Metagenomic and functional insights into root endophytic bacteria associated with drought stress in cowpea

Abstract

Abstract Endophytic bacterial communities enhance plant drought resilience, yet their dynamics in cowpeas ( Vigna unguiculata ) remain poorly understood. To explore this, we analyzed the root endophytic bacteriome under drought stress using 16 S rRNA gene metagenomics and evaluated isolated bacteria for plant growth-promoting traits. Drought significantly reduced both alpha and beta diversity, indicating a loss of microbial richness and evenness and community homogenization. Taxonomic shifts revealed enrichment of Cyanobacteriota, Cyanophyceae, and Marileptolyngbya sina in drought conditions. Forty-seven endophytic isolates were identified and characterized, including Enterobacter spp., Bacillus spp., Leclercia adecarboxylata , and Stenotrophomonas spp. The isolated strains exhibited plant growth-promoting traits in vitro and, in a pot assay, some enhanced wheat biomass under both control and drought conditions. The reduction in diversity due to drought indicates a loss of microbial richness and evenness, along with homogenization of microbial composition, suggesting that drought selectively enriches specific taxa, which may enhance plant stress resilience through specialized metabolic functions. By combining metagenomic profiling with functional assays, this study highlights the role of drought-induced bacterial shifts in supporting plant growth and development. These insights could lead to the development of microbial inoculants to improve crop drought tolerance.