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Volume 72, Issue 2

sp. nov., a halophilic bacterium isolated from sediment collected at a cold seep field in the South China Sea No Access

Abstract

A moderately halophilic bacterium, designated strain KX20305, was isolated from sediment collected from a cold seep field in the South China Sea. Cells of strain KX20305 were Gram-stain-negative, rod-shaped, non-motile, facultatively anaerobic, oxidase- and catalase-positive, and grew optimally at 25–30 °C, pH 6.0–8.0 and with 3–6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KX20305 grouped with members of the genus , including D-24 (98.3 % sequence similarity), KMM 3516 (98.1 %) and CC-CZW007 (97.5 %). Genome sequencing of strain KX20305 revealed a genome size of 3.35 Mb and a DNA G+C content of 38.71 mol%. Genomic average nucleotide identity (orthoANI) values of strain KX20305 with D-24, KMM 3516 and JCM 30378 were 83.8, 81.7 and 75.4 %, respectively, while DNA–DNA hybridization (GGDC) values for strain KX20305 with these strains were 27.2, 25.0 and 19.6 %, respectively. The major fatty acids of strain KX20305 were iso-C, iso-C 3-OH and 10-methyl C/iso-C 9. The predominant respiratory quinone was menaquinone-6 (MK-6). The polar lipids mainly comprised phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. Based on comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain KX20305 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is KX20305 (=KCTC 82699=MCCC 1K06238=JCM 34635).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Aequorivita , chemotaxonomic characterization , cold seep , genome and type strain
Funding
This study was supported by the:
  • the Senior User Project of RV KEXUE (Award KEXUE2019GZ06)
    • Principle Award Recipient: MinxiaoWang
  • National Natural Science Foundation of China (Award 42076091)
    • Principle Award Recipient: MinxiaoWang
  • National Natural Science Foundation of China (Award 42030407)
    • Principle Award Recipient: ChaolunLi
  • Priority Research Program of the Chinese Academy of Sciences (Award XDA22050303)
    • Principle Award Recipient: MinxiaoWang
  • National Key R&D Program of China (Award 2018YFC0310800)
    • Principle Award Recipient: HuanZhang
© 2022 The Authors
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2022-02-08
2024-04-23
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References

