A lot of work has been done on a large number of bacterial species that we know are present in the environment. This work has yielded important results for fundamental science as well as for biotechnological applications. But the environment has much more to offer in terms of bacterial variety, genomic variety and useful genes that remain to be discovered. One way to exploit these possibilities is the study of the soil metagenome, DNA sequences directly isolated from soil samples. The genes that are isolated by the various techniques can be used in genetic engineering to improve bacterial strains that are available and that can be handled. This raises questions about risks, for instance the risk of horizontal transfer of these transgenes between organisms, i.e. between higher organisms and bacteria, as well as between different bacteria. One way to minimise the chances of such horizontal gene transfer (HGT) is to reduce the homology between transgenic DNA in donor organisms and the DNA in recipient organisms. With all the enthusiasm about the environment as a source of biodiversity, it should be recognised that the environment is very promising, but also extremely difficult to investigate, and difficult to control.