To satisfy the food demands of the global population, advanced technology based research is needed, that can extract the information from the plant metabolism and microbial gene pool and use it for improving plant health and productivity. Modern biotechnological tools have the ability to unlock the limitations of agricultural practices. However, the application of these tools is not well equipped. Moreover, eco-friendly agriculture by microbial inoculants is known to have positive influences on soil/plant health. Therefore it is relevant to explore the plant associated microbial niches, especially endophytes, epiphytes, and soil microbes and understand how they are benefitting each other.