Biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing

Applied and Environmental Microbiology

Volumn 75, Issue 20, 2009, Pages 6471-6477

  Uhlik, Ondrej ^a,b   Jecna, Katerina ^a   Mackova, Martina ^a   Vlcek, Cestmir ^c   Hroudova, Miluse ^c   Demnerova, Katerina ^a   Paces, Vaclav ^c   Macek, Tomas ^a,b  

^a INSTITUTE OF CHEMICAL TECHNOLOGY   (Czech Republic)

^b INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^c INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; ALCALIGENES; AMINO ACID SEQUENCE; BETAPROTEOBACTERIA; BIPHENYL DIOXYGENASE; BULK SOILS; CLONE LIBRARY; MICROBIAL COMMUNITIES; PCB CONGENERS; RHIZOSPHERE SOILS; SOIL ENVIRONMENT; STABLE-ISOTOPE PROBING; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISMS;

AGRICULTURAL PRODUCTS; AMINES; AMINO ACIDS; BACTERIOLOGY; CLONING; DNA; GENES; ISOTOPES; METABOLISM; NUCLEIC ACIDS; ORGANIC ACIDS; ORGANIC POLLUTANTS; POLYCHLORINATED BIPHENYLS; PRINTED CIRCUITS;

SOILS;

BIPHENYL; BIPHENYL DIOXYGENASE ALPHA; CARBON; CARBON 13; DIOXYGENASE; ISOTOPE; POLYCHLORINATED BIPHENYL DERIVATIVE; RNA 16S; UNCLASSIFIED DRUG;

AMINO ACID; DNA; ISOTOPIC ANALYSIS; METABOLISM; MICROBIAL ACTIVITY; MICROCOSM; PCB; PERENNIAL PLANT; RHIZOSPHERE; SOIL ECOSYSTEM; SOIL POLLUTION; STABLE ISOTOPE;

ACHROMOBACTER; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BETAPROTEOBACTERIA; CLONE; DEGRADATION; GENUS; HORSERADISH; HYDROGENOPHAGA; METABOLISM; METHYLOPHILUS; METHYLOVORUS; MICROBIAL COMMUNITY; MICROCOSM; MOLECULAR LIBRARY; NONHUMAN; NUCLEOTIDE SEQUENCE; NUTRIENT; PAENIBACILLUS; PSEUDOMONAS ALCALIGENES; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOSPHERE; SOIL AMENDMENT; SOIL POLLUTION; VARIOVORAX;

ARMORACIA; BACTERIA; BASE SEQUENCE; BETAPROTEOBACTERIA; BIPHENYL COMPOUNDS; CARBON ISOTOPES; DNA PRIMERS; DNA, BACTERIAL; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYCHLORINATED BIPHENYLS; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; SOIL POLLUTANTS;

ACHROMOBACTER; ARMORACIA RUSTICANA; BETAPROTEOBACTERIA; HYDROGENOPHAGA; METHYLOPHILUS; METHYLOVORUS; PAENIBACILLUS; PSEUDOMONAS ALCALIGENES; VARIOVORAX;

EID: 70349912423     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00466-09     Document Type: Article

References (36)

