Bacteria that produce a group of enzymes called deaminase can protect plants against many different stressors, such as drought, flooding, heavy metals, high salinity and pathogens. These bacterial enzymes help plants by blocking the production of ethylene, which inhibits root growth and development. Other bacteria that make the sugar trehalose help stabilize plant membranes and enzymes to protect them against damage produced by repeated cycles of drying and rehydration. Similarly, endophytes, fungi that live on and within plant tissues, often form beneficial relationships by making the host plants unattractive to pests, such as mites, that can carry harmful pathogens that inhibit plant growth and reproduction.
Most microbes beneficial to plants live in the soil. Of these, some have a close and mutually beneficial, or symbiotic, relationships with plants. Rhizobia form nodules on the roots of beans and peas to help them fix nitrogen from the air while taking minerals and sugars from the plant. Mycorrhizae create filaments or threads that increase the surface area of roots and help with the uptake of water and nutrients, such as phosphorus and zinc. In return, the fungus receives sugars and other compounds for its own growth.
A variety of organisms in soil help decompose organic matter, such as dead leaves, grass clippings and other elements that may also exist in compost piles. These beneficial microbes transform nutrients in organic matter into mineral forms that plants can use. In addition, as these organisms break down organic matter, their presence simultaneously improves soil structure, resulting in less soil compaction and better water and air movement by turning the organic matter into humus. Humus releases nitrogen, phosphorus and sulfur over time, while helping to retain soil nutrients.
Although some garden supply sources sell microbe inoculants that can help promote soil heath, you can also take steps to create an environment to encourage beneficial microbes. Add organic matter regularly so microbes have a regular food source. Using organic mulch on top of soil stabilizes soil moisture and temperature and prevents compaction. Water frequently to maintain a damp, but not overly wet environment. Avoid unnecessary tilling and pesticide applications, as these two activities can be harmful to beneficial microbes.