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Soils produce 95 percent of the food we consume, healthy soil provides crucial ecosystem services for life, such as water storage, purification and flood regulation, carbon sequestration and consequently climate change mitigation, or nutrient cycling e.t.c. The dangers posed to the environment due to anthropogenic activities necessitate the need for novel strategies for decontamination and clean up. It is challenging to realize and discover the interplay between the biodiversity in polluted environments. The process of clean-up can be done in aerobic or anaerobic systems depending on the microorganisms and the electron acceptors available in the media. This review has examined the sources of pollutants into the environment, mechanism for clean-up, contribution of molecular techniques and how utilization of biodiversity can be an effective technique available for clean-up of polluted sites. Though the idea has a long history, however other relatively new applications are emerging or being developed for optimization of the existing biodiversity - based techniques for clean-up of polluted environments.