28.07.2026
research

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, Anne Menert;
  • CELMS project manager Eeva Heinaru;
  • Doctoral students Karl Jürgenstein, Lea Ets, Tanel Ilmjärv, Ingrem Popazova.

Popazova, I., Ilmjärv, T., Brauer, A., Saumaa, S., Kivisaar, M. (2026). TOL Plasmid pWW0 Transposons Facilitate Adaptation of Pseudomonas putida for Growth on the New Carbon Source m-Cresol. Environmental Microbiology 28, no. 7: e70368. DOI: https://doi.org/10.1111/1462-2920.70368

Jõesaar, M., Viggor, S., Barrow, R.R., Peegel, A., Saan, D., Heinaru, E., Kivisaar, M. (2026). Catabolic gene redundancy enhances metabolic flexibility during degradation of mixed aromatic compounds in Pseudomonas. Journal of Hazardous Materials Advances,
Volume 23, 101336, ISSN 2772-4166. DOI: https://doi.org/10.1016/j.hazadv.2026.101336

Ets, L., Ilves, H., Juhe, L., Ilmjärv, T., Puiggené, Ò., Nikel, P.I., Kivisaar, M. (2026). Adaptive evolution of Pseudomonas putida in the presence of fluoride exposes novel functions of a benzoate transporter. Journal of Bacteriology, 0:e00479-25. DOI: https://doi.org/10.1128/jb.00479-25

Jürgenstein, K., Ilves, H., Luhaäär, C., Brauer, A., Remme, J., Kivisaar, M. (2025). Mutations in ribosomal protein uS5 alter translation fidelity and mutagenesis in Pseudomonas putida. Journal of Bacteriology, 207:e00334-25. DOI:
https://doi.org/10.1128/jb.00334-25

Saumaa, S., Ilmjärv, T., Popazova, I., Ets, L., Brauer, A., Kivisaar, M. (2025) Engineering and laboratory evolution of lactose-utilizing Pseudomonas putida strains. Journal of Biotechnology, 406:225-235. DOI: https://doi.org/10.1016/j.jbiotec.2025.07.015

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

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

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

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

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

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.

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

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

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.

Further information about the microbial collection

Estonian Electronic Microbial Database webpage

Contact (research group leader)
Maia Kivisaar
PhD (Molecular Biology)
Faculty of Science and Technology
Institute of Molecular and Cell Biology
Director
Riia 23–104
Institute of Molecular and Cell Biology
Chair of Genetics
Head of Chair, Professor of Microbial Genetics
Riia 23–104
+372 737 5036
+372 520 4036