Background Our knowledge of plant beneficial bacteria in the rhizosphere is rapidly expanding due to intense interest in utilizing these types of microbes in agriculture. Laboratory and field studies consistently document the growth, health and protective benefits conferred to plants by applying plant growth promoting rhizobacteria (PGPR). PGPR exert their influence on other species, including plants, in the rhizosphere by producing a wide array of extracellular molecules for communication and defense. Scope The types of PGPR molecular products are characteristically diverse, and the mechanisms by which they are acting on the plant are only beginning to be understood. While plants may contribute to shape their microbiome, it is these bacterial products which induce beneficial responses in plants. PGPR extracellular products can directly stimulate plant genetic and molecular pathways, leading to increases in plant growth and induction of plant resistance and tolerance. This review will discuss known PGPR-derived molecules, and how these products are implicated in inducing plant beneficial outcomes through complex plant response mechanisms. Conclusions In order to move PGPR research to the next level, it will be important to describe and document the genetic and molecular mechanisms employed in these interactions. In this way, we will be able to restructure and harness these mechanisms in a way that allows for broad-based applications in agriculture. A greater depth of understanding of how these PGPR molecules are acting on the plant will allow more effective development of rhizobacterial applications in the field.

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Cassava (Manihot esculenta), a major staple food in the developing world, provides a basic carbohydrate diet for over half a billion people living in the tropics. Despite the iron abundance in most soils, cassava provides insufficient iron for humans as the edible roots contain 3–12 times less iron than other traditional food crops such as wheat, maize, and rice. With the recent identification that the beneficial soil bacterium Bacillus subtilis (strain GB03) activates iron acquisition machinery to increase metal ion assimilation in Arabidopsis, the question arises as to whether this plant-growth promoting rhizobacterium also augments iron assimilation to increase endogenous iron levels in cassava. Biochemical analyses reveal that shoot-propagated cassava with GB03-inoculation exhibit elevated iron accumulation after 140 days of plant growth as determined by X-ray microanalysis and total foliar iron analysis. Growth promotion and increased photosynthetic efficiency were also observed for greenhouse-grown plants with GB03-exposure. These results demonstrate the potential of microbes to increase iron accumulation in an important agricultural crop and is consistent with idea that microbial signaling can regulate plant photosynthesis.

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Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.