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Laboratory of Microbial Ecology

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The tremendous diversity of microorganisms is not only astonishing; it is also a key to understanding how organisms evolve and adapt to various environmental conditions. The metabolic activity of microorganisms is essential for maintaining the functions of all ecosystems in the biosphere. Microbial ecology seeks to unveil microorganisms in their natural environments; it looks at how microbes interact with one another and their environment, and what the consequences of these interactions are for ecosystem functions.

vodyIn the Laboratory of Microbial Ecology, we are interested in uncovering some of the hidden gems of microbial diversity. Certain localities of the Czech Republic are very interesting from the microbial ecological point of view; being extreme (brine, radioactive), often unique, spatially isolated biotopes, they are a promising source of hitherto undiscovered microbial diversity. Such habitats include mineral water springs which are used for healing purposes in Karlovy Vary, Jáchymov or Luhačovice, or soils and mofettas from the Soos National reserve. Our objective is to analyze microbial communities in these habitats and understand their physiology, biochemistry and ecology.

exudaceNo less important to us is improving our understanding of plant-microbe interactions. We look at how secondary plant metabolites shape soil microbial community structure and how they induce and/or regulate biodegradative genes in soil bacteria, thereby increasing the contaminant biodegradation potential in the microbial community. In turn, we are looking at how rhizosphere microorganisms promote the growth of plants. At the same time, we are looking at how many and which of these microorganisms colonize the interior of the plants, thus becoming endophytic. The applications of this fundamental research mainly include sustainable agriculture or environmental protection.

kultivaceWe identify metabolically active microbial populations in the context of their environments without the need for their cultivation. Microorganisms whose activity is crucial for a particular bio(geo)chemical process in the ecosystem are often not very abundant in the community. Therefore, we use microbial ecological techniques that allow linking community members with specific functions, including Stable Isotope Probing (SIP) or epicPCR. We thereby identify microorganisms degrading contaminants from the soil, promoting plant growth, etc.

exudaceWe are also aware of the importance of pure culture in microbiology. Therefore, we are trying to modify standard extraction and cultivation procedures in order to increase the efficiency of culturing of microorganisms, be it from soil, water, plant interior or any other habitat. Resuscitation factors or signaling molecules can help us to do so, along with mimicking the conditions of natural environments in which our microbes thrive. Upon successful isolation, the novel pure cultures are classified and characterized.

In order to reach our goals, we try to apply cutting-edge methodologies and techniques, including metataxonomics, metagenomics, stable isotope probing as well as modified culturing approaches. If you are interested in more details on our research, see our current projects.

We are a group of enthusiastic, motivated and hardworking microbial ecologists. If you are a motivated and diligent student who is eager to do solid research, do not hesitate to contact us.

Updated: 18.4.2023 12:07, Author: Michal Strejček

Once ecological mechanisms are understood, ecologists strive to better predict, conserve or manage communities to desired outcomes.

(Ashley Shade, ISME J 2017; 11, 1–6)