Phenolic acids are the main polyphenols made by plants. These compounds have diverse functions and are immensely important in plant-microbe interactions/symbiosis. Phenolic compounds act as signaling molecules in the initiation of legumerhizobia symbioses, establishment of arbuscular mycorrhizal symbioses and can act as agents in plant defense. Flavonoids are a diverse class of polyphenolic compounds that have received considerable attention as signaling molecules involved in plant-microbe interactions compared to the more widely distributed, simple phenolic acids; hydroxybenzoic and hydroxycinnamic acids, which are both derived from the general phenylpropanoid pathway. Plants possess defense mechanisms that they use in response to the attack of pathogens. Secondary metabolites play important roles either as local or systemic resistance factors in protecting the plants against various pathogens. Phenolic compounds play a major role in the induction of resistance in plants. Generally, phenolic compounds released from seeds, roots or residue decomposition can act against soil borne pathogens and root-feeding insects. Roots are a rich source of specific natural products that contribute to the competitiveness of invasive plant species and have a marked effect plant and soilborne organisms. Several studies have shown that plant defense against soil born pathogens, nematodes, phytophagous insects is based on the release and accumulation of phenolic compounds in soil. The activity of particular phenolic compounds depends on their structural diversity. For example, simple and complex phenolic compounds such as cajanin, medicarpin, glyceolin, rotenone, coumestrol, phaseolin, phaseolinin, isoflavonoid, flavonoids act as phytoalexins, phytoanticipins and nematicides against soilborne pathogens and phytophagous insects. Several phenolic acids possess high antifungal activity. Phenolic compounds can offer an alternative to the chemical control of pathogens on agricultural crops. Accumulation of phenolic compounds at the challenge site also reinforces cell wall which is accompanied by localized production of reactive oxygen species driving cell wall cross linking, antimicrobial activity and defense signaling. The presence of microorganisms undoubtedly influences the quality and quantity of flavonoids present in the rhizosphere, both through modification of root exudation patterns and microbial catabolism of exudates. Microbial alteration and attenuation of the signals of phenolic compounds may have ecological consequences for plant-microbe interaction.

Plant phenolic compounds produced during host-pathogen interactions work by several mechanisms in plant defense. It has been suggested that the alteration of flavonoid profiles in response to AMF colonization may be a result of initiation of a general plant defense response which is later suppressed. The potential consequences of microbial transformations of pre-existing phenolic compound pools, namely the production of de novo flavonoids which are either nod gene inducers or repressors and also induce rhizobial resistance toward phytoalexins, or the formation of mono-cyclic hydroxy aromatic metabolites which could have implications for competition for nodule occupancy, and chemotactic responses. Such natural defense mechanisms provided by these biomolecules in the rhizosphere deserves more scientific attention because of its dual ecological potential as a sustainable means of reducing soil borne infections and for increasing the soil fertility in the ecosystems. Interestingly, rhizobia induce a number of defense mechanisms in planta thereby conferring increased disease resistance. Plant growth promoting rhizobacteria (PGPR) are increasingly being used in agriculture with potential beneficial effects on plant growth while limiting deleterious effects of phytopathogens by the production of antimicrobials. Recent advances in genomic research provide vital clues to the enigma of legume—rhizobia recognition by antimicrolbial molecules.