1887

Abstract

A novel Gram-negative, aerobic, non-motile, rod-shaped, bacterial strain (CAU 1598) was isolated from marine sand. Strain CAU 1598 grew well at 30 °C, pH 6.5–7.0 and with 3 % NaCl (w/v). Phylogeny results based on 16S rRNA gene sequencing indicated that the identified strain had the highest similarity (94.3%) to , indicating that strain CAU 1598 belongs to the family . Further, the fatty acid profile of the strain was primarily composed of C iso-C, iso-C, summed feature 3 (consisting of C 7/iso-C 2-OH) and summed feature 9 (consisting of iso-C 9 and/or C 10-methyl), with ubiquinone-8 as the major isoprenoid quinone. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, an unidentified aminolipid and an unidentified lipid. The G+C content of the bacterial genome was 62.6 mol% and its 5.4 Mb length encompassed 144 contigs and 4236 protein-coding genes. These phenotypic, chemotaxonomic and phylogenetic data indicate that CAU 1598 belongs to a new genus and species, for which the name gen. nov., sp. nov. is proposed. The type strain is CAU 1598 (=KCTC 82406=MCCC 1K05673).

Funding
This study was supported by the:
  • Chung-Ang University (Award 2021)
    • Principle Award Recipient: WonyongKim
  • Ministry of Environment of the Republic of Korea (Award NIBR201902203)
    • Principle Award Recipient: WonyongKim
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/content/journal/ijsem/10.1099/ijsem.0.005159
2021-12-15
2024-04-20
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References

  1. Saddler GS, Bradbury JF. Family I. Xanthomonadaceae fam. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. eds Bergey’s Manual of Systematic Bacteriology, 2nd. edn vol. 2 New York: Springer; 2005 p 63
    [Google Scholar]
  2. Wei Z, Wu T, Huang Y, Zhu G, Zhang Y et al. Pseudolysobacter antarcticus gen. nov., sp. nov., isolated from soil in Fildes Peninsula, Antarctica. Int J Syst Evol Microbiol 2020; 70:1861–1867 [View Article] [PubMed]
    [Google Scholar]
  3. Weon H-Y, Yoo S-H, Kim Y-J, Lee C-M, Kim B-Y et al. Rudaea cellulosilytica gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:2308–2312 [View Article] [PubMed]
    [Google Scholar]
  4. Busse HJ, Kämpfer P, Moore ERB, Nuutinen J, Tsitko IV et al. Thermomonas haemolytica gen. nov., sp. nov., a gamma-proteobacterium from kaolin slurry. Int J Syst Evol Microbiol 2002; 52:473–483 [View Article] [PubMed]
    [Google Scholar]
  5. Lane DJ. 16S/23S RNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics 1991 pp 115–175
    [Google Scholar]
  6. Nam SW, Kim W, Chun J. Tsukamurella pseudospumae sp. nov., a novel actinomycete isolated from activated sludge foam. Int J Syst Evol Microbiol 2004; 54:1209–1212 [View Article] [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 [View Article]
    [Google Scholar]
  8. 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 [View Article]
    [Google Scholar]
  9. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  10. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  12. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  13. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian protein metabolism 1969; 3:21–132
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  15. 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 [View Article] [PubMed]
    [Google Scholar]
  16. 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 [View Article] [PubMed]
    [Google Scholar]
  17. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC genomics 2008; 9:1–15 [View Article]
    [Google Scholar]
  18. 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 [View Article] [PubMed]
    [Google Scholar]
  19. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  20. 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 [View Article] [PubMed]
    [Google Scholar]
  21. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  22. 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 [View Article] [PubMed]
    [Google Scholar]
  23. 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 [View Article] [PubMed]
    [Google Scholar]
  24. Kim D, Park S, Chun J. Introducing EzAAI: A pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
    [Google Scholar]
  25. Rosselló-Móra R, Trujillo ME, Sutcliffe IC. Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria. Syst Appl Microbiol 2017; 40:121–122 [View Article]
    [Google Scholar]
  26. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
    [Google Scholar]
  27. Abdalla AK, Ayyash MM, Olaimat AN, Osaili TM, Al-Nabulsi AA et al. Exopolysaccharides as antimicrobial agents: mechanism and spectrum of activity. Front Microbiol 2021; 12:664395. [View Article] [PubMed]
    [Google Scholar]
  28. Grammbitter GL, Shi YM, Shi YN, Vemulapalli SP, Richter C et al. The chemical structure of widespread microbial aryl polyene lipids [preprint]. bioRxiv 20202020.12.19.423268. 10.1101/2020.12.19.423268
    [Google Scholar]
  29. 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 [View Article] [PubMed]
    [Google Scholar]
  30. Li M, Kong D, Wang Y, Ma Q, Han X et al. Photobacterium salinisoli sp. nov., isolated from a sulfonylurea herbicide-degrading consortium enriched with saline soil. Int J Syst Evol Microbiol 2019; 69:3910–3916 [View Article] [PubMed]
    [Google Scholar]
  31. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RG, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC, USA: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  32. Lanyi B. 1 Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1988; 19:1–67
    [Google Scholar]
  33. 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 [View Article]
    [Google Scholar]
  34. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M. eds Chemical Methods in Prokaryotic Systematics New York, USA: Chichester, John Wiley and Sons; 1994 pp 121–161
    [Google Scholar]
  35. Kim J-H, Ward AC, Kim W. Kangiella chungangensis sp. nov. isolated from a marine sand. Antonie van Leeuwenhoek 2015; 107:1291–1298 [View Article]
    [Google Scholar]
  36. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acids Methyl Esters (GC-FAME). Technical Note 101 Newark, D.E, USA: Microbial ID Inc; 2006
    [Google Scholar]
  37. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. Journal of Liquid Chromatography 2006; 5:2359–2367 [View Article]
    [Google Scholar]
  38. Thierry S, Macarie H, Iizuka T, Geißdörfer W, Assih EA et al. Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species. Int J Syst Evol Microbiol 2004; 54:2245–2255 [View Article] [PubMed]
    [Google Scholar]
  39. Kwon S-W, Kim B-Y, Weon H-Y, Baek Y-K, Go S-J. Arenimonas donghaensis gen. nov., sp. nov., isolated from seashore sand. Int J Syst Evol Microbiol 2007; 57:954–958 [View Article] [PubMed]
    [Google Scholar]
  40. Christensen P, Cook FD. Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 1978; 28:367–393 [View Article]
    [Google Scholar]
  41. Xiong L, An L, Zong Y, Wang M, Wang G et al. Luteimonas gilva sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2020; 70:3462–3467 [View Article] [PubMed]
    [Google Scholar]
  42. Lee J-K, Oh J-S, Cho W-D, Roh D-H. Pseudoxanthomonas putridarboris sp. nov. isolated from rotten tree. Int J Syst Evol Microbiol 2017; 67:1807–1812 [View Article] [PubMed]
    [Google Scholar]
  43. Busse HJ, Kämpfer P, Moore ERB, Nuutinen J, Tsitko IV et al. Thermomonas haemolytica gen. nov., sp. nov., a gamma-proteobacterium from kaolin slurry. Int J Syst Evol Microbiol 2002; 52:473–483 [View Article] [PubMed]
    [Google Scholar]
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