Harnessing drought-induced shifts in Cowpea Rhizoplane Bacterial Communities across the vegetative and reproductive stages

Authors: CHINTHALAPUDI, DURGA - Mississippi State University; NARAYANA, NISARGA - Mississippi State University; POUDEL, SUJAN - Mississippi State University; Brooks, John; SHANMUGAM, SHANKAR - Mississippi State University; BHEEMANAHALLI, RAJU - Mississippi State University

Submitted to: Plant Stress
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/9/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: Drought risks food production and food security. Understanding how the food crop relates to the soil microbiome and more specifically to bacteria attached to roots will help us understand how to better protect food production. Simply producing more food is not sustainable, but being able to protect the food we currently can grow from drought or other weather related issues is paramount to exploiting our current agricultural management regimes. In this study we utilized DNA and physiological approaches to understand how genotype and environment play a role in affecting the bacteria of the roots of cowpea crops. Overall, genotype had an effect on selecting and enriching specific bacterial groups, while drought negatively affected cowpea bacterial enzymatic responses as well as overall diversity and structure. Using models we were able to discover which bacterial groups were most effective in protecting against drought.

Technical Abstract: The increasing prevalence of drought poses significant challenges to global food security, necessitating a deeper understanding of plant-microbiome interactions which help crop production. This study investigated the dynamics of drought stress-induced changes in rhizosphere-associated bacterial communities of two cowpea (Vigna unguiculata L.) genotypes (Episelect4 and UCR369) across four growth stages. Community-level physiological profiling using Biolog EcoPlate analysis revealed that drought reduced rhizosphere microbial metabolic activity (carbon substrate utilization) in both genotypes, but UCR369 maintained higher metabolic capability than Episelect4 across growth stages. Further, integration of amplicon metagenomics and physiological data showed that drought significantly altered rhizoplane bacterial communities in cowpea, with distinct genotype-specific responses. There was a decline in Alpha diversity under drought, while community composition shifted based on genotype. Beta diversity results revealed that genotype and drought significantly influenced microbial community structure across growth stages. Proteobacteria dominated the rootzone of the Episelect4 genotype, while UCR369 showed increment of Actinobacteria under drought conditions. Redundancy analysis revealed soil enzyme activities (ß-glucosidase and N-acetyl-glucosaminidase) and physiological traits correlated considerably with microbial community shifts. Interpretable machine learning approach identified Actinobacteriota and Cyanobacteria as the key biomarkers enriched under drought, with genera such as Streptomyces and Ensifer potentially contributing to drought tolerance. The Random Forest model coupled with SHapley Additive exPlanations (SHAP) values demonstrated high predictive accuracy for identifying drought-related biomarkers, aligning with DeSeq2 analysis results. These models provided insights into the potential contributions of specific microbial taxa to cowpea drought tolerance, offering a promising avenue for developing microbiome-based strategies to improve crop resilience and sustainability under drought conditions.