Pavlovska M. Black sea ecosystem recovery under the influence of pollutants of different origin

A comprehensive study of structure and function of the Black sea microbial communities inhabiting the water column and sediments is presented in the thesis. Additionally, microbial metagenomic data is tested for its potential applicability in the Black sea ecological status assessment according to the requirements of the EU Marine Strategy Framework Directive and the Ukrainian Marine Conservation Strategy. Additionally, the response of microbial communities to anthropogenic pressure, particularly their potential and realized activity in xenobiotics degradation, as well as their role in the antibiotic resistance genes dissemination in the aquatic environment, were investigated. A comprehensive analysis of microbial communities’ taxonomic and functional composition and their distribution in different Black sea regions was conducted for the first time using metagenomic methods. The results of our research have revealed that the taxonomic and functional composition of Black Sea microbial communities varies with the vertical stratification of the water column in accordance with the gradient of physicochemical environmental conditions. According to our data, samples from the surface and thermocline formed a single cluster dominated by Flavobacteriaceae, Rhodobacteraceae, and Synechococcaceae. The suboxic zone of the Black Sea was characterized by a trend towards an increased proportion of green sulfur bacteria (Chlorobia (7%)) and non-sulfur bacteria (Anaerolineae (1%)), which are capable of growing in oxygen-depleted environments with low light intensity. Our data indicate that the anoxic zone of the Black Sea is an ecotone environment characterized by a decrease in light availability and increase in hydrogen sulfide concentration with depth. Subsequent correlation analysis revealed a significant relationship between the taxonomic and functional diversity of the investigated microbial communities and the gradient of physicochemical parameters in the environment. The distribution of A714017, Piscirickettsiaceae, Chlorobiaceae, Helicobacteraceae, Desulfobacteraceae, and Desulfarculaceae showed a positive correlation with the proportion of functional components related to anoxygenic photosynthesis, denitrification, and dissimilatory sulfate reduction. Analysis of bacterial activity towards xenobiotics’ degradation was conducted with the purpose to investigate the ecological role of microbial communities in the Black sea water column and sediments. Our study demonstrated the presence of potential capability for xenobiotic degradation in the microbial communities of the Black Sea. The transcription of catabolic genes was assessed in order to determine the realized activity of the Black sea microorganisms in xenobiotics degradation processes of xenobiotics. The differences in the abundance and transcription of genes involved in the degradation of polycyclic aromatic compounds (PAHs) between gram-positive and gram-negative bacteria were demonstrated. In general, the analysis of the Black sea microbial communities’ ecological role revealed the presence of both potential and realized activity directed at the degradation of pollutants. We conducted research on the dissemination of antibiotic resistance genes, which are known to be treated as "pollutants" in international ecological studies. We have demonstrated the presence of an ecological problem regarding the spread of antibiotic resistance in the Black Sea. It has been shown that genes coding for the resistance to beta-lactams, vancomycin, macrolides, and colistin are prevalent in different parts of the Black Sea water column, with a decreasing abundance trend from the shelf zones to the open waters. The calculated abundance of antibiotic resistance genes is high and falls within the range of beta-lactam resistance genes’ (blaOXA) abundance determined for the Danube River basin, which was 2,4 × 10−8 – 3,1 × 10−2 copies/μL. We have demonstrated the presence of an ecological problem regarding the spread of antibiotic resistance in the Black Sea. The prevalence of antibiotic resistance genes can be considered as one of the indicators for the ecological assessment of the Black Sea in the future. The data obtained on the studied Black sea microbial communities’ taxonomic and functional structure and their role in the ecosystem was analyzed for the potential to be used for ecological assessment. According to the calculated microgAMBI values, the ecological status of the Black Sea waters is predominantly "good" (microgAMBI = 1,47 – 2,34), based on the categories defined in the EU Water Framework Directive. Certain discrepancies were identified between the assessment of the environmental status based on chemical parameters and the structure of microbial communities. Certain discrepancies were identified between the assessment of the environmental status based on chemical parameters and the structure of microbial communities.