Salinity is one of the most important abiotic stress factors affecting wheat production. Salt in the soil is a major environmental stressor that can affect the bacterial community in the rhizosphere of wheat. The bacteria in the plant’s rhizosphere promote growth and stress tolerance, which vary by variety and location. Nevertheless, the soil harbors some of the most diverse microbial communities, while the rhizosphere selectively recruits according to the needs of plants in a complex harmonic regulation. The microbial composition and diversity under normal and saline conditions were assessed by comparing the rhizosphere of wheat with soil using 16S rRNA gene amplicon sequencing, highlighting the number of operational taxonomic units (OTUs). Taxonomic analyzes showed that the bacterial community was predominantly and characteristically composed of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Fibrobacteres, representing the usual microbial profile for the rhizosphere of wheat. Idiomarinaceae, Rheinheimera, Halomonas, and Pseudomonas (a strain of Proteobacteria), together with Gracilibacillus (a strain of Firmicutes Bacilli), were recognized as microbial signatures for the rhizosphere microbiome under saline conditions. This was observed even with unchanged soil type and genotype. These patterns occurred despite the same soil type and genotype, with salinity being the only variable. The collective action of these bacterial phyla in the rhizosphere not only improves nutrient availability but also induces systemic resistance in the plants. This synergistic effect improves plant resistance to salt stress and supports the development of salt-tolerant wheat varieties. These microbial signatures could improve our understanding of plant–microbe interactions and support the development of microbiome-based solutions for salt stress.

Wheat is one of the most important cereal crops and an important source of food for billions of people worldwide. However, drought stress can pose a real threat to its productivity and lead to significant yield losses, especially in Egypt. The rhizospheric microbiome of wheat can play an important role in drought stress and help wheat to respond to this abiotic stress. Understanding this microbiome is therefore also important to improve drought stress resilience and productivity. In this study, a metagenomic analysis was performed to investigate how the composition and diversity of microbial communities associated with the wheat rhizosphere change under drought. Taxonomic and phylogenetic analyses revealed a shift in microbial abundance, with Actinobacteria, Bacteroidetes, Proteobacteria and Verrucomicrobia being the four most abundant phyla of the ethnic microbiota. Remarkably, other classes, including Alphaproteobacteria and Cytophagia, were significantly enriched under drought, which could be a promising enhancement of plant stress altruism. Differential abundance analysis showed that the control samples had higher abundance of microbial taxa such as OD1, WS2, Chlorobi, ABY1 and SHA-109 compared to the drought-treated genotypes. Functional prediction analysis using PICRUSt showed that an uncharacterized ATP-binding protein within the AAA + superfamily is overrepresented under drought conditions. This suggests that these genes may play a role in stress adaptation, possibly via energy-dependent regulation of cellular processes involved in plant survival. Our results expand our understanding of the complexity of responses of the wheat rhizosphere microbiome to drought and have practical implications for the development of microbial target combinations to improve wheat tolerance and productivity in the context of climate change challenges.

Stripe rust, caused by Puccinia striiformis f. sp., is a widespread and serious fungal disease that affects wheat ( Triticum aestivum L.) cultivation worldwide. Its rapid development, high adaptability, and ability to cause significant yield losses threaten global food security. Although conventional breeding strategies play a role, they are limited by the evolutionary dynamics of the pathogen. Therefore, genomic and molecular approaches have been employed to improve resistance breeding techniques. This review summarizes relevant research findings on the pathogenicity of Pst and the genetic basis of resistance to stripe rust, categorized as all-stage resistance (ASR) and adult plant resistance (APR). More than 300 QTLs and 86 yellow rust ( Yr ) resistance genes have been identified through marker-assisted selection (MAS), quantitative trait loci (QTL) mapping, and genome-wide association studies (GWAS). Meta-QTL analyses have advanced to the point where fine-tuning candidate gene regions across different backgrounds is possible, facilitating marker-assisted breeding in closed systems. In addition, genomic selection (GS) enables the combined use of major and minor resistance loci when selecting for multiple traits, allowing rapid gene pyramiding to improve durability. Recent developments in CRISPR/Cas9 genome editing and pan-genomics offer the opportunity to induce a broad spectrum of durable resistance in elite wheat lines. Collectively, these integrative genomic approaches hold promise for sustainable strategies to combat the persistent threat of stripe rust and protect wheat production worldwide.

