1887

Abstract

A novel bacterium, designated BD-1, was isolated from a sludge sample. Cells of the novel Gram-stain-negative strain were identified to be facultative anaerobic, non-motile and short rod-shaped. Growth occurred at 15–37 °C (optimum, 30 °C), pH 5.0–10.0 (pH 7.0) and in 0–4.0  % NaCl (2.0 %, w/v). The 16S rRNA gene sequence of strain BD-1 showed the highest sequence similarity to DSM 14619 (97.0 %), followed by DSM 21699 (96.3 %) and less than 96 % to other related strains. The phylogenetic trees revealed that strain BD-1 clustered within the genus . Summed feature 3 (C 7 and/or C 6, 48.2 %), C (23.2 %) and summed feature 8 (C 7 and/or C 6, 8.6 %) were the major fatty acids (>5 %), and ubiquinone-8 was the respiratory quinone. Phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylglycerol were identified as the major polar lipids. Meanwhile, the G+C content of the DNA was 63.6 mol% based on the draft genome analysis. The average nucleotide identity and digital DNA–DNA hybridization values between strain BD-1 and DSM 14619 were 74.5 and 21.4  %, respectively. In addition, the novel strain completely degraded 500 mg l phenylacetic acid within 72 h under the condition of 3 % NaCl. Given the results of genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain BD-1 was considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The strain is a potential resource for the bioremediation of phenylacetic acid contaminated water. The type strain is BD-1 (=CGMCC 1.18541=KCTC 82183).

Funding
This study was supported by the:
  • High-qualified Talents Scientific Research Startup Foundation of Nanyang Normal University (Award 2019ZX015)
    • Principle Award Recipient: HaoZhang
  • Key Scientific Research Projects of Institutions of Higher Learning in Henan province (Award 20A180020)
    • Principle Award Recipient: HaoZhang
  • Natural Science Foundation of Henan Province (Award 212300410215)
    • Principle Award Recipient: HaoZhang
  • The special research fund from Henan Provincial Science and Technology Department (Award 212102110391)
    • Principle Award Recipient: Fa-HuPang
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2021-12-08
2022-01-28
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References

