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Pedobacter pollutisoli sp. nov., Isolated from Tetrabromobisphenol A-Contaminated Soil

  • Yang Mu
  • Zhuang Ke
  • Chen-Xi Feng
  • Xiao-Wei Wang
  • Xiao-Wen Wang
  • Hong-Mei Wang
  • Qing ChenEmail author
  • Jian He
Article

Abstract

A Gram-stain negative, strictly aerobic, non-spore forming, non-motile, rod-shaped bacterium, designated TBBPA-24T, was isolated from tetrabromobisphenol A-contaminated soil in China. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain TBBPA-24T was most closely related to Pedobacter nanyangensis Q4T (96.5%) and Pedobacter ‘zeaxanthinifaciens’ TDMA-5T (96.1%). Chemotaxonomic analysis revealed that strain TBBPA-24T possessed MK-7 as the major respiratory quinone and lipid, aminolipid, phospholipid, phosphatidylethanolamine, and phosphoaminolipid as the major polar lipid. The major fatty acids were iso-C15:0 (40.2%), summed feature 3 (C16:1ω6c and/or C16:1ω7c, 25.6%) and iso-C17:0 3-OH (16.4%). The genomic DNA G+C content of strain TBBPA-24T was 43.9 mol%. Based on the phylogenetic, phenotypic characteristics, and chemotaxonomic data, strain TBBPA-24T is considered a novel species of the genus Pedobacter, for which the name Pedobacter pollutisoli sp. nov. is proposed. The type strain TBBPA-24T (= KCTC 62314T = CCTCC AB 2017244T) is proposed.

Notes

Acknowledgements

This work was financially supported through grants from the National Natural Science Foundation of China (31600080) and the Natural Science Foundation of Shandong Province, China (ZR2016CB29).

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research Involving Human Participants and/or Animals

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

284_2019_1643_MOESM1_ESM.docx (544 kb)
Supplementary material 1 (DOCX 543 KB)

