Abstract
Root endophytic and rhizosphere microorganisms are vital for ecosystem functions such as nutrient cycling, plant health maintenance, and the promotion of sustainable agriculture. In this investigation, a metagenomic strategy was employed to explore the microbial communities associated with oat (Avena sativa L.) and common vetch (Vicia sativa L.), cultivated both as monocultures and in a mixed intercropping system. Four types of microbiomes were examined: (A) root endophytic microbiome in oat–vetch intercropping, (B) root endophytic microbiome in vetch, (C) rhizosphere microbiome in oat–vetch intercropping, and (D) rhizosphere microbiome in vetch. Total DNA was extracted and subjected to next-generation sequencing of the bacterial 16S rRNA gene. The obtained data were analysed using the MG-RAST and QIIME platforms to assess taxonomic composition, alpha and beta diversity, and the relative abundance of microbial taxa. The results revealed distinct differences among the four microbiome types. The oat–vetch intercropping promoted higher microbial diversity and a more balanced community structure compared to monocultures. The enrichment of bacterial and fungal groups involved in nitrogen fixation, phosphate solubilization, and organic matter decomposition highlighted the enhanced biological activity under intercropping. Alpha diversity indices indicated greater species richness and evenness, while beta diversity analyses demonstrated clearly separated clustering patterns among the treatments. The combined metagenomic and functional analyses provide a comprehensive understanding of the dynamics of endophytic and soil microbiomes and demonstrate the potential of the oat–vetch system to enrich beneficial microbial communities, improve soil fertility, and support sustainable agroecosystem management.
Keywords: intercropping, oat (Avena sativa), metagenomics, microbial diversity, soil microbiome, vetch (Vicia sativa)