Pelovirga terrestris gen. nov., sp. nov., anaerobic, alkaliphilic, fumarate-, arsenate-, Fe(III)- and sulfur-reducing bacterium isolated from a terrestrial mud volcano

Khomyakova, Maria; Merkel, Alexander Y.; Копицын, Д. С.; Slobodkin, A. I.

doi:10.1016/j.syapm.2022.126304

Cited by 18 publications

(5 citation statements)

References 60 publications

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“…Many TMVs in this area have pH 8.5–9.1 and contain high concentrations of HCO

and Na + ions (Lavrushin et al, 2021 ). The presence of Methanotrichaceae species had not previously been detected by 16S rRNA gene-based observations in several TMVs of this region (Merkel et al, 2021 ; Khomyakova et al, 2022 ; Slobodkin et al, 2023 ). However, in the other study, Methanothrix (“Methanosaeta”) thermophila accounted for almost 40% of Archaea in one TMV of southwestern Taiwan, suggesting the importance of this microbial group in certain TMVs (Cheng et al, 2012 ).…”

Section: Discussionmentioning

confidence: 75%

Phenotypic and genomic characterization of the first alkaliphilic aceticlastic methanogens and proposal of a novel genus Methanocrinis gen.nov. within the family Methanotrichaceae

Khomyakova,

Merkel,

Slobodkin

et al. 2023

Front. Microbiol.

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Highly purified cultures of alkaliphilic aceticlastic methanogens were collected for the first time using methanogenic enrichments with acetate from a soda lake and a terrestrial mud volcano. The cells of two strains were non-motile rods forming filaments. The mud volcano strain M04Ac was alkalitolerant, with the pH range for growth from 7.5 to 10.0 (optimum at 9.0), while the soda lake strain Mx was an obligate alkaliphile growing in the pH range 7.7–10.2 (optimum 9.3–9.5) in the presence of optimally 0.2–0.3 M total Na+. Genomes of both strains encoded all enzymes required for aceticlastic methanogenesis and different mechanisms of (halo)alkaline adaptations, including ectoine biosynthesis, which is the first evidence for the formation of this osmoprotectant in archaea. According to 16S rRNA gene phylogeny, the strains possessed 98.3–98.9% sequence identity and belonged to the obligately aceticlastic genus Methanothrix with M. harundinaceae as the most closely related species. However, a more advanced phylogenomic reconstruction based on 122 conserved single-copy archaeal protein-coding marker genes clearly indicated a polyphyletic origin of the species included in the genus Methanothrix. We propose to reclassify Methanothrix harrundinacea (type strain 8AcT) into a new genus, Methanocrinis gen. nov., with the type species Methanocrinis harrundinaceus comb. nov. We also propose under SeqCode the complete genome sequences of strain MxTs (GCA_029167045.1) and strain M04AcTs (GCA_029167205.1) as nomenclatural types of Methanocrinis natronophilus sp. nov. and Methanocrinis alkalitolerans sp. nov., respectively, which represent other species of the novel genus. This work demonstrates that the low energy aceticlastic methanogenesis may function at extreme conditions present in (halo)alkaline habitats.

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“…Many TMVs in this area have pH 8.5–9.1 and contain high concentrations of HCO

Section: Discussionmentioning

confidence: 75%

Phenotypic and genomic characterization of the first alkaliphilic aceticlastic methanogens and proposal of a novel genus Methanocrinis gen.nov. within the family Methanotrichaceae

Khomyakova,

Merkel,

Slobodkin

et al. 2023

Front. Microbiol.

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“…Analysis of the prokaryotic diversity in salsa lake sediments of Karabetova Gora mud volcano by high-throughput sequencing of 16S rRNA gene amplicons showed that representatives of OPB41 group constituted 13–14% of all reads ( Khomyakova et al, 2022 ). An enrichment culture was initiated by 10% (w/v) inoculation of a mud sample into anaerobic sterile medium with 3,4-dihydroxybenzoic (protocatechuic) acid and sulfate.…”

Section: Resultsmentioning

confidence: 99%

“…Representatives of the phylum Actinomycetota are not a major component of TMV’s microbial communities, where methane-oxidizing and sulfur-metabolizing prokaryotes usually predominate ( Wang et al, 2014 ; Lin et al, 2018 ; Mardanov et al, 2020 ; Merkel et al, 2021 ; Tu et al, 2022 ). However, in several TMVs the relative abundance of Actinomycetota reaches 12–15% ( Yang et al, 2012 ; Khomyakova et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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“…DNA from mud samples as well as from enrichment cultures was isolated using FastDNA Spin Kit for Soil according to the manufacturer’s protocol (MP Biomedicals, Santa Ana, CA, USA). The V4 region of the 16S rRNA amplicon libraries preparation, sequencing, and analysis were performed as previously described [ 31 ].…”

Section: Methodsmentioning

confidence: 99%

Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria

et al. 2023

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The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood–Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide.

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Pelovirga terrestris gen. nov., sp. nov., anaerobic, alkaliphilic, fumarate-, arsenate-, Fe(III)- and sulfur-reducing bacterium isolated from a terrestrial mud volcano

Cited by 18 publications

References 60 publications

Phenotypic and genomic characterization of the first alkaliphilic aceticlastic methanogens and proposal of a novel genus Methanocrinis gen.nov. within the family Methanotrichaceae

Phenotypic and genomic characterization of the first alkaliphilic aceticlastic methanogens and proposal of a novel genus Methanocrinis gen.nov. within the family Methanotrichaceae

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

Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria

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