1887

Abstract

Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated SSM26 and SSM44, were isolated from a sea surface microlayer sample from the Ross Sea, Antarctica. Analysis of the 16S rRNA gene sequences of strains SSM26 and SSM44 revealed a clear affiliation with the genus . Based on the results of phylogenetic analysis, strains SSM26 and SSM44 showed the closest phylogenetic relationship with the species KCTC 22137 with the 16S rRNA gene sequence similarity level of 98.5 %. Strains SSM26 and SSM44 grew optimally at 30 °C, pH 7.0–7.5 and 0.5–10.0 % NaCl (w/v). The major cellular fatty acids were C ω7 (31.3–34.9 %), C(15.5–20.2 %), summed feature 3 (C ω7c/C ω6; 19.5–25.4 %) and C(6.0–9.3 %). The genomic DNA G+C content of each strain was 56.2 mol%. Genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strains SSM26 and SSM44 constituted a single species that was clearly distinguishable from its phylogenetically close relatives. The combined phenotypic, chemotaxonomic, genomic and phylogenetic data also showed that strains SSM26 and SSM44 could be distinguished from validly published members of the genus . Thus, these strains should be classified as representing a novel species in the genus , for which the name sp. nov. is proposed with the type strain SSM26 (=KCCM 43193=JCM 31284=PAMC 28426) and a sister strain SSM44 (=KCCM 43194=JCM 31285=PAMC 28427).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004240
2020-06-08
2020-12-01
Loading full text...

Full text loading...

References

  1. Migula W. Über ein neues system Der Bakterien. Arb Bakteriol Inst Karlsruhe 1894; 1:235–238
    [Google Scholar]
  2. Palleroni NJ. Genus Pseudomonas Migula 1894, 237AL (Nom. Cons., Opin. 5 of the Jud. Comm. 1952, 121). In Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons; 2015.
    [Google Scholar]
  3. 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 [CrossRef][PubMed]
    [Google Scholar]
  4. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H. Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 2000; 50 Pt 4:1563–1589 [CrossRef][PubMed]
    [Google Scholar]
  5. Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010; 12:1513–1530 [CrossRef][PubMed]
    [Google Scholar]
  6. Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E. Phylogenomics and systematics in Pseudomonas . Front Microbiol 2015; 6:214 [CrossRef][PubMed]
    [Google Scholar]
  7. Harvey GW. Microlayer collection from the sea surface: a new method and initial results. Limnol Oceanogr 1966; 11:608–613 [CrossRef]
    [Google Scholar]
  8. Englen MD, Kelley LC. A rapid DNA isolation procedure for the identification of Campylobacter jejuni by the polymerase chain reaction. Lett Appl Microbiol 2000; 31:421–426 [CrossRef][PubMed]
    [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–175
    [Google Scholar]
  10. Anzai Y, Kudo Y, Oyaizu H. The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 1997; 47:249–251 [CrossRef][PubMed]
    [Google Scholar]
  11. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [CrossRef][PubMed]
    [Google Scholar]
  12. Kim O-S, Cho Y-J, Lee K, Yoon S-H, 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 [CrossRef][PubMed]
    [Google Scholar]
  13. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014; 42:D633–D642 [CrossRef][PubMed]
    [Google Scholar]
  14. 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]
  15. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
    [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  17. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  19. Kim K-H, Roh SW, Chang H-W, Nam Y-D, Yoon J-H et al. Pseudomonas sabulinigri sp. nov., isolated from black beach sand. Int J Syst Evol Microbiol 2009; 59:38–41 [CrossRef][PubMed]
    [Google Scholar]
  20. 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]
  21. Suzuki M, Nakagawa Y, Harayama S, Yamamoto S. Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. Int J Syst Evol Microbiol 2001; 51:1639–1652 [CrossRef][PubMed]
    [Google Scholar]
  22. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 6th ed. Menlo Park, CA: Benjamin/Cummings;; 2002
    [Google Scholar]
  23. Høvik Hansen G, Sørheim R. Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 1991; 13:231–241 [CrossRef]
    [Google Scholar]
  24. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [CrossRef][PubMed]
    [Google Scholar]
  25. Hwang CY, Kim MH, Bae GD, Zhang GI, Kim YH et al. Muricauda olearia sp. nov., isolated from crude-oil-contaminated seawater, and emended description of the genus Muricauda . Int J Syst Evol Microbiol 2009; 59:1856–1861 [CrossRef][PubMed]
    [Google Scholar]
  26. Hwang CY, Lee I, Hwang YJ, Yoon SJ, Lee WS et al. Pseudoalteromonas neustonica sp. nov., isolated from the sea surface microlayer of the Ross Sea (Antarctica), and emended description of the genus Pseudoalteromonas . Int J Syst Evol Microbiol 2016; 66:3377–3382 [CrossRef][PubMed]
    [Google Scholar]
  27. 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 [CrossRef][PubMed]
    [Google Scholar]
  28. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [CrossRef][PubMed]
    [Google Scholar]
  29. 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]
  30. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [CrossRef][PubMed]
    [Google Scholar]
  31. 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 [CrossRef][PubMed]
    [Google Scholar]
  32. 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]
  33. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2020; 36:1925–1927
    [Google Scholar]
  34. 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][PubMed]
    [Google Scholar]
  35. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131..
  36. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001; 25:39–67 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004240
Loading
/content/journal/ijsem/10.1099/ijsem.0.004240
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