Microorganisms can improve crop nutrition and the ability of crops to resist biotic and abiotic stress. Thus, greater utilisation of microorganisms in agricultural systems has the potential to allow reductions in the use of inorganic fertilisers, water, herbicides and pesticides.

The primary harmful effects of microbes upon our existence and civilization is that they are an important cause of disease in animals and crop plants, and they are agents of spoilage and decomposition of our foods, textiles and dwellings.

Beneficial microorganisms include those that create symbiotic associations with plant roots (rhizobia, mycorrhizal fungi, actinomycetes, diazotrophic bacteria), promote nutrient mineralization and availability, produce plant growth hormones, and are antagonists of plant pests, parasites or diseases (biocontrol agents).

In agriculture, microbial products are those made from microorganisms to help protect crops from disease and pests, and to encourage healthy growth.

Soil microbes (bacteria, fungi, and archaea) perform fundamental functions in soils, such as cycling of crucial nutrients like nitrogen and carbon, breaking down crop residues, and stimulating plant growth.

The beneficial uses of bacteria include the production of traditional foods such as yogurt, cheese, and vinegar. Microbes are also important in agriculture for the compost and fertilizer production. Bacteria are used in genetic engineering and genetic changes.

Some of the commonly promoted and used beneficial microorganisms in agriculture worldwide include Rhizobia, Mycorrhizae, Azospirillum, Bacillus, Pseudomonas, Trichoderma, Streptomyces species and many more.

Microbiology is important to food safety, production, processing, preservation, and storage. Microbes such as bacteria, molds, and yeasts are employed for the foods production and food ingredients such as production of wine, beer, bakery, and dairy products.