxidation. This study expands current knowledge on the occurrence, distribution, and activity of microorganisms associated with methane cycle in terrestrial mud volcanoes.

Pseudodesulfovibrio pelocollis sp. nov. a Sulfate-Reducing Bacterium Isolated from a Terrestrial Mud Volcano

Terrestrial mud volcanoes (TMVs), surface expressions of a deep-subterranean sedimentary volcanism, are widespread throughout the world. The methane and sulfur cycles are recognized as the most important biogeochemical cycles in these environments. Only few anaerobic bacterial strains were recovered from TMVs. We have isolated a novel sulfate-reducing bacterium (strain SB368T) from TMV located at Taman Peninsula, Russia. Optimum growth of strain SB368T was observed at 30 °C, pH 8.0 and 1% NaCl. Strain SB368T utilized lactate, pyruvate and fumarate in the presence of sulfate, sulfite or thiosulfate. Growth with molecular hydrogen was observed only in the presence of acetate. Fermentative growth occurred on pyruvate. Phylogenetic analysis revealed that strain SB368T belongs to the genus Pseudodesulfovibrio but is distinct from all described species. Based on its genomic and phenotypic properties, a new species, Pseudodesulfovibrio pelocollis sp. nov. is proposed with strain SB368T (= DSM 111087 T = VKM B-3585 T) as a type strain.

Sedimenticola hydrogenitrophicus sp. nov. a chemolithoautotrophic bacterium isolated from a terrestrial mud volcano, and proposal of Sedimenticolaceae fam. nov. in the order Chromatiales

Chemolithoautotrophic microorganisms can play a significant role in the biogeochemical cycling of elements in deep-subsurface-associated environments. A novel facultatively anaerobic lithoautotrophic bacteria (strains SB48T and SN1189) were isolated from terrestrial mud volcanoes (Krasnodar Krai, Russia). Cells of the strains were straight motile rods. Growth was observed at temperatures up to 35 °C (optimum at 30 °C), pH 6.0-8.5 (optimum at pH 7.5) and NaCl concentrations of 0.5-4.0% (w/v) (optimum at 1.5-2.0% (w/v)). The isolates grew chemolithoautotrophically with molecular hydrogen or thiosulfate as an electron donor, nitrate as an electron acceptor and CO2/HCO3- as a carbon source. They also grew with organic acids, ethanol, yeast extract and peptone. The isolates were capable of either anaerobic respiration with nitrate or nitrous oxide as the electron acceptors or aerobic respiration under microaerobic condition. The total size of the genome of strains SB48T and SN1189 was 4.71 and 5.13 Mbp, respectively. Based on phenotypic and phylogenetic characteristics, strains SB48T and SN1189 represent a novel species of the genus Sedimenticola, S. hydrogenitrophicus (the type strain is SB48T = KCTC 25568 T = VKM B-3680 T). The new isolates are the first representatives of the genus Sedimenticola isolated from a terrestrial ecosystem. Based on phylogenomic reconstruction we propose to include the genus Sedimenticola and the related genera into a new family Sedimenticolaceae fam. nov. within the order Chromatiales.

Desulfatitalea alkaliphila sp. nov., an alkalipilic sulfate- and arsenate- reducing bacterium isolated from a terrestrial mud volcano

A novel alkaliphilic sulfate-reducing bacterium, strain M08but^T, was isolated from a salsa lake of terrestrial mud volcano (Taman Peninsula, Russia). Cells were rod-shaped, motile and Gram-stain-negative. The temperature range for growth was 15-42 °C (optimum at 30 °C). The pH range for growth was 7.0-11.0, with an optimum at pH 8.5-9.0 Strain M08but^T used sulfate, thiosulfate, sulfite, dimethyl sulfoxide and arsenate as electron acceptors. Acetate, formate, butyrate, fumarate, succinate, glycerol and pyruvate were utilized as electron donors with sulfate. Fermentative growth was observed with fumarate, pyruvate, crotonate. Strain M08but^T grew chemolithoautotrophically with H₂ and CO₂. The G + C content of the genomic DNA was 60.1%. The fatty acid profile of strain M08but^T was characterized by the presence of anteiso-C_15:0 as the major component (68.8%). The closest phylogenetic relative of strain M08but^T was Desulfatitalea tepidiphila (the order Desulfobacterales) with 96.3% 16S rRNA gene sequence similarity. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M08but^T is considered to represent a novel species of the genus Desulfatitalea, with proposed name Desulfatitalea alkaliphila sp. nov. The type strain of Desulfatitalea alkaliphila is M08but^T (= KCTC 25382^T = VKM B-3560^T = DSM 113909^T = JCM 39202^T = UQM 41473^T).

Pseudodesulfovibrio nedwellii sp. nov., a mesophilic sulphate-reducing bacterium isolated from a xenic culture of an anaerobic heterolobosean protist

A novel sulphate-reducing bacterium, strain SYK^T, was isolated from a xenic culture of an anaerobic protist obtained from a sulphidogenic sediment of the saline Lake Hiruga in Fukui, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SYK^T clustered with the members of the genus Pseudodesulfovibrio. The closest relative of strain SYK^T was Pseudodesulfovibrio sediminis SF6^T, with 16S rRNA gene sequence identity of 97.43 %. Digital DNA-DNA hybridisation and average nucleotide identity values between SYK^T and species of the genus Pseudodesulfovibrio fell below the respective thresholds for species delineation, indicating that SYK^T represents a novel species of the genus Pseudodesulfovibrio. Cells measured 1.7-3.7×0.2-0.5 µm in size and were Gram-stain-negative, obligately anaerobic, motile by means of a single polar flagellum and had a curved rod or sigmoid shape. Cell growth was observed under saline conditions from pH 6.0 to 9.5 (optimum pH 8.0-9.0) and at a temperature of 10-30 °C (optimum 25 °C). SYK^T used lactate, pyruvate, fumarate, formate and H₂ as electron donors. It used sulphate, sulphite, thiosulphate and sulphur as terminal electron acceptors. Pyruvate and fumarate were fermented. Major cellular fatty acids were anteiso-C_15 : 0, C_16 : 0, anteiso-C_17 : 1ω9c, summed feature 3 (C_16 : 1ω6c and/or C_16 : 1ω7c) and summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c). The DNA G+C content of SYK^T was 49.4 mol%. On the basis of the the genetic and phenotypic features, SYK^T was determined to represent a novel species of the genus Pseudodesulfovibrio for which the name Pseudodesulfovibrio nedwellii sp. nov. is proposed with type strain SYK^T (=DSM 114958^T=JCM 35746^T).

