Skip to main content

Advertisement

SpringerLink
Log in

Massilia aquatica sp. nov., Isolated from a Subtropical Stream in China

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

A Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strain FT127WT was isolated from a subtropical stream in China. Comparison based on 16S rRNA gene sequences showed that strain FT127WT belongs to genus Massilia and shares 98.5% similarity with Massilia buxea A9T as its closest neighbor. The genome size of strain FT127WT was 6.65 Mbp with G + C content of 65.3%. The calculated pairwise OrthoANIu values and digital DNA–DNA hybridization values between strain FT127WT and each of strains M. buxea KCTC 52429T, Massilia armeniaca ZMN-3T, Massilia plicata DSM 17505T and Massilia namucuonensis CGMCC 1.11014T were less than 83.1% and 26.6%, respectively. The reconstructed phylogenomic tree based on concatenated 92 core genes showed that strain FT127WT clusters closely with M. namucuonensis CGMCC 1.11014T. The respiratory quinone of strain FT127WT was Q-8. The major fatty acids were C16:1 ω7c, C16:0 and C12:0. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. Combining above all characteristics, strain FT127WT should represent a novel species within genus Massilia, for which the name Massilia aquatica sp. nov. (type strain FT127WT = GDMCC 1.1690T = KACC 21482T) is proposed.

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

Fig. 1

Similar content being viewed by others

References

  1. La Scola B, Birtles RJ, Mallet MN, Raoult D (1998) Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions. J Clin Microbiol 36:2847–2852

    Article  Google Scholar 

  2. Kämpfer P, Lodders N, Martin K, Falsen E (2011) Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov. Int J Syst Evol Microbiol 61:1528–1533

    Article  Google Scholar 

  3. Singh H, Du J, Won K, Yang JE, Yin C, Kook M, Yi TH (2015) Massilia arvi sp. nov., isolated from fallow-land soil previously cultivated with Brassica oleracea, and emended description of the genus Massilia. Int J Syst Evol Microbiol 65:3690–3696

    Article  CAS  Google Scholar 

  4. Guo BX, Liu YQ, Gu ZQ, Shen L, Liu KS, Wang NL, Xing TT, Liu HC, Zhou YG, Li JL (2016) Massilia psychrophila sp. nov., isolated from an ice core. Int J Syst Evol Microbiol 66:4088–4093

    Article  CAS  Google Scholar 

  5. Sun LN, Yang ED, Cui DX, Ni YW, Wang YB, Sun DD, Wang WY (2017) Massilia buxea sp. nov., isolated from a rock surface. Int J Syst Evol Microbiol 67:4390–4396

    Article  CAS  Google Scholar 

  6. Ren M, Li XY, Zhang YQ, Jin Y, Li SQ, Huang HD (2018) Massilia armeniaca sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 68:2319–2324

    Article  CAS  Google Scholar 

  7. Zhang YQ, Li WJ, Zhang KY, Tian XP, Jiang Y, Xu LH, Jiang CL, Lai R (2006) Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China. Int J Syst Evol Microbiol 56:459–463

    Article  CAS  Google Scholar 

  8. Weon HY, Kim BY, Hong SB, Jeon YA, Koo BS, Kwon SW, Stackebrandt E (2009) Massilia niabensis sp. nov. and Massilia niastensis sp. nov., isolated from air samples. Int J Syst Evol Microbiol 59:1656–1660

    Article  CAS  Google Scholar 

  9. Kong BH, Li YH, Liu M, Liu Y, Li CL, Liu L, Yang ZW, Yu R (2013) Massilia namucuonensis sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 63:352–357

    Article  CAS  Google Scholar 

  10. Baldani JI, Rouws L, Cruz LM, Olivares FL, Schmid M, Hartmann A (2014) The Family Oxalobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes: Alphaproteobacteria and Betaproteobacteria. Springer, Berlin, pp 919–974

    Chapter  Google Scholar 

  11. Dong XZ, Cai MY (2001) Determinative manual for routine bacteriology. Beijing Scientific Press, Beijing

    Google Scholar 

  12. Lu HB, Xue XF, Phurbu D, Xing P, Wu QL (2018) Roseovarius tibetensis sp. nov., a halophilic bacterium isolated from Lake LongmuCo on Tibetan Plateau. J Microbiol 56:783–789

