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The main research interests of the Laboratory of Microbial Ecology can be divided into four 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.
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.
Third, we identify metabolically active microbial populations in the context of their environments without the need for their cultivation. We use techniques such as Stable Isotope Probing (SIP) or epicPCR for these purposes.
Fourth, 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 all of the above-mentioned research areas.
Our research is/was supported by the projects:
- Exelent research – OP JAK, INTER-MICRO, Talking microbes - understanding microbial interactions within One Health framework
- European Commission Grant 101060625, NYMPHE, New system-driven bioremediation of polluted habitats and environment
- Life at the Interface: Ecology of Plant-Associated Microorganisms (Czech Science Foundation grant no. 22-00132S). Given their intertwined evolutionary history and close environmental proximity, plants and microorganisms have developed extensive interactions which are essential for ecosystem functioning. Our goal is to improve our mechanistic understanding of the ecology of plant-associated microorganisms and to explore some of the mechanisms driving processes that are enabled by plant-microbe interactions. More specifically, we aim to elucidate the role of rhizodeposit components in structuring soil microbial communities, determine the extent to which roots impact soil microbial populations, including the assembly of plant-associated microbial communities, as well as reveal the specific role of rhizodeposits in selecting soil bacteria with plant-growth-promoting traits to be recruited for endophytic mutualism. Results of this project should significantly advance our understanding of plant-microbial interactions, having potential implications for plant health and important ecosystem functions, such as horticultural plant growth promotion, environmental restoration and others.
- Who is responsible here? Linking transformation of organochlorines with specific bacterial
populations (Czech Science Foundation grant no. 22-00150S). Organochlorines (OCs), such as chlorinated ethenes and polychlorinated biphenyls, still constitute an important environmental problem due to actual and/or potential contamination of soils or drinking water sources. Although microbial degradation of OCs has been extensively studied, there is paucity of knowledge about the distribution of OC degradation genes at contaminated sites and their link to phylogenetic information in individual taxa. In this project, we aim to understand patterns in the distribution of vital biodegradative functions and the phylogenetic origin of bacteria that perform these functions. Specifically, our main objectives are to: reveal patterns in the distribution of selected OC degradation (bphA and rdhA) genes in indigenous communities at contaminated sites and their link to phylogeny; investigate the contribution of extrachromosomal DNA to the distribution of OC degradation genes in the environment; elucidate the capability of bacterial consortia to adapt to elevated concentrations of OCs by up-regulation and dissemination of particular genes. - Genome dynamics and maintenance in simple and homogeneous natural prokaryotic communities (in collaboration with Faculty of Science of the Charles University, Czech Science Foundation grant no. 23-06568S) Simple and spatially and genetically clearly defined microbial populations represent an optimal model for the study of prokaryotic population genetics. The bacterium Ferrovum myxofaciens from mine biostalactites perfectly meets these criteria. Our previous research has shown that the F. myxofaciens genomes have almost identical gene content but there is significant intrapopulation variability in the distribution of mobile elements and short polymorphisms. This variability probably serves for life strategy diversification or adaptation to different microniches. In this project, we analyze a larger number of better characterized populations from multiple localities which will allow a functional interpretation of their variability. The influence of different genetic variants on the biological properties of F. myxofaciens are be verified on pure cultures derived from natural populations. These analyses may provide new insights into the function of mobile elements and the role of local disruptions of intraspecific gene flow in the formation of prokaryotic populations.
- 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.
- 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.