Environmental biotechnology is biotechnology that is applied to and used to study the natural environment. Environmental biotechnology could also imply that one try to harness biological process for commercial uses and exploitation. The International Society for Environmental Biotechnology defines environmental biotechnology as "the development, use and regulation of biological systems for remediation of contaminated environments (land, air, water), and for environment-friendly processes (green manufacturing technologies and sustainable development)". Environmental biotechnology can simply be described as "the optimal use of nature, in the form of plants, animals, bacteria, fungi and algae, to produce renewable energy, food and nutrients in a synergistic integrated cycle of profit making processes where the waste of each process becomes the feedstock for another process". The IAASTD has called for the advancement of small-scale agro-ecological farming systems and technology in order to achieve food security, climate change mitigation, climate change adaptation and the realisation of the Millennium Development Goals. Environmental biotechnology has been shown to play a significant role in agroecology in the form of zero waste agriculture and most significantly through the operation of over 15 million biogas digesters worldwide. Consider the effluents of starch plant which has mixed up with a local water body like a lake or pond. We find huge deposits of starch which are not so easily taken up for degradation by microorganisms except for a few exemptions. Microorganisms from the polluted site are scan for genomic changes that allow them to degrade/utilize the starch better than other microbes of the same genus. The modified genes are then identified. The resultant genes are cloned into industrially significant microorganisms and are used for economically processes like in pharmaceutical industry, fermentations... etc.. Similar situations can be encountered in the case of marine oil spills which require cleanup, where microbes isolated from oil rich environments like oil wells, oil transfer pipelines.

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