Biology subjects

Saad, M. M.

Publications and source records attributed to Saad, M. M..

4 recordsLinked to original sources

bioRxiv2025

Darwin21 Genome Database: A Curated Whole-Genome Repository of Endophytic Bacteria from Desert Plants

Microbial communities associated with desert plants play a pivotal role in enhancing host survival under extreme environmental stressors, including drought, salinity, and nutrient limitation. The Darwin21 Endophytic Microbial Collection is one of the largest curated repositories of 2,500 cultivable endophytic bacteria isolated from 23 native desert plant species across Saudi Arabia, Jordan, and Pakistan. Representing a broad spectrum of arid microhabitats from inland deserts and mountain wadis to coastal mangroves and date palm oases, the collection supports integrative studies on microbial ecology and plant-microbe interactions in water-limited ecosystems. A central component of this initiative is the Darwin21 Genome Database, which currently hosts whole-genome sequences (WGS) of 534 endophytic bacterial isolates annotated with extensive ecological metadata, assembly statistics, functional traits, and host associations. The database interface provides tools for genome exploration, metadata filtering, and functional gene mining, enabling users to identify taxa and traits of agronomic interest, particularly for applications in sustainable agriculture and sustainable desert revegetation. By combining genomic, ecological, and functional data, the Darwin21 Genome Database serves as a foundational platform for the development of targeted microbial inoculants and fosters data-driven research into desert microbiomes and plant resilience mechanisms. Database URLhttps://www.genomedatabase.org/ O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/672100v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1703432org.highwire.dtl.DTLVardef@172fce7org.highwire.dtl.DTLVardef@39bd1borg.highwire.dtl.DTLVardef@ae3fef_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Oxalotrophic bacteria in desert and drylands: Enzymatic pathways and Carbon sequestration

Oxalotrophy refers to the ability of bacteria to utilize oxalate as a carbon and energy source. This is a critical process with significant implications for the global carbon cycle. Oxalate-degrading bacteria play a key role in carbon sequestration through the oxalate-carbonate pathway (OCP), contributing to stable inorganic carbon pools. In this study, we identified and cataloged 20 enzymes associated with various facets of oxalate metabolism to characterize the oxalotrophic potential of bacteria. Within this group, sets of enzymes were grouped into two functional categories in the context of carbon sequestration: a biomineralization toolkit for converting oxalate to inorganic carbon and an assimilation toolkit for incorporating oxalate into metabolic pathways such as amino acid biosynthesis and energy production. Using bioinformatic approaches, we analyzed a collection of 536 bacterial genomes from desert and dryland strains spanning 81 genera to identify oxalotrophs. To validate our findings, we tested several bacterial strains for growth on media supplemented with exogenous oxalate. Notably, while multiple bacterial strains grew on oxalate media, two Pseudomonas species, namely JZ043 and JZ097, failed to grow despite genomic predictions suggesting otherwise. Further investigation of these strains revealed several non-conservative amino acid substitutions in the glyoxylate carboligase enzyme (EC 4.1.1.47), a key player in oxalate metabolism, suggesting a potential link between these mutations and their inability to metabolize oxalate. Our findings highlight the significance of our approach for identifying oxalotrophic bacteria (OxB) and offer valuable insights into the molecular basis of oxalate metabolism. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/637404v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@13d1408org.highwire.dtl.DTLVardef@ee2e5eorg.highwire.dtl.DTLVardef@1265323org.highwire.dtl.DTLVardef@11c56d0_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Mangrove endophytes enhance yield and convey flooding and salt tolerance to Nipponbare rice

Global climate change increasingly challenges agriculture with flooding and salinity. Among strategies to enhance crop resilience to these stresses, we tested several endophytic bacterial strains from mangroves, which are permanently exposed to flooding and high salinity. We show several strains that can enhance flooding and salinity tolerance in Arabidopsis and rice plants. Two strains and their combination massively enhanced the growth and yield of Oryza sativa cv. Nipponbare under both soil and hydroponic growth conditions with and without salt treatment. The bacteria-induced transcriptome changes in O. sativa roots related to ABA-signaling with lignin and suberin deposition in root tissues explain the altered responses of colonized rice plants to hypoxic and saline stress conditions. While enhancing yield and grain quality, bacterially colonized rice plants also show much earlier flowering, thereby massively shortening the life cycle of rice plants and opening the possibility for an additional harvest per year. These results show that microbes can be a powerful tool for enhancing the yield and resilience of rice to hypoxic and saline stress conditions.

plant biology↗

bioRxiv2023

Microbe-induced plant drought tolerance by ABA-mediated root morphogenesis and epigenetic reprogramming of gene expression

The use of beneficial microbes to mitigate drought stress tolerance of plants is of great potential albeit little understood. We show here that a root endophytic desert bacterium, Pseudomonas argentinensis sp. SA190, enhances drought stress tolerance in Arabidopsis. Transcriptome and genetic analysis demonstrate that SA190-induced root morphogenesis and gene expression is mediated via the plant abscisic acid (ABA) pathway. Moreover, we demonstrate that SA190 primes the promoters of target genes in an epigenetic manner which is ABA-dependent. Application of the SA190 priming technology on crops is demonstrated for alfalfa in field trials, showing enhanced performance under desert agriculture conditions. In summary, a single beneficial root bacterial strain can help to perform agriculture under drought and water limiting conditions. Synopsis O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/522604v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@b0bd17org.highwire.dtl.DTLVardef@14e3262org.highwire.dtl.DTLVardef@cdd103org.highwire.dtl.DTLVardef@5526a0_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIBeneficial root endophyte Pseudomonas argentinensis sp. SA190 confers drought tolerance in plants C_LIO_LISA190 modulates the expression of genes under drought stress in an ABA-dependent manner C_LIO_LISA190 primes genes via H3K4me3 histone mark enrichment C_LIO_LISA190 alters host plant physiology by improving the plant water status C_LIO_LISA190 enhances crop performance in open field conditions with limited irrigation C_LI

plant biology↗