When we think about microbes (bacteria, fungi, and other organisms too small to be seen by the naked eye) we often term them germs and consider them as harmful, even deadly. However, the soil environment just like human beings benefit greatly and even need microorganisms for good health. What type of organisms are we concerned with? These organisms include algae, fungi, bacteria, archaea, nematodes, earthworms, arthropods, and insects. Not all of these are microscopic for at least part of their life cycle but all tend to be thought of in negative terms. So what ecological niches (spots) in the soil do these organisms fill?
• Earthworms break down detritus, organic debris, promote soil structure as they ingest soil for nutrition, help incorporate organic matter into the soil, and improve the number of large pores. They really do no damage.
• Ants and termites while most aren’t thrilled with them are mostly quite beneficial. While some attack plants and sound wood most start recycling organic materials. Of the 2,000 or so species of termites, very few are going to attack sound wood or the wood in your house and are quite important in forest soils.
• Nematodes, roundworms, receive attention for the damage they do such as the soybean cyst nematode and the sting nematode in corn. Scientists estimate there are over 100,000 species and the overwhelming majority of these in the soil and feed on bacteria, fungi, other nematodes, protozoa and insect larvae.
• Protozoa are primarily predators and feed on bacteria. Few have negatives effects on plants or animals.
• While we think of fungi as causing plant and animal diseases or as signs of spoilage, they are key in the health of the soil and crops. While some cause diseases for plants and toxic compounds, they are the most versatile decomposers of organic matter, improve soil structure in their vegetative stage, improve soil fertility and release nutrients from organic matter, and are the source of antibiotics. Perhaps most importantly for many plants, fungi infect plant roots in a symbiotic relationship that effectively increases the size of the plant root system and aid in the uptake of water and nutrients. Many plants can’t survive without them.
• Bacteria and archaea are closely related single celled organisms that serve as a food source for other soil organisms, and help cycle organic matter/nutrients primarily when soil oxygen is limiting. Some are photosynthetic while others can infect the roots of legumes (soybeans and alfalfa) and provide nitrogen to the plant. The Bt in Bt corn and cotton as well as the toxin in the organic insecticide Dipel come from certain species.  
• Insects overall are considered pest but besides the termites and ants mentioned above most are harmless or help the ecosystem stay healthy. Of the millions of insect species most are of no concern which is a good thing, however, those that are pests such as rootworms, wireworms, grubs, etc. require a great deal of attention and management.