1887

Abstract

China is a hotspot for hot springs and during microbial diversity analysis of Tengchong hot spring, Yunnan province, south-west PR China, two strains designated SYSU G01001 and SY-13 were isolated. SYSU G01001 and SY-13 were Gram-stain-positive, motile and spore-forming. Colonies were white, circular, raised and punctiform. SYSU G01001 and SY-13 grew at pH 6.0–9.0 (optimum pH 8.0) and at 23–37 °C (optimum 28 °C). The 16S rRNA gene sequence similarity between SYSU G01001 and SY-13 was 99.6 % but these strains shared low sequence similarity with (97.5 %) indicating that they represented a novel species. On the basis of the results, SYSU G01001 was selected for further investigations and SY-13 was considered to represent a second strain of the species. The cell wall peptidoglycan of SYSU G01001 was -2,6-diaminopimelic acid and MK-7 was the only respiratory quinone. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified aminolipids (AL), two unidentified amino phospholipids (APL), an unidentified phospholipid (PL) and an unidentified polar lipid (L). The G+C content of the genomic DNA was 53.9 mol%. The average nucleotide identity (ANIb and ANIm) values between SYSU G01001 and LMG 29963 were below the cut-off level (95–96 %) recommended as the average nucleotide identity (ANI) criterion for interspecies identity. On the basis of the above results strain SYSU G01001 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SYSU G01001 (=KCTC 33952=CGMCC 1.13870).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004004
2020-01-27
2020-02-28
Loading full text...

Full text loading...

References

  1. Xian WD, Narsing Rao MP, Zhou EM, Xiao M.Diversity of thermophiles in terrestrial hot springs of Yunnan and Tibet, China In Egamberdieva D, Birkeland NK, Panosyan H, Li WJ. (editors) Extremophiles in Eurasian ecosystems: ecology, diversity, and applications. Microorganisms for sustainability8 Singapore: Springer; 2018; pp57–79
    [Google Scholar]
  2. Dong L, Ming H, Zhou E-M, Yin Y-R, Liu L et al. Crenobacter luteus gen. nov., sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2015;65:214–219 [CrossRef]
    [Google Scholar]
  3. Duan Y-Y, Ming H, Dong L, Yin Y-R, Zhang Y et al. Streptomyces calidiresistens sp. nov., isolated from a hot spring sediment. Antonie van Leeuwenhoek 2014;106:189–196 [CrossRef]
    [Google Scholar]
  4. Habib N, Khan IU, Hussain F, Zhou E-M, Xiao M et al. Caldovatus sediminis gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2017;67:4716–4721 [CrossRef]
    [Google Scholar]
  5. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Antonie van Leeuwenhoek 1994;64:253–260 [CrossRef]
    [Google Scholar]
  6. Parte AC. LPSN - list of prokaryotic names with standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018;68:1825–1829 [CrossRef]
    [Google Scholar]
  7. Akaracharanya A, Lorliam W, Tanasupawat S, Lee KC, Lee JS. Paenibacillus cellulositrophicus sp. nov., a cellulolytic bacterium from Thai soil. Int J Syst Evol Microbiol 2009;59:2680–2684 [CrossRef]
    [Google Scholar]
  8. Lee HW, Roh SW, Yim KJ, Shin NR, Lee J et al. Paenibacillus marinisediminis sp. nov., a bacterium isolated from marine sediment. J Microbiol 2013;51:312–317 [CrossRef]
    [Google Scholar]
  9. Dong Lee S. Paenibacillus cavernae sp. nov., isolated from soil of a natural cave. Int J Syst Evol Microbiol 2016;66:598–603 [CrossRef]
    [Google Scholar]
  10. Suominen I et al. Paenibacillus stellifer sp. nov., a cyclodextrin-producing species isolated from paperboard. Int J Syst Evol Microbiol 2003;53:1369–1374 [CrossRef]
    [Google Scholar]
  11. Grady EN, MacDonald J, Liu L, Richman A, Yuan ZC. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 2016;15:203 [CrossRef]
    [Google Scholar]
  12. Dong ZY, Narsing Rao MP, Wang HF, Fang BZ, Liu YH et al. Transcriptomic analysis of two endophytes involved in enhancing salt stress ability of Arabidopsis thaliana. Sci Total Environ 2019;686:107–117 [CrossRef]
    [Google Scholar]
  13. 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 [CrossRef]
    [Google Scholar]
  14. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425
    [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef]
    [Google Scholar]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971;20:406–416 [CrossRef]
    [Google Scholar]
  17. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef]
    [Google Scholar]
  18. Thompson J, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef]
    [Google Scholar]
  19. 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 [CrossRef]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  21. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346–351 [CrossRef]
    [Google Scholar]
  22. Xu P 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 [CrossRef]
    [Google Scholar]
  23. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956;178:703–704 [CrossRef]
    [Google Scholar]
  24. 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 [CrossRef]
    [Google Scholar]
  25. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983;29:319–322 [CrossRef]
    [Google Scholar]
  26. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970;20:435–443 [CrossRef]
    [Google Scholar]
  27. Collins M, Pirouz T, Goodfellow M, Minnikin D. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef]
    [Google Scholar]
  28. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982;5:2359–2367 [CrossRef]
    [Google Scholar]
  29. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979;47:87–95 [CrossRef]
    [Google Scholar]
  30. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Microbiol 1980;48:459–470 [CrossRef]
    [Google Scholar]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
    [Google Scholar]
  32. Siddiqi MZ, Choi G-M, Choi KD, Im W-T. Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil. Int J Syst Evol Microbiol 2017;67:4917–4922 [CrossRef]
    [Google Scholar]
  33. 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 [CrossRef]
    [Google Scholar]
  34. 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 [CrossRef]
    [Google Scholar]
  35. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007;23:673–679 [CrossRef]
    [Google Scholar]
  36. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003;4:41 [CrossRef]
    [Google Scholar]
  37. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007;35:W182–W185 [CrossRef]
    [Google Scholar]
  38. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007;35:3100–3108 [CrossRef]
    [Google Scholar]
  39. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997;25:955–964 [CrossRef]
    [Google Scholar]
  40. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32:929–931 [CrossRef]
    [Google Scholar]
  41. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009;106:19126–19131 [CrossRef]
    [Google Scholar]
  42. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004004
Loading
/content/journal/ijsem/10.1099/ijsem.0.004004
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error