Identification of Endophytic Bacterial Community Associated With Roots of Desert Vegetation

Native plants thriving in extreme environments host unique microbial communities that might play crucial roles in promoting their growth and enhancing tolerance to harsh environmental conditions. In this study, the root-associated microbial communities were analysed from ten desert native plant species. The analysis was conducted using the V3–V4 regions of the 16S rRNA gene to assess the taxonomic diversity, composition, and functional characteristics of root-associated bacterial microbiomes. A total of 1,078,916 high-quality sequences obtained from ten different plants were clustered into 3,842 Amplicon Sequence Variants (ASVs). Alpha and beta diversity indices revealed that trees and grasses exhibited higher diversity and richness in root-associated bacterial microbial community compared to shrubs and herbs. Analysis of Similarities (ANOSIM) and PERMANOVA further confirmed significant differences between the bacterial communities of the four plant types. At the phylum level, Proteobacteria (31%–75%) dominated the microbial communities associated with trees and shrubs. Herbs and grass exhibited a different composition, with Fermicutes (41%) and Actinobacteriota (56%), respectively. In the bacterial order, Lachnospirales (41%–44%) was dominant bacterial community in trees and herbs, Rickettsiales (80%) in shrubs, and Streptomycetales (50%) in the grass. At the genus level, Muribaculum was dominant in trees, while Nocardioides in shrubs, herbs and grass (30%–80%). Functional prediction analyses indicated that nitrogen assimilation was abundant mainly in herbs. While methane and ammonia oxidation processes were enriched in the microbial communities of shrubs and trees. Our findings determine the common bacterial microbiome communities associated with the different desert plant roots that may support their growth in the arid environment. These findings can potentially improve sustainable agricultural practices in arid regions.