Less studied than above-ground interactions, but proving to be increasingly important, are the below-ground interactions that influence plant defense. There is a complex network of signal transduction pathways involved in plant responses to stimuli, and soil microbes can influence these responses. Certain soil microbes aid plant growth, producing increased tolerance to various environmental stressors, and can protect their host plants from many different pathogens by inducing systemic resistance. Organisms in above- and below-ground environments can interact indirectly through plants. Many studies have shown both the positive and negative effects that one organism in one environment can have on other organisms in the same or opposite environment, with the plant acting as the intermediary.
The colonization of plant roots with mycorhizae typically results in a mutualistic relationship between the plant and the fungus, inducing a number of changes in the plant. Such colonization has a mixed impact on herbivores; insects with different feeding methods are affected differently, some positively and others negatively. The mycorhizal species involved also matters. One common species, Rhizophagus irregularis, has been observed to have a negative effect on the feeding success of chewing herbivores, whereas other species studied have positive effects.
The roots of some maize plants produce a defense chemical when roots are damaged by leaf beetle larvae; this chemical attracts the entomopathogenic nematode species Heterorhabditis megidis. Only certain maize varieties produce this chemical; plants that release the chemical see up to five times as much parasitization of leaf beetle larvae as those that do not. Incorporating these varieties or their genes into commercial maize production could increase the efficacy of nematode treatments.
Further studies suggest that the plant-emitted chemicals act as the primary source of attractant to the nematodes. Herbivores are believed to have evolved to evade detection on the part of the nematodes, whereas the plants have evolved to release highly attractive chemical signals. A high degree of specificity is involved; species that make up these tritrophic interactions have evolved with one another over a long period of time and as a result have close interrelationships.
Microorganisms can also influence tritrophic interactions. The bacterium Klebsiella aerogenes produces the volatile 2,3-butanediol, which modulates interactions between plants, pathogens, and insects.  When maize plants are grown in a soil culture containing the bacterium or the plants are inoculated with the bacterium, the maize is more resistant to the fungus Setosphaeria turcica. The bacterium does not deter insect herbivory; it actually increases weight gain and leaf consumption in the caterpillar Spodoptera littoralis. However, the parasitic wasp Cotesia marginiventris is attracted more readily to maize plants grown in soil cultures containing either the volatile-producing bacterium or pure 2,3-butanediol.