Soils are considered principally non-renewable resources. Soil ecosystem services have a large impact on numerous societal demands and are of high economic importance. Within the area of sustainable agriculture, it is expected that agricultural production will increasingly rely on the natural nutrient retention and recycling capabilities of soil. This project seeks to provide a fundamental scientific understanding of soil functioning and the resulting ecosystem services in Brazilian and Dutch bio-economies based on innovative microbial ecology and soil science studies. Focus is in sugarcane crop production systems by linking soil microbial composition and functioning, waste residues recycling, fertilizers, soil factors and greenhouse gases (GHG) emissions through integrating and complementing the strong expertise of Brazilian and Dutch researchers from different areas of agronomy, soil sciences, plant nutrition, biogeochemistry, soil ecology, microbial ecology, ecological genomics, molecular ecology and bioinformatics. We will quantify the microbial functional groups and microbial abundance of C and N cycle genes and measure GHG emissions (CO2, CH4 and N2O) from soils during the productive cycle of the plant under different management practices and verify the temporal and spatial variability of these emissions in the evaluated treatments with different concentrations of sugarcane vinasse residue combined with N mineral fertilizers in combination with straw additions, and determine the conditions under which such GHG emissions can be counteracted, or minimized most. The proposed project will enhance fundamental scientific understanding of the interactive role of the microbial networks operating in soil and the consequences of bio-based agricultural management practices for the functioning of soil systems.

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.