Skip to main content
SpringerLink
Log in

Pseudomonas subflava sp. nov., a new Gram-negative bacterium isolated from Guishan in Yunnan province, south–west China

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A new Gram-negative, rod-shaped, flagellated bacterium was isolated from soil in the Guishan, Xinping County, Yuxi City, Yunnan Province, China, and named YIM B01952T. Growth occurred at 10–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.5) and with up to ≤ 5.0% (w/v) NaCl on Tryptic Soy Broth Agar (TSA) plates. Phylogenetic analysis based on the 16S rRNA gene and draft-genome sequence showed that strain YIM B01952T belonged to the genus Pseudomonas, and was closely related to the type strain of Pseudomonas alcaligenes (sequence similarity was 98.8%). The digital DNA–DNA hybridization (dDDH) value between strain YIM B01952T and the parallel strain P. alcaligenes ATCC 14909T was 49.0% based on the draft genome sequence. The predominant menaquinone was Q-9. The major fatty acids were summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), summed feature 3 (C16:1 ω6c and/or C16:1 ω7c) and C16:0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The genome size of strain YIM B01952T was 4.341 Mb, comprising 4156 predicted genes with a DNA G + C content of 66.4 mol%. In addition, we detected that strain YIM B01952T had some traditional functional genes (plant growth promotion and multidrug resistance), unique genes through genome comparison and analysis with similar strains. Based on genetic analyses and biochemical characterization, the strain YIM B01952T was identified as a novel species in the genus Pseudomonas, for which the name Pseudomonas subflava sp. nov. is proposed. The type strain is YIM B01952T (=CCTCC AB 2021498T = KCTC 92073T).

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
Fig. 2

Similar content being viewed by others

References

  • Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75

    Article  PubMed  PubMed Central  Google Scholar 

  • Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al (2021) antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 49(W1):W29–W35

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68(1):461–466

    Article  CAS  PubMed  Google Scholar 

  • Clark LL, Dajcs JJ, McLean CH, Bartell JG, Stroman DW (2006) Pseudomonas otitidis sp. nov., isolated from patients with otic infections. Int J Syst Evol Microbiol 56(Pt 4):709–714

    Article  CAS  PubMed  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100(2):221–230

    Article  CAS  PubMed  Google Scholar 

  • De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12(1):133–142

    Article  PubMed  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791

    Article  PubMed  Google Scholar 

  • Feng YZ, Chunyu WX, Liang R, Hahnke RL, Schumann P et al (2020) Vallicoccus soli gen. nov., sp. nov., a novel actinobacterium isolated from soil, and description of Vallicoccaceae fam. nov Motilibacterales ord nov. Antonie Van Leeuwenhoek 113:2155–2165

    Article  CAS  PubMed  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Fraser JR, Laurent TC, Laurent UB (1997) Hyaluronan: its nature, distribution, functions and turnover. J Intern Med 242(1):27–33

    Article  CAS  PubMed  Google Scholar 

  • Groth I, Schumann P, Weiss N, Martin K, Rainey FA (1996) Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 46(1):234–239

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu YC, Young LS, Lin SY, Hameed A, Hsu YH et al (2013) Pseudomonas guguanensis sp. nov., a gammaproteobacterium isolated from a hot spring. Int J Syst Evol Microbiol 63(Pt 12):4591–4598

    Article  CAS  PubMed  Google Scholar 

  • Migula W (1894) Über ein neues system der bakterien. Arb Bakteriol Inst Karlsruhe 1:235–238 (in German)

    Google Scholar 

  • Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2(5):233–241

    Article  CAS  Google Scholar 

  • Monias BL (1928) Classification of Bacterium alcaligenes, pyocyaneum and fluorescens. J Infect Dis 43(4):330–334

    Article  Google Scholar 

  • Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32(6):929–931

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068–2069

    Article  CAS  PubMed  Google Scholar 

  • Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57(5):758–771

    Article  PubMed  Google Scholar 

  • Tang SK, Wang Y, Zhang H, Lee JC, Lou K et al (2010) Haloechinothrix alba gen. nov., sp. nov., a halophilic, filamentous actinomycete of the suborder Pseudonocardineae. Int J Syst Evol Microbiol 60(Pt 9):2154–2158

    Article  CAS  PubMed  Google Scholar 

  • Tarhriz V, Nouioui I, Spröer C, Verbarg S, Ebrahimi V et al (2020) Pseudomonas khazarica sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Khazar sea sediments. Antonie Van Leeuwenhoek 113(4):521–532

    Article  CAS  PubMed  Google Scholar 

  • 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(24):4876–4882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tohya M, Watanabe S, Teramoto K, Tada T, Kuwahara-Arai K et al (2020) Pseudomonas yangonensis sp. nov., isolated from wound samples of patients in a hospital in Myanmar. Int J Syst Evol Microbiol 70(6):3597–3605

    Article  CAS  PubMed  Google Scholar 

  • Toru H, Masayuki T, Seiichi T (1983) A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29(4):319–322

    Article  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67(5):1613–1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46(W1):W95–W101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by Major Science and Technology Projects of Yunnan Province (202202AE090015; 202002AA100007), Basic Research Project of Yunnan Province (202001BB050025), and the Top Young Talents of "ten thousand talents plan" in Yunnan Province, China, and the rural revitalization project of Serving Yunnan (CZ22624401).

Author information

Author notes

  1. Cheng Ling and Jiang-Yuan Zhao equally contributed to this work.

Authors and Affiliations

  1. Key Laboratory for Microbial Resources of the Ministry of Education and School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People’s Republic of China

    Cheng Ling, Jiang-Yuan Zhao, Le-Le Li, Zhang-Gui Ding, Meng-Yu Zhang, Jing Tang, Song-Guo Liang, Jian-Yu Li, Xiao-Di Liu, Lu-Yao Feng, Ming-Gang Li & Shu-Kun Tang

  2. Department of Medicine, Qujing Vocational and Technical College, Qujing, 655000, People’s Republic of China

    Le-Le Li

  3. Institute of Agricultural Environmental Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650205, People’s Republic of China

    Lu-Yao Feng, Pei-Wen Yang, Yao Lu, Zhu-Feng Shi & Chui-Si Kong

Authors
  1. Cheng Ling
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jiang-Yuan Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Le-Le Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhang-Gui Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Meng-Yu Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jing Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Song-Guo Liang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jian-Yu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Xiao-Di Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Lu-Yao Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Pei-Wen Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Yao Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Zhu-Feng Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Chui-Si Kong
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Ming-Gang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Shu-Kun Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

CL, J-YZ, and L-LL, M-GL C-SK and S-KT designed the study, carried out the experiments and the data analysis, wrote and revised the manuscript. Z-GD, M-YZ, JT, S-GL, J-YL, X-DL, L-YF, and P-WY, YL, Z-FS participated in the data analysis and revised the manuscript. All authors have read and approved the manuscript.

Corresponding authors

Correspondence to Chui-Si Kong, Ming-Gang Li or Shu-Kun Tang.

Ethics declarations

Conflicts of interest

The authors declare that there are no conflicts of interest.

Additional information

Publisher's Note

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

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 432 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ling, C., Zhao, JY., Li, LL. et al. Pseudomonas subflava sp. nov., a new Gram-negative bacterium isolated from Guishan in Yunnan province, south–west China. Antonie van Leeuwenhoek 116, 557–564 (2023). https://doi.org/10.1007/s10482-023-01826-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-023-01826-z

Keywords

Search

Navigation