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Volume 73, Issue 1

sp. nov., a thermophilic bacterium isolated from a hot spring sediment No Access

Abstract

A novel anaerobic bacterium, designated SYSU GA19001, was isolated from a hot spring sediment sample. Phylogenetic analysis indicated that the isolate belongs to the genus , and showed the highest sequence similarity to CICC 10730 (96.63 %) and PYR-10 (96.11 %). Cells of strain SYSU GA19001 were Gram-stain-positive, spore-forming, rod-shaped (0.6–0.8×2.6–4.0 µm) and motile. Growth was observed at pH 5.0–9.0 (optimum, pH 7.0), 37–55 °C (optimum, 45 °C) and in NaCl concentrations of 0–2.0 % (optimum, 0 %). The genomic DNA G+C content was 31.62 %. The major cellular fatty acids of strain SYSU GA19001 were C, iso-C, C and summed feature 8. The prominent polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol. -diaminopimelic acid was the diamino acid in peptidoglycan. Based on the results of phylogenetic, chemotaxonomic and phenotypic analyses, strain SYSU GA19001 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain of the proposed novel species is SYSU GA19001 (=NBRC 115040= CGMCC 1.17864).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Clostridium caldaquaticum sp. nov. , hot spring and thermophilic
Funding
This study was supported by the:
  • the key Scientific Research Platforms and Program in Ordinary Universities of Guangdong Province (Award 2018KQNCX183)
    • Principle Award Recipient: LanLiu
  • Guangdong Basic and Applied Basic Research Foundation (Award 2019A1515110227)
    • Principle Award Recipient: LanLiu
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2019FY100701)
    • Principle Award Recipient: Jian-YuJiao
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2021FY100900)
    • Principle Award Recipient: Jian-YuJiao
  • National Natural Science Foundation of China (Award 91951205)
    • Principle Award Recipient: LiWen-Jun
© 2023 Sun Yat-Sen University
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2023-01-11
2024-04-29
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References

  1. Lawson P. The taxonomy of the genus clostridium: current status and future perspectives. Microbiology China 2016; 43:1070–1074
     [Google Scholar]
  2. Rodriguez DC, Seyboldt C, Rupnik M, Non-human C. difficile reservoirs and sources: animals, food, environment. In Mastrantonio P, Pupnik M. eds Updates on Clostridium Difficile in Europe Springer; 2018 pp 227–243
     [Google Scholar]
  3. Liu L, Jiao J-Y, Fang B-Z, Lv A-P, Ming Y-Z et al. Isolation of Clostridium from Yunnan-Tibet hot springs and description of Clostridium thermarum sp. nov. with lignocellulosic ethanol production. Syst Appl Microbiol 2020; 43:126104 [View Article]
     [Google Scholar]
  4. Song L, Dong X. Clostridium amylolyticum sp. nov., isolated from H2-producing UASB granules. Int J Syst Evol Microbiol 2008; 58:2132–2135 [View Article]
     [Google Scholar]
  5. Shiratori H, Sasaya K, Ohiwa H, Ikeno H, Ayame S et al. Clostridium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge. Int J Syst Evol Microbiol 2009; 59:1764–1770 [View Article]
     [Google Scholar]
  6. Cirne DG, Delgado OD, Marichamy S, Mattiasson B. Clostridium lundense sp. nov., a novel anaerobic lipolytic bacterium isolated from bovine rumen. Int J Syst Evol Microbiol 2006; 56:625–628 [View Article]
     [Google Scholar]
  7. Bankar SB, Survase SA, Singhal RS, Granström T. Continuous two stage acetone-butanol-ethanol fermentation with integrated solvent removal using Clostridium acetobutylicum B 5313. Bioresour Technol 2012; 106:110–116 [View Article]
     [Google Scholar]
  8. Graham-Rowe D. Agriculture: Beyond food versus fuel. Nature 2011; 474:S6–8 [View Article]
     [Google Scholar]
  9. Pace NR. A molecular view of microbial diversity and the biosphere. Science 1997; 276:734–740 [View Article] [PubMed]
     [Google Scholar]
  10. Whitaker RJ, Grogan DW, Taylor JW. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 2003; 301:976–978 [View Article] [PubMed]
     [Google Scholar]
  11. Hahnke S, Langer T, Koeck DE, Klocke M. Description of Proteiniphilum saccharofermentans sp. nov., Petrimonas mucosa sp. nov. and Fermentimonas caenicola gen. nov., sp. nov., isolated from mesophilic laboratory-scale biogas reactors, and emended description of the genus Proteiniphilum. Int J Syst Evol Microbiol 2016; 66:1466–1475 [View Article]
     [Google Scholar]
  12. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
     [Google Scholar]
  13. May HG. A safe spore stain for class use. Stain Technology 1926; 1:105–106 [View Article]
     [Google Scholar]
  14. Leifson E. Atlas of Bacterial Flagellation New York: Academic Press; 1960 [View Article]
     [Google Scholar]
  15. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article]
     [Google Scholar]
  16. KOVACS N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article]
     [Google Scholar]
  17. Smibert RA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, D.C: American Society of Microbiology; 1994 pp 607–654
     [Google Scholar]
  18. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
     [Google Scholar]
  19. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  20. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  21. Hasegawa T, Takizawa M, Tanida SJ. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  22. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematic New York: John Wiley and Sons; 1991 pp 115–175
     [Google Scholar]
  23. Delcher AL, Salzberg SL, Phillippy AM. Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinformatics 2003; Chapter 10:Unit [View Article]
     [Google Scholar]
  24. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
     [Google Scholar]
  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  27. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biology 1971; 20:406–416 [View Article]
     [Google Scholar]
  28. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  29. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article]
     [Google Scholar]
  30. 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] [PubMed]
     [Google Scholar]
  31. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
     [Google Scholar]
  32. Jiao J-Y, Fu L, Hua Z-S, Liu L, Salam N et al. Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. ISME J 2021; 15:3005–3018 [View Article] [PubMed]
     [Google Scholar]
  33. Jiao J-Y, Liu L, Hua Z-S, Fang B-Z, Zhou E-M et al. Microbial dark matter coming to light: challenges and opportunities. Natl Sci Rev 2021; 8:waa280 [View Article]
     [Google Scholar]
  34. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article] [PubMed]
     [Google Scholar]
  35. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  36. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  37. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article]
     [Google Scholar]
  38. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
     [Google Scholar]
  39. Huang Y, Wei Z, Cong L, Qiu Z, Chen R et al. Clostridium prolinivorans sp. nov., a thermophilic bacterium isolated from an anaerobic reactor degrading propionate. Int J Syst Evol Microbiol 2020; 70:5190–5196 [View Article] [PubMed]
     [Google Scholar]
  40. Liu C, Huang D, Liu L, Zhang J, Deng Y et al. Clostridium swellfunianum sp. nov., a novel anaerobic bacterium isolated from the pit mud of Chinese Luzhou-flavor liquor production. Antonie van Leeuwenhoek 2014; 106:817–825 [View Article]
     [Google Scholar]
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Clostridium caldaquaticum sp. nov., a thermophilic bacterium isolated from a hot spring sediment
Int J Syst Evol Microbiol 73, 005684 (2023); https://doi.org/10.1099/ijsem.0.005684
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