Engineered microbiomes, mainly bacteria and fungi, have been used since decades in numerous fields including medicine, industry and agriculture. For the purpose of phytoprotection or bioremediation, engineered microbiomes – genetically modified or not – are thus released into the environment. Before any release in an uncontained environment, the impacts of engineered organisms on the natural microbial communities need to be considered. Predictive ecology studies help evaluate these potential impacts and to balance their expected benefits against any potential risks.
A solid knowledgebase acquired on microbiomes engineered for land-based agriculture shows that the evaluation of ecological risks is complex and should be based on multiple criteria. This complexity will be illustrated through the example of the soil-dwelling, nitrogen-fixating bacteria Bradyrhizobium, intentionally introduced for Acacia agroforestry. Several studies have been conducted on different temporal and spatial scales, starting from short-term laboratory experiments, down to greenhouses and small-scale field trials in an open environment. Finally, long-term monitoring was performed in very different ecosystems, at a worldwide scale. These case studies help to measure the persistence of introduced organisms, their competition with native species and their subsequent impact on the local microflora, as well as the potential genetic exchange between introduced and native microbiome. There is growing interest to engineer algae or their microbiomes for industrial applications such as biofuel production or the degradation of organic pollutants raises questions on their interactions with natural communities; this is compounded by the development of efficient technologies towards the genetic modification of algae and their microbiome. As in agriculture, and parallel to the current aquaculture boom, the scientific community will have to review, evaluate and monitor the ecological risks associated to engineer algae and their microbiomes.