1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 8

sp. nov., isolated from surface water of the Yellow Sea, and proposal of the genus as a member of the family No Access

Abstract

A Gram-stain-negative, non-motile and aerobic bacterium, designated HHU G3-2, was isolated from surface water of the Yellow Sea, PR China. Strain HHU G3-2 was positive for oxidase activity and negative for catalase. Optimal growth occurred at 28 °C (range, 20–37 °C), pH 7.0 (range, pH 6.0–9.0) and in the presence of 2–5 % (w/v) NaCl (range, 1–7%). Phylogenetic analysis based on 16S rRNA gene sequences and 120 ubiquitous single-copy protein-coding genes indicated that strain HHU G3-2 formed a distinct phylogenetic lineage with JCM 30134, sharing a 16S rRNA gene sequence similarity of 98.05%. Average nucleotide identity and digital DNA–DNA hybridization values between strain HHU G3-2 and JCM 30134 were 75.74 and 17.80%, respectively, which were below the threshold values of 95–96 and 70 %, respectively. The DNA G+C content of the genomic DNA was 51.17 mol%. The major fatty acids (>10 %) were C 8 (19.8 %), summed feature 3 (C 7/C 6; 15.9 %), summed feature 8 (C 7/C 6; 13.8 %) and C (10.3 %). The predominant isoprenoid quinone was ubiquinone-8. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the polyphasic taxonomic data, strain HHU G3-2 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is HHU G3-2 (=MCCC 1K04224=JCM 34652=GDMCC 1.2418=CGMCC 1.17397). In addition, we proposed the genus as a member of the family .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , Aestuariicella albida sp. nov. , bac120 and phylogenetic analysis
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005493
2022-08-18
2024-12-07
Loading full text...

Full text loading...

