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Volume 72, Issue 11

sp. nov., an aerobic denitrifying bacterium isolated from activated sludge No Access

Abstract

An aerobic denitrifying bacterium, designated as strain CPY4, was isolated from activated sludge treating urban sewage under alternating aerobic/anaerobic conditions by an enrichment culture technique. Cells of strain CPY4 were Gram-stain-negative, aerobic, long rod-shaped, motile by means of single polar flagellum and capable of aerobic denitrification with citrate as the carbon source. Growth of strain CPY4 was observed at 10–45 °C (optimum, 30–35 °C), at pH 6.0–10.5 (optimum, pH 8.0–8.5) and in 0–5 % NaCl (optimum, 0–3 %; w/v). The 16S rRNA gene sequence of strain CPY4 showed the highest similarity to ZD1 (97.9 %), followed by 59N8 (97.6 %), JC2671 (97.2 %), ZT1 (97.1 %) and 102-Py4 (96.3 %). Genome comparisons between CPY4 and other species showed highest digital DNA–DNA hybridization with ZD1 (43.8 %) and highest average nucleotide identity (ANIb and ANIm) of genome nucleotide sequences with ZD1(90.7 and 92 %, respectively). Phylogenetic analysis revealed that strain CPY4 fell within the clade comprising the type strains of species and formed a phyletic line with them, which was distinct from other members of the family . The sole respiratory ubiquinone was quinone 8. The predominant fatty acids (>10 % of the total fatty acids) of strain CPY4 were summed feature 8 (C 6 and/or C 7), summed feature 3 (C 6 and/or C 7) and C. The genomic DNA G+C content was 62.7 mol %. In the polar lipid profile, diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl ethanolamine, phospholipids and aminolipids were the major compounds. Based on the genotypic and phenotypic data, strain CPY4 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CPY4 (=JCM 34456=CGMCC 1.18722).

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  • Accepted:
  • Published Online:
Keyword(s): activated sludge , aerobic denitrification , new species and Zobellella
Funding
This study was supported by the:
  • FJIRSM and IUE Joint Research Fund (Award RHZX-2019-005)
    • Principle Award Recipient: YuChang-Ping
  • STS Project of Fujian-CAS (Award 2021T3014)
    • Principle Award Recipient: LiJiangwei
  • National Natural Science Foundation of China (Award 31870475)
    • Principle Award Recipient: HuAnyi
  • National Natural Science Foundation of China (Award 31500420)
    • Principle Award Recipient: LiJiangwei
© 2022 The Authors
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2022-11-11
2024-04-26
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References

  1. Zhang Q-L, Liu Y, Ai G-M, Miao L-L, Zheng H-Y et al. The characteristics of a novel heterotrophic nitrification-aerobic denitrification bacterium, Bacillus methylotrophicus strain L7. Bioresour Technol 2012; 108:35–44 [View Article] [PubMed]
     [Google Scholar]
  2. Joo HS, Hirai M, Shoda M. Characteristics of ammonium removal by heterotrophic nitrification-aerobic denitrification by Alcaligenes faecalis No. 4. J Biosci Bioeng 2005; 100:184–191 [View Article] [PubMed]
     [Google Scholar]
  3. Kim DJ, Lee DI, Keller J. Effect of temperature and free ammonia on nitrification and nitrite accumulation in landfill leachate and analysis of its nitrifying bacterial community by FISH. Bioresour Technol 2006; 97:459–468 [View Article]
     [Google Scholar]
  4. Third KA, Gibbs B, Newland M, Cord-Ruwisch R. Long-term aeration management for improved N-removal via SND in a sequencing batch reactor. Water Res 2005; 39:3523–3530 [View Article] [PubMed]
     [Google Scholar]
  5. Rajta A, Setia H, Shukla S, Bhatia R. Heterotrophic aerobic denitrification by novel bacterium Georgenia daeguensis ARB2 for treatment of nitrate contaminated waters. Int J Environ Sci Technol 2022; 19:3133–3144 [View Article]
     [Google Scholar]
  6. Lin YT, Shieh WY. Zobellella denitrificans gen. nov., sp. nov. and Zobellella taiwanensis sp. nov., denitrifying bacteria capable of fermentative metabolism. Int J Syst Evol Microbiol 2006; 56:1209–1215 [View Article]
     [Google Scholar]
  7. Yi H, Song J, Cho JC, Chun J. Zobellella aerophila sp. nov., isolated from seashore sand, and emended description of the genus Zobellella. Int J Syst Evol Microbiol 2011; 61:2491–2495 [View Article] [PubMed]
     [Google Scholar]
  8. Lee DW, Lee H, Kwon B-O, Khim JS, Yim UH et al. Zobellella maritima sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium, isolated from beach sediment. Int J Syst Evol Microbiol 2018; 68:2279–2284 [View Article] [PubMed]
     [Google Scholar]
  9. Song Z, Sun Q-W, Liang L-X, Zhang X-X, Li L-B et al. Zobellella endophytica sp. nov., isolated from the roots of Phragmites communis in the Kumtag Desert. Int J Syst Evol Microbiol 2018; 68:3807–3811 [View Article] [PubMed]
     [Google Scholar]
  10. Huang Z, Cao G, Chen H, Li Z, Mo C. Synergy and competition for nitrogen removal by heterotrophic nitrification-aerobic denitrification bacteria. Res Environ Sci 2017; 30:765–774
     [Google Scholar]
  11. Liu C, Shao Z. Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 2005; 55:1181–1186 [View Article] [PubMed]
     [Google Scholar]
  12. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  13. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  18. Shi W, Sun Q, Fan G, Hideaki S, Moriya O et al. gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. Nucleic Acids Res 2021; 49:D694–D705 [View Article] [PubMed]
     [Google Scholar]
  19. Luo R, Liu B, Xie Y, Li Z, Huang W et al. Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2015; 4:30 [View Article]
     [Google Scholar]
  20. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015; 43:D261–9 [View Article] [PubMed]
     [Google Scholar]
  21. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361 [View Article] [PubMed]
     [Google Scholar]
  22. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2017; 45:D566–D573 [View Article] [PubMed]
     [Google Scholar]
  23. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580 [View Article] [PubMed]
     [Google Scholar]
  28. Dong X, Cai M. Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation); 2001
     [Google Scholar]
  29. Sasser M. Technical note 101: Identification of bacteria by gas chromatography of cellular fatty acids. MIDI; 1990
  30. Qin D, Ma C, Lv M, Yu CP. Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov., isolated from a wastewater treatment plant. Int J Syst Evol Microbiol 2020; 70:1822–1829 [View Article] [PubMed]
     [Google Scholar]
  31. Komagata K, Suzuki K-I. 4 lipid and cell-wall analysis in bacterial systematics. In Methods in Microbiology Amsterdam: Elsevier; 1988 pp 161–207
     [Google Scholar]
  32. Park S, Jung YT, Choi SJ, Yoon JH. Altererythrobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2017; 67:3446–3451 [View Article] [PubMed]
     [Google Scholar]
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Zobellella iuensis sp. nov., an aerobic denitrifying bacterium isolated from activated sludge
Int J Syst Evol Microbiol 72, 005567 (2022); https://doi.org/10.1099/ijsem.0.005567
/content/journal/ijsem/10.1099/ijsem.0.005567
/content/journal/ijsem/10.1099/ijsem.0.005567
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