1887

Abstract

A Gram-stain-negative, aerobic, rod-shaped, carotenoid-pigmented, motile-by-gliding bacterium, which was designated as SSH13, was isolated from a surface seawater sample collected from Sehwa Beach in the Republic of Korea. Strain SSH13 was oxidase-negative, catalase-positive and grew at 2–37 °C (optimum, 30 °C), in the presence of 0.5–6% NaCl and within a pH range of pH 6–10 (optimum, pH 8). The novel isolate required NaCl for growth and grew optimally with approximately 2 % NaCl. Chemotaxonomic and morphological characteristics were consistent with members of the genus . Furthermore, phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain SSH13 was most closely related to the type strains of the genus . Strain SSH13 had highest 16S rRNA gene sequence similarities to DSM 23188 (95.3 %) and KCTC 12774 (95.0 %). The major fatty acids of SSH13 were summed feature 3 (C 7 and/or C 6) and iso-C. Strain SSH13 contained phosphatidylethanolamine as a major polar lipid. Menaquinone-7 was the predominant respiratory quinone. The average nucleotide identity values between strain SSH13 and T-3 and SST-19 were 72.9 and 72.6 %, respectively. The DNA G+C content of the genomic DNA was 52.8 mol%. The present study aimed to determine the multiple-antibiotic resistance ofthe novel bacterium. Based on phylogenetic and phenotypic analyses, strain SSH13 is considered to represent a novel species of the genus , for which the name sp. nov. (type strain SSH13=KACC 21167=NBRC 113866) is proposed.

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2020-10-15
2020-12-01
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References

  1. Sly LI, Taghavi M, Fegan M, Baumann P, Baumann L. Phylogenetic heterogeneity within the genus Herpetosiphon: transfer of the marine species Herpetosiphon cohaerens, Herpetosiphon nigricans and Herpetosiphon persicus to the genus Lewinella gen. nov. in the Flexibacter-Bacteroides-Cytophaga phylum. Int J Syst Bacteriol 1998; 48:731–737 [CrossRef][PubMed]
    [Google Scholar]
  2. Khan ST, Fukunaga Y, Nakagawa Y, Harayama S. Emended descriptions of the genus Lewinella and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica, and description of Lewinella lutea sp. nov. and Lewinella marina sp. nov. Int J Syst Evol Microbiol 2007; 57:2946–2951 [CrossRef][PubMed]
    [Google Scholar]
  3. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:1095–1098 [CrossRef][PubMed]
    [Google Scholar]
  4. 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]
  5. Lee SD. Lewinella agarilytica sp. nov., a novel marine bacterium of the phylum Bacteroidetes, isolated from beach sediment. Int J Syst Evol Microbiol 2007; 57:2814–2818 [CrossRef][PubMed]
    [Google Scholar]
  6. Kang H, Kim H, Joung Y, Joh K. Lewinella maritima sp. nov., and Lewinella lacunae sp. nov., novel bacteria from marine environments. Int J Syst Evol Microbiol 2017; 67:3603–3609 [CrossRef][PubMed]
    [Google Scholar]
  7. Jung Y-T, Lee J-S, Yoon J-H. Lewinella aquimaris sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:3989–3994 [CrossRef][PubMed]
    [Google Scholar]
  8. Sung H-R, Lee J-M, Kim M, Shin K-S. Lewinella xylanilytica sp. nov., a member of the family Saprospiraceae isolated from coastal seawater. Int J Syst Evol Microbiol 2015; 65:3433–3438 [CrossRef][PubMed]
    [Google Scholar]
  9. Park S, Won SM, Yoon J-H. Lewinella litorea sp. nov., isolated from marine sand. Int J Syst Evol Microbiol 2020; 70:246–250 [CrossRef][PubMed]
    [Google Scholar]
  10. Oh H-M, Lee K, Cho J-C. Lewinella antarctica sp. nov., a marine bacterium isolated from Antarctic seawater. Int J Syst Evol Microbiol 2009; 59:65–68 [CrossRef][PubMed]
    [Google Scholar]
  11. Fraser PD, Bramley PM. The biosynthesis and nutritional uses of carotenoids. Prog Lipid Res 2004; 43:228–265 [CrossRef][PubMed]
    [Google Scholar]
  12. Kim I, Kim J, Chhetri G, Seo T. Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil. J Microbiol 2019; 57:1079–1085 [CrossRef][PubMed]
    [Google Scholar]
  13. Kim J, Chhetri G, Kim I, Kim H, Kim MK et al. Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. J Microbiol 2019; 57:959–966 [CrossRef][PubMed]
    [Google Scholar]
  14. Yoon SH, Ha SM, 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]
  15. 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]
  16. 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]
  17. 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 [CrossRef][PubMed]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  22. 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]
  23. 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]
  24. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [CrossRef][PubMed]
    [Google Scholar]
  25. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [CrossRef]
    [Google Scholar]
  26. Yoon SH, Ha SM, 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]
  27. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [CrossRef][PubMed]
    [Google Scholar]
  28. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [CrossRef][PubMed]
    [Google Scholar]
  29. 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]
  30. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [CrossRef][PubMed]
    [Google Scholar]
  31. Smibert RM, Krieg NR. Phenotypic Characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: ASM Press; 1994 pp 607–654
    [Google Scholar]
  32. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. 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
    [Google Scholar]
  33. Chhetri G, Kim J, Kim H, Kim I, Seo T. Pontibacter oryzae sp. nov., a carotenoid-producing species isolated from a rice paddy field. Antonie van Leeuwenhoek 2019; 112:1705–1713 [CrossRef][PubMed]
    [Google Scholar]
  34. Joss A, Keller E, Alder AC, Göbel A, McArdell CS et al. Removal of pharmaceuticals and fragrances in biological wastewater treatment. Water Res 2005; 39:3139–3152 [CrossRef][PubMed]
    [Google Scholar]
  35. Fisher JF, Meroueh SO, Mobashery S. Bacterial resistance to beta-lactam antibiotics: compelling opportunism, compelling opportunity. Chem Rev 2005; 105:395–424 [CrossRef][PubMed]
    [Google Scholar]
  36. Komagata K, Suzuki KI. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  37. 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 [CrossRef]
    [Google Scholar]
  38. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [CrossRef]
    [Google Scholar]
  39. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [CrossRef][PubMed]
    [Google Scholar]
  40. Lee D, Jang JH, Cha S, Seo T. Telluribacter humicola gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea. Antonie van Leeuwenhoek 2016; 109:1525–1533 [CrossRef][PubMed]
    [Google Scholar]
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