The Role of Secretion Systems, Effectors, and Secondary Metabolites of Beneficial Rhizobacteria in Interactions With Plants and Microbes

Abstract

Beneficial rhizobacteria dwell in plant roots and promote plant growth, development, and resistance to various stress types. In recent years there have been large-scale efforts to culture root-associated bacteria and sequence their genomes to uncover novel beneficial microbes. However, only a few strains of rhizobacteria from the large pool of soil microbes have been studied at the molecular level. This review focuses on the molecular basis underlying the phenotypes of three beneficial microbe groups; (1) plant-growth promoting rhizobacteria (PGPR), (2) root nodulating bacteria (RNB), and (3) biocontrol agents (BCAs). We focus on bacterial proteins and secondary metabolites that mediate known phenotypes within and around plants, and the mechanisms used to secrete these. We highlight the necessity for a better understanding of bacterial genes responsible for beneficial plant traits, which can be used for targeted gene-centered and molecule-centered discovery and deployment of novel beneficial rhizobacteria.

Keywords: beneficial bacteria; biocontrol agents; effectors; plant growth promoting bacteria; rhizosphere; root nodulating bacteria; secretion systems.

Figure 1

The interaction of the three groups of beneficial bacteria with other species; plant growth promoting rhizobacteria (PGPR), root nodulating bacteria (RNB), and biocontrol agents (BCAs) and their neighboring cells. PGPR produce various secondary metabolites including phytohormones which are regulating several processes in the plant development such as seed germination, stem, leaf, and root morphology. Another feature of PGPR is the solubilization of nutrients. RNB contain several secretion systems that can transport effectors directly into the host cell to regulate certain processes. Type I protein secretion system (TISS) of Rhizobium leguminosarum bv. Viciae is responsible for biofilm formation via the effectors PlyA, PlyB, and Rhizobium-adhering proteins (RapS). The T1SS is recognizable due to the outer membrane protein TolC. Type III secretion system (T3SS) and type IV secretion system (T4SS) are secreting effectors which can trigger protein regulation and induce plant immune responses. At least one effector travels into the plant cell nucleus. BCAs produce antibacterial and antifungal protein toxins and small molecules. Proteinaceous toxins are transferred through the Type VI secretion system (T6SS), a powerful nanoweapon, into the host cell. Specific antimicrobials can kill phytopathogens like fungi, oomycetes, and bacteria. In addition, biocontrol agents can trigger the plant immunity pathway induced systemic resistance (ISR), which leads to the production of antimicrobials which can eliminate a broad spectrum of organisms.