The Janzen-Connell hypothesis is one of the most important hypotheses in ecology, but is mostly tested indirectly without accounting for the underlying plant-associated organisms, or only for highly host-specific organisms. Advances in massive sequencing allow to sample, for example, the fungi communities associated with different plant species, and spatial analysis can reveal spatial patterns in the number of organisms (species) shared by plant species and their neighbours. We show how combining these tools provides new perspectives for testing the Janzen Connell hypothesis. We illustrate our approach using a natural experiment in two fully-mapped Mediterranean forest plots, where the dominant dry- and fleshy-fruited species have distinctly different seed deposition patterns, leading to contrasting expectation about the emerging spatial structures. Our analysis confirmed these expectations and provided deep insights into how the neighbourhood load of plant-associated fungi and herbivorous insects changes during plant ontogeny and how seed dispersal mechanisms modulates Janzen-Connell effects.