Plant-growth promoting microbes (PGPM) are a viable alternative to traditional fertilizers for enhancing plant productivity and improving soil quality without environmental pollution. The use of PGPM in agriculture has been hampered by a lack of reproducible results and the difficulty of transferring this technology to the field. This inconsistent success primarily reflects competition or resistance of the original soil microbiome to inoculants, as well as the negative effects of management practices such as fertilization on plant interactions with the soil microbiome and the efficiency of ecosystem services delivered by PGPM. We were the first to circumvent this problem under field conditions by manipulating the soil microbiome to successfully obtain consistent, positive effects of inoculated microbes on plant productivity (Cipriano et al., 2016;https://doi.org/10.1093/femsec/fiw197). However, the influence of the indigenous soil microbiome on plants remains largely unknown. We propose to investigate this tripartite, PGPM-plant-soil microbiome interaction in plant quality and productivity using state-of-the-art ‘omics’ and bioinformatics approaches to investigate facilitation (positive interactions) and competition (negative interactions) by both microbes and PGPM within the plant realized niche following gradients of both soil diversity and nutrient availability. This research will facilitate the development of innovative methods for agricultural and horticultural starting material production using PGPM for sustainable crop production by combining techniques to reduce nutrient input and enhance the efficiency and long-lasting effects of PGPM. This research proposal will integrate approaches to obtain a fundamental understanding of these tripartite interactions in a smart microbiome engineered plant production system for sustainable high-quality crop production.

A current challenge for modern agriculture is to meet the food production needs for an increasing global population while improving resource use efficiency and attenuating impacts on human health and environment. In order to maximize reliability and stability in agriculture, optimization of crop management and resource use efficiency have been considered the best approaches for a sustainable increase of crop yields under variable agro-ecological conditions, environments and years. For this purpose, one interesting and sustainable method is the use of natural plant biostimulants, a diverse class of products and microorganisms that enhance plant growth and other plant parameters, such as flowering, fruit set, crop productivity and nutrient use efficiency. In this context, several studies already demonstrated that plant biostimulants can induce morpho-anatomical, biochemical, physiological and molecular plant responses, not only improving crop productivity but also promoting protection against abiotic stresses, such as drought and salinity. Among the different biostimulant classes there are protein hydrolysates (PH), mixtures of polypeptides, oligopeptides and aminoacids originated from partially hydrolyzed animal and vegetal tissues. Even though the effect of PH were already observed in diverse crops, the mechanisms and behind their action are still scarcely studied, and their action can vary depending on their origin, characteristics, crop species, cultivars, growing conditions, time and mode of applications, among other parameters. The objective of this project is to evaluate the effect of protein hydrolysates in the growth, nutrient content and microbial communities of crops, if microbes are responsible for these effects, which are the mechanisms and if such effects are long-lasting.

Land degradation usually leads to a reduction in soil fertility, decline of plant productivity, and loss of biodiversity. Introducing beneficial microbial inoculants to degraded lands represents a promising and sustainable strategy. The aim of this project is to reveal the ecological roles of microbial inoculants and soil-resident microbial community in restoring both belowground biodiversity and aboveground productivity in the degraded land.