Microbiome Structures and Beneficial Bacteria in Soybean Roots Under Field Conditions of Prolonged High Temperatures and Drought Stress

Abstract

Drought stress has a significant impact on agricultural productivity, affecting key crops such as soybeans, the second most widely cultivated crop in the United States. Endophytic and rhizospheric microbial diversity analyses were conducted with soybean plants cultivated during the 2023 growing season amid extreme weather conditions of prolonged high temperatures and drought in Louisiana. Specifically, surviving and non-surviving soybean plants were collected from two plots of a Louisiana soybean field severely damaged by extreme heat and drought conditions in 2023. Although no significant difference was observed between surviving and non-surviving plants in microbial diversity of the rhizosphere, obvious differences were found in the structure of the endophytic microbial community in root tissues between the two plant conditions. In particular, the bacterial genera belonging to Proteobacteria, <i>Pseudomonas</i> and <i>Pantoea</i>, were predominant in the surviving root tissues, while the bacterial genus <i>Streptomyces</i> was conspicuously dominant in the non-surviving (dead) root tissues. Co-occurrence patterns and network centrality analyses enabled us to discern the intricate characteristics of operational taxonomic units (OTUs) within endophytic and rhizospheric networks. Additionally, we isolated and identified bacterial strains that enhanced soybean tolerance to drought stresses, which were sourced from soybean plants under a drought field condition. The 16S rDNA sequence analysis revealed that the beneficial bacterial strains belong to the genera <i>Acinetobacter</i>, <i>Pseudomonas</i>, <i>Enterobacter</i>, and <i>Stenotrophomonas</i>. Specific bacterial strains, particularly those identified as <i>Acinetobacter pittii</i> and <i>Pseudomonas</i> sp., significantly enhanced plant growth metrics and reduced drought stress indices in soybean plants through seed treatment. Overall, this study advances our understanding of the soybean-associated microbiome structure under drought stress, paving the way for future research to develop innovative strategies and biological tools for enhancing soybean resilience to drought.