Modern society introduces a variety of contaminating chemicals to surface soils through chemical pest management, manure application, and deposition of biosolids from wastewater treatment plants. Many of these contaminants are degraded slowly or incompletely in the environment, and may therefore diffuse to surface waters or leach to lower soil horizons, and ultimately contaminate aquifers. As a result, soil contamination, e.g. by pesticides, hydrocarbons, and veterinary as well as human pharmaceuticals is creating a legitimate concern in the public: Are residential soils safe? Can agricultural soils continue to generate safe crops for human consumption? Will the underlying aquifers continue to provide safe drinking waters?
It is becoming increasingly clear that microbiological transformations are typically more significant (in both extent and rate of reaction) than chemically or physically induced transformations of contaminants in the environment. Most importantly, it is the intricate interactions between available compounds and available degrader organisms that determine whether the contaminant will be transformed by the microorganisms or remain a long-lived concern in production of crops or drinking water.
Hence, it is becoming obvious that we need to move from a large-scale “black box” approach to a much more detailed understanding when trying to identify the bottlenecks that limit microbial biodegradation. In environmental microbiology, new methods have thus become available that allow one to detect, identify, quantify, and even localize both the presence and activity of key organisms involved in such processes. They show us a heterogeneous micro-scale distribution of microorganisms and habitats in the soil environment. Concomitantly the improved analytical techniques have lead to several reports on temporal or spatial occurrences of transformation products, with their own possible negative environmental effects.
At present, it remains a challenge for environmental microbiologists to elucidate the true limiting factors that control biodegradation in Nature. Convergence in the development of microbial, biochemical, and physiochemical analytical methods provides the opportunity to visualize degrader microorganisms and their activities in their natural environments at the relevant scale of spatial resolution. An equally large challenge is then to translate the information, which we obtain at the micro-scale into soil management strategies that can optimize biodegradation of contaminated environments to the benefit of the community.