1887

Abstract

A Gram-stain-negative bacterial strain, designated JW-3, was isolated from a soil sample collected from farmland in Yantai, Shandong Province, PR China. Cells of strain JW-3 are motile rods and strictly aerobic, showing catalase- and oxidase-positive reactions. Strain JW-3 could grow at 16–37 °C (optimum, 30 °C), at pH 6.0–9.0 (pH 7.0) and in the presence of 0–1 % (w/v) NaCl (0.5 %, in Luria–Bertani broth). The major fatty acids were summed feature 3 (C 7 and/or C 6; 35.5 %), iso-C (16.7 %) and C (10.8 %). The major respiratory quinone was ubiquinone-8 (Q8). The polar lipids of strain JW-3 consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified phospholipids, two unidentified lipids, two unidentified glycolipids and a partial unidentified aminophospholipid. Strain JW-3 was most closely related to KA5-B with 97.67 % 16S rRNA gene sequence similarity. Results of phylogenetic analyses, based on 16S rRNA gene sequencing, showed that strain JW-3 forms a distinct phylogenic lineage within the genus of the family . The DNA G+C content of strain JW-3 was 62.57 mol%, based on its draft genome sequence. Average nucleotide identity values and digital DNA–DNA hybridization values for draft genomes, between strain JW-3 and strain KA5-B, were 84.54 and 30.80 %, respectively. Based on its phenotypic, chemotaxonomic and molecular features, and DNA–DNA hybridization results, strain JW-3 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is JW-3 (=CCTCC AB 2018184=KCTC 62820).

Keyword(s): new taxa , Steroidobacter and taxonomy
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2019-11-01
2022-01-18
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References

  1. Fahrbach M, Kuever J, Remesch M, Huber BE, Kämpfer P et al. Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium. Int J Syst Evol Microbiol 2008; 58:2215–2223 [View Article][PubMed]
    [Google Scholar]
  2. Sakai M, Hosoda A, Ogura K, Ikenaga M. The growth of Steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to Rhizobiales. Microbes Environ 2014; 29:89–95 [View Article][PubMed]
    [Google Scholar]
  3. Yang H, Wang X, Zheng J, Wang G, Hong Q et al. Biodegradation of acetamiprid by Pigmentiphaga sp. D-2 and the degradation pathway. Int Biodeterior Biodegradation 2013; 85:95–102 [View Article]
    [Google Scholar]
  4. Liu XM, Chen K, Meng C, Zhang L, Zhu JC et al. Pseudoxanthobacter liyangensis sp. nov., isolated from dichlorodiphenyltrichloroethane-contaminated soil. Int J Syst Evol Microbiol 2014; 64:3390–3394 [View Article][PubMed]
    [Google Scholar]
  5. du H, Jiao N, Hu Y, Zeng Y. Diversity and distribution of pigmented heterotrophic bacteria in marine environments. FEMS Microbiol Ecol 2006; 57:92–105 [View Article][PubMed]
    [Google Scholar]
  6. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  7. 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]
    [Google Scholar]
  8. 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]
  9. 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]
  10. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  11. Nogi Y, Yoshizumi M, Hamana K, Miyazaki M, Horikoshi K. Povalibacter uvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes. Int J Syst Evol Microbiol 2014; 64:2712–2717 [View Article][PubMed]
    [Google Scholar]
  12. Dellaporta SL, Wood J, Hicks JB. A plant DNA minipreparation: Version II. Plant Mol Biol Report 1983; 1:19–21 [View Article]
    [Google Scholar]
  13. 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]
  14. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
    [Google Scholar]
  15. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  16. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015; 43:6761–6771 [View Article][PubMed]
    [Google Scholar]
  17. Stackebrandt E, Goebel BM. Taxonomic Note: A place for dna-dna reassociation and 16s rrna sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  18. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
    [Google Scholar]
  19. Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP et al. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 2000; 38:3623–3630[PubMed]
    [Google Scholar]
  20. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993[PubMed]
    [Google Scholar]
  21. Zhang YQ, Yu LY, Wang D, Liu HY, Sun CH et al. Roseomonas vinacea sp. nov., a Gram-negative coccobacillus isolated from a soil sample. Int J Syst Evol Microbiol 2008; 58:2070–2074 [View Article][PubMed]
    [Google Scholar]
  22. Deng SK, Ye XM, Chu CW, Jiang J, He J et al. Chryseomicrobium aureum sp. nov., a bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2014; 64:2682–2687 [View Article][PubMed]
    [Google Scholar]
  23. Ye XM, Chu CW, Shi C, Zhu JC, He Q et al. Lysobacter caeni sp. nov., isolated from the sludge of a pesticide manufacturing factory. Int J Syst Evol Microbiol 2015; 65:845–850 [View Article][PubMed]
    [Google Scholar]
  24. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  25. Tindall BJ. A comparative study of the lipid composition of halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  26. Collins MD. Isoprenoid quinone analysis in bacterial classification and identification. Chemical Methods in Bacterial Systematics 1985
    [Google Scholar]
  27. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of bradyrhizobium japonicum . Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  28. Chun J, Lee JH, Jung Y, Kim M, Kim S et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [View Article][PubMed]
    [Google Scholar]
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