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Current Microbiology

, Volume 70, Issue 1, pp 110–118 | Cite as

Paradevosia shaoguanensis gen. nov., sp. nov., Isolated from a Coking Wastewater

  • Shuang Geng
  • Xin-Chi Pan
  • Ran Mei
  • Ya-Nan Wang
  • Ji-Quan Sun
  • Xue-Ying Liu
  • Yue-Qin Tang
  • Xiao-Lei WuEmail author
Article

Abstract

A Gram staining negative, rod-shaped, aerobic bacterial strain J5-3T with a single polar flagellum was isolated from coking wastewater collected from Shaoguan, Guangdong, China. It was motile and capable of optimal growth at pH 6–8, 30 °C, and 0–2 % (w/v) NaCl. Its predominant fatty acids were 11-methyl C18:1 ω7c (29.2 %), C16:0 (20.6 %), C19:0 cyclo ω8c (18.2 %), C18:0 (11.0 %), and C18:1 ω7c/C18:1 ω6c (10.9 %) when grown on trypticase soy agar. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids (GL1, GL2), and two unknown phospholipid (PL1, PL2). The predominant ubiquinone was Q-10, and the genome DNA G+C content was 61.7 mol %. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain J5-3T belonged to the family Hyphomicrobiaceae in Alphaproteobacteria. It shared the 16S rRNA gene sequence similarities of 93.8–96.1 % with the genus Devosia, 94.5–94.8 % with the genus Pelagibacterium, and <92.0 % with all the other type strains in family Hyphomicrobiaceae. It can be distinguished from the closest phylogenetic neighbors based on several phenotypic and genotypic features, including α-galactosidase activity, tetracycline susceptibility, major fatty acid composition, polar lipid profile, DNA gyrase B subunit (gyrB) gene sequence, and random-amplified polymorphic DNA profile. Therefore, we consider strain J5-3T to represent a novel species of a novel genus within the family Hyphomicrobiaceae, for which the name Paradevosia shaoguanensis gen. nov., sp. nov. is proposed. The type strain of Paradevosia shaoguanensis is J5-3T (=CGMCC 1.12430T =LMG 27409T).

Keywords

gyrB Gene Major Polar Lipid China General Microbiological Culture Collection Center Coke Wastewater Single Polar Flagellum 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The authors thank the Institute of Microbiology, Chinese Academy of Sciences, for providing the transmission electron microscopy facility. This study was supported by the National Natural Science Foundation of China (31225001), and the National High Technology Research and Development Program (“863” Programs: 2012AA02A703 and 2013AA065701).

Supplementary material

284_2014_689_MOESM1_ESM.doc (2 mb)
Supplementary material 1 (DOC 2082 kb)

