Pelomicrobium methylotrophicum gen. nov., sp. nov. a moderately thermophilic, facultatively anaerobic, lithoautotrophic and methylotrophic bacterium isolated from a terrestrial mud volcano

  • G. B. SlobodkinaEmail author
  • A. Y. Merkel
  • A. A. Novikov
  • E. A. Bonch-Osmolovskaya
  • A. I. Slobodkin
Original Paper


A novel moderately thermophilic, bacterium, strain SM250T, was isolated from a terrestrial mud volcano, Taman peninsula, Krasnodar region, Russia. Cells of strain SM250T were Gram-negative non-spore forming motile straight rods. Growth was observed at temperatures 30–63 °C (optimum at 50 °C), pH 6.5–10.0 (optimum at pH 8.5) and NaCl concentrations 0–4.5% (w/v) (optimum at 1.0–1.5% (w/v)). The novel isolate grows by aerobic respiration or anaerobic respiration with nitrate as the terminal electron acceptor. Strain SM250T grows by the utilization of methanol, formate and a number of other organic compounds or lithoautotrophically with hydrogen, elemental sulfur or thiosulfate as electron donors. The total size of the genome of the novel isolate was 3,327,116 bp and a genomic DNA G + C content was 64.8 mol%. Analysis of the 16S rRNA gene sequences revealed that strain SM250T belongs to the class Hydrogenophilia within the phylum Proteobacteria, with less than 91% of 16S rRNA gene sequence similarity to any species with validly published name. We propose to assign strain SM250T to a new species of a novel genus Pelomicrobium methylotrophicum gen. nov., sp. nov. The type strain is SM250T (= KCTC 62861T = VKM B-3274T).


Hydrogen oxidation Sulfur oxidation Nitrate reduction CO2 fixation Proteobacteria Hydrogenophilales 



The work of G.B.S., A.I.S. and E.A.B.-O. was supported by the Russian Science Foundation, project no. 17-74-30025. The work of A.Y.M (genome sequencing and assembly) was supported by the Ministry of Science and Higher Education of the Russian Federation. The work of A.A.N (chemotaxonomic studies) was supported by the President of Russia (grant MК-3801.2018.4; agreement 075-15-2019-1025.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.


