Alfalfa Cover Crops Influence the Soil Fungal Community and Function in Apple Orchards in Arid Desert Oases in Northwest China

Abstract

The present study investigated the effects of alfalfa cover crops on soil fungal communities and function in apple orchards in arid desert oases. A five-year apple orchard was subjected to two treatments: Intercropping with an alfalfa cover crop (A) and clean tillage (QG). The soil fungal ITS (internal transcribed spacer) region was analyzed using Illumina MiSeq high-throughput sequencing technology, and fungal function was determined using FUNGuild. Changes in the fungal community structure, diversity, and metabolic function in the 0–60 cm soil layer of the apple orchard were compared. The results showed that the alfalfa cover crops enhanced fungal richness but reduced diversity. The alfalfa cover crops improved fungal copy numbers but reduced the relative abundance of the dominant phylum, Ascomycota. Correlations between soil fungi and soil factors revealed that total nitrogen and total carbon were the most important nutrient factors in positively regulating the fungal community. The main negative factors were soil total salts and pH. The FUNGuild functional prediction showed that Ectomycorrhizal-Wood Saprotroph and Endophyte-Undefined Saprotroph only appeared in the alfalfa cover crops. The abundance of endophytes was enhanced (p < 0.05), but the abundance of plant pathogens and wood saprotrophs decreased (p < 0.01). Alfalfa cover crops could increase the copy numbers and richness in arid oasis apple orchards.