References

  1. 1.
    Andrews JM (2008) BSAC standardized disc susceptibility testing method (version 7). J Antimicrob Chemother 62:256–278PubMedCrossRefGoogle Scholar
  2. 2.
    Cai M, Wang L, Cai H, Li Y, Wang YN, Tang YQ, Wu XL (2011) Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soil. Int J Syst Evol Microbiol 61:1767–1775PubMedCrossRefGoogle Scholar
  3. 3.
    Embley TM (1991) The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol 13:171–174PubMedCrossRefGoogle Scholar
  4. 4.
    Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376PubMedCrossRefGoogle Scholar
  5. 5.
    Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  6. 6.
    Fraser SL, Jorgensen JH (1997) Reappraisal of the antimicrobial susceptibilities of Chtyseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 41:2738–2741PubMedCentralPubMedGoogle Scholar
  7. 7.
    Garrity GM, Bell JA, Lilburn T (2005) Family VIII. Hyphomicrobiaceae Babudieri. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 476–477Google Scholar
  8. 8.
    Geng S, Pan XC, Mei R, Wang YN, Sun JQ, Liu XY, Tang YQ, Wu XL (2014) Ottowia shaoguanensis sp. nov., isolated from coking wastewater. Curr Microbiol 68:324–329PubMedCrossRefGoogle Scholar
  9. 9.
    Gong XC, Liu ZS, Guo P, Chi CQ, Chen J, Wang XB, Tang YQ, Wu XL, Liu CZ (2012) Bacteria in crude oil survived autoclaving and stimulated differentially by exogenous bacteria. PLoS ONE 7:e40842PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Hwang CY, Cho BC (2008) Cucumibacter marinus gen. nov., sp. nov., a marine bacterium in the family Hyphomicrobiaceae. Int J Syst Evol Microbiol 58:1591–1597PubMedCrossRefGoogle Scholar
  11. 11.
    Jadhav VV, Jamle MM, Pawar PD, Devare MN, Bhadekar RK (2010) Fatty acid profiles of PUFA producing antarctic bacteria: correlation with RAPD analysis. Ann Microbiol 60:693–699CrossRefGoogle Scholar
  12. 12.
    Kaiser JP, Feng YC, Bollag JM (1996) Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions. Microbiol Rev 60:483–498PubMedCentralPubMedGoogle Scholar
  13. 13.
    Kates M (1986) Techniques of lipidology: isolation, analysis, and identification of lipids, 2nd edn. Elsevier Ltd, Amsterdam, pp 100–110Google 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 62:716–721PubMedCrossRefGoogle Scholar
  15. 15.
    Komagata K, Suzuki K (1987) Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 19:161–207CrossRefGoogle Scholar
  16. 16.
    Kumar M, Verma M, Lal R (2008) Devosia chinhatensis sp. nov., isolated from a hexachlorocyclohexane (HCH) dump site in India. Int J Syst Evol Microbiol 58:861–865PubMedCrossRefGoogle Scholar
  17. 17.
    Mandel M, Igambi L, Bergenda J, Dodson ML, Scheltge E (1970) Correlation of melting temperature and cesium chloride buoyant density of bacterial deoxyribonucleic acid. J Bacteriol 101:333–338PubMedCentralPubMedGoogle Scholar
  18. 18.
    Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218CrossRefGoogle Scholar
  19. 19.
    Moschetti G, Blaiotta G, Aponte M, Catzeddu P, Villani F, Deiana P, Coppola S (1998) Random amplified polymorphic DNA and amplified ribosomal DNA spacer polymorphism: powerful methods to differentiate Streptococcus thermophilusstrains. J Appl Microbiol 85:25–36PubMedCrossRefGoogle Scholar
  20. 20.
    Nakagawa Y, Sakane T, Yokota A (1996) Transfer of ‘‘Pseudomonas riboflavina’’ (Foster 1944), a gram-negative, motile rod with long-chain 3-hydroxy fatty acids, to Devosia riboflavina gen. nov., sp. nov., nom. rev. Int J Syst Bacteriol 46:16–22PubMedCrossRefGoogle Scholar
  21. 21.
    Rambeloarisoa E, Rontani JF, Giusti G, Duvnjak Z, Bertrand JC (1984) Degradation of crude oil by a mixed population of bacteria isolated from sea-surface foams. Mar Biol 83:69–81CrossRefGoogle Scholar
  22. 22.
    Reginensi SM, Gonzalez MJ, Olivera JA, Sosa M, Juliano P, Bermudez J (2011) RAPD-based screening for spore-forming bacterial populations in Uruguayan commercial powdered milk. Int J Food Microbiol 148:36–41PubMedCrossRefGoogle Scholar
  23. 23.
    Ren Y, Wei CH, Wu CF, Li BG (2007) Environmental and biological characteristics of coking wastewater. Acta Sci Circumst 27:1094–1100Google Scholar
  24. 24.
    Rzhetsky A, Nel M (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10:1073–1095PubMedGoogle Scholar
  25. 25.
