gen. nov., sp. nov., an anaerobic thermophilic bacterium utilizing methoxylated benzoates Free

Abstract

A novel anaerobic, thermophilic bacterium (strain A05 MB) was isolated from Daginsky thermal springs (Sakhalin, Russia) on 2-methoxybenzoate as a substrate. Cells of the strain were motile long rods, 3.0–5.0 µm in length and 0.5–0.6 µm in diameter. The temperature range for growth was 47–68 °C, with an optimum at 60 °C. The pH range for growth was 4.5–8.0, with an optimum at pH 5.5–6.0. Strain A05 MB did not require NaCl for growth. The strain utilized methoxylated aromatic compounds (2-methoxybenzoate and 3,4-dimethoxybenzoate), a number of carbohydrates (glucose, fructose, mannose, trehalose, xylose, sucrose, galactose, ribose, maltose, raffinose, lactose, cellobiose and dextrin) and proteinaceous substrates (yeast extract, beef extract, peptone and tryptone). The end products of glucose fermentation were acetate, ethanol and CO. The DNA G+C content of strain A05 MB was 40.2 mol% (whole-genome analysis). 16S rRNA gene sequence analysis revealed that strain A05MB belongs to the order (phylum ). The closest relative of strain A05 MB was (94.3 % 16S rRNA gene sequence similarity). Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain A05 MB is considered to represent a novel species of a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain of is A05 MB (=KCTC 15839=VKM B-3388).

Funding
This study was supported by the:
  • President of Russia (Award МК-6493.2018.3; agreement 075-15-2019-1036)
    • Principle Award Recipient: D.S. Kopitsyn
  • Ministry of Science and Higher Education of the Russian Federation
    • Principle Award Recipient: A.Y. Merkel
  • Russian Science Foundation (Award 17-74-30025)
    • Principle Award Recipient: E.A. Bonch-Osmolovskaya
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004019
2020-01-29
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/3/2066.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004019&mimeType=html&fmt=ahah

