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Volume 65, Issue Pt_9

sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid Free

Abstract

Strain Kp5.2 is an aerobic, Gram-negative soil bacterium that was isolated in Freiberg, Saxony, Germany. The cells were motile and rod-shaped. Optimal growth was observed at 20–30 °C. The fatty acids of strain Kp5.2 comprised mainly Cω7 and summed feature 3 (Cω7/iso-C 2-OH). The major respiratory quinone was Q-10. The major polar lipids of strain Kp5.2 were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The G+C content of the genomic DNA was 63.7 %. Sequencing of the 16S rRNA gene of strain Kp5.2 allowed its classification into the family , and the sequence showed the highest similarity to those of members of the genus , with SC13E-S71 (99.15 % similarity), Gsoil 124 (98.96 %), S37 (98.90 %) and BZ30 (98.51 %) as the nearest neighbours. DNA–DNA hybridization and further characterization revealed that strain Kp5.2 can be considered to represent a novel species of the genus . Hence, the name sp. nov. is proposed, with the type strain Kp5.2 ( = DSM 28731 = LMG 28478).

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2015-09-01
2024-04-25
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References

  1. Alias-Villegas C., Jurado V., Laiz L., Saiz-Jimenez C. ( 2013;). Sphingopyxis italica sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 63 2565–2569 [View Article] [PubMed] .
     [Google Scholar]
  2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. ( 1990;). Basic local alignment search tool. J Mol Biol 215 403–410 [View Article] [PubMed] .
     [Google Scholar]
  3. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. ( 1997;). Gapped blast psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25 3389–3402 [View Article] [PubMed] .
     [Google Scholar]
  4. Busse H.-J., Kämpfer P., Denner E.B.M. ( 1999;). Chemotaxonomic characterisation of Sphingomonas . J Ind Microbiol Biotechnol 23 242–251 [View Article] [PubMed] .
     [Google Scholar]
  5. Campbell J.W., Morgan-Kiss R.M., Cronan J.E. Jr ( 2003;). A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic beta-oxidation pathway. Mol Microbiol 47 793–805 [View Article] [PubMed] .
     [Google Scholar]
  6. Cashion P., Holder-Franklin M.A., McCully J., Franklin M. ( 1977;). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81 461–466 [View Article] [PubMed] .
     [Google Scholar]
  7. De Ley J., Cattoir H., Reynaerts A. ( 1970;). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12 133–142 [View Article] [PubMed] .
     [Google Scholar]
  8. Dorn E., Hellwig M., Reineke W., Knackmuss H.-J. ( 1974;). Isolation and characterization of a 3-chlorobenzoate degrading pseudomonad. Arch Microbiol 99 61–70 [View Article] [PubMed] .
     [Google Scholar]
  9. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368–376 [View Article] [PubMed] .
     [Google Scholar]
  10. Gaby W.L., Hadley C. ( 1957;). Practical laboratory test for the identification of Pseudomonas aeruginosa . J Bacteriol 74 356–358 [PubMed].
     [Google Scholar]
  11. Gerhardt P., Murray R.G.E., Costilow R.N., Nester E.W., Wood W.A., Krieg N.R., Phillips G.B. ( 1981). Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology;.
     [Google Scholar]
  12. Godoy F., Vancanneyt M., Martínez M., Steinbüchel A., Swings J., Rehm B.H.A. ( 2003;). Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov. Int J Syst Evol Microbiol 53 473–477 [View Article] [PubMed] .
     [Google Scholar]
  13. Gordon D. ( 2003;). Viewing and editing assembled sequences using Consed. . In Current Protocols in Bioinformatics, pp. 11.2.1–11.2.43 Chichester: Wiley; [View Article].
     [Google Scholar]
  14. Gordon D., Abajian C., Green P. ( 1998;). Consed: a graphical tool for sequence finishing. Genome Res 8 195–202 [View Article] [PubMed] .
     [Google Scholar]
  15. Gram C. ( 1884;). Über die isolirte Färbung der Schizomyceten in Schnitt-und Trockenpräparaten. Fortschr Med 2 185–884 (in German) .
     [Google Scholar]
  16. Halebian S., Harris B., Finegold S.M., Rolfe R.D. ( 1981;). Rapid method that aids in distinguishing Gram-positive from Gram-negative anaerobic bacteria. J Clin Microbiol 13 444–448 [PubMed].
     [Google Scholar]
  17. Huss V.A.R., Festl H., Schleifer K.H. ( 1983;). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4 184–192 [View Article] [PubMed] .
     [Google Scholar]
  18. Kämpfer P., Kroppenstedt R.M. ( 1996;). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42 989–1005 [View Article].
     [Google Scholar]
  19. Kimura M. ( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 111–120 [View Article] [PubMed] .
     [Google Scholar]
  20. Kluge A.G., Farris F.S. ( 1969;). Quantitative phyletics and the evolution of anurans. Syst Zool 18 1–32 [View Article].
     [Google Scholar]
