III The use of micro-organisms for bioremediation

Designing bacteria for the environment: From trial and error to earnest engineering

Victor de Lorenzo

Systems Biology Program, Centro Nacional de Biotecnologia CSIC, Cantoblanco-Madrid, Spain

Since the mid-1970s, genetic engineering and the possibility of accidental or deliberate environmental release of modified micro-organisms has been the centre of debates concerning the consequences of altering the ordinary course of nature. For a sound discussion on risks, it is of essence to separate substantive scientific and technical issues from non-informed perceptions of the general public. This chapter advocates this question to be framed on the already extensive history and wealth of data on the design, performance and risk studies made since the early 1980s on genetically modified organisms and more specifically, on available records on genetically engineered micro-organisms (GEMs) designed for non-contained applications as in situ bioremediation agents. Existing information provides a suitable background for tackling the uncertainties raised by newly engineered agents, including those that may stem from synthetic biology.


There are at least three ways in which genetically modified bacteria can help remove toxic waste. The first is, of course, by the use of environmentally friendly bio-processes and products which are designed ab initio precisely to avoid the production of noxious by-products (Schmid et al., 2001). The second case is the recycling or reuse of waste in source for either generation of added value products (e.g. conversion of lignocellulose into biofuels) or for mineralisation into CO2 and H2O (Keasling and Chou, 2008; Lee et al., 2008). Finally, there are frequent scenarios in which given chemicals have been released accidentally or chronically to soil or water ecosystems. This pollutes the area with concentrations of the compounds that are high enough to cause a detrimental effect on the biology of the site, but low enough not to warrant an intensive and costly, ex situ treatment. These cases are typical candidates for bioremediation interventions (Pieper and Reineke, 2000).

The conceptual frames behind such actions have evolved considerably since 1989, the time of the Exxon Valdez disaster (Harvey et al., 1990), as the deliberate addition of biodegrading bacteria (so-called bio-augmentation) has, in most cases, not been useful (Peterson et al., 2003). For the sake of enumerating biotechnological challenges related to microbial diversity, it should be mentioned that after a long period of stagnation, the field is experiencing a rebirth under the aegis of newly developed insights, for instance in systems and synthetic biology. New bioremediation approaches stem from the growing knowledge on the genomes of soil and marine bacteria and from the analyses of their whole transcriptomes, proteomes and metabolomes (Lovley, 2003; Watanabe and Hamamura, 2003; Pieper and Reineke, 2000; Katsivela et al., 2005; de Lorenzo, 2008). This wealth of data allows the construction of metabolic models that identify bottlenecks in biodegradation reactions. In some cases, these can be overcome through protein design and metabolic engineering aimed at fixing the problems found in natural bacteria. In other instances, the choice is the amendment of the afflicted site with given nutrients that may limit growth or catalysis of the indigenous micro-organisms otherwise (Wenderoth et al., 2003; El Fantroussi and Agathos, 2005). It is also feasible to associate degrading bacteria to plant roots (rhizoremediation), and even the expression of catabolic genes of bacterial origin in transgenic plants (Kuiper et al., 2004; Van Dillewijn et al., 2007).

These approaches are likely to produce successes in the degradation of otherwise recalcitrant pollutants in situ, such as chlorinated aliphatics and polychlorinated biphenyls as well as for binding heavy metals. However, bioremediation is not just the encounter of one bacterium with one chemical in a Petri dish. Real environmental cleanup involves various layers of multi-scale complexity involved in removal of toxic waste from polluted sites. Genetics and metabolism are the central, but not the only, aspects of bioremediation. A number of pre-catalysis processes upstream (diffusion in solid matrixes, bioavailability, weathering, abiotic catalysis of pollutants) and downstream post-catalysis (stress, production of toxic intermediates, predation, competition) constrain the outcome of the whole action (de Lorenzo, 2008). To this end, one needs to integrate multi-scale data from the all the biological, chemical and physical actors of the process - a challenging field of action for systems biology.

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