References

  1. 1.
    An DS, Kim SG, Ten LN, Cho CH (2009) Pedobacter daechungensis sp. nov., from freshwater lake sediment in South Korea. Int J Syst Evol Microbiol 59:69–72CrossRefGoogle Scholar
  2. 2.
    Asker D, Beppu T, Ueda K (2008) Nubsella zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Sphingobacteriaceae isolated from freshwater. Int J Syst Evol Microbiol 58:601–606CrossRefGoogle Scholar
  3. 3.
    Baik KS, Park YD, Kim MS, Park SC, Moon EY, Rhee MS, Choi JH, Seong CN (2007) Pedobacter koreensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 57:2079–2083CrossRefGoogle Scholar
  4. 4.
    Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070Google Scholar
  5. 5.
    Buck JD (1982) Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993Google Scholar
  6. 6.
    Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230CrossRefGoogle Scholar
  7. 7.
    Felsenstein J (1981)) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefGoogle Scholar
  8. 8.
    Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  9. 9.
    Gallego V, Garcıà MT, Ventosa A (2006) Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 56:1853–1858CrossRefGoogle Scholar
  10. 10.
    Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL, Holben WE, Gannon JE (2009) Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int J Syst Evol Microbiol 59:1720–1726CrossRefGoogle Scholar
  11. 11.
    Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  12. 12.
    Hoang VA, Kim YJ, Nguyen NL, Min JW, Yang DC (2013) Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 63:1273–1279CrossRefGoogle Scholar
  13. 13.
    Hwang CY, Choi DH, Cho BC (2006) Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 56:1831–1836CrossRefGoogle Scholar
  14. 14.
    Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721CrossRefGoogle Scholar
  15. 15.
    Kook MC, Park YJ, Yi TH (2014) Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 64:1789–1794CrossRefGoogle Scholar
  16. 16.
    Lane DL (1991) 16S/23S rRNA sequencing. In: Stackebrandt ER, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175Google Scholar
  17. 17.
    Li R, Zheng JW, Wang R, Song Y, Chen Q, Yang X, Li SP, Jiang JD (2010) Biochemical degradation pathway of dimethoate by Paracoccus sp. Lgjj-3 isolated from treatment wastewater. Int J Biodeterior Biodegrad 64:51–57CrossRefGoogle Scholar
  18. 18.
    Mandel M, Marmur J (1968) Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B:195–206CrossRefGoogle Scholar
  19. 19.
    Mccarthy AJ, Cross T (1984) A taxonomic study of Thermomonospora and other monosporic Actinomycetes. Microbiol-SGM 130:5–25CrossRefGoogle Scholar
  20. 20.
    Muurholm S, Cousin S, Päuker O, Brambilla E, Stackebrandt E (2007) Pedobacter duraquae sp. nov. Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet. Int J Syst Evol Microbiol 57:2221–2227CrossRefGoogle Scholar
  21. 21.
    Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory, Cold Spring HarborGoogle Scholar
  22. 22.
    Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE: MIDIGoogle Scholar
  23. 23.
    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  24. 24.
    Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K, Joubert JJ (1998) 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 Bacteriol 48:165–177CrossRefGoogle Scholar
  25. 25.
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using Maximum Likelihood, evolutionary Distance, and Maximum Parsimony methods. Mol Biol Evo 28:2731–2739CrossRefGoogle Scholar
  26. 26.
    Ten LN, Liu QM, Im WT, Lee M, Yang DC, Lee ST (2006) Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 56:2565–2570CrossRefGoogle Scholar
  27. 27.
    Tindall BJ (1990) A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130CrossRefGoogle Scholar
  28. 28.
    Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202CrossRefGoogle Scholar
  29. 29.
    Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefGoogle Scholar
  30. 30.
    Roh SW, Quan ZX, Nam YD, Chang HW, Kim KH, Kim MK, Im WT, Jin L, Kim SH (2008) Pedobacter agri sp. nov., from soil. Int J Syst Evol Microbiol 58:1640–1643CrossRefGoogle Scholar
  31. 31.
    Oh HW, Kim BC, Park DS, Jeong WJ, Kim H, Lee KH, Kim SU (2013) Pedobacter luteus sp. nov., isolated from soil. Int J Syst Evol Microbiol 63:1304–1310CrossRefGoogle Scholar
  32. 32.
    Yang DJ, Hong JK (2017) Pedobacter solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 67:4814–4819CrossRefGoogle Scholar
  33. 33.
    Yang JE, Son HM, Lee JM, Shin HS, Park SY, Lee DG, Kook MC, Yi TH (2013) Pedobacter ginsenosidimutans sp. nov., with ginsenoside-converting activity. Int J Syst Evol Microbiol 63:4396–4401CrossRefGoogle Scholar
  34. 34.
    Zhang DC, Schinner F, Margesin R (2010) Pedobacter bauzanensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 60:2592–2595CrossRefGoogle Scholar
  35. 35.
    Zhang B, Liu ZQ, Zheng YG (2017) Pedobacter quisquiliarum sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol.  https://doi.org/10.1099/ijsem.0.002531 Google Scholar
  36. 36.
    Zhang H, Zhang J, Song M, Cheng MG, Wu YD, Guo SH, Li Q, Hong Q, Huang X (2015) Pedobacter nanyangensis sp. nov., isolated from herbicide-contaminated soil. Int J Syst Evol Microbiol 65:3517–3521CrossRefGoogle Scholar
  37. 37.
    Zhou Z, Jiang F, Wang S, Peng F, Dai J, Li W, Fang C (2012) Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus. Int J Syst Evol Microbiol 62:1963–1969CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Yang Mu
    • 2
  • Zhuang Ke
    • 2
  • Chen-Xi Feng
    • 1
  • Xiao-Wei Wang
    • 1
  • Xiao-Wen Wang
    • 1
  • Hong-Mei Wang
    • 1
  • Qing Chen
    • 1
    • 2
    Email author
  • Jian He
    • 2
  1. 1.College of Life SciencesZaozhuang UniversityZaozhuangPeople’s Republic of China
  2. 2.Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life SciencesNanjing Agricultural UniversityNanjingPeople’s Republic of China

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