Bacteria are single-celled microorganisms that are vital for cycling nutrients in the soil. There are thousands of species of bacteria. In general, beneficial bacteria are usually aerobic, requiring oxygen to survive, while disease-causing ones thrive in low-oxygen environments. Many species of bacteria serve as decomposers, eating up dead plant matter and concentrating the nutrients in their bodies—one of the first steps in returning those plant building blocks to the soil. Bacteria bind all kinds of compounds into organic forms that will not leach out of the soil. Another group of bacteria collaborates with legumes to capture or "fix" atmospheric nitrogen and add it to the soil.
Fungi are strandlike microorganisms that help hold soil particles together and improve soil structure. They consume the harder-to-digest organic materials, such as dead leaves, pine needles, and fallen tree trunks. One type of fungi establishes mutually beneficial mycorrhizal relationships with plants, which allows the fungi to hold and transfer nutrients directly to plant roots. While many species of fungi are beneficial, others are responsible for plant diseases.
Protozoa include microorganisms like flagellates, amoebae, and ciliates, all of which eat bacteria. As protozoa consume bacteria, they release excess nutrients in soluble forms that can be utilized by plants. Protozoa also work with bacteria and fungi to build air passageways, letting oxygen, water, and roots move easily through the soil.
Microarthropods are an assortment of very tiny organisms that include soil mites, springtails, and soil-dwelling insects. There are many different kinds of these critters, but, in general, their function is to eat fungi, or each other, and release nutrients in a plant-available form. And while they are doing that, they also build structure in the soil.
Like so many things in life, the secret is balance. We need members from each of these groups of organisms in our soil working in concert with each other and the plants they feed. To a large extent, plants control and select for the growth of the microorganisms they need.
But gardening and farming that relies on heavy doses of synthetic chemicals and fertilizers destroys beneficial life in the soil, leaving plants without this important support system. Chemically maintained soils have been reduced to dirt over the course of a half-century, with little or no beneficial life to combat disease organisms or insect pests, and nothing left in the soil to cycle nutrients.
The best way to obtain and nourish the full set of life-sustaining microbes is by adding locally made compost. Both worm composting and thermal composting provide a great diversity of beneficial organisms. In worm compost, the worms consume the pathogens and pests. Thermal composting, also called hot composting, means the pile reaches and maintains a temperature high enough to kill weed seeds, pathogens, and pests. In both cases, the beneficial organisms thrive and help maintain the aerobic conditions of the compost when it is applied to the garden.
Good compost will then replace the life—and the foods that feed that life—currently missing from many gardens, and will turn that dirt back into living soil.