    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  26. 26.
    Smibert RM, Krieg NR (1994) Phenotypic characterization. Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654Google Scholar
  27. 27.
    Sun JQ, Xu L, Tang YQ, Chen FM, Liu WQ, Wu XL (2011) Degradation of pyridine by one Rhodococcus strain in the presence of chromium (VI) or phenol. J Hazard Mater 191:62–68PubMedCrossRefGoogle Scholar
  28. 28.
    Sun JQ, Xu L, Tang YQ, Chen FM, Zhao JJ, Wu XL (2014) Bacterial pyridine hydroxylation is ubiquitous in environment. Appl Microbiol Biotechnol 98:455–464PubMedCrossRefGoogle Scholar
  29. 29.
    Takai K, Inoue A, Horikoshi K (2002) Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal vent system. Int J Syst Evol Microbiol 52:1089–1095PubMedCrossRefGoogle Scholar
  30. 30.
    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 Evol 28:2731–2739PubMedCentralPubMedCrossRefGoogle Scholar
  31. 31.
    Tang SK, Li WJ, Wang D, Zhang YG, Xu LH, Jiang CL (2003) Studies of the biological characteristics of some halophilic and halotolerant actinomycetes isolated from saline and alkaline soils. Actinomycetologica 17:6–10CrossRefGoogle Scholar
  32. 32.
    Wang YN, Chi CQ, Cai M, Lou ZY, Tang YQ, Zhi XY, Li WJ, Wu XL, Du X (2010) Amycolicicoccus subflavus gen. nov., sp. nov., an actinomycete isolated from a saline soil contaminated by crude oil. Int J Syst Evol Microbiol 60:638–643PubMedCrossRefGoogle Scholar
  33. 33.
    Watt PM, Hickson ID (1994) Structure and function of type II DNA topoisomerases. Biochem J 303:681–695PubMedCentralPubMedGoogle Scholar
  34. 34.
    Welsch J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218CrossRefGoogle Scholar
  35. 35.
    Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA, Sackin MJ (1983) Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743–1813PubMedGoogle Scholar
  36. 36.
    Xu HY, Chen LP, Fu SZ, Fan HX, Zhou YG, Liu SJ, Liu ZP (2009) Zhangella mobilis gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae isolated from coastal seawater. Int J Syst Evol Microbiol 59:2297–2301PubMedCrossRefGoogle Scholar
  37. 37.
    Xu XW, Huo YY, Wang CS, Oren A, Cui HL, Vedler E, Wu M (2011) Pelagibacterium halotolerans gen. nov., sp. nov. and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae. Int J Syst Evol Microbiol 61:1817–1822PubMedCrossRefGoogle Scholar
  38. 38.
    Xue DW, Feng SG, Zhao HY, Jiang H, Shen B, Shi N, Lu JJ, Liu JJ, Wang HZ (2010) The linkage maps of Dendrobium species based on RAPD and SRAP markers. J Genet Genomics 37:197–204PubMedCrossRefGoogle Scholar
  39. 39.
    Yamamoto S, Harayama S (1995) PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61:1104–1109PubMedCentralPubMedGoogle Scholar
  40. 40.
    Yee B, Oertli GE, Fuerst JA, Staley JT (2010) Reclassification of the polyphyletic genus Prosthecomicrobium to form two novel genera, Vasilyevaea gen. nov. and Bauldia gen. nov. with four new combinations: Vasilyevaea enhydra comb. nov., Vasilyevaea mishustinii comb. nov., Bauldia consociata comb. nov. and Bauldia litoralis comb. nov. Int J Syst Evol Microbiol 60:2960–2966PubMedCentralPubMedCrossRefGoogle Scholar
  41. 41.
    Yoon JH, Kang SJ, Park S (2007) Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia. Int J Syst Evol Microbiol 57:1310–1314PubMedCrossRefGoogle Scholar
  42. 42.
    Zhang DC, Redzic M, Liu HC, Zhou YG, Schinner F, Margesin R (2012) Devosia psychrophila sp. nov. and Devosia glacialis sp. nov., from alpine glacier cryoconite, and an emended description of the genus Devosia. Int J Syst Evol Microbiol 62:710–715PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Shuang Geng
    • 1
  • Xin-Chi Pan
    • 1
  • Ran Mei
    • 1
  • Ya-Nan Wang
    • 2
  • Ji-Quan Sun
    • 1
    • 3
  • Xue-Ying Liu
    • 1
  • Yue-Qin Tang
    • 4
  • Xiao-Lei Wu
    • 1
    • 3
    Email author
  1. 1.College of EngineeringPeking UniversityBeijingPeople’s Republic of China
  2. 2.Institute of BiologyHenan Academy of SciencesZhengzhouPeople’s Republic of China
  3. 3.Institute of Engineering (Baotou), College of EngineeringPeking UniversityBaotouPeople’s Republic of China
  4. 4.College of Architecture and EnvironmentSichuan UniversityChengduPeople’s Republic of China

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