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Micro-organisms play a fundamental role in the environment. Yet their role is the result of complex biogeochemical processes by consortia of micro-organisms and the function of individual species is not clear in many cases. This publication provides an overview of the current situation and relevant developments in environmental microbiology, as well as its potential application, which covers: use of micro-organisms for agriculture, production purposes, bioremediation, and cleaning purpose; environmental applications of microbial symbionts of insects; and environmental risk/safety assessment of the deliberate release of engineered micro-organisms.