An ecosystem contains living organisms all of which depend on the interaction with one another. The rhizosphere housing the root of cultivated crops contains several groups of organisms ranging from microbes to vertebrates. Most of which depend on plants directly or indirectly for their survival. Agricultural crops interact with other organisms present in their environment. Such interactions may be beneficial or harmful to the crops grown in the ecosystem. Biotic component including opportunistic fungi, plant, and nematode influences the metabolisms and yield of cultivated crops. As the crops grow with time in their life cycle, they may be susceptible to the influence of these opportunistic organisms on the field. Factors such as growth stage, unfavourable weather condition, and wounding may reduce the immunity of the plants and therefore leading to the infection of the crop plant by opportunistic organisms. Therefore, this chapter explores the various physical and biochemical interactions between agricultural plant and opportunistic microorganisms.