1887

Abstract

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacterium, designated CWB-1, was isolated from a haloalkaline lake sediment sample collected from the bottom of Chaiwopu Lake, Urumchi, Xinjiang Province, PR China. Strain CWB-1 grew at 4–40 °C (optimum, 30–35 °C), pH 6.5–9.0 (optimum, pH 6.5–7.0) and with 0.5–5.5 % (w/v) NaCl (optimum, 2.5–3.0 %). Phylogenetic analyses based on the 16S rRNA gene sequence and the whole genome sequence both revealed that strain CWB-1 belonged to the family . The strain had the highest similarity of the 16S rRNA gene sequence to PAMC 27130 (92.8 %). The genome of strain CWB-1 was 3 548 011 bp long with 36.3 % DNA G+C content. The predominant fatty acids (>10 %) in the CWB-1 cells were iso-C, iso-C 3-OH and summed feature 1 (iso-C H/C 3-OH). The major respiratory quinone was menaquinone-6 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. Based on the phylogenetic analyses, as well as the phenotypic characteristics, a novel genus and species of the family , gen. nov., sp. nov., is proposed. The type strain is CWB-1 (=KCTC 72450=CGMCC 1.17149).

Funding
This study was supported by the:
  • Yue-zhong Li , National Key Research and Development Programs of China , (Award 2018YFA0900400 and 2018YFA0901704)
  • Yue-zhong Li , Key Program of Shandong Natural Science Foundation , (Award ZR2016QZ002)
  • Yue-zhong Li , National Outstanding Youth Science Fund Project of National Natural Science Foundation of China , (Award 31670076 and 31471183)
  • Yue-zhong Li , Special investigation on scientific and technological basic resources , (Award 2017FY100302)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004421
2020-09-04
2020-09-18
Loading full text...

Full text loading...

References

  1. Bernardet J-F, 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 [CrossRef][PubMed]
    [Google Scholar]
  2. Bowman JP, Nichols DS. Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia. Int J Syst Evol Microbiol 2005; 55:1471–1486 [CrossRef][PubMed]
    [Google Scholar]
  3. Bernardet JF, Nakagawa Y. An introduction to the family Flavobacteriaceae. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E. (editors) The Prokaryotes: a Handbook on the Biology of Bacteria 7, 3rd ed. New York: Springer.; 2006 pp 455–480
    [Google Scholar]
  4. Bernardet JF. Family I. Flavobacteriaceae Reichenbach 1992. In Krieg NR, Ludwig W, Whitman WB, Hedlund BP, Paster BJ et al. (editors) Bergey’s Manual of Systematic Bacteriology 4, 2nd ed. New York: Springer; 2011 pp 106–111
    [Google Scholar]
  5. Wainright SC. Sediment-to-water fluxes of particulate material and microbes by resuspension and their contribution to the planktonic food web. Mar Ecol Prog Ser 1990; 62:271–281 [CrossRef]
    [Google Scholar]
  6. Feng Zongwei 冯宗炜, Deng LJ et al. Archaea diversity in water of two typical brackish lakes in Xinjiang. Acta Ecologica Sinica 2012; 32:6811–6818 [CrossRef]
    [Google Scholar]
  7. Meng YJ. Protection and restoration of Chaiwopu lake national wetland park in Urumqi, Xinjiang. Wetland science & management 2020; 16:1673–3290
    [Google Scholar]
  8. Wu J, Ma L. Characteristics of the climate and environment in arid regions over the past 150 years recorded by the core sediments of Chaiwopu lake, Xinjiang, China. Quaternary sciences 2010; 30:1001–7410
    [Google Scholar]
  9. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP et al. Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 2001; 51:357–363 [CrossRef][PubMed]
    [Google Scholar]
  10. 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][PubMed]
    [Google Scholar]
  11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  12. 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][PubMed]
    [Google Scholar]
  13. Baek K, Lee YM, Hwang CY, Park H, Jung Y-J et al. Psychroserpens jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment. Int J Syst Evol Microbiol 2015; 65:183–188 [CrossRef][PubMed]
    [Google Scholar]
  14. Bowman JP, McCammon SA, Brown JL, Nichols PD, McMeekin TA. Psychroserpens burtonensis gen. nov., sp. nov., and Gelidibacter algens gen. nov., sp. nov., psychrophilic bacteria isolated from Antarctic lacustrine and sea ice habitats. Int J Syst Bacteriol 1997; 47:670–677 [CrossRef][PubMed]
    [Google Scholar]
  15. Webster JA, Hugh R. Flavobacterium aquatile and Flavobacterium meningosepticum: Glucose Nonfermenters with Similar Flagellar Morphologies. Int J Syst Bacteriol 1979; 29:333–338 [CrossRef]
    [Google Scholar]
  16. Sun Y, Chen B-Y, Du Z-J. Winogradskyella aurantia sp. nov., isolated from a marine solar saltern. Antonie van Leeuwenhoek 2017; 110:1445–1452 [CrossRef][PubMed]
    [Google Scholar]
  17. 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][PubMed]
    [Google Scholar]
  18. Zuo G, Hao B. CVTree3 web server for Whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 2015; 13:321–331 [CrossRef][PubMed]
    [Google Scholar]
  19. Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 2013; 4:4–2304 [CrossRef][PubMed]
    [Google Scholar]
  20. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  21. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [CrossRef][PubMed]
    [Google Scholar]
  22. 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 [CrossRef][PubMed]
    [Google Scholar]
  23. Richter M, Rosselló-Móra R, Michael R, Ramon RM. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  24. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e7312 [CrossRef][PubMed]
    [Google Scholar]
  25. Li Y, Tang B-L, Ren X-B, Dang Y-R, Sun L-L et al. Complete genome sequence of Flavobacterium arcticum SM1502T, exhibiting adaption to the Arctic marine salty environment. Mar Genomics 2019; 47:100670–100705 [CrossRef]
    [Google Scholar]
  26. Kumar M, Grzelakowski M, Zilles J, Clark M, Meier W. Highly permeable polymeric membranes based on the incorporation of the functional water channel protein aquaporin Z. Proc Natl Acad Sci U S A 2007; 104:20719–20724 [CrossRef][PubMed]
    [Google Scholar]
  27. Claus D. A standardized Gram staining procedure. World J Microbiol Biotechnol 1992; 8:451–452 [CrossRef][PubMed]
    [Google Scholar]
  28. Zhang R, Zhang X-Y, Sun X-K, Mu D-S, Du Z-J et al. Flavobacterium cerinum sp. nov., isolated from Arctic tundra soil. Int J Syst Evol Microbiol 2019; 69:3745–3750 [CrossRef][PubMed]
    [Google Scholar]
  29. Yan L, Wang J, Chen Z, Guan Y, Li J. Microbacterium nanhaiense sp. nov., an actinobacterium isolated from sea sediment. Int J Syst Evol Microbiol 2015; 65:3697–3702 [CrossRef][PubMed]
    [Google Scholar]
  30. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria. Proceedings of the Royal Society of Medicine 59 1965 p 468
    [Google Scholar]
  31. Du Z-J, Wang Z-J, Zhao J-X, Chen G-J. Woeseia oceani gen. nov., sp. nov., a chemoheterotrophic member of the order Chromatiales, and proposal of Woeseiaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:107–112 [CrossRef][PubMed]
    [Google Scholar]
  32. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004421
Loading
/content/journal/ijsem/10.1099/ijsem.0.004421
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL
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