1887

Abstract

A Gram-negative, aerobic bacterium, designated as SH-1, was isolated from the gut content of a whiteleg shrimp, collected in a shrimp farm in South Korea. The bacterial cells were ovoid rod-shaped, non-motile, oxidase-positive and catalase-negative. Growth was observed at 20–35 °C (optimum, 30 °C), pH 5.0–9.5 (pH 8.5) and in the presence of 0–6 % (w/v) NaCl (2–3 %). The major polar lipids were phosphatidylglycerol, phosphatidylinositolmannoside, unidentified aminolipid and two unidentified lipids. The G+C content was 66.1 mol% and the predominant respiratory quinone was Q-10. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SH-1 was placed in a distinct clade with PX7 (96.97 % sequence similarity), DSM 21219 (96.03 %) and BH-SD19 (95.02 %) in the family and distantly related with them to be a new genus. The digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) values calculated from whole-genome-sequence comparison between the SH-1 and the close species were in the ranges of 19.0–19.8, 73.8–74.9 and 64.1–65.9 %, respectively. Based on the polyphasic analysis presented in this study, we suggest that strain SH-1 represents a novel genus and species in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is SH-1 (=KCTC 62276=MCCC 1K04072).

Funding
This study was supported by the:
  • Kyoung-Ho Kim , Ministry of Education , (Award 2016R1D1A3B04935909)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004269
2020-06-15
2020-09-28
Loading full text...

Full text loading...

References

  1. Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I et al. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. Isme J 2017; 11:1483–1499 [CrossRef][PubMed]
    [Google Scholar]
  2. Kim KK, Lee J-S, Lee KC, Oh H-M, Kim S-G. Pontibaca methylaminivorans gen. nov., sp. nov., a member of the family Rhodobacteraceae . Int J Syst Evol Microbiol 2010; 60:2170–2175 [CrossRef][PubMed]
    [Google Scholar]
  3. Elifantz H, Horn G, Ayon M, Cohen Y, Minz D. Rhodobacteraceae are the key members of the microbial community of the initial biofilm formed in Eastern Mediterranean coastal seawater. FEMS Microbiol Ecol 2013; 85:348–357 [CrossRef][PubMed]
    [Google Scholar]
  4. Liu J, Wang K, Wang Y, Chen W, Jin Z et al. Strain-specific changes in the gut microbiota profiles of the white shrimp Litopenaeus vannamei in response to cold stress. Aquaculture 2019; 503:357–366 [CrossRef]
    [Google Scholar]
  5. Kim Y-S, Kim K-H. The complete genome sequence of Rhodobacteraceae bacterium strain SH-1 isolated from a gut content of whiteleg shrimp Litopenaeus vannamei . Korean J Microbiol 2019; 55:
    [Google Scholar]
  6. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [CrossRef][PubMed]
    [Google Scholar]
  7. 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][PubMed]
    [Google Scholar]
  8. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [CrossRef][PubMed]
    [Google Scholar]
  9. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic acids symposium series London: Information Retrieval Ltd; 1999 pp c1979–c2000
    [Google Scholar]
  10. 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]
  11. 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]
  12. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  13. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  14. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes:. PeerJ Preprints 20162167–9843
    [Google Scholar]
  15. 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][PubMed]
    [Google Scholar]
  16. 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]
  17. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [CrossRef][PubMed]
    [Google Scholar]
  18. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [CrossRef][PubMed]
    [Google Scholar]
  19. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393–2411 [CrossRef][PubMed]
    [Google Scholar]
  20. 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]
  21. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI inc;
    [Google Scholar]
  22. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [CrossRef]
    [Google Scholar]
  23. Komagata K, Suzuki K-I. Lipid and Cell-Wall Analysis in Bacterial Systematics Methods in microbiology: Elsevier; 1988 pp 161–207
    [Google Scholar]
  24. Reddy C, Beveridge TJ, Breznak JA, Marzluf G. Methods for General and Molecular Microbiology American Society for Microbiology Press; 2007 pp 364–365
    [Google Scholar]
  25. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC. The family Rhodobacteraceae. The Prokaryotes: Alphaproteobacteria and Betaproteobacteria; 2014439–512
  26. Wang NN, Sang J, Wang XQ, YX L, ZJ D et al. Primorskyibacter marinus sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2018; 68:3169–3174
    [Google Scholar]
  27. Ji X, Zhang C, Zhang X, Xu Z, Ding Y et al. Pelagivirga sediminicola gen. nov., sp. nov. isolated from the Bohai Sea. Int J Syst Evol Microbiol 2018; 68:3494–3499 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004269
Loading
/content/journal/ijsem/10.1099/ijsem.0.004269
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