sp. nov., isolated from oil-contaminated soil Free

Abstract

A Gram-stain-negative, rod-shaped, non-motile and non-spore-forming bacterium, designated HAL-9, was isolated from oil-contaminated soil in Daqing oilfield, Heilongjiang Province, PR China. Strain HAL-9 was able to degrade quizalofop--ethyl and diclofop-methyl. Growth was observed at 10–35 °C (optimum, 30 °C), pH 6.0–10.0 (optimum, pH 7.0) and salinity of 0 %–5.0 % (w/v; optimum 1.0 %). The results of phylogenetic analysis based on the 16S rRNA gene indicated that strain HAL-9 belongs to the genus and showed the highest sequence similarity (98.3 %) to Y3L14, followed by DSM 11724 (95.1 %) and DSM 22361 (95.1 %). Menaquinone-7 (MK-7) was the only isoprenoid quinone. The predominant cellular fatty acids were summed feature 3 (C 7 and/or C 6), iso-C and iso-C 3-OH. The major polar lipids were phosphatidylethanolamine, three phosphoglycolipids and three unidentified lipids. The draft genome of strain HAL-9 was 5.41 Mb. The G+C content of strain HAL-9 was 40.6 mol%. Furthermore, the average nucleotide identity and DNA–DNA hybridization values between strain HAL-9 and Y3L14 were 86.2 % and 32.8 %, respectively, which were below the standard thresholds for species differentiation. On the basis of phenotypic, genotypic and phylogenetic evidence, strain HAL-9 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is HAL-9 (=ACCC 61581=CCTCC AB 2019176=KCTC 72287).

Funding
This study was supported by the:
  • 31560033 (Award 31560033)
    • Principle Award Recipient: Cheng hong Wang
  • 2018ZX0800907B-002 (Award 2018ZX0800907B-002)
    • Principle Award Recipient: Jian He
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004000
2020-01-22
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/3/1931.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004000&mimeType=html&fmt=ahah

References

  1. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N. Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting gram-negative rods in CDC groups IIk-2 and IIb. Int J Syst Evol Microbiol 1983; 33:580–598 [View Article]
    [Google Scholar]
  2. Takeuchi M, Yokota A. Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum . J Gen Appl Microbiol 1992; 38:465–482 [View Article]
    [Google Scholar]
  3. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K et al. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Evol Microbiol 1998; 48:165–177 [View Article]
    [Google Scholar]
  4. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article]
    [Google Scholar]
  5. Zhang J, Zheng J-W, Cho BC, Hwang CY, Fang C et al. Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge. Int J Syst Evol Microbiol 2012; 62:683–687 [View Article]
    [Google Scholar]
  6. Nam I-H, Kim Y, Cho D, Kim J-G, Song H et al. Effects of heavy metals on biodegradation of fluorene by a Sphingobacterium sp. strain (KM-02) isolated from polycyclic aromatic hydrocarbon-contaminated mine soil. Environ Eng Sci 2015; 32:891–898 [View Article]
    [Google Scholar]
  7. Ghosh S, Sadowsky MJ, Roberts MC, Gralnick JA, LaPara TM. Sphingobacterium sp. strain PM2-P1-29 harbours a functional tet(X) gene encoding for the degradation of tetracycline. J Appl Microbiol 2009; 106:1336–1342 [View Article]
    [Google Scholar]
  8. Beveridge TJ, Lawrence JR, Murray RGE. Sampling and staining for light microscopy. Methods for General and Molecular Microbiology, 3rd edn. American Society of Microbiology; 2007 pp 19–33
    [Google Scholar]
  9. Fraser SL, Jorgensen JH. Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 1997; 41:2738–2741 [View Article]
    [Google Scholar]
  10. Bernardet J-F, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article]
    [Google Scholar]
  11. Dong XZ, Cai MY. General Bacterial Identification System Handbook Beijing, China: Scientific Press; 2001 pp 377–385
    [Google Scholar]
  12. Zhang J, Chen S-A, Zheng J-W, Cai S, Hang B-J et al. Catellibacterium nanjingense sp. nov., a propanil-degrading bacterium isolated from activated sludge, and emended description of the genus Catellibacterium . Int J Syst Evol Microbiol 2012; 62:495–499 [View Article]
    [Google Scholar]
  13. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. , MIDI Technical Note 101. Newark, DE: MIDI, Inc; 1990
  14. 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]
  15. Kates M. Techniques of Lipidology, 2nd ed. Amsterdam: Elsevier; 1986
    [Google Scholar]
  16. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
    [Google Scholar]
  17. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
    [Google Scholar]
  18. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: a Laboratory Manual 3, 2nd ed. Cold Springs Harb Lab Press; 1989
    [Google Scholar]
  19. 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 [View Article]
    [Google Scholar]
  20. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article]
    [Google Scholar]
  21. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article]
    [Google Scholar]
  22. 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]
    [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]
    [Google Scholar]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  25. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Molecular Biology and Evolution 1992; 9:945
    [Google Scholar]
  26. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  27. 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]
    [Google Scholar]
  28. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  29. Cheng JF, Guo JX, Bian YN, Chen ZL, Li CL et al. Sphingobacterium athyrii sp. nov., a cellulose- and xylan-degrading bacterium isolated from a decaying fern (Athyrium wallichianum Ching). Int J Syst Evol Microbiol 2019; 69:752–760 [View Article]
    [Google Scholar]
  30. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article]
    [Google Scholar]
  31. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article]
    [Google Scholar]
  32. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article]
    [Google Scholar]
  33. Wu J, Hong Q, Sun Y, Hong Y, Yan Q et al. Analysis of the role of LinA and LinB in biodegradation of δ-hexachlorocyclohexane. Environ Microbiol 2007; 9:2331–2340 [View Article]
    [Google Scholar]
  34. Wang B-zhan, Guo P, Hang B-jian, Li L, He J et al. Cloning of a novel pyrethroid-hydrolyzing carboxylesterase gene from Sphingobium sp. strain JZ-1 and characterization of the gene product. Appl Environ Microbiol 2009; 75:5496–5500 [View Article]
    [Google Scholar]
  35. Nie Z-J, Hang B-J, Cai S, Xie X-T, He J et al. Degradation of cyhalofop-butyl (CyB) by Pseudomonas azotoformans strain QDZ-1 and cloning of a novel gene encoding CyB-hydrolyzing esterase. J Agric Food Chem 2011; 59:6040–6046 [View Article]
    [Google Scholar]
  36. Chen D, Kong X, Wu S, Huang J, Cheng X et al. An esterase AppH for the hydrolysis of 2-(4-aryloxyphenoxy) propionate herbicides in Sphingobium sp. strain C3. Int Biodeterior Biodegradation 2019; 136:34–40 [View Article]
    [Google Scholar]
  37. 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]
    [Google Scholar]
  38. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article]
    [Google Scholar]
  39. 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]
    [Google Scholar]
  40. Xu L, Sun J-Q, Wang L-J, Liu X-Z, Ji Y-Y et al. . Aliidiomarina soli sp. nov., isolated from saline-alkaline soil. Int J Syst Evol Microbiol 2017; 67:724–728 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004000
Loading
/content/journal/ijsem/10.1099/ijsem.0.004000
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed