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.

Microp- Diversity and functions of the potato microbiome in the centre of origin

Microp- Stress-induced communication between plants and microbes

MiRA- Microbe-induced Resistance to Agricultural pests

VolControl will examine the possibility to enhance control of soil-borne fungal crop diseases via stimulation of production of pathogen-suppressing volatiles by soil microbes. The working hypothesis is that these volatiles will be released by bacteria upon decomposition of selected organic materials that contain precursors of suppressive volatiles. During the first phase of the project, different organic materials will be screened and the ones that give the most promising results will be further tested for disease suppressing performance in greenhouse - and field trials. In addition, information will be provided on the identity of the produced suppressing volatiles and the microbes that release these volatiles. The project will be done in close collaboration with participating companies to optimize application perspectives

This is a sub-project of a WUR-NIOO project entitled "Closing the loop: exploiting sustainable insect production to improve soil, crop and animal health", coordinated by Prof. Marcel Dicke. Insects can transform waste streams into high-value proteins for food and feed. Consequently, insects provide valuable contributions to a circular economy. The project aims to investigate the valorisation of the rest-stream of insect production, i.e. moulting skins and faeces (‘frass’) to enhance soil health and crop health (https://doi.org/10.1016/j.tplants.2022.01.007).
In the NIOO project, we study the decomposition rate of frass and moulting skins of three insects species (black soldier fly, mealworm, cricket) in arable soil as well as the composition of the fungal and bacterial decomposers. In addition, we study if the insect materials, which are rich in chitin, can be used to control soil-borne fungal plant diseases.

PhyloFunDB. This project aims at creating and maintaining phylogenetically validated reference databases of various microbial functional genes and creating the tools to make the databases available for the scientific community

This project aims at degrading asbestos fibers using a combination of plants, fungi and bacteria.

Plant virus genomes are highly diverse and can evolve rapidly, as highlighted by recent metagenomics advances. However, most research on plant viruses focuses on agricultural systems, and we therefore know little about virus diversity and evolution in natural ecosystems.