sp. nov., isolated from cave soil Free

Abstract

A Gram-stain-positive, motile, rod-shaped and endospore-forming strain, SYSU K30002, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-west China. SYSU K30002 grew at 28–40 °C (optimum, 37 °C), at pH 5.0–8.0 (optimum, pH 7.0) and in the presence of 0–4 % (w/v) NaCl (optimum in the absence of NaCl). The cell-wall peptidoglycan type was A4 (Lys–Asp). The cell-wall sugars of SYSU K30002 were ribose, galactose and mannose, and MK-7 was the menaquinone. The major fatty acids were iso-C, C 7 alcohol and iso-C. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. The G+C content of the genomic DNA was 36.1 mol%. The average nucleotide identity values between SYSU K30002 and its closest relatives were below the cut-off level (95–96 %) for species delineation. Based on phenotypic, chemotaxonomic and genome comparisons, strain SYSU K30002 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SYSU K30002 (=KCTC 33955=CGMCC 1.13504).

Funding
This study was supported by the:
  • Key-Area Research and Development Program of Guangdong Province (Award 2018B020206001)
    • Principle Award Recipient: Wen-Jun Li
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2020-04-24
2024-03-29
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References

  1. Ahmed I, Yokota A, Yamazoe A, Fujiwara T. Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov. Int J Syst Evol Microbiol 2007; 57:1117–1125 [View Article][PubMed][PubMed]
    [Google Scholar]
  2. 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 [View Article][PubMed][PubMed]
    [Google Scholar]
  3. Duan YQ, He S-T, Li Q-Q, Wang M-F, Wang W-Y et al. Lysinibacillus tabacifolii sp. nov., a novel endophytic bacterium isolated from Nicotiana tabacum leaves. J Microbiol 2013; 51:289–294 [View Article][PubMed][PubMed]
    [Google Scholar]
  4. Kim SJ, Jang YH, Hamada M, Ahn JH, Weon HY et al. Lysinibacillus chungkukjangi sp. nov., isolated from Chungkukjang, Korean fermented soybean food. J Microbiol 2013; 51:400–404 [View Article][PubMed][PubMed]
    [Google Scholar]
  5. Sun J-Q, Xu L, Wu X-L. Lysinibacillus alkalisoli sp. nov., isolated from saline-alkaline soil. Int J Syst Evol Microbiol 2017; 67:67–71 [View Article][PubMed][PubMed]
    [Google Scholar]
  6. Lee CS, Jung Y-T, Park S, Oh T-K, Yoon J-H. Lysinibacillus xylanilyticus sp. nov., a xylan-degrading bacterium isolated from forest humus. Int J Syst Evol Microbiol 2010; 60:281–286 [View Article][PubMed][PubMed]
    [Google Scholar]
  7. Kämpfer P, Martin K, Glaeser SP. Lysinibacillus contaminans sp. nov., isolated from surface water. Int J Syst Evol Microbiol 2013; 63:3148–3153 [View Article][PubMed][PubMed]
    [Google Scholar]
  8. Rao MPN, Dong Z-Y, Zhang H, Niu X-K, Zhang K et al. Bacillus antri sp. nov., isolated from cave soil. Int J Syst Evol Microbiol 2019; 69:2335–2339 [View Article][PubMed][PubMed]
    [Google Scholar]
  9. Dong Z-Y, Narsing Rao MP, Wang H-F, Fang B-Z, Liu Y-H et al. Transcriptomic analysis of two endophytes involved in enhancing salt stress ability of Arabidopsis thaliana . Sci Total Environ 2019; 686:107–117 [View Article][PubMed][PubMed]
    [Google Scholar]
  10. 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][PubMed][PubMed]
    [Google Scholar]
  11. Thompson JD, 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 [View Article][PubMed][PubMed]
    [Google Scholar]
  12. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed][PubMed]
    [Google Scholar]
  13. 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][PubMed]
    [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed][PubMed]
    [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed][PubMed]
    [Google Scholar]
  16. 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][PubMed]
    [Google Scholar]
  17. 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][PubMed][PubMed]
    [Google Scholar]
  18. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article][PubMed][PubMed]
    [Google Scholar]
  19. 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][PubMed]
    [Google Scholar]
  20. 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; 59:2025–2032 [View Article][PubMed][PubMed]
    [Google Scholar]
  21. 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][PubMed]
    [Google Scholar]
  22. 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 [View Article]
    [Google Scholar]
  23. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
    [Google Scholar]
  24. 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 [View Article]
    [Google Scholar]
  25. 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]
  26. Yu J, Guan X, Liu C, Xiang W, Yu Z et al. Lysinibacillus endophyticus sp. nov., an indole-3-acetic acid producing endophytic bacterium isolated from corn root (Zea mays cv. Xinken-5). Antonie van Leeuwenhoek 2016; 109:1337–1344 [View Article][PubMed][PubMed]
    [Google Scholar]
  27. Jung MY, Kim J-S, Paek WK, Styrak I, Park I-S et al. Description of Lysinibacillus sinduriensis sp. nov., and transfer of Bacillus massiliensis and Bacillus odysseyi to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov. with emended description of the genus Lysinibacillus . Int J Syst Evol Microbiol 2012; 62:2347–2355 [View Article][PubMed][PubMed]
    [Google Scholar]
  28. 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][PubMed]
    [Google Scholar]
  29. 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 [View Article][PubMed][PubMed]
    [Google Scholar]
  30. 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 [View Article][PubMed][PubMed]
    [Google Scholar]
  31. 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 [View Article][PubMed][PubMed]
    [Google Scholar]
  32. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [View Article][PubMed][PubMed]
    [Google Scholar]
  33. 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 [View Article][PubMed][PubMed]
    [Google Scholar]
  34. 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][PubMed]
    [Google Scholar]
  35. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R et al. Circos: an information aesthetic for comparative genomics. Genome Res 2009; 19:1639–1645 [View Article][PubMed][PubMed]
    [Google Scholar]
  36. Eren AM, ÖC E, Quince C, Vineis JH, Morrison HG et al. Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ 2015; 8:e1319
    [Google Scholar]
  37. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using diamond. Nat Methods 2015; 12:59–60 [View Article][PubMed][PubMed]
    [Google Scholar]
  38. van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks. Methods Mol Biol 2012; 804:281–295 [View Article][PubMed][PubMed]
    [Google Scholar]
  39. 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 [View Article][PubMed][PubMed]
    [Google Scholar]
  40. 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][PubMed]
    [Google Scholar]
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