References

  1. Spring S, Scheuner C, Goker M, Klenk HP. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 2015; 6:281 [View Article]
     [Google Scholar]
  2. Liao H, Lin X, Li Y, Qu M, Tian Y. Reclassification of the taxonomic framework of orders Cellvibrionales, Oceanospirillales, Pseudomonadales, and Alteromonadales in class Gammaproteobacteria through phylogenomic tree analysis. mSystems 2020; 5:e00543-20 [View Article]
     [Google Scholar]
  3. Parte AC. LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article]
     [Google Scholar]
  4. Lo N, Kim KH, Baek K, Jia B, Jeon CO. Aestuariicella hydrocarbonica gen. nov., sp nov., an aliphatic hydrocarbon-degrading bacterium isolated from a sea tidal flat. Int J Syst Evol Microbiol 2015; 65:1935–1940 [View Article]
     [Google Scholar]
  5. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article]
     [Google Scholar]
  6. 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] [PubMed]
     [Google Scholar]
  7. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  8. 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]
  9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  10. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  11. 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 [View Article] [PubMed]
     [Google Scholar]
  12. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  13. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 2013; 20:714–737 [View Article] [PubMed]
     [Google Scholar]
  14. Okonechnikov K, Golosova O, Fursov M, Team U. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012; 28:1166–1167 [View Article] [PubMed]
     [Google Scholar]
  15. 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 [View Article] [PubMed]
     [Google Scholar]
  16. 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 [View Article] [PubMed]
     [Google Scholar]
  17. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  18. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  19. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
     [Google Scholar]
  20. Parks DH, Rinke C, Chuvochina M, Chaumeil P-A, Woodcroft BJ et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2017; 2:1533–1542 [View Article] [PubMed]
     [Google Scholar]
  21. Zhang DF, Cui XW, Zhao Z, Zhang AH, Huang JK et al. Sphingomonas hominis sp. nov., isolated from hair of a 21-year-old girl. Antonie van Leeuwenhoek 2020; 113:1523–1530 [View Article]
     [Google Scholar]
  22. 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 [View Article]
     [Google Scholar]
  23. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:1–19 [View Article]
     [Google Scholar]
  24. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article]
     [Google Scholar]
  25. Margush T, Mcmorris F. Consensus-trees. Bull Math Biol 1981; 43:239–244 [View Article]
     [Google Scholar]
  26. Carbon S, Douglass E, Dunn N, Good B, Harris NL et al. The Gene Ontology resource: 20 years and still going strong. Nucleic Acids Res 2019; 47:D330–D338 [View Article] [PubMed]
     [Google Scholar]
  27. Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000; 28:27–30 [View Article] [PubMed]
     [Google Scholar]
  28. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015; 43:D261–9 [View Article] [PubMed]
     [Google Scholar]
  29. van Beilen JB, Funhoff EG, van Loon A, Just A, Kaysser L et al. Cytochrome P450 alkane hydroxylases of the CYP153 family are common in alkane-degrading eubacteria lacking integral membrane alkane hydroxylases. Appl Environ Microbiol 2006; 72:59–65 [View Article] [PubMed]
     [Google Scholar]
  30. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [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 [View Article] [PubMed]
     [Google Scholar]
  32. Huang ZB, Lai QL, Zhang DM, Shao ZZ. Agaribacterium haliotis gen. nov., sp. nov., isolated from abalone faeces. Int J Syst Evol Microbiol 2017; 67:3819–3823 [View Article] [PubMed]
     [Google Scholar]
  33. Wang G, Zheng X, Xu S, Dang G, Su H et al. Exilibacterium tricleocarpae gen. nov., sp. nov., a marine bacterium from coralline algae Tricleocarpa sp. Int J Syst Evol Microbiol 2020; 70:3427–3432 [View Article] [PubMed]
     [Google Scholar]
  34. Lucena T, Arahal DR, Sanz-Sáez I, Acinas SG, Sánchez O et al. Thalassocella blandensis gen. nov., sp. nov., a novel member of the family Cellvibrionaceae. Int J Syst Evol Microbiol 2020; 70:1231–1239 [View Article]
     [Google Scholar]
  35. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  36. 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]
  37. Collins MD, Jones D. A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 1981; 51:129–134 [View Article] [PubMed]
     [Google Scholar]
  38. Iwaki H, Takada K, Hasegawa Y. Maricurvus nonylphenolicus gen. nov., sp nov., a nonylphenol-degrading bacterium isolated from seawater. FEMS Microbiol Lett 2012; 327:142–147 [View Article]
     [Google Scholar]
  39. Iwaki H, Fujioka M, Hasegawa Y. Isolation and characterization of marine nonylphenol-degrading bacteria and description of Pseudomaricurvus alkylphenolicus gen. nov., sp. nov. Curr Microbiol 2014; 68:167–173 [View Article] [PubMed]
     [Google Scholar]
  40. Seo HS, Yang SH, Lee JH, Kwon KK. Pseudomaricurvus alcaniphilus sp. nov., a marine bacterium isolated from tidal flat sediment and emended descriptions of the genus Pseudomaricurvus, Pseudomaricurvus alkylphenolicus Iwaki et al. 2014 and Maricurvus nonylphenolicus Iwaki et al. 2012. Int J Syst Evol Microbiol 2015; 65:3591–3596 [View Article] [PubMed]
     [Google Scholar]
  41. Chen M-H, Sheu S-Y, Arun AB, Young C-C, Chen CA et al. Pseudoteredinibacter isoporae gen. nov., sp. nov., a marine bacterium isolated from the reef-building coral Isopora palifera. Int J Syst Evol Microbiol 2011; 61:1887–1893 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005493
Loading
Aestuariicella albida sp. nov., isolated from surface water of the Yellow Sea, and proposal of the genus Aestuariicella as a member of the family Cellvibrionaceae
Int J Syst Evol Microbiol 72, 005493 (2022); https://doi.org/10.1099/ijsem.0.005493
/content/journal/ijsem/10.1099/ijsem.0.005493
/content/journal/ijsem/10.1099/ijsem.0.005493
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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