  1. Alain K, Holler T, Musat F, Elvert M, Treude T, Krüger M (2006) Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania. Environ Microbiol 8:574–590. CrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  3. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477CrossRefPubMedGoogle Scholar
  4. Benson DA, Boguski MS, Lipman DJ, Oullette BFF, Rapp BA, Wheeler DL (1999) GenBank. Nucleic Acids Res 27:12–17CrossRefPubMedGoogle Scholar
  5. Boden R, Hutt LP, Rae AW (2017) Reclassification of Thiobacillus aquaesulis (Wood and Kelly 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the ‘Proteobacteria’, and four new families within the orders Nitrosomonadales and Rhodocyclales. Int J Syst Evol Microbiol 67:1191–1205. CrossRefGoogle Scholar
  6. Chaney AL, Marbach EP (1962) Modified reagents for determination of urea and ammonium. Clin Chem 8:130–132Google Scholar
  7. Chang YH, Cheng TW, Lai WJ, Tsai WY, Sun CH, Lin LH, Wang PL (2012) Microbial methane cycling in a terrestrial mud volcano in eastern Taiwan. Environ Microbiol 14:895–908. CrossRefGoogle Scholar
  8. Cheng TW, Chang YH, Tang SL, Tseng CH, Chiang PW, Chang KT, Sun CH, Chen YG, Kuo HC, Wang CH, Chu PH, Song SR, Wang PL, Lin LH (2012) Metabolic stratification driven by surface and subsurface interactions in a terrestrial mud volcano. ISME J 6:2280–2290. CrossRefPubMedCentralPubMedGoogle Scholar
  9. Chistoserdova L (2011) Modularity of methylotrophy, revisited. Environ Microbiol 13:2603–2622. CrossRefGoogle Scholar
  10. Crowther GJ, Kosály G, Lidstrom ME (2008) Formate as the main branch point for methylotrophic metabolism in Methylobacterium extorquens AM1. J Bacteriol 190:5057–5062CrossRefPubMedGoogle Scholar
  11. Dimitrov LI (2002) Mud volcanoes–the most important pathway for degassing deeply buried sediments. Earth Sci Rev 59:49–76CrossRefGoogle Scholar
  12. Etiope G, Milkov AV (2004) A new estimate of global methane flux from onshore and shallow submarine mud volcanoes to the atmosphere. Environ Geol 46:997–1002CrossRefGoogle Scholar
  13. Garrity GM, Bell JA, Lilburn T (2005) Methylophilaceae fam. nov. In: Bergey’s manual of systematics of archaea and bacteria. Wiley.
  14. Hayashi NR, Ishida T, Yokota A, Kodama T, Igarashi Y (1999) Hydrogenophilus thermoluteolus gen. nov., sp. nov., a thermophilic, facultatively chemolithoautotrophic, hydrogen-oxidizing bacterium. Int J Syst Bacteriol 49:783–786. CrossRefGoogle Scholar
  15. Kalyuzhnaya MG, De Marco P, Bowerman S, Pacheco CC, Lara JC, Lidstrom ME, Chistoserdova L (2006) Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates. Int J Syst Evol Microbiol 56:2517–2522. CrossRefGoogle Scholar
  16. Kokoschka S, Dreier A, Romoth K, Taviani M, Schafer N, Reitner J, Hoppert M (2015) Isolation of anaerobic bacteria from terrestrial mud volcanoes (Salse di Nirano, Northern Apennines, Italy). Geomicrobiol J 32:355–364. CrossRefGoogle Scholar
  17. Kopf A (2002) Significance of mud volcanism. Rev Geophys 40:1005. CrossRefGoogle Scholar
  18. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. CrossRefPubMedGoogle Scholar
  19. Manaia CM, Nogales B, Nunes OC (2003) Tepidiphilus margaritifer gen. nov., sp. nov., isolated from a thermophilic aerobic digester. Int J Syst Evol Microbiol 53:1405–1410. CrossRefGoogle Scholar
  20. Mazzini A, Etiope G (2017) Mud volcanism: an updated review. Earth Sci Rev 168:81–112CrossRefGoogle Scholar
  21. Miyake D, Ichiki S, Tanabe M, Oda T, Kurod H, Nishihara H, Sambongi Y (2007) Thiosulfate oxidation by a moderately thermophilic hydrogen-oxidizing bacterium, Hydrogenophilus thermoluteolus. Arch Microbiol 188(2):199–204CrossRefGoogle Scholar
  22. Nakatsu CH, Hristova K, Hanada S, Meng XY, Hanson JR, Scow KM, Kamagata Y (2006) Methylibium petroleiphilum gen. nov., sp nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria. Int J Syst Evol Microbiol 56:983–989. CrossRefGoogle Scholar
  23. Poddar A, Lepcha RN, Subrata KD (2014) Taxonomic study of the genus Tepidiphilus: transfer of Petrobacter succinatimandens to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov., emended description of the genus Tepidiphilus and description of Tepidiphilus thermophilus sp. nov., isolated from a terrestrial hot spring. Int J Syst Evol Microbiol 64:228–235. CrossRefGoogle Scholar