References

  1. Bache R, Pfennig N. Selective isolation of Acetobacterium woodii on methoxylated aromatic acids and determination of growth yields. Arch Microbiol 1981; 130:255–261 [View Article]
    [Google Scholar]
  2. Tasaki M, Kamagata Y, Nakamura K, Mikami E. Utilization of methoxylated benzoates and formation of intermediates by Desulfotomaculum thermobenzoicum in the presence or absence of sulfate. Arch Microbiol 1992; 157:209–212 [View Article]
    [Google Scholar]
  3. Neumann A, Engelmann T, Schmitz R, Greiser Y, Orthaus A et al. Phenyl methyl ethers: novel electron donors for respiratory growth of Desulfitobacterium hafniense and Desulfitobacterium sp. strain PCE-S. Arch Microbiol 2004; 181:245–249 [View Article]
    [Google Scholar]
  4. Mayumi D, Mochimaru H, Tamaki H, Yamamoto K, Yoshioka H et al. Methane production from coal by a single methanogen. Science 2016; 354:222–225 [View Article]
    [Google Scholar]
  5. Grech-Mora I, Fardeau M-L, Patel BKC, Ollivier B, Rimbault A et al. Isolation and characterization of Sporobacter termitidis gen. nov., sp. nov., from the digestive tract of the Wood-Feeding termite Nasutitermes lujae . Int J Syst Bacteriol 1996; 46:512–518 [View Article]
    [Google Scholar]
  6. Kuhner CH, Frank C, Griesshammer A, Schmittroth M, Acker G et al. Sporomusa silvacetica sp, nov., an acetogenic bacterium isolated from aggregated forest soil. Int J Syst Bacteriol 1997; 47:352–358 [View Article]
    [Google Scholar]
  7. Dehning I, Stieb M, Schink B. Sporomusa malonica sp. nov., a homoacetogenic bacterium growing by decarboxylation of malonate or succinate. Arch Microbiol 1989; 151:421–426 [View Article]
    [Google Scholar]
  8. Mechichi T, Labat M, Patel BK, Woo TH, Thomas P et al. Clostridium methoxybenzovorans sp. nov., a new aromatic o-demethylating homoacetogen from an olive mill wastewater treatment digester. Int J Syst Bacteriol 1999; 49:1201–1209 [View Article]
    [Google Scholar]
  9. Daniel SL, Keith ES, Yang H, Lin YS, Drake HL. Utilization of methoxylated aromatic compounds by the acetogen Clostridium thermoaceticum: expression and specificity of the co-dependent O-demethylating activity. Biochem Biophys Res Commun 1991; 180:416–422 [View Article]
    [Google Scholar]
  10. Slobodkin AI, Reysenbach A-L, Slobodkina GB, Baslerov RV, Kostrikina NA et al. Thermosulfurimonas dismutans gen. nov., sp. nov., an extremely thermophilic sulfur-disproportionating bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2012; 62:2565–2571 [View Article]
    [Google Scholar]
  11. Wolin EA, Wolin MJ, Wolfe RS. Formation of methane by bacterial extracts. J Biol Chem 1963; 238:2882–2886
    [Google Scholar]
  12. Slobodkina GB, Baslerov RV, Novikov AA, Viryasov MB, Bonch-Osmolovskaya EA et al. Inmirania thermothiophila gen. nov., sp. nov., a thermophilic, facultatively autotrophic, sulfur-oxidizing gammaproteobacterium isolated from a shallow-sea hydrothermal vent. Int J Syst Evol Microbiol 2016; 66:701–706 [View Article]
    [Google Scholar]
  13. Wunderlin T, Junier T, Roussel-Delif L, Jeanneret N, Junier P. Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes . Environ Microbiol Rep 2013; 5:911–924 [View Article]
    [Google Scholar]
  14. Onyenwoke RU, Brill JA, Farahi K, Wiegel J. Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch (Firmicutes). Arch Microbiol 2004; 182:182–192 [View Article]
    [Google Scholar]
  15. Härtig C. Rapid identification of fatty acid methyl esters using a multidimensional gas chromatography-mass spectrometry database. J Chromatogr A 2008; 1177:159–169 [View Article]
    [Google Scholar]
  16. Collins MD. Analysis of isoprenoid quinones. Methods Microbiol 1985; 18:329–363
    [Google Scholar]
  17. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article]
    [Google Scholar]
  18. Benson DA, Boguski MS, Lipman DJ, Ostell J, Ouellette BF et al. Genbank. Nucleic Acids Res 1999; 27:12–17 [View Article]
    [Google Scholar]
  19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article]
    [Google Scholar]
  20. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
    [Google Scholar]
  21. Nakamura T, Yamada KD, Tomii K, Katoh K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 2018; 34:2490–2492 [View Article]
    [Google Scholar]
  22. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article]
    [Google Scholar]
  23. Lefort V, Longueville J-E, Gascuel O. Sms: smart model selection in PhyML. Mol Biol Evol 2017; 34:2422–2424 [View Article]
    [Google Scholar]
  24. Anisimova M, Gil M, Dufayard J-F, Dessimoz C, Gascuel O. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol 2011; 60:685–699 [View Article]
    [Google Scholar]
  25. Hordijk W, Gascuel O. Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics 2005; 21:4338–4347 [View Article]
    [Google Scholar]
  26. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
    [Google Scholar]
  27. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article]
    [Google Scholar]
  28. Slobodkina GB, Kolganova TV, Kostrikina NA, Bonch-Osmolovskaya EA, Slobodkin AI. Caloribacterium cisternae gen. nov., sp. nov., an anaerobic thermophilic bacterium from an underground gas storage reservoir. Int J Syst Evol Microbiol 2012; 62:1543–1547 [View Article]
    [Google Scholar]
  29. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article]
    [Google Scholar]
  30. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article]
    [Google Scholar]
  31. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article]
    [Google Scholar]
  32. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008; 25:1307–1320 [View Article]
    [Google Scholar]
  33. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article]
    [Google Scholar]
  34. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article]
    [Google Scholar]
  35. Studenik S, Vogel M, Diekert G. Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2. J Bacteriol 2012; 194:3317–3326 [View Article]
    [Google Scholar]
  36. Wiegel J. Family I Thermoanaerobacteraceae fam.nov. In: De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W. et al. (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York. 2009; 1225. Validation List no. 132. Int J Syst Evol Microbiol 2010469–472
    [Google Scholar]
  37. Lee Y, Jain M, Lee C, Zeikus J. Taxonomic distinction of saccharolytic thermophilic anaerobes: description of Thermoanaerobacterium xylanolyticum gen.nov., sp.nov., and Thermoanaerobacterium saccharolyticum gen.nov., sp.nov.; Reclassification of Thermoanaerobium brockii, Clostridium thermosulfurogenes, and Clostridium thermohydrosulfuricem E100–69 as Thermoanaerobacter brockii comb.nov., Thermoanaerobacterium thermosulfurigenes comb.nov., and Thermoanaerobacter thermohudrosulfuricus comb.nov., respectively; and transfer of Clostridium thermohydrosulfuricum 39E to Thermoanaerobacter ethanolicus . Int J Syst Evol Microbiol 1993; 43:41–51
    [Google Scholar]
  38. Cann IK, Stroot PG, Mackie KR, White BA, Mackie RI. Characterization of two novel saccharolytic, anaerobic thermophiles, Thermoanaerobacterium polysaccharolyticum sp. nov. and Thermoanaerobacterium zeae sp. nov., and emendation of the genus Thermoanaerobacterium . Int J Syst Evol Microbiol 2001; 51:293–302 [View Article]
    [Google Scholar]
  39. Lee Y-J, Mackie RI, Cann IKO, Wiegel J. Description of Caldanaerobius fijiensis gen. nov., sp. nov., an inulin-degrading, ethanol-producing, thermophilic bacterium from a Fijian hot spring sediment, and reclassification of Thermoanaerobacterium polysaccharolyticum and Thermoanaerobacterium zeae as Caldanaerobius polysaccharolyticus comb. nov. and Caldanaerobius zeae comb. nov. Int J Syst Evol Microbiol 2008; 58:666–670 [View Article]
    [Google Scholar]
  40. S–Y L, Rainey FA, Morgan HW, Mayer F, Wiegel J. Thermoanaerobacterium aotearoense sp. nov., a slightly acidophilic, anaerobic thermophile isolated from various hot springs in New Zealand, and emendation of the genus Thermoanaerobacterium . Int J Syst Bacteriol 2009; 46:388–396
    [Google Scholar]
  41. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004019
Loading
/content/journal/ijsem/10.1099/ijsem.0.004019
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed