“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)
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Technická 5
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EB29_Franconibacter_helveticus_MspExport.btmsp
EB31_Franconibacter_helveticus_MspExport.btmsp
EB32_Franconibacter_helveticus_MspExport.btmsp
EB33_Franconibacter_helveticus_MspExport.btmsp
EB35_Franconibacter_helveticus_MspExport.btmsp
EB38_Franconibacter_pulveris_MspExport.btmsp
EB39_Franconibacter_pulveris_MspExport.btmsp
EB41_Franconibacter_pulveris_MspExport.btmsp
EB42_Franconibacter_pulveris_MspExport.btmsp
EB44_Siccibacter_turicensis_MspExport.btmsp
EB45_Siccibacter_turicensis_MspExport.btmspAlso available at Zenodo
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Advanced Biochemistry, Applied Enzymology, Environmental Microbiology, Food microbiology and Genetic engineering are delivered in English for foreign students.
The department is accredited for doctoral education of biochemists and microbiologists.
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stdClass Object ( [nazev] => Laboratory of Microbial Ecology [seo_title] => Laboratory of Microbial Ecology [seo_desc] => [autor] => [autor_email] => [obsah] =>Home Projects Publications
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.
In 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.
No 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.
We 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.
We 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.
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(Ashley Shade, ISME J 2017; 11, 1–6)
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assistant professors
postdoc
Ana Catalina Lara Rodriguez, Ph.D.PhD students
professor
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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: