Drought is one of the most serious abiotic stressors in the environment, restricting agricultural production by reducing plant growth, development, and productivity. To investigate such a complex and multifaceted stressor and its effects on the plants, a systems biology-based approach is necessitated, entailing the generation of co-expression networks, identification of highly-priority transcription factors (TFs) dynamic mathematical modeling, and computational simulations. Here, we studied a high-resolution drought transcriptome of Arabidopsis. We revealed distinct temporal transcriptional signatures and demonstrated the involvement of specific biological pathways. Generation of a large-scale co-expression network followed by network centrality analyses identified 117 TFs that possess critical properties of hubs, bottlenecks, and high clustering coefficients nodes. Dynamic transcriptional regulatory modeling on integrated TF-target and transcriptome datasets uncovered major transcriptional events during the course of drought stress. Mathematical transcriptional simulations allowed us to ascertain the activation status of major TFs as well as the transcriptional intensity and amplitude of their target genes. Finally, we validated our predictions by providing experimental evidence of gene expression under drought stress for a set of four TFs and their major target genes using qRT-PCR. Taken together, we provided a systems-level perspective on the dynamic transcriptional regulation during drought stress in Arabidopsis and uncovered numerous novel TFs that can potentially be used in future genetic crop engineering programs.

Salt marshes are highly dynamic and biologically diverse ecosystems that serve as natural habitats for numerous salt-tolerant plants (halophytes). We investigated the bacterial communities associated with the roots and leaves of plants growing in the coastal salt marshes of the Daphne Bay area in Alabama, United States. We compared external (epiphytic) and internal (endophytic) communities of both leaf and root plant organs. Using 16S rDNA amplicon sequencing methods, we identified 10 bacterial phyla and 59 different amplicon sequence variants (ASVs) at the genus level. Bacterial strains belonging to the phyla Proteobacteria, Bacteroidetes, and Firmicutes were highly abundant in both leaf and root samples. At the genus level, sequences of the genus Pseudomonas were common across all four sample types, with the highest abundance found in the leaf endophytic community. Additionally, Pantoea was found to be dominant in leaf tissue compared to roots. Our study revealed that plant habitat (internal vs. external for leaves and roots) was a determinant of the bacterial community structure. Co-occurrence network analyses enabled us to discern the intricate characteristics of bacterial taxa. Our network analysis revealed varied levels of ASV complexity in the epiphytic networks of roots and leaves compared to the endophytic networks. Overall, this study advances our understanding of the intricate composition of the bacterial microbiota in habitats (epiphytic and endophytic) and organs (leaf and root) of coastal salt marsh plants and suggests that plants might recruit habitat- and organ-specific bacteria to enhance their tolerance to salt stress.