Novel Molecular Tools to Assess Microbial Activity in Contaminated Environments

Microorganisms are the ultimate survivalists and account for the major portion of Earth’s biological diversity. They play critical roles in many global biogeochemical cycles (carbon, nitrogen, sulfur, and iron to name but a few). A gram of soil can contain 103–106 different bacterial species, and microorganisms (bacteria as well as archaea and fungi) have been observed in diverse terrestrial and aquatic environments ranging from deep oceanic hydrothermal vents to isolated voids in polar ice sheets. Given this extreme diversity across the globe, attention has been given to the development of techniques to identify and characterize bacterial communities, encouraged also by the prospect to find new species, enzymes, or proteins that can be used in industrial applications. Over the last 20 years, the science and application of molecular-based approaches has evolved from a perspective of determining the biological structure to elucidating the entire genome and its functions. This chapter will focus on discussing different widely used approaches and recent advancements made to detect and quantify “microbial activity” in contaminated environments using biochemical and molecular tools. Understanding how contaminants are biologically influenced in the environment will require a detailed understanding of both chemical and biological function within various environmental compartments. Combined these techniques can be used to address multiple environmental issues and will aid in the development of new remediation technologies.