  21. Kroppenstedt R.M. ( 1985;). Fatty acid and menaquinone analysis of actinomycetes and related organisms. . In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series vol. 20), pp. 173–199. Edited by Goodfellow M., Minnikin D. E. New York: Academic Press;.
     [Google Scholar]
  22. Kuykendall L.D., Roy M.A., O'Neill J.J., Devine T.E. ( 1988;). Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 38 358–361 [View Article].
     [Google Scholar]
  23. Lee H.W., Ten I.L., Jung H.M., Liu Q.M., Im W.T., Lee S.T. ( 2008;). Sphingopyxis panaciterrae sp. nov., isolated from soil from ginseng field. J Microbiol Biotechnol 18 1011–1015 [PubMed].
     [Google Scholar]
  24. Meyer F., Goesmann A., McHardy A.C., Bartels D., Bekel T., Clausen J., Kalinowski J., Linke B., Rupp O., other authors, other authors. ( 2003;). GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31 2187–2195 [View Article] [PubMed] .
     [Google Scholar]
  25. Miller L.T. ( 1982;). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16 584–586 [PubMed].
     [Google Scholar]
  26. Oelschlägel M., Gröning J.A.D., Tischler D., Kaschabek S.R., Schlömann M. ( 2012;). Styrene oxide isomerase of Rhodococcus opacus 1CP, a highly stable and considerably active enzyme. Appl Environ Microbiol 78 4330–4337 [View Article] [PubMed] .
     [Google Scholar]
  27. Oelschlägel M., Zimmerling J., Schlömann M., Tischler D. ( 2014;). Styrene oxide isomerase of Sphingopyxis sp. Kp5.2. Microbiology 160 2481–2491 [View Article] [PubMed] .
     [Google Scholar]
  28. Oelschlägel M., Kaschabek S.R., Zimmerling J., Schlömann M., Tischler D. ( 2015;). Co-metabolic formation of substituted phenylacetic acids by styrene-degrading bacteria. Biotechnol Rep (Amst) 6 20–26 [View Article].
     [Google Scholar]
  29. Rachel R., Meyer C., Klingl A., Gürster S., Heimerl T., Wasserburger N., Burghardt T., Küper U., Bellack A., other authors. ( 2010;). Analysis of the ultrastructure of archaea by electron microscopy. Methods Cell Biol 96 47–69 [PubMed]. [CrossRef]
    [Google Scholar]
  30. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406–425 [PubMed].
     [Google Scholar]
  31. Sambrook J., Russell D.W., Irwin N., Janssen K.A. ( 2001). Molecular Cloning: a Laboratory Manual , 3rd edn. Cold Spring Harbor Laboratory, NY: Cold Spring Harbor;.
     [Google Scholar]
  32. Snell K.D., Feng F., Zhong L., Martin D., Madison L.L. ( 2002;). YfcX enables medium-chain-length poly(3-hydroxyalkanoate) formation from fatty acids in recombinant Escherichia coli fadB strains. J Bacteriol 184 5696–5705 [View Article] [PubMed] .
     [Google Scholar]
  33. Takeuchi M., Hamana K., Hiraishi A. ( 2001;). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51 1405–1417 [PubMed]. [CrossRef]
    [Google Scholar]
  34. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 2725–2729 [View Article] [PubMed] .
     [Google Scholar]
  35. Teufel R., Mascaraque V., Ismail W., Voss M., Perera J., Eisenreich W., Haehnel W., Fuchs G. ( 2010;). Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc Natl Acad Sci U S A 107 14390–14395 [View Article] [PubMed] .
     [Google Scholar]
  36. Tindall B.J. ( 1990a;). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13 128–130 [View Article].
     [Google Scholar]
  37. Tindall B.J. ( 1990b;). Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66 199–202 [View Article].
     [Google Scholar]
  38. Tindall B.J., Sikorski J., Smibert R.M., Krieg N.R. ( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology , 3rd edn.., pp. 330–393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology; [View Article].
     [Google Scholar]
  39. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.H., Moore W.E.C., Murray R.G.E., other authors. ( 1987;). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37 463–464 [View Article].
     [Google Scholar]
  40. Wilson K. ( 2001;). Preparation of genomic DNA from bacteria. . In Current Protocols in Molecular Biology, pp. 2.4.1–2.4.5 Chichester: Wiley; [View Article].
     [Google Scholar]
  41. Yabuuchi E., Yano I., Oyaizu H., Hashimoto Y., Ezaki T., Yamamoto H. ( 1990;). Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas . Microbiol Immunol 34 99–119 [View Article] [PubMed] .
     [Google Scholar]
  42. Yang S.-Y., Li J., He X.-Y., Cosloy S.D., Schulz H. ( 1988;). Evidence that the fadB gene of the fadAB operon of Escherichia coli encodes 3-hydroxyacyl-coenzyme A (CoA) epimerase, (3-cis- (2-trans-enoyl-CoA isomerase, and enoyl-CoA hydratase in addition to 3-hydroxyacyl-CoA dehydrogenase. J Bacteriol 170 2543–2548 [PubMed].
     [Google Scholar]
  43. Zhang D.C., Liu H.C., Xin Y.H., Zhou Y.G., Schinner F., Margesin R. ( 2010;). Sphingopyxis bauzanensis sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 60 2618–2622 [View Article] [PubMed] .
     [Google Scholar]
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Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid
Int J Syst Evol Microbiol 65, 3008 (2015); https://doi.org/10.1099/ijs.0.000371
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