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Applied and Environmental Microbiology, October 2009, p. 6471-6477, Vol. 75, No. 20
0099-2240/09/$08.00+0     doi:10.1128/AEM.00466-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Biphenyl-Metabolizing Bacteria in the Rhizosphere of Horseradish and Bulk Soil Contaminated by Polychlorinated Biphenyls as Revealed by Stable Isotope Probing{triangledown} ,{dagger}

Ondrej Uhlik,1,2 Katerina Jecna,1 Martina Mackova,1 Cestmir Vlcek,3 Miluse Hroudova,3 Katerina Demnerova,1 Vaclav Paces,3 and Tomas Macek1,2*

Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, Institute of Chemical Technology Prague, Technicka 3, 166 28 Prague 6, Czech Republic,1 IOCB & ICT Joint Laboratory, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic,2 Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic3

Received 25 February 2009/ Accepted 13 August 2009

DNA-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (Armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (PCBs) compared to members of the microbial community in initial, uncultivated bulk soil. On the basis of early and recurrent detection of their 16S rRNA genes in clone libraries constructed from [13C]DNA, Hydrogenophaga spp. appeared to dominate biphenyl catabolism in the horseradish rhizosphere soil, whereas Paenibacillus spp. were the predominant biphenyl-utilizing bacteria in the initial bulk soil. Other bacteria found to derive carbon from biphenyl in this nutrient-amended microcosm-based study belonged mostly to the class Betaproteobacteria and were identified as Achromobacter spp., Variovorax spp., Methylovorus spp., or Methylophilus spp. Some bacteria that were unclassified at the genus level were also detected, and these bacteria may be members of undescribed genera. The deduced amino acid sequences of the biphenyl dioxygenase {alpha} subunits (BphA) from bacteria that incorporated [13C]into DNA in 3-day incubations of the soils with [13C]biphenyl are almost identical to that of Pseudomonas alcaligenes B-357. This suggests that the spectrum of the PCB congeners that can be degraded by these enzymes may be similar to that of strain B-357. These results demonstrate that altering the soil environment can result in the participation of different bacteria in the metabolism of biphenyl.

* Corresponding author. Mailing address: Institute of Organic Chemistry and Biochemistry, v.v.i., Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic. Phone: 420 220183340. Fax: 420 220183582. E-mail: macek{at}uochb.cas.cz

{triangledown} Published ahead of print on 21 August 2009.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, October 2009, p. 6471-6477, Vol. 75, No. 20
0099-2240/09/$08.00+0     doi:10.1128/AEM.00466-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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