Skip to main content
SpringerLink
Log in

Parahaliea maris sp. nov., isolated from surface seawater and emended description of the genus Parahaliea

  • Microbial Systematics and Evolutionary Microbiology
  • Published:
Journal of Microbiology Aims and scope Submit manuscript

Abstract

A Gram-stain-negative strictly aerobic, short-rod-shaped, and non-motile bacterial strain designated HSLHS9T was isolated from surface seawater collected from the South China Sea. Strain HSLHS9T could grow at 15–41°C (optimum 28°C), at pH 5.0–9.0 (optimum 6.0–7.0), and in 0–7% (w/v) NaCl (optimum 2–3%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HSLHS9T shared high identities with the closely related Parahaliea aestuarii S2-26T (98.6%) and Parahaliea mediterranea 7SM29T (97.8%) and formed a distinct lineage within the genus Parahaliea. Wholegenome sequencing of strain HSLHS9T revealed the size of 4.8 Mbp and DNA G + C content of 61.8 mol%. Strain HSLHS9T shared the digital DNA-DNA hybridization values of 22.4% and 23.0%, and the average nucleotide identities of 79.7% and 79.9%, respectively, with the two type strains above. The predominant cellular fatty acids of the strain were summed feature 8 (C18:1ω6c and/or C18:1ω7c), summed feature 3 (C16:1ω7c and/or C16:1ω6c), C17:1ω8c, and C16:0. The sole isoprenoid quinone was identified as Q-8. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminolipid, and two glycolipids. Based on taxonomic data obtained in this study, it is suggested that strain HSLHS9T represents a novel species of the genus Parahaliea, for which the name Parahaliea maris sp. nov. is proposed. The type strain is HSLHS9T (= MCCC 1A06717T = KCTC 52307T). An emended description of the genus Parahaliea is also provided.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Auch, A.F., von Jan, M., Klenk, H.P., and Göker, M. 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genomic Sci.2, 117–134.

    Article  PubMed  PubMed Central  Google Scholar 

  • Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D., et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol.19, 455–477.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chang, Y.Q., Meng, X., Du, Z.Z., and Du, Z.J. 2019. Kineobactrum sediminis gen. nov., sp. nov., isolated from marine sediment. Int. J. Syst. Evol. Microbiol.69, 2395–2400.

    Article  CAS  PubMed  Google Scholar 

  • Collins, M.D., Pirouz, T., Goodfellow, M., and Minnikin, D.E. 1977. Distribution of menaquinones in actinomycetes and corynebacteria. J. Gen. Microbiol.100, 221–230.

    Article  CAS  PubMed  Google Scholar 

  • Csotonyi, J.T., Stackebrandt, E., Swiderski, J., Schumann, P., and Yurkov, V. 2011. Chromocurvus halotolerans gen. nov., sp. nov., a gammaproteobacterial obligately aerobic anoxygenic phototroph, isolated from a Canadian hypersaline spring. Arch. Microbiol.193, 573–582.

    Article  CAS  PubMed  Google Scholar 

  • Czelusniak, J., Goodman, M., Moncrief, N.D., and Kehoe, S.M. 1990. Maximum parsimony approach to construction of evolutionary trees from aligned homologous sequences. Methods Enzymol.183, 601–615.

    Article  CAS  PubMed  Google Scholar 

  • Euzéby, J. 2009. List of new names and new combinations previously effectively, but not validly, published. Int. J. Syst. Evol. Microbiol.59, 1555–1556.

    Article  Google Scholar 

  • Euzéby, J. 2012. List of new names and new combinations previously effectively, but not validly, published. Int. J. Syst. Evol. Microbiol.62, 1017–1019.

    Article  Google Scholar 

  • Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol.17, 368–376.

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution39, 783–791.

    Article  PubMed  Google Scholar 

  • Garrity, G.M., Bell, J.A., and Lilburn, T. 2015. Gammaproteobacteria class. nov. In Whitman, W.B. and John Wiley and Sons, Inc., Bergey’s Manual of Systematics of Archaea and Bacteria, Bergey’s Manual Trust.

  • Jung, H.S., Jeong, S.E., Kim, K.H., and Jeon, C.O. 2017. Parahaliea aestuarii sp. nov., isolated from the Asan Bay estuary. Int. J. Syst. Evol. Microbiol.67, 1431–1435.

    Article  CAS  PubMed  Google Scholar 

  • Konkit, M., Kim, J.H., and Kim, W. 2016. Marimicrobium arenosum gen. nov., sp. nov., a moderately halophilic bacterium isolated from sea sand. Int. J. Syst. Evol. Microbiol.66, 856–861.

    Article  CAS  PubMed  Google Scholar 

  • Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol.35, 1547–1549.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lai, Q., Liu, Y., Yuan, J., Du, J., Wang, L., Sun, F., and Shao, Z. 2014. Multilocus sequence analysis for assessment of phylogenetic diversity and biogeography in Thalassospira bacteria from diverse marine environments. PLoS One9, e106353.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lin, C.Y., Zhang, X.Y., Liu, A., Liu, C., Song, X.Y., Su, H.N., Qin, Q.L., Xie, B.B., Zhang, Y.Z., and Chen, X.L. 2015. Haliea atlantica sp. nov., isolated from seawater, transfer of Haliea mediterranea to Parahaliea gen. nov. as Parahaliea mediterranea comb. nov. and emended description of the genus Haliea. Int. J. Syst. Evol. Microbiol.65, 3413–3418.

