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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 4

sp. nov., isolated from a hot spring in Yunnan Province, south-west China No Access

Abstract

Two Gram-positive, rod-shaped, endospore-forming strains, YIM B05601 and YIM B05602, were isolated from soil sampled at Hamazui hot spring, Tengchong City, Yunnan Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus , appearing most closely related to YIM B00362 (96.9 % sequence similarity). Genome-based phylogenetic analysis confirmed that strains YIM B05601 and YIM B05602 formed a distinct phylogenetic cluster within the genus . The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values of strains YIM B05601 and YIM B05602 with the related species YIM B00362 were within the ranges of 74.43–74.57 % and 12.1–18.5 %, respectively, which clearly indicated that strains YIM B05601, YIM B05602 represented a novel species. Strains YIM B05601 and YIM B05602 exhibited 99.6 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 99.8 and 100 %, respectively, suggesting that they belong to the same species. Optimum growth for both strains occurred at pH 7.0 and 45 °C. The diagnostic diamino acid in the cell-wall peptidoglycan of strains YIM B05601 and YIM B05602 was -diaminopimelic acid. MK-7 was the predominant menaquinone. The polar lipids of strain YIM B05602 were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, four unidentified glycolipids, an unidentified polarlipid and phosphatidylinositol mannoside. The major fatty acids of the two stains were iso-C and anteiso-C. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizations, strains YIM B05601 and YIM B05602 could be classified as a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YIM B05602 (=CGMCC 1.60051=KCTC 43460=NBRC 115924).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genomics , Paenibacillus , phylogeny and taxonomy
Funding
This study was supported by the:
  • the Natural Science Foundation of Anhui Province Department of Education (Award KJ2020A0058)
    • Principle Award Recipient: Yong-MeiMiao
  • National Natural Science Foundation of China (Award 31860017)
    • Principle Award Recipient: MinYin
  • National Natural Science Foundation of China (Award 82160674)
    • Principle Award Recipient: MinYin
  • National Natural Science Foundation of China (Award 31760003)
    • Principle Award Recipient: Shu-KunTang
  • Major Science and Technology Projects of Yunnan Province (Award 202002AA100007)
    • Principle Award Recipient: Shu-KunTang
© 2024 The Authors
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2024-04-12
2024-04-29
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References