  1. Bowman JP, Nichols DS. Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats. Int J Syst Evol Microbiol 2002; 52:1533–1541 [View Article] [PubMed]
     [Google Scholar]
  2. Park SC, Baik KS, Kim MS, Kim SS, Kim SR et al. Aequorivita capsosiphonis sp. nov., isolated from the green alga Capsosiphon fulvescens, and emended description of the genus Aequorivita. Int J Syst Evol Microbiol 2009; 59:724–728 [View Article] [PubMed]
     [Google Scholar]
  3. Liu J-J, Zhang X-Q, Pan J, Sun C, Zhang Y et al. Aequorivita viscosa sp. nov., isolated from an intertidal zone, and emended descriptions of Aequorivita antarctica and Aequorivita capsosiphonis. Int J Syst Evol Microbiol 2013; 63:3192–3196 [View Article] [PubMed]
     [Google Scholar]
  4. Zhang S, Zhou H, Sun C, Hu Z, Wang H. Aequorivita lutea sp. nov., a novel bacterium isolated from the estuarine sediment of the Pearl River in China, and transfer of Vitellibacter todarodis and Vitellibacter aquimaris to the genus Aequorivita as Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov. Int J Syst Evol Microbiol 2020; 70:3117–3122 [View Article] [PubMed]
     [Google Scholar]
  5. Wang Q, Cai S-D, Liu J, Zhang D-C. Aequorivita sinensis sp. nov., isolated from sediment of the East China Sea, and reclassification of Vitellibacter todarodis as Aequorivita todarodis comb. nov. and Vitellibacter aquimaris as Aequorivita aquimaris comb. nov. Int J Syst Evol Microbiol 2020; 70:3323–3327 [View Article] [PubMed]
     [Google Scholar]
  6. Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M et al. Genome-based taxonomic classification of bacteroidetes. Front Microbiol 2016; 7:2003 [View Article] [PubMed]
     [Google Scholar]
  7. Nedashkovskaya OI, Suzuki M, Vysotskii MV, Mikhailov VV. Vitellibacter vladivostokensis gen. nov., sp. nov., a new member of the phylum Cytophaga-Flavobacterium-Bacteroides. Int J Syst Evol Microbiol 2003; 53:1281–1286 [View Article]
     [Google Scholar]
  8. Kim B-S, Kim O-S, Moon EY, Chun J. Vitellibacter aestuarii sp. nov., isolated from tidal-flat sediment, and an emended description of the genus Vitellibacter. Int J Syst Evol Microbiol 2010; 60:1989–1992 [View Article] [PubMed]
     [Google Scholar]
  9. Park S, Lee K-C, Bae KS, Yoon J-H. Vitellibacter soesokkakensis sp. nov., isolated from the junction between the ocean and a freshwater spring and emended description of the genus Vitellibacter. Int J Syst Evol Microbiol 2014; 64:588–593 [View Article] [PubMed]
     [Google Scholar]
  10. Rajasabapathy R, Mohandass C, Yoon J-H, Dastager SG, Liu Q et al. Vitellibacter nionensis sp. nov., isolated from a shallow water hydrothermal vent. Int J Syst Evol Microbiol 2015; 65:692–697 [View Article] [PubMed]
     [Google Scholar]
  11. Lin S-Y, Hameed A, Wen C-Z, Liu Y-C, Hsu Y-H et al. Vitellibacter echinoideorum sp. nov., isolated from a sea urchin (Tripneustes gratilla). Int J Syst Evol Microbiol 2015; 65:2320–2325 [View Article] [PubMed]
     [Google Scholar]
  12. Kim HC, Kim Y-O, Park S, Nam B-H, Kim D-G et al. Vitellibacter todarodis sp. nov., isolated from intestinal tract of a squid (Todarodes pacificus). Int J Syst Evol Microbiol 2018; 68:1233–1237 [View Article] [PubMed]
     [Google Scholar]
  13. Thevarajoo S, Selvaratnam C, Goh KM, Hong KW, Chan XY et al. Vitellibacter aquimaris sp. nov., a marine bacterium isolated from seawater. Int J Syst Evol Microbiol 2016; 66:3662–3668 [View Article] [PubMed]
     [Google Scholar]
  14. 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 [View Article] [PubMed]
     [Google Scholar]
  15. 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] [PubMed]
     [Google Scholar]
  16. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article] [PubMed]
     [Google Scholar]
  17. 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]
  18. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article] [PubMed]
     [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 2018; 46:2159–2168 [View Article] [PubMed]
     [Google Scholar]
  22. 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 [View Article] [PubMed]
     [Google Scholar]
  23. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
     [Google Scholar]
  24. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
     [Google Scholar]
  25. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29 [View Article]
     [Google Scholar]
  26. 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]
  27. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006; 34:D354–7 [View Article] [PubMed]
     [Google Scholar]
  28. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:D277–80 [View Article] [PubMed]
     [Google Scholar]
  29. Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 2002; 18:77–82 [View Article] [PubMed]
     [Google Scholar]
  30. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000; 28:45–48 [View Article] [PubMed]
     [Google Scholar]
  31. 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 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
  33. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12 [View Article] [PubMed]
     [Google Scholar]
  34. Harris RS. Improved Pairwise Alignment of Genomic DNA The Pennsylvania State University; 2007
     [Google Scholar]
  35. Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. In Proceedings of the Pacific Symposium 2001 pp 115–126 [View Article]
     [Google Scholar]
  36. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article]
     [Google Scholar]
  37. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article]
     [Google Scholar]
  38. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article]
     [Google Scholar]
  39. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article]
     [Google Scholar]
  40. Zhang C, Scornavacca C, Molloy EK, Mirarab S. ASTRAL-Pro: quartet-based species-tree inference despite paralogy. Mol Biol Evol 2020; 37:3292–3307 [View Article]
     [Google Scholar]
  41. 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]
  42. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  43. Zhang X. Marine Microbiology, 2nd edn. Beijing: Science Press; 2016
     [Google Scholar]
  44. Dong X, Cai M. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  45. Sun Q-L, Sun L. Description of Algoriphagus iocasae sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2017; 67:243–249 [View Article] [PubMed]
     [Google Scholar]
  46. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 1990; 20:1–6
     [Google Scholar]
  47. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  48. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  49. Kates M. Techniques of Llipidology, 2nd edn. Amsterdam: Elsevier; 1986
     [Google Scholar]
  50. Lai Q, Liu X, Yuan J, Xie S, Shao Z. Pararhodobacter marinus sp. nov., isolated from deep-sea water of the Indian Ocean. Int J Syst Evol Microbiol 2019; 69:932–936 [View Article] [PubMed]
     [Google Scholar]
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Aequorivita iocasae sp. nov., a halophilic bacterium isolated from sediment collected at a cold seep field in the South China Sea
Int J Syst Evol Microbiol 72, 005199 (2022); https://doi.org/10.1099/ijsem.0.005199
/content/journal/ijsem/10.1099/ijsem.0.005199
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