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The lagoons and lakes found in at different stages of isolation from the White Sea are a special group of hydrological objects. Their evolution is associated with the uplift of the Kandalaksha Bay coast. Stratified structure in such water bodies is formed under the influence of conditions affecting not only physicochemical characteristics of the water but biological ones as well. Green sulfur bacteria are anoxygenic phototrophic microorganisms that live in the chemocline zone (the water layer with transition from aerobic conditions to anaerobic) and in the anaerobic zone in the stratified lakes separating from the White Sea. Fluorescence spectra of green sulfur bacteria show two longwave bands: (1) emission with maximum at 740-770 nm that corresponds to BChl d and e fluorescence and (2) emission with maximum at 815 nm that corresponds to BChl a fluorescence. The maximum of the first emission band can be shifted depending on the type of bacteria and their pigment composition. In this work we report on spectroscopic studies performed in 2015-2016 on water samples from different depths taken fro the water bodies at different stages of isolation from the White Sea. Fluorescence measurements were performed using luminescence spectrometer Solar CM2203. Absorption spectra were registered by spectrophotometers Unico and Solar PB2201. Aceton-methanol (7:2) extracts of water samples were prepared to calculate the concentration of BChls. Depth distributions of BChl fluorescence, BChl concentrations were plotted and compared with physical and hydrochemical characteristics of waters. The work was supported by the Russian Foundation for Basic Research, project no. 16-05- 00548a.