Soil Bacterial and Fungal Community Composition in Top- and Subsoil From Irrigated Mediterranean Orchards

The soil microbiome, crucial for nutrient cycling and soil health, has been extensively studied in topsoil, yet the subsoil microbiome remains relatively unexamined despite its potential contributions to agroecosystem functionality. This research aimed to bridge this knowledge gap by investigating the interconnections between soil properties and the microbial communities residing in the topsoil and the subsoil of irrigated orchards under a semiarid Mediterranean climate. We collected soil samples from two depths, topsoil (0–10 cm) and subsoil (30–50 cm), noting elevated salinity levels in the topsoil due to irrigation practices. Utilizing high-throughput 16S rRNA gene and ITS1 region amplicon sequencing, we characterized the bacterial and fungal communities across these two depths. Our findings indicated that soil pH (higher in subsoil), electrical conductivity (higher in topsoil) and soil organic carbon (higher in topsoil) were the primary physicochemical drivers of microbial community composition shifts between top- and subsoil. Genera such as Rhizobium, Skermanella, Microvirga and Rubrobacter (bacteria) and Aspergillus , Gibellulopsis, Alternaria, Preussia and Monocillium (fungi) were identified as key genera more abundant in the topsoil, while MB-A2-108, Streptomyces and Bacillus (bacteria), and Mortierella, Fusarium, Necosmospora, Chaetomium and Emericellopsis (fungi), were key genera more abundant in the subsoil, associated with key studied soil properties. So they can be considered as key microorganisms contributing to soil processes in the topsoil and the subsoil. Our study gives insights about how soil bacterial and fungal communities respond differently to changes in the soil physicochemical properties across topsoil and subsoil, with salinity as important driver, reflecting the crucial need to develop a better understanding of how environmental changes impact soil properties and the microbiome throughout the soil profile.