Microbial genetics research group
Bacteria evolve rapidly under stress conditions where their growth is inhibited due to unfavorable environment. Under growth-restricting conditions (e.g., nutrient depletion, during colonization of host organism, exposure to antimicrobial compounds or environmental pollutants) microbial populations can rapidly evolve due to increased mutation frequency. The horizontal transfer of genes or the expression of new genes introduced in laboratory conditions can also cause stress and increased mutation frequency in bacteria. In our research group, the molecular mechanisms of bacterial evolution are investigated in bacteria belonging to the genus Pseudomonas. We are focused in the identification of genes affecting the mutation frequency in the soil bacterium P. putida and in human opportunistic pathogen P. aeruginosa. We also explore the mechanisms of evolution of bacteria that degrade compounds that pollute the environment by conducting laboratory evolution experiments. In addition, we elucidate stress responses and adaptation mechanisms associated with the construction of new metabolic pathways in the bacterium P. putida.
The research group also deals with the identification of biodegradative pathways of environment polluting compounds such as phenols and alkanes, and the structure, functioning and redundancy of plasmids in environmental microbes. Possibilities of cleaning contaminated water and soil using the bioaugmentation method are being investigated. New research topics are the decomposition of lignocellulose, the characterization of bacterial strains producing biosurfactants and the use of C1 substrates by microorganisms.
The results of our study could have applications in biotechnology, environmental protection and human health.
Image used in header: Evolution in a bacterial colony (author: Heili Ilves)
Group members
- Research scientists Heili Ilves, Signe Saumaa, Merike Jõesaar, Signe Viggor;
- CELMS project manager Eeva Heinaru;
- Doctoral students Karl Jürgenstein, Lea Ets, Tanel Ilmjärv, Ingrem Popazova.
1. Viggor, S., Jõesaar, M., Peterson, C., Teras, R., Kivisaar, M. (2023) Potential of indigenous strains isolated from the wastewater treatment plant of a crude oil refinery. Microorganisms, 11(3):752, DOI: https://doi.org/10.3390/microorganisms11030752
2. Jürgenstein, K., Tagel, M., Ilves, H., Leppik, M., Kivisaar, M., Remme, J. (2022) Variance in translational fidelity of different bacterial species is affected by pseudouridines in the tRNA anticodon stem-loop. RNA Biol. 2022 Jan;19(1):1050-1058. DOI: https://doi.org/10.1080/15476286.2022.2121447
3. Nandy, S., Arora, U., Tarar, P., Viggor, S., Jõesaar, M., Kivisaar, M., Kapley, A. (2021) Monitoring the growth, survival and phenol utilization of the fluorescent-tagged Pseudomonas oleovorans immobilized and free cells. Bioresource Technology 338, 125568. DOI: https://doi.org/10.1016/j.biortech.2021.125568
4. Tagel, M., Ilves, H., Leppik, M., Jürgenstein, K., Remme, J., Kivisaar, M. (2020) Pseudouridines of tRNA anticodon stem-loop have unexpected role in mutagenesis in Pseudomonas sp. Microorganisms. 9(1):25, DOI: https://doi.org/10.3390/microorganisms9010025
5. Kivisaar, M. (2020) Narrative of a versatile and adept species Pseudomonas putida. J. Medical Microbiol. 69:324-338. DOI: https://doi.org/10.1099/jmm.0.001137
6. Mikkel, K., Tagel, M., Ilves, H., Ukkivi, K., Kivisaar, M. (2019) Integration Host Factor IHF facilitates homologous recombination and mutagenic processes in Pseudomonas putida. DNA Repair. DOI: https://doi.org/10.1016/j.dnarep.2019.102745.
7. Ukkivi K., Kivisaar, M. (2018). Involvement of transcription-coupled factor Mfd and DNA helicase UvrD in mutational processes in Pseudomonas putida. DNA Repair, 72:18-27. DOI: https://doi.org/10.1016/j.dnarep.2018.09.011
8. Ilmjärv, T., Naanuri, E., Kivisaar, M. (2017). Contribution of increased mutagenesis to the evolution of pollutants-degrading indigenous bacteria. PLoS ONE, e0182484. DOI: https://doi.org/10.1371/journal.pone.0182484
Horizon 2020 (814418) "Synthetic biology- guided engineering of Pseudomonas putida for biofluorination" (SinFonia) (ended)
Horizon Europe (101070281) "BIOS: The bio-intelligent DBTL cycle, a key enabler catalysing the industrial transformation towards sustainable biomanufacturing" (running)
Molecular mechanisms of evolution of bacteria under stressful conditions (Estonian Research Council: PRG707) (running)
Collection of microbial strains (CELMS)
The research group member Signe Viggor is responsible for preserving and supplementing the Estonian national collection of natural and laboratory microbial strains (Collection of non-medical environmental and laboratory microbial strains, CELMS). The collection mainly contains natural bacterial strains isolated from various contaminated areas (both water and soil).
In compiling the collection, the main focus has been on the collection and thorough characterization of microbes that produce biodegradative and/or beneficial compounds using both classical microbiological and molecular biological methods. Whole genome sequences have also been determined for some strains.