1887

Abstract

A novel bacterial strain, designated NS28, was isolated from interfacial sediment sampled at Taihu Lake, PR China. Cells were rod-shaped, Gram-negative, aerobic and non-motile on Reasoner's 2A medium. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NS28 was most closely related to species from the genus , with 98.4 and 96.0 % 16S rRNA gene sequence similarity to its closest phylogenetic neighbours CGMCC 1.12895 and CCTCC AB 2017091, respectively. MK-7 was the only cellular menaquinone. The major fatty acids were summed feature 3 (Cω7 and/or Cω6), iso-C and Cω5. The major polar lipids were phosphatidylethanolamine, one phospholipid, one aminolipid, one lipid and two unidentified lipids. Genomic analysis of strain NS28 indicated that the total genome size was 6 477 094 bp with a G+C content of 44.8 mol%, 5380 protein-coding genes, 79 contigs and an N50 length of 299584 bp. On the basis of the genomic DNA sequence, the average nucleotide identity values were 90.5 and 74.1 % with CGMCC 1.12895 and CCTCC AB 2017091, respectively. Digital DNA-DNA hybridization results of strain NS28 with CGMCC 1.12895 and CCTCC AB 2017091 were 40.9 and 18.6 %, respectively. Based on the phenotypic, chemotaxonomic, phylogenetic and genome sequence data presented here, it is proposed that strain NS28 represents a novel species of the genus for which the name is proposed . The type strain is NS28 (=NBRC 113854=MCCC 1K03764).

Funding
This study was supported by the:
  • Jian-Hang Qu , National Natural Science Foundation of China , (Award 31370147)
  • Jian-Hang Qu , Key Scientific Research Project of Colleges and Universities in Henan Province , (Award 20A180009)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003876
2019-11-21
2021-01-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/2/1064.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003876&mimeType=html&fmt=ahah

References

  1. Chelius MK, Triplett EW. Dyadobacter fermentans gen. nov., sp. nov., a novel gram-negative bacterium isolated from surface-sterilized Zea mays stems. Int J Syst Evol Microbiol 2000; 50 Pt 2:751–758 [CrossRef]
    [Google Scholar]
  2. Reddy GS, Garcia-Pichel F. Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000. Int J Syst Evol Microbiol 2005; 55:1295–1299 [CrossRef]
    [Google Scholar]
  3. Chaturvedi P, Reddy GS, Shivaji S. Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India. Int J Syst Evol Microbiol 2005; 55:2113–2117 [CrossRef]
    [Google Scholar]
  4. Liu QM, Im WT, Lee M, Yang DC, Lee ST. Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2006; 56:1939–1944 [CrossRef]
    [Google Scholar]
  5. Baik KS, Kim MS, Kim EM, Kim HR, Seong CN. Dyadobacter koreensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2007; 57:1227–1231 [CrossRef]
    [Google Scholar]
  6. Dong Z, Guo X, Zhang X, Qiu F, Sun L et al. Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China. Int J Syst Evol Microbiol 2007; 57:862–865 [CrossRef]
    [Google Scholar]
  7. Tang Y, Dai J, Zhang L, Mo Z, Wang Y et al. Dyadobacter alkalitolerans sp. nov., isolated from desert sand. Int J Syst Evol Microbiol 2009; 59:60–64 [CrossRef]
    [Google Scholar]
  8. Zhang DC, Liu HC, Xin YH, Zhou YG, Schinner F et al. Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2010; 60:1640–1643 [CrossRef]
    [Google Scholar]
  9. Lee M, Woo SG, Park J, Yoo SA. Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil. Int J Syst Evol Microbiol 2010; 60:2577–2582 [CrossRef]
    [Google Scholar]
  10. Chen L, Jiang F, Xiao M, Dai J, Kan W et al. Dyadobacter arcticus sp. nov., isolated from Arctic soil. Int J Syst Evol Microbiol 2013; 63:1616–1620 [CrossRef]
    [Google Scholar]
  11. Chun J, Kang JY, Joung Y, Kim H, Joh K et al. Dyadobacter jejuensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:1788–1792 [CrossRef]
    [Google Scholar]
  12. Shen L, Liu Y, Yao T, Wang N, Xu B et al. Dyadobacter tibetensis sp. nov., isolated from glacial ice core. Int J Syst Evol Microbiol 2013; 63:3636–3639 [CrossRef]
    [Google Scholar]
  13. Wang L, Chen L, Ling Q, Li C-chen, Tao Y et al. Dyadobacter jiangsuensis sp. nov., a methyl red degrading bacterium isolated from a dye-manufacturing factory. Int J Syst Evol Microbiol 2015; 65:1138–1143 [CrossRef]
    [Google Scholar]
  14. Tian M, Zhang RG, Han L, Zhao XM, Lv J. Dyadobacter sediminis sp. nov., isolated from a subterranean sediment sample. Int J Syst Evol Microbiol 2015; 65:827–832 [CrossRef]
    [Google Scholar]
  15. Gao JL, Sun P, Wang XM, Qiu TL, Lv FY et al. Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:4022–4026 [CrossRef]
    [Google Scholar]
  16. Song Z, Song Y, Yu Y, Choi L, Wang G et al. Dyadobacter luticola sp. nov., isolated from a sewage sediment sample. Int J Syst Evol Microbiol 2019; 69:465–469 [CrossRef]
    [Google Scholar]
  17. Dahal RH, Kim J. Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil. Arch Microbiol 2018; 200:1067–1074 [CrossRef]
    [Google Scholar]
  18. Qu JH, Zhang LJ, Fu YH, Li XD, Li HF et al. A novel genus of the class Actinobacteria, Longivirga aurantiaca gen. nov., sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2018; 68:942–946 [CrossRef]
    [Google Scholar]
  19. Birnboim HC, Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 1979; 7:1513–1523 [CrossRef]
    [Google Scholar]
  20. Moreno C, Romero J, Espejo RT. Polymorphism in repeated 16S rRNA genes is a common property of type strains and environmental isolates of the genus Vibrio. Microbiology 2002; 148:1233–1239 [CrossRef]
    [Google Scholar]
  21. Yoon SH, 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]
  22. McGinnis S, Madden TL. Blast: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004; 32:W20–W25 [CrossRef]
    [Google Scholar]
  23. 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]
  24. 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]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef]
    [Google Scholar]
  26. Buck JD, Nonstaining BJD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993
    [Google Scholar]
  27. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  28. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
    [Google Scholar]
  29. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  30. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Tech Bull Regist Med Technol 1966; 45:493–496 [CrossRef]
    [Google Scholar]
  31. Boontosaeng T, Nimrat S, Vuthiphandchai V. Pigments production of bacteria isolated from dried seafood and capability to inhibit microbial pathogens. IOSR J Environ Sci Toxicol Food Technol 2016; 10:30–34
    [Google Scholar]
  32. Komagata K, Suzuki K. 4 lipid and cell-wall analysis in bacterial Systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  33. Pospiech A, Neumann B. A versatile quick-prep of genomic DNA from gram-positive bacteria. Trends Genet 1995; 11:217–218 [CrossRef]
    [Google Scholar]
  34. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014; 30:2114–2120 [CrossRef]
    [Google Scholar]
  35. 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]
  36. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. Ncbi prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [CrossRef]
    [Google Scholar]
  37. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. Refseq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [CrossRef]
    [Google Scholar]
  38. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [CrossRef]
    [Google Scholar]
  39. 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 [CrossRef]
    [Google Scholar]
  40. 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]
    [Google Scholar]
  41. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003876
Loading
/content/journal/ijsem/10.1099/ijsem.0.003876
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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