The so-called biologically mediated reactions are also very significant in the involvement of microorganisms in the biogeochemical cycles. In these reactions, microbes form an environment in which certain forms of minerals are stable according to the fields of thermodynamic stability. It is most important for rare elements, whose amount is insufficient to ensure the existence of certain specific groups. These trace elements act as indicators of the environment. Uranium is one of the examples. Another example is the deposition of metals in the zone of sulfate reduction. Such microbially mediated pathways form many sedimentary deposits. The so-called biogeo-chemical barriers represent the sites of drastic changes in the environment, which cause precipitation of minerals. Biogeochemical barriers are sustained by countercurrents of solutes and by the activity of microorganisms. There are different kinds of barriers: oxido-reductive, alkaline, sulfidic, etc. Chemocline in the lakes is an example. Change in the state of environment often causes transition from migrating chemical species to insoluble one.
The cycle of calcium belongs to biologically mediated reactions. It begins by CO2 weathering of rocks. The essential point here is the concentration of carbon in the biomass and concentrated release of CO2 during decomposition. Formation of active products of decomposition as acids or chelators is also important. Released Ca2+ comes into waterways as Ca(HCO3)2 and migrates to the ocean. Here it might be used by calcareous eukaryotes for the formation of skeleton and release of CO2. The main part of CaCO3 at present is biogenic by origin. Another possibility is the release of CO2 in warm shallow water when its solubility decreases and the reaction, Ca(HCO3)2 !#CaCO3 + "CO2 + H2O develops. The surface of precipitated CaCO3 is covered by a microbial biofilm. It gives to the precipitate a laminated texture due to the slime produced. If the microbial biofilm is formed by cyanobacteria, then the additional sink of CO2 assimilated in Corg might result in a drop of pH and precipitation of carbonate. The layered structures of precipitated carbonates are known as stromatolites. They are recorded for Proterozoic as the most important deposits. Their abundance indicates that they represent significant deposits of CO2. Stromatolites correlate with deposits of dolomites, but sometimes pieces of black chert are included and in these cherts, silicified microfossils of cyanobacteria are observed. Preservation is excellent and one can identify taxa, with the aid of books on systematics, of extant cyano-bacteria to approximately 2.4 billion years ago. The scale of stromatolite formation delineating ancient warm shallow water environment is of the order of millions of square kilometers. Height of such deposits is up to hundreds of meters. Mass development of stromatolites ended with the end of bacterial exclusive domination in the biosphere. Calcium cycle contributes to the neutrophilic conditions on the Earth.
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