The microbial organisms transform the substance through metabolic or enzymatic processes. It is based on two processes: growth and cometabolism. In growth, an organic pollutant is used as sole source of carbon and energy. This process results in a complete degradation of organic pollutants. Soil organic matter and soil organisms are inextricably connected. Microbial biomass is the living component of soil organic matter, and microorganisms are the catalysts for most nutrient-releasing processes. They make it possible for crops to grow and for soils to be productive. Due to their close proximity to plant roots, soil microbes significantly affect soil and crop health. Some of the activities they perform include nitrogen-fixation, phosphorus solubilization, suppression of pests and pathogens, improvement of plant stress, and decomposition that leads to soil aggregation. Bacteria and fungi are responsible for most of the mineralization of organic matter in soils. Microorganisms release enzymes that oxidize the organic compounds in organic matter. A decomposer is essentially an organism that breaks down organic material such as the remains of dead and decaying animals and plants and other organisms in the ecosystem.

Microorganisms are essential to soil formation and soil ecology because they control the flux of nutrients to plants promote nitrogen fixation, and promote soil detoxification of inorganic and naturally occurring organic pollutants. The living portion represents about 5 percent of the total soil organic matter. Micro-organisms, earthworms and insects help break down crop residues and manures by ingesting them and mixing them with the minerals in the soil, and in the process recycling energy and plant nutrients. Bioremediation is a process that uses mainly microorganisms, plants, or microbial or plant enzymes to detoxify contaminants in the soil and other environments. The microbial organisms transform the substance through metabolic or enzymatic processes. It is based on two processes: growth and cometabolism. In growth, an organic pollutant is used as sole source of carbon and energy. This process results in a complete degradation of organic pollutants. Various microorganisms can degrade environmental pollutants with promising skills like bacteria, fungi, algae, and protozoa. Certain parameters must be established to provide the highest biodegradation rate of degradable microorganisms under the optimum conditions. Microorganism used some substances in pesticides as nutrients and decompose them into small molecules, and the main ways of degradation were mineralization and co-metabolism.Microbial turnover forms the backbone of soil organic matter (SOM) formation and it has been recently proposed that SOM molecular complexity is a key driver of stability. Despite this, the links between microbial diversity, chemical complexity and biogeochemical nature of SOM remain missing. Organic matter decomposition serves two functions for the microorganisms, providing energy for growth and suppling carbon for the formation of new cells. Soil organic matter (SOM) is composed of the "living" (microorganisms), the "dead" (fresh residues), and the "very dead" (humus) fractions. They include algae, bacteria, cyanobacteria, fungi, yeasts, myxomycetes and actinomycetes that are able to decompose almost any existing natural material. Micro-organisms transform organic matter into plant nutrients that are assimilated by plants.