There is relationship equilibrium among soil particles, living organisms and geo-chemicals that make agricultural ecosystem functioning. Many components and conditions play significant role for development of soil biota along with increasing soil microbial diversity and soil richness. Chemotrophic microorganisms, obtaining energy from oxidation of chemicals surrounded by them, these organisms involved in agricultural soils and playing significant role in Carbon, Nitrogen, Phosphorus, Sulphur and other elemental cycles. In recent years, de-esterification, degradation, biotransformation, bioaugmentaiton are requried steps of metabolism of certain herbicides, pesticides and other agrochemicals. For stability of these chemicals pH require maintain with acidic buffer solutions, and there are certain microorganism which possess functional groups for de-composting with these agrochemicals. Moreover, these microorganisms potential with most stable in climate conditions regardless other physic-geochemical factors of heat, salt, water holding and field capacity of soil. The organisms functioning in agro-ecosystem by degradation of chemicals and actively participating to improve soil fertility. Now it is necessary to determine all microbial community present in soil for degradation pattern of agrochemicals present in those agricultural sites. Community level study can detect with help of genetic studies that provide functional genomic information. The presence of bacteria, fungi and plant studied with genomic study profile which suggests microbial transformation and incorporation of function in ecosystem that provide effectiveness for agro-ecosystems.