Drivers of Soil Community Composition in Apple Orchards: Insights From Environmental Metabarcoding

Soil biodiversity in apple orchards plays a vital role for productivity. We studied the biodiversity of prokaryotes, protists and fungi of 26 apple orchards belonging to the same regional growers' association in Northern-Italy by environmental DNA metabarcoding (16S, 18S, ITS). We assessed alpha- and beta-diversity, distance decay relationships, immigration rates and community assembly processes, variance partitioning between space and environment and putative prokaryotic and fungal functions from the upper 20 cm of soil during summer 2023. Despite uniform management practices, orchards showed a huge variability in alpha diversity, with single orchards having only a small part of total diversity. Protists showed the lowest mean beta-diversity, followed by prokaryotes and fungi. Although immigration rates were low across all organismal groups-reflecting the low number of taxa co-occurring across all orchards-prokaryotes and protists still displayed relatively higher rates than fungi, in support of the size-plasticity hypothesis. Community assembly was governed primarily by stochastic processes, even though deterministic processes were also important. Turnover dominated community composition for all organismal groups. Putative functions of prokaryotes pertained mainly to carbon and nitrogen cycling. Our study provided mechanistic insights into the diversity of soil organisms across different trophic levels found in apple orchards.