1887

Abstract

A Gram-stain-negative, aerobic, motile, short-rod-shaped bacterium with nicosulfuron-degrading ability, designated strain LAM1902, was isolated from a microbial consortium enriched with nicosulfuron as a sole nitrogen and energy source. The optimal temperature and pH for growth of strain LAM1902 were 30 °C and pH 6.0, respectively. Strain LAM1902 could grow in the presence of NaCl with concentration up to 4.0 % (w/v). Comparative analysis of 16S rRNA gene sequences revealed that LAM1902 was closely related to the members of the family to the genus , with the highest similarity to DSM 14399 (99.6 %), WZBFD3-5A2 (99.3 %) and Esp-1 (98.8 %). Multi-locus sequence analysis based on both concatenated sequences of the 16S rRNA gene and three housekeeping genes (, and ) further confirmed the intrageneric phylogenetic position of strain LAM1902. The genomic DNA G+C content of LAM1902 was 64.8 mol%. The low values of DNA–DNA hybridization (less than 43.7 %) and average nucleotide identity (less than 90.9 %) also showed that the strain was distinctly different from known species of the genus . The major fatty acids were C, C cyclo and anteiso C. Ubiquinone Q-9 was detected as the predorminant respiratory quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on phylogenetic, phenotypic and chemotaxonomic analyses and genome comparisons, we conclude that strain LAM1902 represents a novel species, for which the name sp. nov. is proposed. The type strain is LAM1902 (=JCM 33860=KCTC 72830).

Funding
This study was supported by the:
  • Fundamental Research Funds for Central Non-profit Scientific Institution (Award 1610132020009)
    • Principle Award Recipient: ZhiyongRuan
  • National Key R&D Program of China (Award 2017YFD0800702)
    • Principle Award Recipient: ZhiyongRuan
  • National Natural Science Foundation of China (Award 31860025)
    • Principle Award Recipient: QinghuaZhang
  • National Natural Science Foundation of China (Award 31670006)
    • Principle Award Recipient: ZhiyongRuan
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004632
2021-01-07
2024-11-11
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/2/ijsem004632.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004632&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. Carrión O, Miñana-Galbis D, Montes MJ, Mercadé E. Pseudomonas deceptionensis sp. nov., a psychrotolerant bacterium from the Antarctic. Int J Syst Evol Microbiol 2011; 61:2401–2405 [View Article][PubMed]
    [Google Scholar]
  3. 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]
  4. Silby MW, Winstanley C, Godfrey SAC, Levy SB, Jackson RW. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev 2011; 35:652–680 [View Article][PubMed]
    [Google Scholar]
  5. Sneath PH, Stevens M, Sackin MJ. Numerical taxonomy of Pseudomonas based on published records of substrate utilization. Antonie van Leeuwenhoek 1981; 47:423–448 [View Article][PubMed]
    [Google Scholar]
  6. Oyaizu H, Komagata K. Grouping of Pseudomonas species on the basis of cellular fatty acid composition and the quinone system with special reference to the existence of 3-hydroxy fatty acids. J Gen Appl Microbiol 1983; 29:17–40 [View Article]
    [Google Scholar]
  7. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H. Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 2000; 50:1563–1589 [View Article][PubMed]
    [Google Scholar]
  8. Mulet M, Lalucat J, García-Valdés E, Magdalena M, Jorge L. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010; 12:1513–1530 [View Article][PubMed]
    [Google Scholar]
  9. Regitano JB, Koskinen WC. Characterization of nicosulfuron availability in aged soils. J Agric Food Chem 2008; 56:5801–5805 [View Article][PubMed]
    [Google Scholar]
  10. Brusa T, Ferrari F, Bolzacchini E, Rindone B. Study on the microbiological degradation of bensulfuronmethyl. Ann Microbiol 2001; 12:205–214
    [Google Scholar]
  11. 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]
  12. Sun C, Fu G-Y, Zhang C-Y, Hu J, Xu L et al. Isolation and complete genome sequence of Algibacter alginolytica sp. nov., a novel seaweed-degrading Bacteroidetes bacterium with diverse putative polysaccharide utilization loci. Appl Environ Microbiol 2016; 82:2975–2987 [View Article][PubMed]
    [Google Scholar]
  13. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18–23 [View Article][PubMed]
    [Google Scholar]
  14. Sakamoto M, Suzuki M, Umeda M, Ishikawa I, Benno Y. Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov. Int J Syst Evol Microbiol 2002; 52:841–849 [View Article][PubMed]
    [Google Scholar]
  15. 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]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  17. 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]
  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 [View Article][PubMed]
    [Google Scholar]
  19. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  20. 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; 14:60–73 [View Article][PubMed]
    [Google Scholar]
  21. Lang E, Griese B, Spröer C, Schumann P, Steffen M et al. Characterization of 'Pseudomonas azelaica' DSM 9128, leading to emended descriptions of Pseudomonas citronellolis Seubert 1960 (Approved Lists 1980) and Pseudomonas nitroreducens Iizuka and Komagata 1964 (Approved Lists 1980), including Pseudomonas multiresinivorans as its later heterotypic synonym. Int J Syst Evol Microbiol 2007; 57:878–882 [View Article][PubMed]
    [Google Scholar]
  22. Wang Y-N, He W-H, He H, Du X, Jia B et al. Pseudomonas nitritireducens sp. nov., a nitrite reduction bacterium isolated from wheat soil. Arch Microbiol 2012; 194:809–813 [View Article][PubMed]
    [Google Scholar]
  23. Gupta SK, Kumari R, Prakash O, Lal R. Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site. Int J Syst Evol Microbiol 2008; 58:1339–1345 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. Moore L, Moore E, Murray R, Stackebrandt E, Starr M. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  26. Wang X, Wang Y, Yang X, Sun H, Li B et al. Photobacterium alginatilyticum sp. nov., a marine bacterium isolated from bottom seawater. Int J Syst Evol Microbiol 2017; 67:1912–1917 [View Article][PubMed]
    [Google Scholar]
  27. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd edn. Baltimore: Williams & Wilkins; 1967
    [Google Scholar]
  28. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  29. Nokhal TH, Schlegel HG. Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 1983; 33:26–37 [View Article]
    [Google Scholar]
  30. 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 [View Article]
    [Google Scholar]
  31. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986; 123:31–36 [View Article][PubMed]
    [Google Scholar]
  32. Kates M. Techniques of Lipidology, 2nd ed. Amsterdam: Elsevier; 1986
    [Google Scholar]
  33. 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]
  34. Moore ERB, Tindall BJ, Dos M, Santos VAP, Pieper DH. et al. Nonmedical: Pseudomonas. In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. (editors) The Prokaryotes:Volume 6: Proteobacteria: Gamma Subclass New York, NY: Springer New York; 2006 pp 646–703
    [Google Scholar]
  35. Zhou S, Song J, Dong W, Mu Y, Zhang Q, Ruan ZY et al. Nicosulfuron biodegradation by a novel cold-adapted strain Oceanisphaera psychrotolerans LAM-WHM-ZC. J Agric Food Chem 2017; 65:10243–10249 [View Article][PubMed]
    [Google Scholar]
  36. Li M, Song J, Ma Q, Kong D, Zhou Y, MM L, Ruan ZY et al. Insight into the characteristics and new mechanism of nicosulfuron biodegradation by a Pseudomonas sp. LAM1902. J Agric Food Chem 2020; 68:826–837 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004632
Loading
/content/journal/ijsem/10.1099/ijsem.0.004632
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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