sp. nov., isolated from activated sludge Free

Abstract

A Gram-stain-negative, aerobic, non-flagellated and filamentous-shaped bacterium, HX-16-21, was isolated from activated sludge. Strain HX-16-21 was able to degrade gentisate, protocatechuic acid and -hydroxybenzoic acid and herbicides quizalofop-p-ethyl and diclofop-methyl. The strain shared 97.2 % 16S rRNA gene sequence similarity to CCTCC AB 2015052 and less than 97 % similarities to other type strains. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HX-16-21 belonged to the genus and formed a subclade with CCTCC AB 2015052. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and six unidentified lipids. The major fatty acids were iso-C, iso-C G and iso-C 3-OH. The predominant respiratory quinone was menaquinone 7 (MK-7). The draft genome of strain HX-16-21 was 8.1 Mb, and the G+C content was 43.5 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain HX-16-21 and CCTCC AB 2015052 were 80.6 and 26.8 %, respectively. Based on both phenotypic and phylogenetic evidence, strain HX-16-21 is considered to represent a novel species in the genus , for which the name sp. nov. is proposed. The type strain is HX-16-21 (=KCTC 72288=ACCC 61580).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31770117)
    • Principle Award Recipient: Jian He
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2020-02-10
2024-03-29
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References

  1. Weon H-Y et al. Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 2006; 56:1777–1782 [View Article]
    [Google Scholar]
  2. Di ZK, Yang W, Tang Y, Dai J, Lei Z et al. Niastella populi sp. nov., isolated from soil of Euphrates poplar (Populus euphratica) forest, and emended description of the genus Niastella . Int J Syst Evol Microbiol 2010; 60:542–545
    [Google Scholar]
  3. Kim S-J, Hong S-B, Kwon S-W, Ahn J-H, Seok S-J et al. Niastella gongjuensis sp. nov., isolated from greenhouse soil. Int J Syst Evol Microbiol 2015; 65:3115–3118 [View Article]
    [Google Scholar]
  4. Chen L, Wang D, Yang S, Wang G. Niastella vici sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2016; 66:1768–1772 [View Article]
    [Google Scholar]
  5. Yan Z-F, Lin P, Wang Y-S, Gao W, Li C-T et al. Niastella hibisci sp. nov., isolated from rhizosphere soil of mugunghwa, the Korean national flower. Int J Syst Evol Microbiol 2016; 66:5218–5222 [View Article]
    [Google Scholar]
  6. Choi S, Kang JW, Lee JH, Seong CN. Dokdonia lutea sp. nov., isolated from Sargassum fulvellum seaweed. Int J Syst Evol Microbiol 2017; 67:4482–4486 [View Article]
    [Google Scholar]
  7. Jun Z, Shu-An C, Jin-Wei Z, Shu C, Bao-Jian H 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
    [Google Scholar]
  8. Bernardet JF, Nakagawa Y, Holmes B. 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
    [Google Scholar]
  9. Ohta H, Hattori T. Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium. Antonie van Leeuwenhoek 1983; 49:429–446
    [Google Scholar]
  10. Zhang L, Chen X-L, Hu Q, Chen K, Yan X et al. Haoranjiania flava gen. nov., sp. nov., a new member of the family Chitinophagaceae, isolated from activated sludge. Int J Syst Evol Microbiol 2016; 66:4686–4691 [View Article]
    [Google Scholar]
  11. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  12. 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]
  13. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  14. Saha P, AkmS M, Krishnamurthi S, Bhattacharya A, Chakrabarti T. Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India. Int J Syst Evol Microbiol 2005; 55:2577–2581 [View Article]
    [Google Scholar]
  15. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: a Laboratory Manual 3, 2nd edn. Cold Springs Harb Lab Press Cold Springs Harb NY; 2001
    [Google Scholar]
  16. 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]
  17. 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]
  18. Wang B-z, Guo P, Hang B-j, 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
    [Google Scholar]
  19. Hang B-J, Hong Q, Xie X-T, Huang X, Wang C-H et al. SulE, a sulfonylurea herbicide De-Esterification esterase from Hansschlegelia zhihuaiae S113. Appl Environ Microbiol 2012; 78:1962–1968 [View Article]
    [Google Scholar]
  20. Zhang J, Yin J-G, Hang B-J, Cai S, He J et al. Cloning of a novel arylamidase gene from Paracoccus sp. strain FLN-7 that hydrolyzes amide pesticides. Appl Environ Microbiol 2012; 78:4848–4855 [View Article]
    [Google Scholar]
  21. Yoon J-H, Lee ST, Park Y-H. Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 1998; 48:187–194 [View Article]
    [Google Scholar]
  22. 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]
    [Google Scholar]
  23. Thompson J, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article]
    [Google Scholar]
  24. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425
    [Google Scholar]
  25. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526
    [Google Scholar]
  26. Wolde-meskel E, Terefework Z, Å F, Lindström K. Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia. Int J Syst Evol Microbiol 2005; 55:1439–1452 [View Article]
    [Google Scholar]
  27. 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]
  28. 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]
  29. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article]
    [Google Scholar]
  30. 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]
  31. 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]
  32. 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]
  33. Zhang J, Zheng J-W, Liang B, Wang C-H, Cai S et al. Biodegradation of chloroacetamide herbicides by Paracoccus sp. FLY-8 in vitro. J Agric Food Chem 2011; 59:4614–4621 [View Article]
    [Google Scholar]
  34. Liu HM, Lou X, ZJ G et al. Isolation of an aryloxyphenoxy propanoate (AOPP) herbicide-degrading strain Rhodococcus ruber JPL-2 and the cloning of a novel carboxylesterase gene (feh). Braz J Microbiol 2015; 46:425–432
    [Google Scholar]
  35. Zhang H, Li M, Li J, Wang G, Liu Y et al. Purification and properties of a novel quizalofop-p-ethyl-hydrolyzing esterase involved in quizalofop-p-ethyl degradation by Pseudomonas sp. J-2. Microb Cell Fact 2017; 16:80–90 [View Article]
    [Google Scholar]
  36. 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]
  37. 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]
    [Google Scholar]
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