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You are here: UCT Prague - FFBTDepartment of Biochemistry and Microbiology → Laboratory of Microbial Ecology → Laboratory of Microbial Ecology
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Laboratory of Microbial Ecology

The main research interests of the Laboratory of Microbial Ecology can be divided into three subsections:

First, we are looking into the ecology of plant-microbe interactions. We are working under the hypotheses that secondary plant metabolites (SPM), including lignin degradation intermediates and other phenolics as well as terpenes, significantly affect the biodegradation potential of soil microbial communities. We also predict that biodegradative functions, originally evolved for SPM degradation, and plant-growth promoting functions are often attributed to the same plant-associated microbial populations. We hypothesize that this functional association helps the plant to selectively enrich microbial populations which promote its growth through SPM exudation. At the same time, SPMs indirectly help the plant thrive in contaminated soil by increasing the biodegradation potential of soil microbial communities. This research is currently supported by two projects.

Ecological functions of soil microorganisms governed by secondary plant metabolites (Czech Science Foundation grant no. 20-00291S). A vast source of SPMs in soils is lignin, a complex ubiquitous plant biopolymer composed of phenylpropanoid monomers. Structural similarity of SPMs, including lignin degradation intermediates, to known anthropogenic pollutants might explain why anthropogenic pollutants can be cometabolized in the presence of SPMs. In this proposed project we will test the hypotheses (i) that SPMs as original evolutionarily substrates of biodegradative enzymes significantly affect the biodegradation potential of soil microbial communities; and (ii) that biodegradative functions, originally evolved for SPM degradation, and plant-growth promoting functions, which are often attributed to the same plant-associated microbial populations, together help the plant to selectively enrich microbial populations which promote its growth through SPM exudation.

Microbial Cometabolism: Promoting Biodegradation of Pollutants (Ministry of Education, Youth and Sports of the CR grant no. LTAUSA19013). The objective of the project is to test the hypothesis that secondary plant metabolites can promote cometabolism of persistent organic pollutants in the environment and thereby significantly influence the biodegradation potential of autochthonous microbial communities. In order to accomplish this objective, we (i) selectively enrich soil bacterial consortia that degrade selected pollutants (polychlorinated biphenyls, PCBs, and polyaromatic hydrocarbons, PAHs) when grown on secondary plant metabolites and (ii) test whether the consortia involved in secondary plant metabolite metabolism increase the efficiency of biodegradation of PCBs and PAHs in soils.

Second, we are looking into the microbial ecology of geologically unique biotopes. We are working under the hypotheses that microorganisms found in these biotopes will be unique from many points of view – phylogenetically with respect to as-yet-undetected taxa, metabolically with respect to the production of biologically active compounds, and ecologically with respect to unusual life strategies and interactions. We also predict that cutting-edge microbial ecological techniques, specifically targeted metagenomic, metagenomic/metatranscriptomic and metabolomic approaches, will enable us to decipher the microbial ecology of these biotopes. This research is currently supported by two projects.

Microbiomes of Selected Extreme Biotopes – Their Phylogenetic Diversity and Functional Potential (Ministry of Education, Youth and Sports of the CR grant no. LTAUSA19028). The objective of the project is to characterize microbial populations in extreme biotopes – chronosequence of permafrost (permafrost of differing age) from central Alaska, and soils from salt marshes and moffettes of the Soos National Natural Reserve, Czech Republic. The characterization is conducted by two major routes – metagenomics and modified cultivation techniques. The basic modification of the cultivation techniques is the use of resuscitation-promoting factor and adjustment of cultivation media so that they better mimic natural conditions the bacteria are subjected to in their habitat; the goal is to increase the efficiency of the cultivation and isolate dormant or otherwise difficult-to-culture or, if possible, as-yet-uncultured bacteria.

Ecology of extremophilic microorganisms in Czech spring waters of cultural heritage significance (Czech Science Foundation grant no. 18-00036S). There is a diverse range of deep springs in the Czech Republic, each of which, whether hot, radon or brine, is characterized by an extreme, yet stable and unique, environment that has enabled its indigenous microorganisms to evolve for thousands of years. We therefore hypothesize that microorganisms found in these waters will be unique from many points of view – phylogenetically with respect to as-yet-undetected taxa, metabolically with respect to the production of biologically active compounds, and ecologically with respect to unusual life strategies and interactions. We also predict that cutting-edge microbial ecological techniques, specifically targeted metagenomic, metatranscriptomic and metabolomic approaches, will enable us to decipher the microbial ecology of these waters.

Third, we are looking into how to modify standard extraction and cultivation procedures in order to increase the efficiency of culturing of microorganisms. This work relates to both of the above-mentioned research areas.

Updated: 11.5.2020 19:07, Author: Dalibor Trapl