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Our research revealed changes in the composition of the Baltic Sea microbial populations, namely, an increase in numbers of the physiological group of microorganisms that develop owing to organic compounds contaminating chemical weapon dump sites. We found that mustard gas hydrolysis products (MGHPs) - tolerant microorganisms were predominant in nearbottom water in many stations in the Baltic Sea dumping areas. The proportion of this group of indicator bacteria both in the total number of microorganisms and the amount of heterotrophic bacteria tended to increase. Comparison of the number of the indicator bacteria with the total number of heterotrophs allowed estimating the degree of contamination of marine ecosystem and characterizing the response of microbiota to the effect of warfare agents. Microbiological investigations revealed the concentration of MGHPs-tolerant microorganisms up to 20 - 98% of total number of heterotrophs in Gotland Deep, Strait of Skagerrack and Bornholm Basin. The ldquoabnormalrdquo sites characterized with a poor spectrum of heterotrophic microorganisms. At some stations the dominance of minimal number of species in near-bottom waters was observed. The species diversity of the microbial population in the dump sites was reduced because of an increase in the number of MGHPs-tolerant microorganisms. Thus, high number of microorganisms tolerant to MGHPs in near-bottom waters indicates possible leaking of CW agents into the environment and contamination of water and sediments with mustard gas and products of its hydrolysis in dumping areas.