Deciphering the soil microbiome for optimized intercropping

Modern intensive agriculture is in dire need of a solution to stop the downwards spiral of yield loss caused by deterioration of biodiversity and ecosystem functioning. In addition, climate change and stringent pesticide bans are closing avenues of yield gain needed to feed the increasing world population. Intercropping, the practice of cultivating multiple crops simultaneously, is one of the most promising alternative agricultural methods to increase both sustainability and yield stability. One vital aspect of intercropping that has yet to be characterized is its relationship with, and effect on, soil biodiversity. The soil microbiome, comprising of fungi, bacteria, protists and nematodes plays a major role in ecosystem functioning and stability, boosting crop and soil performance. Thus far, the link between soil biodiversity and crop diversification through intercropping remains poorly explored. In this multidisciplinary project, we will characterize the effect of intercropping on the soil microbiome, and in turn, the role of the soil microbiome in crop performance under intercropping. First, we will perform a large scale field screening on 16 intercrop pairings, sampled at the largest privately owned organic farm of the Netherlands, where intercropping has been on trial for 8 years. Using metabarcoding analysis, we aim to characterize soil microbiome community composition and gain insight into soil biodiversity and host influence under intercropping compared to monoculture. In a follow up greenhouse experiment, we will sample on host to host scale in a spatiotemporal manner, to collect metabarcoding, metagenomics and meta-transcriptomics data. This extensive -omics data will allow us to closely follow microbial community diversity and functional diversity across plant development and the host to host gradient. We aim to provide insights into the importance of soil biodiversity on crop performance in intercropping, to support the optimization and integration of intercropping into modern agriculture.