  1. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek 1993; 64:253–260 [View Article] [PubMed]
     [Google Scholar]
  2. Thin KK, He S-W, Ma R, Wang X, Han J-G et al. Paenibacillus rhizolycopersici sp. nov., an oligotrophic bacterium isolated from a tomato plant in China. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
     [Google Scholar]
  3. Xue H, Tu Y, Ma T, Jiang N, Piao C et al. Taxonomic study of three novel Paenibacillus species with cold-adapted plant growth-promoting capacities isolated from root of Larix gmelinii. Microorganisms 2023; 11:130 [View Article] [PubMed]
     [Google Scholar]
  4. Kim J, Chhetri G, Kim I, So Y, Seo T. Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils. Int J Syst Evol Microbiol 2022; 72:005640 [View Article] [PubMed]
     [Google Scholar]
  5. Wang J, Deng M, Zhou E-M, Ran L, Miao C-P et al. Paenibacillus hamazuiensis sp. nov., a bacterium isolated from Hamazui hot spring in Yunnan province, south-west China. Arch Microbiol 2022; 204:676 [View Article] [PubMed]
     [Google Scholar]
  6. Gao Q-J, Mo K-L, Hu Y-H, Liu Z-Y, Huang H-Q. Paenibacillus sabuli sp. nov., isolated from the South China Sea. Int J Syst Evol Microbiol 2022; 72:005568 [View Article] [PubMed]
     [Google Scholar]
  7. Nguyen MH, Dinh MTN, Lee KC, Kim J-S, Nguyen TKN et al. Paenibacillus vietnamensis sp. nov., isolated from the rhizosphere soil of Arachis hypogaea. Int J Syst Evol Microbiol 2022; 72:005537 [View Article]
     [Google Scholar]
  8. Kämpfer P, Lipski A, Lamothe L, Clermont D, Criscuolo A et al. Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root. Arch Microbiol 2022; 204:630 [View Article] [PubMed]
     [Google Scholar]
  9. Deng N, Huang H, Hu Y, Wang X, Mo K. Paenibacillus arenilitoris sp. nov., isolated from seashore sand and genome mining revealed the biosynthesis potential as antibiotic producer. Antonie van Leeuwenhoek 2022; 115:1307–1317 [View Article] [PubMed]
     [Google Scholar]
  10. Li R, Zhang Z-T-L, Wang Y, Jiang G-Q, Yin M et al. Paenibacillus alkalitolerans sp. nov., a bacterium isolated from a salt lake of Turpan City in Xinjiang Province, north-west China. Folia Microbiol 2023; 68:115–120 [View Article] [PubMed]
     [Google Scholar]
  11. Cho E-S, Hwang CY, Kwon HW, Seo M-J. Paenibacillus mellifer sp. nov., isolated from gut of the honey bee Apis mellifera. Arch Microbiol 2022; 204:558 [View Article] [PubMed]
     [Google Scholar]
  12. Chauhan NS, Joseph N, Shaligram S, Chavan N, Joshi A et al. Paenibacillus oleatilyticus sp. nov., isolated from soil. Arch Microbiol 2022; 204:516 [View Article] [PubMed]
     [Google Scholar]
  13. Dong Lee S. Paenibacillus cavernae sp. nov., isolated from soil of a natural cave. Int J Syst Evol Microbiol 2016; 66:598–603 [View Article] [PubMed]
     [Google Scholar]
  14. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  15. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  16. 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] [PubMed]
     [Google Scholar]
  17. Fitch W. Citation-classic - toward defining the course of evolution - minimum change for a specific tree topology. Curr Con/Agri Biol Environ Sci 1987; 27:14
     [Google Scholar]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  20. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  21. Lim HJ, Lee E-H, Yoon Y, Chua B, Son A. Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 2016; 120:379–387 [View Article] [PubMed]
     [Google Scholar]
  22. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
     [Google Scholar]
  23. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
     [Google Scholar]
  24. Avram O, Rapoport D, Portugez S, Pupko T. M1CR0B1AL1Z3R-a user-friendly web server for the analysis of large-scale microbial genomics data. Nucleic Acids Res 2019; 47:W88–W92 [View Article] [PubMed]
     [Google Scholar]
  25. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  26. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015; 43:D261–D269 [View Article] [PubMed]
     [Google Scholar]
  27. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
     [Google Scholar]
  28. Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al. The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res 2020; 48:D606–D612 [View Article] [PubMed]
     [Google Scholar]
  29. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  30. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
     [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  32. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
     [Google Scholar]
  33. Amoozegar MA, Bagheri M, Makhdoumi-Kakhki A, Didari M, Schumann P et al. Oceanobacillus limi sp. nov., a moderately halophilic bacterium from a salt lake. Int J Syst Evol Microbiol 2014; 64:1284–1289 [View Article] [PubMed]
     [Google Scholar]
  34. 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]
  35. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  36. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986; 123:251–256 [View Article] [PubMed]
     [Google Scholar]
  37. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  38. Tang S-K, Wang Y, Chen Y, Lou K, Cao L-L et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 2009; 59:2025–2031 [View Article] [PubMed]
     [Google Scholar]
  39. Moss CW, Dees SB. Identification of microorganisms by gas chromatographic-mass spectrometric analysis of cellular fatty acids. J Chromatogr 1975; 112:594–604 [View Article] [PubMed]
     [Google Scholar]
  40. Tuo L, Yan X-R, Li F-N, Yang C, An M-B et al. Amnibacterium flavum sp. nov., a novel endophytic actinobacterium isolated from bark of Nerium indicum Mill. Int J Syst Evol Microbiol 2019; 69:285–290 [View Article] [PubMed]
     [Google Scholar]
  41. Mise K, Iwasaki W. Environmental atlas of prokaryotes enables powerful and intuitive habitat-based analysis of community structures. iScience 2020; 23:101624 [View Article] [PubMed]
     [Google Scholar]
  42. 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]
  43. Li Q-Q, Han M-X, Fang B-Z, Jiao J-Y, Liu L et al. Nocardia cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample. Int J Syst Evol Microbiol 2017; 67:2998–3003 [View Article] [PubMed]
     [Google Scholar]
  44. Akaracharanya A, Lorliam W, Tanasupawat S, Lee KC, Lee J-S. Paenibacillus cellulositrophicus sp. nov., a cellulolytic bacterium from Thai soil. Int J Syst Evol Microbiol 2009; 59:2680–2684 [View Article] [PubMed]
     [Google Scholar]
  45. Narsing Rao MP, Dong Z-Y, Kan Y, Zhang K, Fang B-Z et al. Description of Paenibacillus antri sp. nov. and Paenibacillus mesophilus sp. nov., isolated from cave soil. Int J Syst Evol Microbiol 2020; 70:1048–1054 [View Article] [PubMed]
     [Google Scholar]
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Paenibacillus thermotolerans sp. nov., isolated from a hot spring in Yunnan Province, south-west China
Int J Syst Evol Microbiol 74, 006336 (2024); https://doi.org/10.1099/ijsem.0.006336
/content/journal/ijsem/10.1099/ijsem.0.006336
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