1. Baker, G. C., J. J. Smith, and D. A. Cowan. 2003. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55:541-555.
2. Blanchard, M., M. J. Teil, E. Guigon, K. Larcher-Tiphagne, D. Ollivon, B. Garban, and M. Chevreuil. 2007. Persistent toxic substance inputs to the River Seine basin (France) via atmospheric deposition and urban sludge application. Sci. Total Environ. 375:232-243.
3. Braune, B. M., M. L. Mallory, G. H. Grant, R. J. Letcher, and K. G. Drouillard. 2007. Levels and trends of organochlorines and brominated flame retardants in ivory gull eggs from the Canadian Arctic, 1976 to 2004. Sci. Total Environ. 378:403-417.
4. Cebron, A., L. Bodrossy, N. Stralis-Pavese, A. C. Singer, I. P. Thompson, J. I. Prosser, and J. C. Murrell. 2007. Nutrient amendments in soil DNA stable isotope probing experiments reduce the observed methanotroph diversity. Appl. Environ. Microbiol. 73:798-807.
5. Cole, J. R., B. Chai, R. J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, G. M. Garrity, and J. M. Tiedje. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33:D294-D296.
6. de Carcer, D. A., M. Martin, M. Mackova, T. Macek, U. Karlson, and R. Rivilla. 2007. The introduction of genetically modified microorganisms designed for rhizoremediation induces changes on native bacteria in the rhizosphere but not in the surrounding soil. ISME J. 1:215-223.
7. Demnerova, K., M. Mackova, V. Spevakova, K. Beranova, L. Kochankova, P. Lovecka, E. Ryslava, and T. Macek. 2005. Two approaches to biological decontamination of groundwater and soil polluted by aromatics - characterization of microbial populations. Int. Microbiol. 8:205-211.
8. Erickson, B. D., and F. J. Mondello. 1992. Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multi-component polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400. J. Bacteriol. 174:2903-2912.
9. Furukawa, K., H. Suenaga, and M. Goto. 2004. Biphenyl dioxygenases: functional versatilities and directed evolution. J. Bacteriol. 186:5189-5196. (Pubitemid 39038121)
10. Hernandez, B. S., S. C. Koh, M. Chial, and D. D. Focht. 1997. Terpeneutilizing isolates and their relevance to enhanced biotransformation of polychlorinated biphenyls in soil. Biodegradation 8:153-158.
11. Holoubek, I. 2001. Polychlorinated biphenyl (PCB) contaminated sites worldwide, p. 17-26. In L. W. Robertson and L. G. Hansen (ed.), PCBs. Recent advances in environmental toxicology and health effects. University of Kentucky Press, Lexington.
12. Kahl, S., and B. Hofer. 2003. A genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities. Microbiology 149:1475-1481. (Pubitemid 36764070)
13. Lambo, A. J., and T. R. Patel. 2006. Cometabolic degradation of polychlorinated biphenyls at low temperature by psychrotolerant bacterium Hydrogenophaga sp. IA3-A. Curr. Microbiol. 53:48-52.
14. Lambo, A. J., and T. R. Patel. 2006. Isolation and characterization of a biphenyl-utilizing psychrotrophic bacterium, Hydrogenophaga taeniospiralis IA3-A, that cometabolizes dichlorobiphenyls and polychlorinated biphenyl congeners in Aroclor 1221. J. Basic Microbiol. 46:94-107.
15. Lambo, A. J., and T. R. Patel. 2007. Biodegradation of polychlorinated biphenyls in Aroclor 1232 and production of metabolites from 2,4,4′-trichlorobiphenyl at low temperature by psychrotolerant Hydrogenophaga sp. strain IA3-A. J. Appl. Microbiol. 102:1318-1329.
16. Lebeuf, M., M. Noel, S. Trottier, and L. Measures. 2007. Temporal trends (1987-2002) of persistent, bioaccumulative and toxic (PBT) chemicals in beluga whales (Delphinapterus leucas) from the St. Lawrence Estuary, Canada. Sci. Total Environ. 383:216-231.
17. Leigh, M. B., V. H. Pellizari, O. Uhlik, R. Sutka, J. Rodrigues, N. E. Ostrom, J. Zhou, and J. M. Tiedje. 2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J. 1:134-148.
18. Macek, T., P. Kotrba, A. Svatos, M. Novakova, K. Demnerova, and M. Mackova. 2008. Novel roles for genetically modified plants in environmental protection. Trends Biotechnol. 26:146-152.
