Organisms in the soil are both numerous and diverse. They range in size from the one-celled bacteria, algae, fungi, and protozoa, to the more complex nematodes and micro-arthropods, and to the larger organisms such as earthworms, insects, small vertebrates, and plants. Soil microbes (or microorganisms) are too small (i.e., smaller than 0. 1 mm) to be seen with the unaided eye. Bacteria are the most abundant microorganisms in soil, with a population of 10¹⁰–10¹¹ individuals and 6,000–50,000 species per gram of soil and a biomass of 40-500 grams per m².

If we are to understand microbial functions in soil and effects of management practices on soil quality, we need to consider more than just the number of individuals in a gram of soil. We also need analytical methods that will allow us to identify changes in the composition of the microbial community. Some of the more recently developed molecular genetic methodologies are proving useful in characterizing soil populations.

DNA sequencing is currently  used to for taxonomic classification of microbes. Sequence information on nucleic acids (DNA- deoxyribonucleic acid and RNA – ribonucleic acid) associated with many microbial organisms is being generated rapidly. These sequences are analyzed by gene probe and polymerase chain reactions (PCR) technologies, which in turn allow us to detect organisms that previously could not be isolated or cultured.

Soil microbes play both beneficial (decomposition and nutrient cycling) and detrimental roles as pathogens and contributors to soil environmental problems such as global warming and groundwater contamination. The physical, chemical, and biological soil properties and their interactions with the resident community of soil microorganisms have a profound impact on growth and activity of microorganisms. As our understanding of these complex relationships develops, we should be able to develop soil management practices that are sustainable and that lead to maintenance and improvement of soil quality.