Alteration of rare taxa and co-occurrence microbial networks in an almond orchard in semiarid climate after three years of intercropping with Thymus hyemalis and Capparis spinosa

In recent years, there has been growing interest in environmentally friendly agricultural systems, with intercropping emerging as a promising option for protecting soil health. However, it is not well understood how intercropping can affect soil microbial communities and functionality, especially in orchards. Therefore, this study aimed to evaluate the effects of intercropping Capparis spinosa (D1) and Thymus hyemalis (D2) during three years with almond trees in a semi-arid Mediterranean climate on the soil bacterial and fungal communities. Results showed that both intercropping systems (D1 and D2) altered microbial composition, favouring the increase of specific plant growth and promoting microorganisms (i.e., could add some taxa here: Amycolatopsis, Bosea, Dyadobacter, Janthinobacterium, and Leifsonia). However, the effects were less evident in the D1 treatment, with most parameters—especially potential prokaryotic functionality and co-occurrence networks—showing significant differences between the D2 and almond monoculture. The largest differences were observed in D2, with significant changes in potential functionality, including increases in nitrogen fixation and fermentation, as well as in co-occurrence networks, potentially increasing the co-occurrence network stability. Thus, we can conclude that intercropping within almond orchards can positively alter the microbial community by increasing plant growth promoting soil microorganisms including arbuscular mycorrhizas and these effects are more pronounced by using T. hyemalis as an intercropping plant.