  1. Teufel R, Mascaraque V, Ismail W, Voss M, Perera J et al. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc Natl Acad Sci USA 2010; 107:14390–14395 [View Article] [PubMed]
    [Google Scholar]
  2. Erb TJ, Ismail W, Fuchs G. Phenylacetate metabolism in thermophiles: characterization of phenylacetate-CoA ligase, the initial enzyme of the hybrid pathway in Thermus thermophilus. Curr Microbiol 2008; 57:27–32 [View Article] [PubMed]
    [Google Scholar]
  3. Huang F, Li X, Guo J, Feng H, Yang F. Aromatic hydrocarbon compound degradation of phenylacetic acid by indigenous bacterial Sphingopyxis isolated from Lake Taihu. J Toxicol Environ Health A 2019; 82:1164–1171 [View Article]
    [Google Scholar]
  4. Hong Q, He J, Liu Z, Zhang GS, Shun L. One phenyl acetic acid-degrading moderate halophilic bacterium (BYS-1) isolated from sludge. J Nanjing Agri University 2003; 26:55–58 [View Article]
    [Google Scholar]
  5. Zhang H, Hua Z, Niu Q, Dong W, Zhou J et al. Isolation, identification, degradation mechanism and application of a fenoxaprop ethyl-degrading strain Rhodococcus sp. DSB-1 Acta Microbiol Sinica 2020; 60:2226–2241 [View Article]
    [Google Scholar]
  6. Bartolomé-Martín D, Martínez-García E, Mascaraque V, Rubio J, Perera J et al. Characterization of a second functional gene cluster for the catabolism of phenylacetic acid in Pseudomonas sp. strain Y2. Gene 2004; 341:167–179 [View Article] [PubMed]
    [Google Scholar]
  7. Grishin AM, Ajamian E, Tao L, Zhang L, Menard R et al. Structural and functional studies of the Escherichia coli phenylacetyl-CoA monooxygenase complex. J Biol Chem 2011; 286:10735–10743 [View Article] [PubMed]
    [Google Scholar]
  8. Cox JS, Moncja K, Mckinnes M, Van Dyke MW. Identification and characterization of preferred DNA-binding sites for the Thermus thermophilus HB8 transcriptional regulator TTHA0973. IJMS 2019; 20:3336 [View Article]
    [Google Scholar]
  9. Spring S, Jäckel U, Wagner M, Kämpfer P. Ottowia thiooxydans gen. nov., sp. nov., a novel facultatively anaerobic, N2O-producing bacterium isolated from activated sludge, and transfer of Aquaspirillum gracile to Hylemonella gracilis gen. nov., comb. nov. Int J Syst Evol Microbiol 2004; 54:99–106 [View Article] [PubMed]
    [Google Scholar]
  10. Cao J, Lai Q, Liu Y, Li G, Shao Z. Ottowia beijingensis sp. nov., isolated from coking wastewater activated sludge, and emended description of the genus Ottowia. Int J Syst Evol Microbiol 2014; 64:963–967 [View Article] [PubMed]
    [Google Scholar]
  11. Heo J, Cho H, Hong S-B, Kim J-S, Kwon S-W et al. Ottowia oryzae sp. nov., isolated from Andong sikhye, a Korean traditional rice beverage. Int J Syst Evol Microbiol 2018; 68:3096–3100 [View Article] [PubMed]
    [Google Scholar]
  12. Yi KJ, Im W-T, Kim D-W, Kim S-K. Ottowia konkukae sp. nov., isolated from rotten biji (tofu residue). Int J Syst Evol Microbiol 2018; 68:3458–3462 [View Article] [PubMed]
    [Google Scholar]
  13. Felföldi T, Kéki Z, Sipos R, Márialigeti K, Tindall BJ et al. Ottowia pentelensis sp. nov., a floc-forming betaproteobacterium isolated from an activated sludge system treating coke plant effluent. Int J Syst Evol Microbiol 2011; 61:2146–2150 [View Article] [PubMed]
    [Google Scholar]
  14. Geng S, Pan X-C, Mei R, Wang Y-N, Sun J-Q et al. Ottowia shaoguanensis sp. nov., isolated from coking wastewater. Curr Microbiol 2014; 68:324–329 [View Article] [PubMed]
    [Google Scholar]
  15. Shi S-B, Li G-D, Yang L-F, Liu C, Jiang M-G et al. Ottowia flava sp. nov., isolated from fish intestines. Antonie van Leeuwenhoek 2019; 112:1567–1575 [View Article] [PubMed]
    [Google Scholar]
  16. Beveridge TJ, Lawrence JR, Murray R. Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology, 3rd. edn New York: Wiley; 2007 pp 19–33
    [Google Scholar]
  17. Ribeiro TG, Clermont D, Branquinho R, Machado E, Peixe L et al. Citrobacter europaeus sp. nov., isolated from water and human faecal samples. Int J Syst Evol Microbiol 2017; 67:170–173 [View Article]
    [Google Scholar]
  18. Smibert RM, Krieg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology Wiley; 1994 pp 607–654
    [Google Scholar]
  19. Marmur J. A procedure for the isolation of deoxyribonucleic acid from microorganisms. Meth Enzymol 1963; 6:726–738 [View Article]
    [Google Scholar]
  20. Sipos R, Székely AJ, Palatinszky M, Révész S, Márialigeti K et al. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol Ecol 2007; 60:341–350 [View Article]
    [Google Scholar]
  21. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing ezTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
    [Google Scholar]
  22. Thompson J. 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]
  23. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article] [PubMed]
    [Google Scholar]
  24. 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] [PubMed]
    [Google Scholar]
  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 10:1073–1095 [View Article]
    [Google Scholar]
  26. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 5:1073–1095 [View Article]
    [Google Scholar]
  27. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  28. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  29. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  30. Collins MD, Goodfellow M, Minnikin DE. Isoprenoid quinones in the classification of coryneform and related bacteria. J Gen Microbiol 1979; 110:127–136 [View Article] [PubMed]
    [Google Scholar]
  31. 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] [PubMed]
    [Google Scholar]
  32. Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000; 28:27–30 [View Article]
    [Google Scholar]
  33. 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 [View Article]
    [Google Scholar]
  34. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  35. He J, Cui Z, Liu Z, Li SP. Isolation and characterization of a salt-tolerant strain A1 (Arthrobacter sp.A1) for the degradation of phenyl acetic acid. Acta Sci Circumstantiae 2002; 22:374–379 [View Article]
    [Google Scholar]
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