Salt stress poses a significant threat to wheat productivity, particularly in arid and semi-arid regions such as Egypt, where soil salinity severely limits crop yield and long-term agricultural sustainability. With increasing recognition of the plant-associated microbiome as a key component of crop resilience, this study investigated the potential of plant growth-promoting bacteria (PGPB) and plant–microbe interactions to alleviate salt-induced stress in two contrasting Egyptian wheat cultivars: the salt-tolerant Sakha 93 and the salt-sensitive Sids1. Bacterial isolates from both rhizospheric and endophytic niches were collected from saline-irrigated wheat and identified using 16S rRNA gene sequencing. Functional characterization identified Pseudomonas stutzeri and Pantoea agglomerans as promising PGPB candidates based on their ability to produce indole acetic acid, ACC deaminase, and siderophores, fix nitrogen, and tolerate high salinity. In greenhouse trials under salinity gradients (0–15 dS/m), both strains improved wheat growth metrics, though Pantoea agglomerans , particularly in Sakha 93, led to significant increases in biomass, root length, seed yield, and proline content. Pseudomonas stutzeri showed beneficial but comparatively moderate effects. These results suggest that endophytic PGPB, especially under saline conditions, may confer enhanced stress tolerance due to superior colonization and physiological modulation. The findings support the use of halotolerant microbial bioinoculants in combination with salt-tolerant genotypes as a viable strategy to enhance wheat resilience and productivity in saline environments.

Rhizosphere microbiome engineering is a promising approach that can enhance crop resilience and input use efficiency by redirecting plant–microbe–soil interactions toward predictable functions. Here, we review the mechanistic bases underlying rhizosphere assembly and stability, including root exudate-mediated selection, priority effects, keystone taxa, and metabolite-driven signaling, and connect these principles to proposed design rules for microbial inoculants. We present a generalizable Design–Build–Test–Learn (DBTL) framework for engineering synthetic microbial consortia, covering trait-to-module mapping (nutrient acquisition, phytohormone modulation, ACC deaminase activity, stress-protective metabolites, and biocontrol), compatibility screening, minimal yet robust community architectures, and iterative optimization driven by multi-omics and high-throughput phenotyping. Translation to field settings is framed as an engineering challenge defined by formulation and administration limitations, including carrier type, seed coating and encapsulation methods, shelf life, strain invasiveness, and permanence of colonization amid environmental diversity. We also summarize how integrative measurement pipelines (amplicon and shotgun sequencing, transcriptomics, metabolomics, and network or causal analyses) can advance microbiome studies from correlation to actionability. We describe how precision agriculture (sensors, remote sensing, and variable-rate inputs) and AI/ML (split-sample comparisons, transfer learning, and active learning) approaches can accelerate strain discovery, mixture optimization, and adaptive experimentation, driven by the need for stringent controls, metadata-rich reporting, and cross-site comparability. Use cases focus on stress conditions (drought, salinity, thermal extremes, and biotic stress) to demonstrate how microbial functions translate to agronomic outcomes and to highlight critical bottlenecks for reproducible, scalable microbiome products.

Climate change causes an increase in the intensity of adverse abiotic and biotic stresses that could severely threaten agriculture production and food security including production, access, and prices. The world's population is anticipated to reach 9.8 billion by 2050, while food production would decline by 20%. The risk of continuous change in the environment has attracted the attention of plant scientists, who are using all available technologies to enhance crop quality and yield. Omics approaches are crucial for studying stress tolerance mechanisms and exploring candidate genes. Several efforts have been made to face these emerging challenges using traditional breeding, genetically modified organisms, and genome editing. Over the last decade, the integration of CRISPR/Cas genome editing into modern breeding programs has had a great impact on crop improvement by targeting precise changes to genomes. Genome editing is a good candidate for developing beneficial climate-resilient crops targeting biotechnological tools. Recently, new techniques in genome editing have been developed, including epigenome modifiers, and base and prime editing which are promising developments for improving plant performance and crop productivity. This chapter unravels the whole picture of the application of genome editing to address climate change and improve crops. <!----> <!----> <!----> <!---->