It is known that the existence of a wide range of environmental change is possible thanks to the boom, environmental changes acting modifications. Theory of modifications indicates some parameters of ecosystems that characterize her condition. However, use them in practice virtually impossible (for example, the definition of biodiversity in forest ecosystems). Though. researchers point to the analogy between evolution and ontogeny organisms biocenosis. The proposed approach on the basis of this theory are parameters that characterize the ecosystems and made the appropriate settings for microorganisms that characterize their status. Theory models drew attention to the possibility of using indicators of ecosystem characteristics for organisms. It is shown that the pilot of the work can be performed only if you use spectral methods for analysis of cells without destruction and wise.