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We studied the biodiversity of prokaryotes, protists and fungi of 26 apple orchards belonging to the same regional growers' association in Northern\u2010Italy by environmental DNA metabarcoding (16S, 18S, ITS). We assessed alpha\u2010 and beta\u2010diversity, 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\u2009cm 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\u2010diversity, followed by prokaryotes and fungi. 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