Microorganisms are involved in many functions which impact plant growth, productivity and tissue quality and the signals that control this interaction with plants is critical. These interactions have global implications for the ecology of natural ecosystems and food security through impacts on crops. Some plant-microbe interactions are beneficial, such as those with nitrogen fixing bacteria or mycorrhizal fungi, while others are detrimental such as those with pathogenic bacteria and fungi. The presence of microorganisms in some cases (i.e. mycorrhizal fungi) is critical in order for plants to survive under extremely P-deficient conditions. For these and other reasons, the impact of plant signals on the survival, success, community behavior and function of species of microorganisms and vice versa is of great interest. Study of impacts on the biodiversity and functionality of the microbial biomass in soils and on plant surfaces such as root and leaves yields insight into such systems. If we can gain understanding into how plants and microorganisms communicate with each other, or how their individual signaling pathways interfere with one another at a biochemical, protein and transcriptional level, then we may be able to manipulate both beneficial and detrimental interactions. If we can do this successfully, we may have a range of opportunities to improve agricultural sustainability and environmental security into the future. This special issue will concentrate on the cutting-edge research in this field of plant-microbe interactions with a view to making recommendations that will enhance agricultural sustainability and food security.In this special issue we present eight papers, which demonstrate how specific individual and communities of microorganisms, including bacteria and fungi, have profound effects on the traits expressed by, biosynthetic pathways regulated by and transcriptional responses of the host plant. We then go on to present some research which harnesses this understanding to enhance plants resistance to pathogens. The papers present research which is focused on both pathogenic and beneficial microorganisms interacting with a range of host plants including ornamentals, those which produce pharmaceuticals, agricultural plants, both legume and cereals, and model plants. The research also covers the role of microorganisms in general growth promotion and tolerance to biotic stress, disease and fungal infection resistance, and abiotic stress including salt tolerance and promotion of nitrogen fixation. Collectively, this research demonstrates that it is possible to develop a fundamental understanding of the biochemical and molecular signals involved in plant responses to microorganisms and translate this into a predictable plant trait response, which has the potential to enhance a plants tolerance to stress.With respect to how plant traits respond to microbial signals we present two papers (Patil et al. 2016;Tsavkelova et al. 2016). In Patil et al. (2016, 136 Pseudomonas isolates were classified based on pl...