Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 70, Issue 12

sp. nov., isolated from Baiyangdian Lake in Xiong'an New Area Free

Abstract

An aerobic, Gram-stain-negative, rod-shaped bacterium, designated as strain R-22–3 w-18, was isolated from Baiyangdian Lake in Xiong'an New Area, PR China. Growth was observed at 15–37 °C (optimum, 30 °C) and pH 7.0–10.0 (optimum, pH 8.0). 16S rRNA gene sequence analysis placed the strain in a separate branch in the group, with DSM12111 as its closest phylogenetic relative (98.2 %). Whole-genome comparisons, using average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) analyses, confirmed low genome relatedness to the closely related species [below the recommended thresholds of 95 % (ANI), 95 % (AAI) and 70 % (DDH) for species delineation]. Phenotypic characterization tests could also distinguish this strain from other related species of the genus . Therefore, based on genetic and phenotypic evidence, it is clear that strain R-22–3 w-18 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is R-22–3 w-18 (=CGMCC 1.17250=KCTC 72658).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Baiyangdian Lake , lake water and Pseudomonas xionganensis sp. nov.
Funding
This study was supported by the:
  • National Natural Science Foudation of China (Award No. 31872632)
    • Principle Award Recipient: Chao Wang
  • Science and Technology Basic Resources Investigation Project (Award No. 2017FY100300)
    • Principle Award Recipient: Jie Feng
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004485
2020-09-30
2025-03-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/12/6052.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004485&mimeType=html&fmt=ahah

References

  1. Migula W. Über ein neues system Der Bakterien. Arb Bakteriol Inst Karlsruhe 1894; 1:235–238
     [Google Scholar]
  2. Palleroni NJ. Pseudomonas. In Brenner DJ, Krieg NR, Staley JT. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. New York: Springer; 2005 pp 323–379
     [Google Scholar]
  3. Spiers AJ, Buckling A, Rainey PB. The causes of Pseudomonas diversity. Microbiology 2000; 146:2345–2350 [View Article][PubMed]
     [Google Scholar]
  4. Yamamoto S, Kasai H, Arnold DL, Jackson RW, Vivian A et al. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 2000; 146:2385–2394 [View Article][PubMed]
     [Google Scholar]
  5. Wei Y, Mao H, Xu Y, Zou W, Fang J et al. Pseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench. Int J Syst Evol Microbiol 2018; 68:2462–2467 [View Article]
     [Google Scholar]
  6. Zhang L, Gao JS, Zhang S, Ali Sheirdil R, Wang XC, Zhang XX et al. Paenibacillus rhizoryzae sp. nov., isolated from rice rhizosphere. Int J Syst Evol Microbiol 2015; 65:3053–3059 [View Article][PubMed]
     [Google Scholar]
  7. Gupta SK, Kumari R, Prakash O, Lal R, Sanjay KG. Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site. Int J Syst Evol Microbiol 2008; 58:1339–1345 [View Article][PubMed]
     [Google Scholar]
  8. Willems A, Falsen E, Pot B, Jantzen E, Hoste B et al. Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov. Int J Syst Bacteriol 1990; 40:384–398 [View Article][PubMed]
     [Google Scholar]
  9. Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H et al. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 1992; 36:1251–1275 [View Article][PubMed]
     [Google Scholar]
  10. Brown GR, Sutcliffe IC, Cummings SP. Reclassification of [Pseudomonas] doudoroffii (Baumann et al. 1983) into the genus Oceanomonas gen. nov. as Oceanomonas doudoroffii comb. nov., and description of a phenol-degrading bacterium from estuarine water as Oceanomonas baumannii sp. nov. Int J Syst Evol Microbiol 2001; 51:67–72 [View Article][PubMed]
     [Google Scholar]
  11. Peix A, Ramírez-Bahena M-H, Velázquez E. Historical evolution and current status of the taxonomy of genus Pseudomonas . Infect Genet Evol 2009; 9:1132–1147 [View Article][PubMed]
     [Google Scholar]
  12. Tamaoka J, Ha DM, Komagata K. Reclassification of Pseudomonas acidovorans den Dooren de Jong 1926 and Pseudomonas testosteroni Marcus and Talalay 1956 as Comamonas acidovorans comb. nov. and Comamonas testosteroni comb. nov., with an Emended Description of the Genus Comamonas . Int J Syst Bacteriol 1987; 37:52–59 [View Article]
     [Google Scholar]
  13. Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010; 12:1513–1530 [View Article][PubMed]
     [Google Scholar]
  14. Wei Y, Mao H, Xu Y, Zou W, Fang J et al. Pseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench. Int J Syst Evol Microbiol 2018; 68:2462–2467 [View Article][PubMed]
     [Google Scholar]
  15. Xu Y, Xu X, Lan R, Xiong Y, Ye C et al. An O island 172 encoded RNA helicase regulates the motility of Escherichia coli O157:H7. PLoS One 2013; 8:e64211 [View Article][PubMed]
     [Google Scholar]
  16. King EO, Ward MK, Raney DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 1954; 44:301–307[PubMed]
     [Google Scholar]
  17. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Rufibacter glacialis sp. nov., a psychrotolerant bacterium isolated from glacier soil. Int J Syst Evol Microbiol 2016; 66:315–318 [View Article][PubMed]
     [Google Scholar]
  18. Vaskovsky VE, Terekhova TA. HPTLC of phospholipid mixtures containing phosphatidylglycerol. J High Resolut Chromatogr 1979; 2:671–672 [View Article]
     [Google Scholar]
  19. Collins MD. Isoprenoid quinone analysis in classification and identification. Chemical Methods in Bacterial Systematics 1985 pp 267–287
     [Google Scholar]
  20. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 2006; 12:2359–2367
     [Google Scholar]
  21. Hu YT, Zhou PJ, Zhou YG, Liu ZH, Liu SJ. Saccharothrix xinjiangensis sp. nov., a pyrene-degrading actinomycete isolated from Tianchi Lake, Xinjiang, China. Int J Syst Evol Microbiol 2004; 54:2091–2209 [View Article][PubMed]
     [Google Scholar]
  22. Niemann S, Pühler A, Tichy HV, Simon R, Selbitschka WJ et al. Evaluation of the resolving power of three DNA fingerprinting methods to discriminate among isolates of a natural. Journal of Applied Microbiology 1997; 4:477–484
     [Google Scholar]
  23. 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]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  25. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  26. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  27. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  28. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed]
     [Google Scholar]
  29. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
     [Google Scholar]
  30. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article][PubMed]
     [Google Scholar]
  31. Na SI, Kim YO, Yoon S-H, Ha SM, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
     [Google Scholar]
  32. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
     [Google Scholar]
  33. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  34. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  35. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
     [Google Scholar]
  36. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kampfer P et al. Report of the AD hoc Committee for the re-evaluation of the species definition in bacteriology. Int.Int J Syst Evol Microbiol 2002; 52:1043–1047
     [Google Scholar]
  37. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR 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]
/content/journal/ijsem/10.1099/ijsem.0.004485
Loading
Pseudomonas xionganensis sp. nov., isolated from Baiyangdian Lake in Xiong'an New Area
Int J Syst Evol Microbiol 70, 6052 (2020); https://doi.org/10.1099/ijsem.0.004485
/content/journal/ijsem/10.1099/ijsem.0.004485
/content/journal/ijsem/10.1099/ijsem.0.004485
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error