Ecology - Cyanobacteria Group @ FCCT UL








Environment

Understanding environment is understanding physical habitats, knowing living organisms and interactions among them. Although cyanobacteria are not confined to water only, they are most abundant in aquatic ecosystems. Their role in oceans where as plankton they serve as oxygen producers and represent the baseline of the food chain is indispensable, but they are important in freshwaters as well.

sampling

Students samplling planktonic microalgae at Podpeško Lake near Ljubljana in summer 2014.

With help of the colleagues from the analytical chemistry group, we can get extremely precise information about the chemical composition of environmental waters in which cyanobacteria live. We did a range of simulation experiments in which we tested for influence of various compounds regularly found in nature, on the growth rate of cyanobacteria. It is clear that we are far from having a full picture of these factors.

Our next goal was determining the presence of specific cyanobacteria in the environment. Sampling was followed by microscopic investigations of concentrated samples, but soon we realized that we need more precise tools to determine the presence of these species in the samples. So we decided to develop a DNA barcoding tool to discriminate among members of the Synechocystis genus.


DNA-barcoding

Using universal primers we amplified rRNA coding regions of the genome of 11 cyanobacterial species / strains. Amplification products were plasmid-cloned and sequences were determined and compared to databases. It turned out that we had a very limited amount of sequencing data except for the type species and three fully sequenced genomes. Our data show that Synechocystis is a very diverse genus that eventually should be split into several genera and that by PCR alone it is possible to discriminate between several clusters in the genus. For strain identification, the ITS (internal transcribed spacer) region has to be sequenced. Interestingly, we found several SNPs (single nucleotide polymorphisms) in the variable regions that were amplified from a single strain, pointing to the fact that rRNA coding regions in the genome are not identical and/or that genomic copies present in the cell are not identical. A manuscript has just been sent for evaluation to a research journal.


Biofilms

Environmental triggers can cause sedimentation and attachment of planktonic cyanobacteria to surfaces. Moreover, cyanobacteria form biofilms in which they are protected from the environment. Which are the triggers and what are the biochemical changes that take place in the biofilm formation? These are just a few of the questions we asked and we are trying to find answers with the limited resources we have.


Interactions

Cyanobacterial growth rate depends not only on the medium chemical composition but also on interactions among organisms. In complex environments this is not easy to study, so we are setting up laboratory experiment to test for these interactions.