DNA sequencing is a powerful method to unravel the genetic diversity of micro-organisms in nature. In recent years, revolutionary next-generation sequencing technologies have become widely used in various microbiological disciplines, including microbial taxonomy and ecology. This chapter reviews the species concept of prokaryotes, including bacteria and Archaea, and presents the development of a comprehensive methodology for monitoring microbes in soil. Next-generation sequencing-enabled metagenomics should be useful and can be widely applied to modern microbiology and biotechnology.

Due to the inter-dependent network of organisms, a microbe’s interaction with the physical environment and its continuous evolution through mutation and horizontal gene transfer, microbial diversity is never static, which makes an analytical approach almost impossible for assessing the risk of the environmental use of microbes. One possible alternative approach could build on concepts developed by the OECD in the early 1990s: familiarity and substantial equivalence. According to the Cartagena Protocol on Biosafety, “the objective of a risk assessment is to identify and evaluate the potential adverse effects of living modified organisms on the conservation and sustainable use of biological diversity in the likely potential receiving environment, taking also into account risks to human health”. The “potential adverse effects” are not always easy to identify and interpreting them in different circumstances has been a long-standing question. Ambiguity surrounding this key word appears to have caused regulatory uncertainty. This chapter addresses the target of risk assessment of environmental application of microbes and the difficulty of using an analytical approach in assessing the risk of micro-organisms used in the environment.

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.

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.