Advertisement

Nonlabens xiamenensis sp. nov., isolated from coastal seawater

  • Zhaobin Huang
  • Yaping Du
  • Qiliang Lai
  • Zongze ShaoEmail author
Original Paper
  • 29 Downloads

Abstract

A Gram-stain negative, rod-shaped and non-flagellated bacterium, designated strain 1Q3T, was isolated from coastal seawater in Xiamen Island, China, and subjected to taxonomic characterisation using a polyphasic approach. Strain 1Q3T was found to be aerobic, non-gliding and to lack flexirubin-type pigments. Catalase activity was found to be negative and oxidase positive. The strain has the ability to degrade protein. The nearly complete 16S rRNA gene sequence of strain 1Q3T shows high sequence similarities with Nonlabens aestuariivivens OITF-31T (96.1%), Nonlabens halophilus CAU 1131T and Nonlabens spongiae UST030701-156T (95.7% and 95.5%, respectively). Phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic analysis based on a 92 bacterial core gene set indicated that strain 1Q3T should be affiliated to the genus Nonlabens, but forms a distinct monophyletic branch, which is separated from the other members within the genus Nonlabens. The predominant fatty acids (> 10%) were identified as iso-C17:0 3-OH, iso-C15:0 and anteiso-C15:0. The predominant respiratory quinone was found to be MK-6. The polar lipids were identified as phosphatidylethanolamine, a phospholipid, an aminolipid and three unidentified polar lipids. The draft genome size of strain 1Q3T is 3.7 Mb with genomic G + C content of 41.1 mol%. Based on these results, strain 1Q3T is concluded to represent a novel species within the genus Nonlabens, for which the name Nonlabens xiamenensis sp. nov. is proposed with the type strain 1Q3T (= MCCC 1A14023T = KCTC 62889T).

Keywords

Nonlabens xiamenensis Flavobacteriaceae Polyphasic taxonomy 

Notes

Acknowledgements

This work was supported by the projects of National Infrastructure of Natural Resources for Science and Technology Program of China (NIMR-2018-9) and Xiamen Ocean Economic Innovation and Development Demonstration Project (16PZP001SF16).

Authors’ contributions

ZH isolated this strain, and performed the phenotypic, physiological and biochemical characterisation. YD performed the part of biochemical characterisation. QL analysed the fatty acids profiles. ZH and ZS wrote the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

10482_2019_1258_MOESM1_ESM.pdf (329 kb)
Supplementary material 1 (PDF 328 kb)

References

  1. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477CrossRefGoogle Scholar
  2. Bernardet JF, Nakagawa Y, Holmes B, Subcommittee on the Taxonomy of F, Cytophaga-Like Bacteria of the International Committee on Systematics of P (2002a) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070Google Scholar
  3. Bernardet JF, Nakagawa Y, Holmes B, Subcommittee on the Taxonomy of F, Prokaryotes C-lbotICoSo (2002b) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070Google Scholar
  4. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075CrossRefGoogle Scholar
  5. Komagata K, Suzuki K-I (1988) 4 Lipid and cell-wall analysis in bacterial systematics. Curr Methods Classif Identif Microorg.  https://doi.org/10.1016/s0580-9517(08)70410-0 Google Scholar
  6. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  7. Kwon YM, Yang SH, Kwon KK, Kim SJ et al (2014) Nonlabens antarcticus sp. nov., a psychrophilic bacterium isolated from glacier ice, and emended descriptions of Nonlabens marinus Park et al. 2012 and Nonlabens agnitus Yi and Chun 2012. Int J Syst Evol Microbiol 64:400–405CrossRefGoogle Scholar
  8. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucl Acids Res 35:3100–3108CrossRefGoogle Scholar
  9. Lau SC, Tsoi MM, Li X, Plakhotnikova I, Dobretsov S, Wong PK, Pawlik JR, Qian PY (2005) Nonlabens tegetincola gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a microbial mat in a subtropical estuary. Int J Syst Evol Microbiol 55:2279–2283CrossRefGoogle Scholar
  10. Lau SC, Tsoi MM, Li X, Plakhotnikova I, Dobretsov S, Wu M, Wong PK, Pawlik JR, Qian PY (2006) Stenothermobacter spongiae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a marine sponge in the Bahamas, and emended description of Nonlabens tegetincola. Int J Syst Evol Microbiol 56:181–185CrossRefGoogle Scholar
  11. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60CrossRefGoogle Scholar
  12. Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J (2018) UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285CrossRefGoogle Scholar
  13. Oh M, Kim JH, Bora N, Kim W (2017) Nonlabens halophilus sp. nov., isolated from reclaimed land. Int J Syst Evol Microbiol 67:138–143CrossRefGoogle Scholar
  14. Park S, Yoshizawa S, Chiura HX, Muramatsu Y, Nakagawa Y, Kogure K, Yokota A (2012) Nonlabens marinus sp. nov., a novel member of the Flavobacteriaceae isolated from the Pacific Ocean. Antonie Van Leeuwenhoek 102:669–676CrossRefGoogle Scholar
  15. Park S, Kang CH, Yoon JH (2013) Nonlabens arenilitoris sp. nov., a member of the family Flavobacteriaceae isolated from seashore sand. Antonie Van Leeuwenhoek 103:1125–1132CrossRefGoogle Scholar
  16. Park S, Ha MJ, Yoon SY, Jung YT, Yoon JH (2017) Nonlabens aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 67:1535–1539CrossRefGoogle Scholar
  17. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055CrossRefGoogle Scholar
  18. Yi H, Chun J (2012) Unification of the genera Nonlabens, Persicivirga, Sandarakinotalea and Stenothermobacter into a single emended genus, Nonlabens, and description of Nonlabens agnitus sp. nov. Syst Appl Microbiol 35:150–155CrossRefGoogle Scholar
  19. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017a) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617CrossRefGoogle Scholar
  20. Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Zhaobin Huang
    • 1
    • 2
  • Yaping Du
    • 1
    • 2
  • Qiliang Lai
    • 1
    • 2
  • Zongze Shao
    • 1
    • 2
    Email author
  1. 1.Key Laboratory of Marine Genetic RecoursesThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
  2. 2.Fujian Key Laboratory of Marine Genetic ResourcesXiamenChina

Personalised recommendations