While some microorganisms in the soil use crops as their food and lead to disease in plants, most organisms that live in the soil are beneficial to crops. Some, like bacteria, nematodes, and fungi, are microscopic, while others such as earthworms and various insect larvae are visible to the naked eye.
Earthworms and nightcrawlers benefit the soil in many ways. Their burrowing helps to mix the soil and improve the ability of the soil to drain, soil aeration, and soil structure. Earthworms and nightcrawlers feed on organic matter above the soil surface and consume soil minerals as they burrow. They defecate fecal matter on the surface called casts that are rich in plant nutrients.
Soil also contains certain bacteria and fungi that feed on and get energy from dead and decaying organic matter called saprophytes. These soil saprophytes are often referred to as decomposers and recyclers because they feed on parts of dead plants in the soil, decompose the organic matter, and recycle them into helpful byproducts like humus. In doing so, they also break down complex organic molecules into simple mineral nutrients that can be consumed by plants, which improves soil fertility. Saprophytes also improve soil structure by churning the soil and excreting gummy substances that help aggregate or bind the soil together.
There are other types of bacteria and fungi that do not feed on dead or decaying organic matter, yet are still beneficial to plants. Some can pull nitrogen (N2) from the air, which cannot be consumed by plants, and convert it to ammonium (NH4+) or nitrate (NO3+), which can be consumed by plant roots.
Most terrestrial or land plant species used for gardening and landscaping form a symbiotic relationship between their root system and certain fungi in the soil. These root and fungi relationships are called mycorrhizae (“myco” means fungus and “rhiza” means root). The fungi colonize the roots of the host plant and extend its root system through mycorrhizal fungal filaments.
The plants produce sugars or carbohydrates through photosynthesis and supply them to these fungi. In return, the fungi take mineral nutrients and water from the soil to supply to the roots of the plants, often much more efficiently than the plants’ own roots.