  • Minnikin, D.E., O’Donnell, A.G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., and Parlett, J.H. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods2, 233–241.

    Article  CAS  Google Scholar 

  • Oren, A. and Garrity, G.M. 2013. List of new names and new combinations previously effectively, but not validly, published. Int. J. Syst. Evol. Microbiol.63, 3131–3134.

    Article  Google Scholar 

  • Oren, A. and Garrity, G.M. 2015. List of new names and new combinations previously effectively, but not validly, published. Int. J. Syst. Evol. Microbiol.65, 2017–2025.

    Article  Google Scholar 

  • Park, S., Yoshizawa, S., Inomata, K., Kogure, K., and Yokota, A. 2012. Halioglobus japonicus gen. nov., sp. nov. and Halioglobus pacificus sp. nov., members of the class Gammaproteobacteria isolated from seawater. Int. J. Syst. Evol. Microbiol.62, 1784–1789.

    Article  CAS  PubMed  Google Scholar 

  • Parks, D.H., Imelfort, M., Skennerton, C.T., Hugenholtz, P., and Tyson, G.W. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res.25, 1043–1055.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Richter, M. and Rosselló-Móra, R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA106, 19126–19131.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4, 406–425.

    CAS  PubMed  Google Scholar 

  • Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc.

  • Shi, R., Xu, S., Qi, Z., Zhu, Q., Huang, H., and Weber, F. 2019. Influence of suspended mariculture on vertical distribution profiles of bacteria in sediment from Daya Bay, Southern China. Mar. Pollut. Bull.146, 816–826.

    Article  CAS  PubMed  Google Scholar 

  • Spring, S., Lunsdorf, H., Fuchs, B.M., and Tindall, B.J. 2009. The photosynthetic apparatus and its regulation in the aerobic gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov. PLoS One4, e4866.

    Article  PubMed  PubMed Central  Google Scholar 

  • Spring, S., Riedel, T., Spröer, C., Yan, S., Harder, J., and Fuchs, B.M. 2013. Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans. BMC Microbiol.13, 118.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spring S., Scheuner, C., Göker, M., and Klenk, H.P. 2015. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front. Microbiol.6, 281.

    Article  PubMed  PubMed Central  Google Scholar 

  • Urios, L., Intertaglia, L., Lesongeur, F., and Lebaron, P. 2008. Haliea salexigens gen. nov., sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea. Int. J. Syst. Evol. Microbiol.58, 1233–1237.

    Article  CAS  PubMed  Google Scholar 

  • Vashist, P., Nogi, Y., Ghadi, S.C., Verma, P., and Shouche, Y.S. 2013. Microbulbifer mangrovi sp. nov., a polysaccharide-degrading bacterium isolated from an Indian mangrove. Int. J. Syst. Evol. Microbiol.63, 2532–2537.

    Article  CAS  PubMed  Google Scholar 

  • Wattam, A.R., Abraham, D., Dalay, O., Disz, T.L., Driscoll, T., Gabbard, J.L., Gillespie, J.J., Gough, R., Hix, D., Kenyon, R., et al. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res.42, D581–D591.

    Article  CAS  PubMed  Google Scholar 

  • Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandler, O., Krichevsky, M.I., Moore, L.H., Moore, W.E.C., Murray, R.G.E., Stackebrandt, E., et al. 1987. Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol.37, 463–464.

    Article  Google Scholar 

  • Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol.173, 697–703.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williams, K.P., Gillespie, J.J., Sobral, B.W.S., Nordberg, E.K., Snyder, E.E., Shallom, J.M., and Dickerman, A.W. 2010. Phylogeny of gammaproteobacteria. J. Bacteriol.192, 2305–2314.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017a. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol.67, 1613–1617.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoon, S.H., Ha, S.M., Lim, J., Kwon, S., and Chun, J. 2017b. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek110, 1281–1286.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was jointly supported by the GDAS’ Project of Science and Technology Development [2019GDASYL-0401002], the Guangdong Province Science and Technology Innovation Strategy Special Fund [2018B020205003] and the Science and Technology Plan Project of Guangdong Province [2019B-030316017].

Author information

Authors and Affiliations

  1. State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, P. R. China

    Yang Liu, Juan Du, Jun Zhang & Honghui Zhu

  2. Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, P. R. China

    Qiliang Lai & Zongze Shao

Authors
  1. Yang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Juan Du
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jun Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Qiliang Lai
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zongze Shao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Honghui Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Zongze Shao or Honghui Zhu.

Additional information

Conflicts of Interest

The authors declare that there is no conflict of interest.

Supplemental material for this article may be found at http://www.springerlink.com/content/120956.

Electronic Supplementary Material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, Y., Du, J., Zhang, J. et al. Parahaliea maris sp. nov., isolated from surface seawater and emended description of the genus Parahaliea. J Microbiol. 58, 92–98 (2020). https://doi.org/10.1007/s12275-020-9405-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-020-9405-z

Keywords

Search

Navigation