Neighbour Effects and Dynamics of Plant-Associated Microbiomes in a Strip-Crop System

While multi-cropping systems, such as strip-cropping, assemble complex microbial communities that contribute to ecosystem resilience, we have limited understanding of their assembly and functions at field scale. Here, we examined the dynamics and site-specific assembly of soil and phyllosphere microbiomes in a rotational faba bean (Vicia faba) and spring barley (Hordeum vulgare) strip-system during two seasons. Using bacterial 16S and fungal ITS amplicon sequencing, we analysed microbial communities across gradients from the centre towards strip edges. We found that phyllosphere microbiomes are more affected by strip-cropping than soil microbiomes. Neighbouring crops harbour different microbial communities, but with increasing proximity, their phyllosphere microbiomes share more specific microbial taxa. Likewise, we observed gradient-specific microbial distribution, including fungal pathogen taxa. For instance, Puccinia was more abundant in the centre of the spring barley strips and gradually declined towards the edge. Correlation and co-occurrence network analyses revealed distinct microbial interaction patterns across soil and phyllosphere gradients. These networks were more resilient at the edge of the strips compared to central networks of spring barley. Altogether, our findings revealed neighbour-effects modulating host-associated microbiomes across strips that could be harnessed for designing optimal cropping systems, for example, to reduce leaf pathogens.