Biology subjects

Majeed, A.

Publications and source records attributed to Majeed, A..

4 recordsLinked to original sources

bioRxiv2024

Co-occurrence Networks and Topological Analyses Revealed Microbiome Structures in Soybean Roots from a Louisiana Soybean Field Severely Damaged by Prolonged High Temperatures and Drought Stress

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. We conducted endophytic and rhizospheric microbial diversity analyses in soybean plants cultivated during the 2023 growing season, amid extreme weather conditions of prolonged high temperatures and drought in Louisiana. Specifically, we collected surviving and non-surviving soybean plants from two plots of a Louisiana soybean field severely damaged from the extreme heat and drought condition in 2023. We did not observe any significant difference in the microbial diversity of rhizosphere between surviving and non-surviving plants. However, we found obvious differences in the structure of endophytic microbial community in root tissues between the two plant conditions. Especially, the bacterial genera of Proteobacteria, Pseudomonas and Pantoea, were predominant in the surviving root tissues, while the bacterial genus Streptomyces 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. Overall, this study advances our understanding of the intricate relationship between bacteria and plants under drought stress, paving the way for future research to investigate the importance of microbial diversity in drought affected regions such as Louisiana.

microbiology↗

bioRxiv2024

Single nuclei multiomics reveals the drought-driven gene regulatory atlas in Arabidopsis

The regulation of gene expression in plant responses to drought has been thoroughly investigated in previous studies. Despite this, a detailed understanding of the cell type-specific regulatory mechanisms, encompassing multi-layered biological processes, is lacking. In this study, we report the use of single-nucleus multiomic analysis in Arabidopsis seedlings in response to drought stress. Our single-nuclei RNA (snRNA) analysis delineated 14 distinct clusters representing major root and shoot cell types and discovered new cell type-specific drought markers. Integration of snRNA with single-nuclei ATAC (snATAC) data in leaf epidermis, root endodermis, and guard cells revealed accessible chromatin regions (ACRs)-linked genes predominantly enriched in pathways responsive to drought, heat, and light. Motif enrichment analysis and gene regulatory network (GRN) inference highlighted key transcription factors (TFs) and regulatory networks related to ethylene signaling pathways in endodermis as well as circadian rhythms in both endodermis and guard cells. Pseudotime analysis identified critical transcriptomic progression from metabolic process to stress response within three cell types. Overall, this study elucidates drought-related regulatory mechanisms in Arabidopsis at single-cell resolution, providing valuable insights into the fundamental regulatory events involved in stress responses. It also serves as a reference for future single-cell multiomic investigations in crop plants. One Sentence SummarySingle cell multiomic analysis under drought stress

plant biology↗

bioRxiv2023

Comprehensive Codon Usage Analysis Across Diverse Plant Lineages

The variation of codon usage patterns in response to the evolution of organisms is an intriguing question to answer. The purpose of this study was to investigate the relevance of the evolutionary events of vascularization and seed production with the codon usage patterns in different plant lineages. We found that the optimal codons of non-vascular lineages generally end with GC, whereas those of the vascular lineages end with AU. Correspondence analysis and model-based clustering showed that the evolution of the codon usage pattern follows the evolutionary event of the vascularization more precisely than that of the seed production. The dinucleotides CpG and TpA were under-represented in all the lineages, whereas the dinucleotide TpG was found over-represented in all the lineages, except algae. Evolutionary-related lineages showed similar codon pair bias (CPB). The dinucleotide CpA showed a similar representation as those of its parent codon pairs. Although natural selection predominates over mutational pressure in determining the codon usage bias (CUB), the relative influence of mutational pressure is higher in the non-vascular lineages than in the vascular lineages.

evolutionary biology↗

bioRxiv2023

A new competitive strategy to unveil the antibiotic-producing Actinobacteria

The bacterial phylum Actinobacteria encompasses microorganisms with incomparable metabolic versatility and deep resource of medicines. However, the recent decrease in the discovery rate of antibiotics warrants innovative strategies to harness actinobacterial resources for lead discovery. Indeed, microbial culturing efforts measuring the outcomes of specific genera lagged behind the detected microbial potential. Herein, we used a distinct competitive strategy that exploits competitive microbial interactions to accelerate the diversification of strain libraries producing antibiotics. This directed-evolution-based strategy shifted the diversity of Actinobacteria over the experimental time course (0-8 days) and led to the isolation of Actinobacterial strains with distinct antimicrobial spectrum against pathogens. To understand the competitive interactions over experimental time, the metagenomic community sequencing revealed that actinobacterial members from families Nocardiaceae and Cellulomonadaceae with relatively increased abundances towards end, are thus competitively advantageous. Whilst comparing the Actinobacteria retrieved in the competitive strategy to that of the routinely used isolation method, the Actinobacteria genera identified from competitive communities differed relatively in abundances as well as antimicrobial spectrum compared to actinobacterial strains retrieved in classical method. In sum, we present a strategy that influences microbial interactions to accelerate the likelihood of potential actinobacterial strains with antimicrobial potencies.

microbiology↗