Profitable and environmentally friendly agriculture is not only measured in terms of high yield, but also in a “healthy” root environment. One of the most challenging areas of science today is understanding the “microbiome” of diverse ecological niches. The microbiome is a special complex of microorganism populations that is a dynamic reflection of environmental conditions and impacts, competition, and change over time. An improved understanding of the microbiome around the roots and the rhizosphere can contribute the missing dimensions that are needed to identify the various and overall elements to be accounted for in shifting from conventional agriculture to conservational agriculture. The microbiome around the roots has a central role in the ability of the plant to exploit resources and the environment, and today is recognized as being an important measure of soil fertility and health. The currently accepted idea is that increased diversity of microbial populations in the soil leads to greater fertility. Moreover, it has been proven that the plant can effect the microbial population structure around its roots by exuding chemical compounds that encourage growth of specific microbial taxa. Systems of interaction and mutual development can contribute to plant health and increase the rate of plant growth and development. Furthermore, these interactions can induce plant responses that are deleterious to herbivorous insects, by favoring spread of diseases or physiological processes that form defense compounds in the foliage. Today, the application of microorganisms for improving the quantity and quality of crop yield is at the forefront of the development of environmentally friendly agricultural products. Induction of changes in the microbiome through one-time addition with a small amount of soil containing a diverse microbial population, or adding specific microbial taxa or other soil supplements, could change the microbial community and performance of the plant community in the field for years to come.
Developments in genomics could enable monitoring of microbial processes in the soil through identification of the genetic composition of its microbial population. Use of modeling approaches based on genomics could allow prediction of population dynamics in the soil, connecting changes in soil microorganism composition with changes in the crop responses.