Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil

0390198 - ÚMG 2013 RIV US eng J - Journal Article
Uhlík, O. - Wald, J. - Strejček, M. - Musilová, L. - Rídl, Jakub - Hroudová, Miluše - Vlček, Čestmír - Cardenas, E. - Mackova, M. - Macek, T.
Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil.
PLoS ONE. Roč. 7, č. 7 (2012), e40653. ISSN 1932-6203. E-ISSN 1932-6203
R&D Projects: GA MŠMT 2B08031
Grant - others:EK(XE) 265946; MŠMT(CZ) ME09024; GA ČR(CZ) GA525/09/1058
Program: GA
Institutional research plan: CEZ:AV0Z50520514
Institutional support: RVO:68378050
Keywords : biodegradation * Proteobacteria * bioremediation
Subject RIV: EB - Genetics ; Molecular Biology
Impact factor: 3.730, year: 2012

Bacteria were identified associated with biodegradation of aromatic pollutants biphenyl, benzoate, and naphthalene in a long-term polychlorinated biphenyl- and polyaromatic hydrocarbon-contaminated soil. In order to avoid biases of culture based approaches, stable isotope probing was applied in combination with sequence analysis of 16 S rRNA gene pyrotags amplified from 13C-enriched DNA fractions. Special attention was paid to pyrosequencing data analysis in order to eliminate the errors caused by either generation of amplicons (random errors caused by DNA polymerase, formation of chimeric sequences) or sequencing itself. Therefore, sample DNA was amplified, sequenced, and analyzed along with the DNA of a mock community constructed out of 8 bacterial strains. This warranted that appropriate tools and parameters were chosen for sequence data processing. 13C-labeled metagenomes isolated after the incubation of soil samples with all three studied aromatics were largely dominated by Proteobacteria, namely sequences clustering with the genera Rhodanobacter Burkholderia, Pandoraea, Dyella as well as some Rudaea- and Skermanella-related ones. Pseudomonads were mostly labeled by 13C from naphthalene and benzoate. The results of this study show that many biphenyl/benzoate-assimilating bacteria derive carbon also from naphthalene, pointing out broader biodegradation abilities of some soil microbiota. The results also demonstrate that, in addition to traditionally isolated genera of degradative bacteria, yet-to-be cultured bacteria are important players in bioremediation. Overall, the study contributes to our understanding of biodegradation processes in contaminated soil. At the same time our results show the importance of sequencing and analyzing a mock community in order to more correctly process and analyze sequence data.
Permanent Link: http://hdl.handle.net/11104/0219111