ABSTRACT
Acknowledgments .................................................................................................. 354 References .............................................................................................................. 354
The pristine soil microbiome constitutes one of the largest and most diverse microbial communities on earth (Curtis et al. 2002). It remains substantially unexplored in terms of functional diversity (Crawford et al. 2005). The structure and the physiology of the soil microbial compartment are shaped by exposure to a wide range of environmental factors, including chemicals originating from microbial, plant, animal, and human activities (Dumbrell et al. 2009). The fate of chemical compounds released into the environment as a consequence of human activities and lifestyle has become a serious concern, mainly due to their impact on health (Williams et al. 2009). The soil microbial compartment resorts to complementary, nonexclusive strategies to deal with pollution: development of resistance, by way of neutralisation or degradation of the toxicant, and development of tolerance, defined as the ability of both strains and communities to withstand toxic insults inflicted by pollutants on the ecosystem. Sequencing of the soil community metagenome has revealed the unexpected density of resistance genes that constitute the natural antibiotic “resistome,” which originates from the fact that over 80% of antibiotics in clinical use originated either directly as soil natural products or as their semisynthetic derivatives (D’Costa et al. 2007; Martinez et al. 2009). Similarly, the need for rehabilitation of environmental contamination caused by manufactured chemicals, which do not occur in significant levels in nature, has contributed to the study of microorganisms, genes, and enzymes that provide efficient degradation pathways for organic chemicals (Copley 2009), or contribute to the dissemination of adaptation to toxic metal contaminants, including radionuclides (Sobecky and Coombs 2009). Characterising the resistance to contaminants and the capacity to degrade them has been a mainstay for research in microbial ecology. This particularly pertains to the isolation and detailed characterisation of numerous “superbugs” highly resistant to high concentrations of trace metals and organic pollutants (Singer et al. 2005; Pandey et al. 2009) and, for the latter class of compounds, the mineralisation of them. In comparison, the subject of tolerance of bacterial strains or bacterial communities to environmental contamination has not yet been given the same level of attention. As a result of growing awareness of environmental issues, and of the need to develop tools for the management of polluted sites and risk evaluation, the focus of investigations has shifted to the measurement, understanding, and quantification of the extent and modes of development of overall tolerance in microbial communities, without necessarily considering the presence or the expression of degradation or resistance genes to tolerate exposure to toxic contaminants. One major challenge remains-to disentangle changes caused by an anthropogenic disturbance, such as industrial or diffuse contamination, from stochastic variability within the microbial compartment as a consequence of normal fluctuations of environmental conditions, in order to establish cause-effect relationships between the presence of toxicants in a given environment and the overall structure and function of the microbial compartment.
