The soil performs a variety of key functions: (i) provides the food, fuel, and fiber needs of the world's population, (ii) regulates the quality of the air and water, (iii) decomposes organic wastes, (iv) recycles nutrients, and (v) acts as a sink for pollutants (including global gases). Soil degradation is increasingly recognized as an urgent environmental issue and a crucial need exists for the capacity to evaluate soil health. After all, soil health is a key component in sustaining the different world's ecosystems and the myriad of natural and socioeconomic systems they support. In this respect, soil health has been defined as the "continued capacity of a specific kind of soil to function as a vital living system, within natural or managed ecosystem boundaries, to sustain plant and animal productivity, to maintain or enhance the quality of air and water environments, and to support human health and habitation". A biological indicator is an organism, a part of an organism, or a community of organisms, used to obtain information about environmental quality. The assessment of microbial biodiversity has the potential to provide useful insight into the health and functioning of soil. Our inability to culture most microorganisms that are present in soils has, until recently, impaired studying the relationships between the structure and the function of soil microbial communities. This shortcoming has been recently overcome by using several molecular techniques that allow the detection, enumeration, and characterization of soil microorganisms without cultivation.