Abstract

There is increased need to identify sustainable agricultural methods which avoid environmental degradation. Previous studies have focused on the effect of specific agricultural interventions on large organisms, but we have fewer data evaluating how microbes, which are key components of ecosystems, might be affected. Additionally, previous studies have been constrained as they only examined one habitat in an ecosystem and have not gone on to evaluate the effect of agricultural approach on harvested crops. Here we take an ecosystems approach and evaluate the net effect of conventional versus biodynamic management on agricultural ecosystems by quantifying fungal communities in multiple habitats using metagenomics. We go on to measure biodiversity in the crop and key chemical quality parameters in the product consumed by humans. We find that the method of management significantly affects communities in soil, on plant structures, and on the developing crop in subtle but importantly different ways in terms of number, type, and abundance of species. However, management approach has no effect on communities in the final harvested juice, nor on product traits aligned with quality. This shows that while management approach impacts different habitats in the environment in different ways, this does not automatically flow onto the harvested crop.