Approaches for diversity analysis of cultivable and non-cultivable bacteria in real soil
2009
Stursa, P.,Vysoka Skola Chemicko-technologicka, Prague (Czech Republic). Ustav Biochemie a Mikrobiologie | Uhlik, O.,Vysoka Skola Chemicko-technologicka, Prague (Czech Republic). Ustav Biochemie a Mikrobiologie | Kurzawova, V.,Vysoka Skola Chemicko-technologicka, Prague (Czech Republic). Ustav Biochemie a Mikrobiologie | Koubek, J.,Vysoka Skola Chemicko-technologicka, Prague (Czech Republic). Ustav Biochemie a Mikrobiologie | Ionescu, M.,Vysoka Skola Chemicko-technologicka, Prague (Czech Republic). Ustav Biochemie a Mikrobiologie | Strohalm, M.,Vysoka Skola Chemicko-technologicka, Prague (Czech Republic). Ustav Biochemie a Mikrobiologie | Lovecka, P.,Vysoka Skola Chemicko-technologicka, Prague (Czech Republic). Ustav Biochemie a Mikrobiologie | Macek, T.,Akademie Ved, Prague (Czech Republic). Ustav Organicke Chemie a Biochemie | Mackova, M.,Vysoka Skola Chemicko-technologicka, Prague (Czech Republic). Ustav Biochemie a Mikrobiologie
The development of molecular phylogenetics has recently enabled to characterize naturally occurring microbial biota without cultivation. In this work we show some aspects, advantages and disadvantages of classical and new approaches in taxonomical and functional description of bacteria present in natural microbial assemblages on the example of cultivable bacteria isolated from rhizosphere of plants, tobacco and black nightshade, planted in PCB contaminated soil. Biochemical analysis of isolates showed 8 different bacterial species. This identification was compared by discrimination using MALDI-TOF mass spectrometry. The identity was then evaluated after sequencing of 16S rDNA. Six strains from the original number of 8 were positively identified after 16S rDNA sequencing. Our analyses confirmed close relations of all species (two of the isolates exhibited the same characteristics and were discriminated as the same species - Pseudomonas stutzeri) and also of Burkholderia xenovorans LB 400, a well-known PCB degrader. Nevertheless, only two isolates gave a positive reaction after amplification of the biphenyl dioxygenase gene and exhibited the potential to degrade PCB. These results indicate that only a subset of the recovered molecular information derived from active population based on molecular and functional analysis is relevant to microbial ecology.
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