19. Macek, T., M. Mackova, and J. Kas. 2000. Exploitation of plants for the removal of organics in environmental remediation. Biotechnol. Adv. 18:23-34.
20. Macek, T., O. Uhlik, K. Jecna, M. Novakova, P. Lovecka, J. Rezek, V. Dudkova, P. Stursa, B. Vrchotova, D. Pavlikova, K. Demnerova, and M. Mackova. 2009. Advances in phytoremediation and rhizoremediation, p. 257-277. In A. Singh, R. C. Kuhad, and O. P. Ward (ed.), Advances in applied bioremediation. Springer, Berlin, Germany.
21. Mackova, M., D. Dowling, and T. Macek. 2006. Phytoremediation and rhizoremediation. Theoretical background. Springer, Dordrecht, The Netherlands.
22. Mondello, F. J., M. P. Turcich, J. H. Lobos, and B. D. Erickson. 1997. Identification and modification of biphenyl dioxygenase sequences that determine the specificity of polychlorinated biphenyl degradation. Appl. Environ. Microbiol. 63:3096-3103.
23. Novakova, M., M. Mackova, Z. Chrastilova, J. Viktorova, M. Szekeres, K. Demnerova, and T. Macek. 2009. Cloning the bacterial bphC gene into Nicotiana tabacum to improve the efficiency of PCB phytoremediation. Biotechnol. Bioeng. 102:29-37.
24. Park, J. S., L. Linderholm, M. J. Charles, M. Athanasiadou, J. Petrik, A. Kocan, B. Drobna, T. Trnovec, A. Bergman, and I. Hertz-Picciotto. 2007. Polychlorinated biphenyls and their hydroxylated metabolites (OHPCBs) in pregnant women from eastern Slovakia. Environ. Health Perspect. 115:20-27.
25. Pavlikova, D., T. Macek, M. Mackova, and M. Pavlik. 2007. Monitoring native vegetation on a dumpsite of PCB-contaminated soil. Int. J. Phytoremediat. 9:71-78.
26. Rezek, J., T. Macek, M. Mackova, J. Triska, and K. Ruzickova. 2008. Hydroxy- PCBs, methoxy-PCBs and hydroxy-methoxy-PCBs: metabolites of polychlorinated biphenyls formed in vitro by tobacco cells. Environ. Sci. Technol. 42:5746-5751.
27. Ryslava, E., T. Macek, M. Mackova, and Z. Krejcik. 2004. Detection of polychlorinated biphenyl-degrading bacteria in soil, p. 839-842. In W. Verstraete (ed.), Environmental biotechnology. Taylor & Francis Group plc, London, United Kingdom.
28. Sakai, M., S. Ezaki, N. Suzuki, and R. Kurane. 2005. Isolation and characterization of a novel polychlorinated biphenyl-degrading bacterium, Paenibacillus sp. KBC101. Appl. Microbiol. Biotechnol. 68:111-116.
29. Shyu, C., T. Soule, S. J. Bent, J. A. Foster, and L. J. Forney. 2007. MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. Microb. Ecol. 53:562-570.
30. Sylvestre, M., M. Sirois, Y. Hurtubise, J. Bergeron, D. Ahmad, F. Shareck, D. Barriault, I. Guillemette, and J. M. Juteau. 1996. Sequencing of Comamonas testosteroni strain B-356-biphenyl/chlorobiphenyl dioxygenase genes: evolutionary relationships among Gram-negative bacterial biphenyl dioxygenases. Gene 174:195-202.
31. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
32. Tillmann, S., C. Strompl, K. N. Timmis, and W. R. Abraham. 2005. Stable isotope probing reveals the dominant role of Burkholderia species in aerobic degradation of PCBs. FEMS Microbiol. Ecol. 52:207-217.
33. Uhlik, O., K. Jecna, M. B. Leigh, M. Mackova, and T. Macek. 2009. DNAbased stable isotope probing: a link between community structure and function. Sci. Total Environ. 407:3611-3619.
34. Vaillancourt, F. H., M. A. Haro, N. M. Drouin, Z. Karim, H. Maaroufi, and L. D. Eltis. 2003. Characterization of extradiol dioxygenases from a polychlorinated biphenyl-degrading strain that possess higher specificities for chlorinated metabolites. J. Bacteriol. 185:1253-1260.
35. Vezina, J., D. Barriault, and M. Sylvestre. 2008. Diversity of the C-terminal portion of the biphenyl dioxygenase large subunit. J. Mol. Microbiol. Biotechnol. 15:139-151.
36. Yu, Y., M. Breitbart, P. McNairnie, and F. Rohwer. 2006. FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics 7:57. (Pubitemid 43308993)