1887

Abstract

A Gram-stain-negative aerobic bacterium, strain 11K1, was isolated from a rhizosphere soil of broad bean collected from Qujing, Yunnan, PR China and characterized by using polyphasic taxonomy. The bacterial cells of strain 11K1 were rod-shaped, motile by two polar flagella and positive for oxidase and catalase. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain had the highest similarities to DSM 13194 (99.52 %), CFBP 5737 (99.45 %), subsp. s NBRC 3904 (99.31 %), DSM 13647 (99.25 %) and JCM11938 (99.24 %). Multilocus sequence analysis using the 16S rRNA, , and gene sequences demonstrated that strain 11K1 was a member of the subgroup within the lineage, but was distant from all closely related species. The average nucleotide identity and DNA–DNA hybridization values were lower than recommended thresholds of 95 and 70 %, respectively, for species delineation. The major isoprenoid quinone of strain 11K1 was ubiquinone (Q-9) and the major cellular fatty acids were C, summed feature 3 (C ω7/C ω6), summed feature 8 (C ω7/C ω6) and C cyclo. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and two unidentified lipids. Based on the results of phenotypic characterization, phylogenetic analysis and genome comparison, strain 11K1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 11K1 (=GDMCC 1.1743=KACC 21650).

Funding
This study was supported by the:
  • Li-Qun Zhang , National Natural Science Foundation of China , (Award 31872020)
  • Li-Qun Zhang , Special Fund for Agro-scientific Research in the Public Interest , (Award 201503109)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004373
2020-08-10
2021-02-26
Loading full text...

Full text loading...

References

  1. Migula W. Uber einneues system Der Bakterien. Arb Bakteriol Inst Karlsruhe 1894; 1:235–238
    [Google Scholar]
  2. Zhao H, Liu Y-P, Zhang L-Q. In silico and genetic analyses of cyclic lipopeptide synthetic gene clusters in Pseudomonas sp. 11K1. Front Microbiol 2019; 10:544 [CrossRef][PubMed]
    [Google Scholar]
  3. Lanotte P, Watt S, Mereghetti L, Dartiguelongue N, Rastegar-Lari A et al. Genetic features of Pseudomonas aeruginosa isolates from cystic fibrosis patients compared with those of isolates from other origins. J Med Microbiol 2004; 53:73–81 [CrossRef][PubMed]
    [Google Scholar]
  4. Janek T, Łukaszewicz M, Rezanka T, Krasowska A. Isolation and characterization of two new lipopeptide biosurfactants produced by Pseudomonas fluorescens BD5 isolated from water from the Arctic Archipelago of Svalbard. Bioresour Technol 2010; 101:6118–6123 [CrossRef][PubMed]
    [Google Scholar]
  5. Achouak W, Sutra L, Heulin T, Meyer JM, Fromin N et al. Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., two root-associated bacteria isolated from Brassica napus and Arabidopsis thaliana . Int J Syst Evol Microbiol 2000; 50 Pt 1:9–18 [CrossRef][PubMed]
    [Google Scholar]
  6. Azhar EI, Papadioti A, Bibi F, Ashshi AM, Raoult D et al. Pseudomonas saudimassiliensis’ sp. nov. a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia. New Microbes New Infect 2017; 16:43–44 [CrossRef]
    [Google Scholar]
  7. Gross H, Loper JE. Genomics of secondary metabolite production by Pseudomonas spp. Nat Prod Rep 2009; 26:1408–1446 [CrossRef][PubMed]
    [Google Scholar]
  8. Tamaoka J, Ha DM, Komagata K. Reclassification of Pseudomonas acidovorans den Dooren de Jong 1926 and Pseudomonas testosterone Marcus and Talalay 1956 as Comamonas acidovorans comb. nov. and Comamonas testostersni comb. nov., with an emended description of the genus. Int J Syst Evol Microbiol 1987; 1:52–59
    [Google Scholar]
  9. 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 [CrossRef][PubMed]
    [Google Scholar]
  10. Mulet M, Lalucat J, Garcia-Valdes E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010; 6:1513–1530
    [Google Scholar]
  11. Hesse C, Schulz F, Bull CT, Shaffer BT, Yan Q et al. Genome-based evolutionary history of Pseudomonas spp. Environ Microbiol 2018; 20:2142–2159 [CrossRef][PubMed]
    [Google Scholar]
  12. Lalucat J, Mulet M, Gomila M, García-Valdés E. Genomics in bacterial taxonomy: impact on the genus Pseudomonas . Genes 2020; 11:139–17 [CrossRef][PubMed]
    [Google Scholar]
  13. Pascual J, Lucena T, Ruvira MA, Giordano A, Gambacorta A et al. Pseudomonas litoralis sp. nov., isolated from Mediterranean seawater. Int J Syst Evol Microbiol 2012; 62:438–444 [CrossRef][PubMed]
    [Google Scholar]
  14. 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 [CrossRef][PubMed]
    [Google Scholar]
  15. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  17. 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 [CrossRef][PubMed]
    [Google Scholar]
  18. 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 [CrossRef][PubMed]
    [Google Scholar]
  19. 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 [CrossRef][PubMed]
    [Google Scholar]
  20. 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 [CrossRef][PubMed]
    [Google Scholar]
  21. 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 [CrossRef]
    [Google Scholar]
  22. 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]
  23. Sun J, Wang W, Ying Y, Zhu X, Liu J et al. Pseudomonas profundi sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2018; 68:1776–1780 [CrossRef][PubMed]
    [Google Scholar]
  24. Tarrand JJ, Gröschel DH. Rapid, modified oxidase test for oxidase-variable bacterial isolates. J Clin Microbiol 1982; 16:772–774 [CrossRef][PubMed]
    [Google Scholar]
  25. Jeffries CD, Holtmian DF, Guse DG. Rapid method for determining the activity of microorganisms on nucleic acids. J Bacteriol 1957; 73:590–591 [CrossRef][PubMed]
    [Google Scholar]
  26. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [CrossRef]
    [Google Scholar]
  27. Collins MD, Jones D. A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 1981; 51:129–134 [CrossRef][PubMed]
    [Google Scholar]
  28. Minnikin DE, Abdolrahimzadeh H. Thin-Layer chromatography of bacterial lipids on sodium acetate-impregnated silica gel. J Chromatogr 1971; 63:452–454 [CrossRef][PubMed]
    [Google Scholar]
  29. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 1990; 101:1–7
    [Google Scholar]
  30. Chen P, Li S, Li QX, Peizhen Chen PZ, SP L, QX L. Pseudomonas tianjinensis sp. nov., isolated from domestic sewage. Int J Syst Evol Microbiol 2018; 68:2760–2769 [CrossRef][PubMed]
    [Google Scholar]
  31. Arnau VG, Sánchez LA, Delgado OD. Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment. Int J Syst Evol Microbiol 2015; 65:424–431 [CrossRef][PubMed]
    [Google Scholar]
  32. Sikorski J, Stackebrandt E, Wackernagel W. Pseudomonas kilonensis sp. nov., a bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 2001; 51:1549–1555 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004373
Loading
/content/journal/ijsem/10.1099/ijsem.0.004373
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