The first cultivated representatives of the actinobacterial lineage OPB41 isolated from subsurface environments constitute a novel order Anaerosomatales

The continental subsurface harbors microbial populations highly enriched in uncultured taxa. OPB41 is an uncultured order-level phylogenetic lineage within the actinobacterial class Coriobacteriia. OPB41 bacteria have a wide geographical distribution, but the physiology and metabolic traits of this cosmopolitan group remain elusive. From two contrasting subsurface environments, a terrestrial mud volcano and a deep subsurface aquifer, located in the central part of Eurasia, within the Caucasus petroleum region, we have isolated two pure cultures of anaerobic actinobacteria belonging to OPB41. The cells of both strains are small non-motile rods forming numerous pili-like appendages. Strain M08DHBT is mesophilic, while strain Es71-Z0120T is a true thermophile having a broad temperature range for growth (25-77°C). Strain M08DHBT anaerobically reduces sulfur compounds and utilizes an aromatic compound 3,4-dihydroxybenzoic acid. Strain Es71-Z0120T is an obligate dissimilatory Fe(III) reducer that is unable to utilize aromatic compounds. Both isolates grow lithotrophically and consume molecular hydrogen or formate using either thiosulfate, elemental sulfur, or Fe(III) as an electron acceptor. Genomes of the strains encode the putative reductive glycine pathway for autotrophic CO2 fixation, Ni-Fe hydrogenases, putative thiosulfate/polysulfide reductases, and multiheme c-type cytochromes presumably involved in dissimilatory Fe(III) reduction. We propose to assign the isolated strains to the novel taxa of the species-order levels and describe strain M08DHBT as Anaerosoma tenue gen. nov., sp. nov., and strain Es71-Z0120T as Parvivirga hydrogeniphila gen. nov., sp. nov., being members of Anaerosomatales ord. nov. This work expands the knowledge of the diversity, metabolic functions, and ecological role of the phylum Actinomycetota.

Lithoautotrophic lifestyle of the widespread genus Roseovarius revealed by physiological and genomic characterization of Roseovarius autotrophicus sp. nov

The genus Roseovarius, a member of the ecologically important Roseobacter-clade, is widespread throughout the world. A facultatively anaerobic lithoautotrophic bacterium (strain SHN287T), belonging to the genus Roseovarius, was isolated with molecular hydrogen as an electron donor and nitrate as an electron acceptor from a terrestrial mud volcano. Strain SHN287T possessed metabolic features not reported for Roseovarius such as chemolithoautotrophic growth with oxidation of molecular hydrogen or sulfur compounds, anaerobic growth and denitrification. Based on the phenotypic and phylogenetic characteristics, the new isolate is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius autotrophicus sp. nov. is proposed. The type strain is SHN287T (= KCTC 15916T = VKM B-3404T). An amended description of the genus Roseovarius is provided. Comparison of 46 Roseovarius genomes revealed that (i) a full set of genes for the Calvin-Benson cycle is present only in two strains: SHN287T and Roseovarius salinarum; (ii) respiratory H2-uptake [NiFe] hydrogenases are specific for a phylogenetically distinct group, including SHN287T-related strains; (iii) the Sox enzymatic complex is encoded in most of the studied genomes; and (iv) denitrification genes are widespread and randomly distributed among the genus. The metabolic characteristics found in R. autotrophicus sp. nov. expand the ecological role of the genus Roseovarius.

Pseudodesulfovibrio sediminis sp. nov., a mesophilic and neutrophilic sulfate-reducing bacterium isolated from sediment of a brackish lake

A novel mesophilic and neutrophilic sulfate-reducing bacterium, strain SF6^T, was isolated from sediment of a brackish lake in Japan. Cells of strain SF6^T were motile and rod-shaped with length of 1.2-2.5 μm and width of 0.6-0.9 μm. Growth was observed at 10-37 °C with an optimum growth temperature of 28 °C. The pH range for growth was 5.8-8.2 with an optimum pH of 7.0. The most predominant fatty acid was anteiso-C_15:0. Under sulfate-reducing conditions, strain SF6^T utilized lactate, ethanol and glucose as growth substrate. Chemolithoautotrophic growth on H₂ was not observed, although H₂ was used as electron donor. Fermentative growth occurred on pyruvate. As electron acceptor, sulfate, sulfite, thiosulfate and nitrate supported heterotrophic growth of the strain. The complete genome of strain SF6^T is composed of a circular chromosome with length of 3.8 Mbp and G+C content of 54 mol%. Analyses of the 16S rRNA gene and whole genome sequence indicated that strain SF6^T belongs to the genus Pseudodesulfovibrio but distinct form all existing species in the genus. On the basis of its genomic and phenotypic properties, strain SF6^T (= DSM111931^T = NBRC 114895^T) is proposed as the type strain of a new species, with name of Pseudodesulfovibrio sediminis sp. nov.