1887

Abstract

A novel Gram-negative, obligate aerobic, mobile, rod-shaped and non-spore-forming bacterial strain, WCHP16, was isolated from the wastewater treatment plant at West China Hospital in Chengdu, PR China. It was characterized using a polyphasic approach. Analysis of its 16S rRNA gene sequence showed that strain WCHP16 belonged to the genus with the highest similarity to JJ3 (99.34 %), VM14 (99.0 %), NBRC 103162 (99.0 %) and RYU5 (99.0 %). Phylogenomic analysis based on 107 core gene sequences demonstrated that WCHP16 was a member of the group but was distant from all closely related species. Whole-genome comparisons, using average nucleotide identity based on (ANIb) and DNA–DNA hybridization (DDH), confirmed low genome relatedness to all the known species (below the recommended thresholds of 95 % [ANIb] and 70 % [DDH] for species delineation). Phenotypic characterization tests showed that the utilization of phenylacetic acid and capric acid, but not -arabitol, and inability to produce fluorescent (King B medium) in combination could distinguish this strain from other related species of the genus . Therefore, based on genetic and phenotypic evidence, it is clear that strain WCHP16 represents a novel species, for which the name sp. nov. is proposed. The type strain is WCHP16 (GDMCC1.1215=CCTCC AB 2017103=KCTC 52991).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 81772233, 81661130159 and 81861138055)
    • Principle Award Recipient: Zhiyong Zong
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004272
2020-06-18
2021-08-02
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/7/4199.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004272&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. Introduction to the family pseudomonadaceae . In Stolp H, Trüper HG, Balows A, Starr MP, Schlegel HG. (editors) The Prokaryotes Berlin Heidelberg: Springer; 1981 pp 655–665
    [Google Scholar]
  3. Anwar N, Abaydulla G, Zayadan B, Abdurahman M, Hamood B et al. Pseudomonas populi sp. nov., an endophytic bacterium isolated from Populus euphratica . Int J Syst Evol Microbiol 2016; 66:1419–1425 [View Article][PubMed]
    [Google Scholar]
  4. Palleroni NJ. Pseudomonas. In Brenner DJ, Krieg NR, Staley JT. (editors) Bergey’s Manual of Systematic Bacteriology 2, 2nd ed. New York: Springer; 2005 pp 323–379
    [Google Scholar]
  5. Iglewski B. Chapter 27 pseudomonas . In Baron S. editor Medical Microbiology, 4th ed. Galveston: University of Texas Medical Branch at Galveston; 1996
    [Google Scholar]
  6. 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]
  7. Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H et al. Proposal of Burkholderiagen. 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]
  8. 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]
  9. 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]
  10. Tamaoka J, Ha D-M, 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]
  11. 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]
  12. Mulet M, Gomila M, Scotta C, Sánchez D, Lalucat J et al. Concordance between whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry and multilocus sequence analysis approaches in species discrimination within the genus Pseudomonas . Syst Appl Microbiol 2012; 35:455–464 [View Article][PubMed]
    [Google Scholar]
  13. Wang X, SW H, Guo HB, Thin KK, Gao JS et al. Pseudomonas rhizoryzae sp. nov., isolated from rice. Int J Syst Evol Microbiol 2019
    [Google Scholar]
  14. Hofmann K, Huptas C, Doll EV, Scherer S, Wenning M. Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate. Int J Syst Evol Microbiol 2019
    [Google Scholar]
  15. Kämpfer P. The characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:7 [View Article][PubMed]
    [Google Scholar]
  16. Moore ERB, Mihaylova SA, Vandamme P, Krichevsky MI, Dijkshoorn L. Microbial systematics and taxonomy: relevance for a microbial commons. Res Microbiol 2010; 161:430–438 [View Article][PubMed]
    [Google Scholar]
  17. Lane DJ. 16S/23S rRNA Sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991
    [Google Scholar]
  18. Hu Y, Feng Y, Zhang X, Zong Z, sp Adefluvii. Nov., recovered from hospital sewage. Int J Syst Evol Microbiol 2017; 67:1709–1713
    [Google Scholar]
  19. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  20. Chojnacki S, Cowley A, Lee J, Foix A, Lopez R. Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. Nucleic Acids Res 2017; 45:W550–W553 [View Article][PubMed]
    [Google Scholar]
  21. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  22. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  26. Ankenbrand MJ, Keller A. bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome 2016; 59:783–791 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. Rosselló-Móra R, Amann R. Past and future species definitions for bacteria and archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article][PubMed]
    [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  30. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  31. Wayne LG. International committee on systematic bacteriology: Announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Zentralblatt für Bakteriologie, Mikrobiologie und Hygiene Series A: Medical Microbiology, Infectious Diseases, Virology . Parasitology 1988; 268:433–434
    [Google Scholar]
  32. 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]
  33. Cowan PI. And steel's manual for the identification of medical bacteria. J Clin Pathol 1993; 46:975
    [Google Scholar]
  34. Pandey KK, Mayilraj S, Chakrabarti T. Pseudomonas indica sp. nov., a novel butane-utilizing species. Int J Syst Evol Microbiol 2002; 52:1559–1567 [View Article][PubMed]
    [Google Scholar]
  35. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 1990; 101:1–7
    [Google Scholar]
  36. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004272
Loading
/content/journal/ijsem/10.1099/ijsem.0.004272
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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