  24. Rabus R, Wöhlbrand L, Thies D, Meyer M, Reinhold-Hurek B, Kämpfer P (2019) Aromatoleum gen. nov., a novel genus accommodating the phylogenetic lineage including Azoarcus evansii and related species, and proposal of Aromatoleum aromaticum sp. nov., Aromatoleum petrolei sp. nov., Aromatoleum bremense sp. nov., Aromatoleum toluolicum sp. nov. and Aromatoleum diolicum sp. nov. Int J Syst Evol Microbiol 69:982–997. CrossRefGoogle Scholar
  25. Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 9:945–967Google Scholar
  26. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. CrossRefPubMedCentralPubMedGoogle Scholar
  27. Salinas MB, Fardeau ML, Cayol JL, Casalo L, Patel BKC, Thomas P, Garcia JL, Ollivier B (2004) Petrobacter succinatimandens gen. nov., sp. nov., a moderately thermophilic, nitrate-reducing bacterium isolated from an Australian oil well. Int J Syst Evol Microbiol 54:645–649. CrossRefGoogle Scholar
  28. Slobodkin AI, Tourova TP, Kuznetsov BB, Kostrikina NA, Chernyh NA, Bonch-Osmolovskaya EA (1999) Thermoanaerobacter siderophilus sp. nov., a novel dissimilatory Fe(III)-reducing anaerobic thermophilic bacterium. Int J Syst Bacteriol 49:1471–1478. CrossRefGoogle Scholar
  29. Slobodkin AI, Reysenbach A-L, Slobodkina GB, Baslerov RV, Kostrikina NA, Wagner ID, Bonch-Osmolovskaya EA (2012) Thermosulfurimonas dismutans gen. nov., sp. nov. a novel extremely thermophilic sulfur-disproportionating bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 62:2565–2571. CrossRefGoogle Scholar
  30. Slobodkina GB, Kolganova TV, Kostrikina NA, Bonch-Osmolovskaya EA, Slobodkin AI (2012) Caloribacterium cisternae gen. nov., sp. nov., an anaerobic thermophilic bacterium from an underground gas storage reservoir. Int J Syst Evol Microbiol 62:1543–1547. CrossRefGoogle Scholar
  31. Smalley NE, Taipale S, De Marco P, Doronina NV, Kyrpides N, Shapiro N, Woyke T, Kalyuzhnaya MG (2015) Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of Methyloversatilis discipulorum sp. nov. Int J Syst Evol Microbiol 65:2227–2233. CrossRefGoogle Scholar
  32. Stöhr R, Waberski A, Liesack W, Völker H, Wehmeyer U, Thomm M (2001) Hydrogenophilus hirschii sp. nov., a novel thermophilic hydrogen-oxidizing β-proteobacterium isolated from Yellowstone National Park. Int J Syst Evol Microbiol 51:481–488. CrossRefGoogle Scholar
  33. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526PubMedGoogle Scholar
  34. Tu T-H, Wu L-W, Lin Y-S, Imachi H, Lin L-H, Wang P-L (2017) Microbial community composition and functional capacity in a terrestrial ferruginous, sulfate-depleted mud volcano. Front Microbiol 8:2137. CrossRefPubMedCentralPubMedGoogle Scholar
  35. Vésteinsdóttir H, Reynisdóttir DB, Örlygsson J (2011) Hydrogenophilus islandicus sp. nov., a thermophilic hydrogen-oxidizing bacterium isolated from an Icelandic hot spring. Int J Syst Evol Microbiol 61:290–294. CrossRefGoogle Scholar
  36. Wolin EA, Wolin MJ, Wolfe RS (1963) Formation of methane by bacterial extracts. J Biol Chem 238:2882–2886Google Scholar
  37. Wrede C, Brady S, Rockstroh S, Dreier A, Kokoschka S, Heinzelmann SM, Heller C, Reitner J, Taviani M, Daniel R, Hoppert M (2012) Aerobic and anaerobic methane oxidation in terrestrial mud volcanoes in the Northern Apennines. Sediment Geol 263(264):210–219CrossRefGoogle Scholar
  38. Yang H-M, Lou K, Sun J, Zhang T, Ma X-L (2012) Prokaryotic diversity of an active mud volcano in the Usu City of Xinjiang, China. J Basic Microbiol 52(79–85):79. CrossRefGoogle Scholar
  39. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. CrossRefPubMedCentralPubMedGoogle Scholar

Copyright information

© Springer Japan KK, part of Springer Nature 2019

Authors and Affiliations

  • G. B. Slobodkina
    • 1
    Email author
  • A. Y. Merkel
    • 1
  • A. A. Novikov
    • 2
  • E. A. Bonch-Osmolovskaya
    • 1
  • A. I. Slobodkin
    • 1
  1. 1.Winogradsky Institute of MicrobiologyResearch Center of Biotechnology of the Russian Academy of SciencesMoscowRussia
  2. 2.Gubkin UniversityMoscowRussia

Personalised recommendations