    Article  CAS  Google Scholar 

  13. Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A (1982) Numerical taxonomy of moderately halophilic Gram-negative rods. J Gen Microbiol 128:1959–1968

    Google Scholar 

  14. Zhong ZP, Liu Y, Wang F, Zhou YG, Liu HC, Liu ZP (2016) Lacimicrobium alkaliphilum gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from a salt lake. Int J Syst Evol Microbiol 66:422–429

    Article  CAS  Google Scholar 

  15. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 38:358–361

    Article  CAS  Google Scholar 

  16. Sasser M (1990) Identification of bacteria through fatty acid analysis. In: Klement Z, Rudolph K, Sands DC (eds) Methods in phytobacteriology. Akademiai Kaido, Budapest, pp 199–204

    Google Scholar 

  17. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  18. Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202

    Article  CAS  Google Scholar 

  19. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid sequencing techniques in bacterial systematics. Wiley, New York, pp 115–175

    Google Scholar 

  20. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2016) Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  Google Scholar 

  21. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  Google Scholar 

  22. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  Google Scholar 

  23. Kimura M (1979) The neutral theory of molecular evolution. Sci Am 241:98–100, 102, 108

  24. Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  25. Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of Anurans. Syst Zool 18:1–32

    Article  Google Scholar 

  26. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  Google Scholar 

  27. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870

    Article  CAS  Google Scholar 

  28. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD et al (2012) SPAdes: a new genome assembly algorithm and its applications to single cell sequencing. J Comput Biol 19:455–477

    Article  CAS  Google Scholar 

  29. Tatiana T, Michael D, Azat B, Vyacheslav C, Eric PN, Leonid Z, Alexandre L, Kim DP, Mark B, James O (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624

    Article  Google Scholar 

  30. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P (2017) Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol 34:2115–2122

    Article  CAS  Google Scholar 

  31. Kanehisa M, Sato Y, Morishima K (2015) BlastKOALA and GhostKOALA: KEGG tools for functional characterisation of genome and metagenome sequences. J Mol Biol 428:726–731

    Article  Google Scholar 

  32. Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1–6

    Article  Google Scholar 

  33. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  34. 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 56:280–285

    Article  CAS  Google Scholar 

  35. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murry RGE, 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 

  36. Michael R, Ramon RM (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    Article  Google Scholar 

Download references

Acknowledgements

This work was funded by Guangdong Provincial Programs for Science and Technology Development (2019B110205004; 2018B030324002), National Natural Science Foundation of China (91851202; 51678163), GDAS’ Special Project of Science and Technology Development (2019GDASYL-0301002; 2020GDASYL-20200402001). The reference strain M. armeniaca ZMN-3 T was kindly donated by Dr. Hai-Dong Huang (Tianjin Agricultural University, Tianjin 300384, PR China).

Author information

Authors and Affiliations

  1. Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People’s Republic of China

    Hui-Bin Lu, Tong-Chu Deng & Mei-Ying Xu

  2. State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, People’s Republic of China

    Hui-Bin Lu, Tong-Chu Deng & Mei-Ying Xu

  3. Guangdong Open Laboratory of Applied Microbiology, Guangzhou, 510070, People’s Republic of China

    Hui-Bin Lu, Tong-Chu Deng & Mei-Ying Xu

Authors
  1. Hui-Bin Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tong-Chu Deng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mei-Ying Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Strain FT127WT was isolated by H-BL. Data collection and analysis were performed by H-BL and T-CD. The first draft of the manuscript was written by H-BL and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Mei-Ying Xu.

Ethics declarations

Conflicts of interest

The authors declare that they have no direct or indirect conflict of interest.

Research Involving Human Participants or Animals

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

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence and draft genome sequence of strain FT127WT are MN865813 and WWCU00000000, respectively.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 4053 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lu, HB., Deng, TC. & Xu, MY. Massilia aquatica sp. nov., Isolated from a Subtropical Stream in China. Curr Microbiol 77, 3185–3191 (2020). https://doi.org/10.1007/s00284-020-02104-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-020-02104-1

Search

Navigation