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Bacterial diversity in the active stage of a bioremediation system for mineral oil hydrocarbon-contaminated soils

Interdisziplinäres Ökologisches Zentrum, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany

Correspondence
Michael Schlömann
michael.schloemann{at}ioez.tu-freiberg.de

Soils contaminated with mineral oil hydrocarbons are often cleaned in off-site bioremediation systems. In order to find out which bacteria are active during the degradation phase in such systems, the diversity of the active microflora in a degrading soil remediation system was investigated by small-subunit (SSU) rRNA analysis. Two sequential RNA extracts from one soil sample were generated by a procedure incorporating bead beating. Both extracts were analysed separately by generating individual SSU rDNA clone libraries from cDNA of the two extracts. The sequencing results showed moderate diversity. The two clone libraries were dominated by Gammaproteobacteria, especially Pseudomonas spp. Alphaproteobacteria and Betaproteobacteria were two other large groups in the clone libraries. Actinobacteria, Firmicutes, Bacteroidetes and Epsilonproteobacteria were detected in lower numbers. The obtained sequences were predominantly related to genera for which cultivated representatives have been described, but were often clustered together in the phylogenetic tree, and the sequences that were most similar were originally obtained from soils and not from pure cultures. Most of the dominant genera in the clone libraries, e.g. Pseudomonas, Acinetobacter, Sphingomonas, Acidovorax and Thiobacillus, had already been detected in (mineral oil hydrocarbon) contaminated environmental samples. The occurrence of the genera Zymomonas and Rhodoferax was novel in mineral oil hydrocarbon-contaminated soil.

The GenBank/EMBL/DDBJ accession numbers for the representative sequences obtained in this study are AM237215–AM237284, AM279418, AM279419, and AM237445–AM237448.

Maximum-likelihood phylogenetic trees of ‘Bacteroidetes’ and Epsilonproteobacteria sequences, and a P test for comparison of Rositz1 and Rositz23 libraries, are available as supplementary data with the online version of this paper.

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