The environmental risk assessment of a genetically modified micro-organism (GMM) needs to consider its potential interactions with indigenous microbial communities in a given habitat. Interactions can relate to the survival of the GMM and/or the transfer of recombinant genes to indigenous community members. While there is already considerable knowledge about the biology and ecology of some species used as hosts for genetic modifications to inform their environmental risk assessments, in-depth studies on the biology, genetics and eco-physiology of other GM species may still be required before considering their use in not-strictly contained systems, for example for biofuel production or as biocontrol agents. Containment can be achieved when using GMM symbionts which are non-viable outside of their hosts, as demonstrated with Wolbachia sp. and insects. Given the potential of non-symbiotic micro-organisms to spread in the environment, it appears desirable that a GM should not persist after its intended purpose of application has been achieved, even if it’s presence does not necessarily translate to a risk, as it may have no adverse properties. In summary, in addition to a detailed characterisation of the genetic and biological properties of a GMM, in-depth knowledge about its interactions with its target and non-target environments is not only crucial to improve its efficiency, but also important to assess their environmental risks.