Salinization of soil with sodium chloride ions inhibits plant functions, causing reduction of yield of crops. Salt tolerant microorganisms have been studied to enhance crop growth under salinity. This review describes the performance of endophytic fungi applied to crops as a supplement to plant genetics or soil management to alleviate salt stress in crops. This is achieved via inducing systemic resistance, increasing the levels of beneficial metabolites, activating antioxidant systems to scavenge ROS, and modulating plant growth phytohormones. Colonization by endophytic fungi improves nutrient uptake and maintains ionic homeostasis by modulating ion accumulation, thereby restricting the transport of Na⁺ to leaves and ensuring a low cytosolic Na⁺:K⁺ ratio in plants. Participating endophytic fungi enhance transcripts of genes encoding the high Affinity Potassium Transporter 1 (HKT1) and the inward-rectifying K⁺ channels KAT1 and KAT2, which play key roles in regulating Na⁺ and K⁺ homeostasis. Endophytic-induced interplay of strigolactones play regulatory roles in salt tolerance by interacting with phytohormones. Future research requires further attention on the biochemical, molecular and genetic mechanisms crucial for salt stress resistance requires further attention for future research. Furthermore, to design strategies for sustained plant health with endophytic fungi, a new wave of exploration of plant-endophyte responses to combinations of stresses is mandatory.

In natural environments, interaction between plant roots and microorganisms are common. These interactions between microbial species and plants inhabited by them are being studied using various techniques. Metabolomics research based on mass spectrometric techniques is one of the crucial approaches that underpins system biology and relies on precision instrument analysis. In the last decade, this emerging field has received extensive attention. It provides a qualitative and quantitative approach for determining the mechanisms of symbiosis of bacteria and fungi with plants and also helps to elucidate the tolerance mechanisms of host plants against various abiotic stresses. However, this -omics application and its tools in plant–microbe interaction studies is still underutilized compared with genomic and transcriptomic methods. Therefore, it is crucial to bring this field forward to bear on the study of plant resistance and susceptibility. This review describes the current status of methods and progress in metabolomics applications for plant–microbe interaction studies discussing current challenges and future prospects.

Optimizing nitrogen (N) availability to plants is crucial for achieving maximum crop yield and quality. However, ensuring the appropriate supply of N to crops is challenging due to the various pathways through which N can be lost, such as ammonia (NH₃) volatilization, nitrous oxide emissions, denitrification, nitrate (NO₃⁻) leaching, and runoff. Additionally, N can become immobilized by soil minerals when ammonium (NH₄⁺) gets trapped in the interlayers of clay minerals. Although synchronizing N availability with plant uptake could potentially reduce N loss, this approach is hindered by the fact that N loss from crop fields is typically influenced by a combination of management practices (which can be controlled) and weather dynamics, particularly precipitation, temperature fluctuations, and wind (which are beyond our control). In recent years, the use of urease and nitrification inhibitors has emerged as a strategy to temporarily delay the microbiological transformations of N-based fertilizers, thereby synchronizing N availability with plant uptake and mitigating N loss. Urease inhibitors slow down the hydrolysis of urea to NH₄⁺ and reduce nitrogen loss through NH₃ volatilization. Nitrification inhibitors temporarily inhibit soil bacteria (Nitrosomonas spp.) that convert NH₄⁺ to nitrite (NO₂⁻), thereby slowing down the first and rate-determining step of the nitrification process and reducing nitrogen loss as NO₃⁻ or through denitrification. This review aims to provide a comprehensive understanding of urease and nitrification inhibitor technologies and their profound implications for plants and root nitrogen uptake. It underscores the critical need to develop design principles for inhibitors with enhanced efficiency, highlighting their potential to revolutionize agricultural practices. Furthermore, this review offers valuable insights into future directions for inhibitor usage and emphasizes the essential traits that superior inhibitors should possess, thereby paving the way for innovative advancements in optimizing nitrogen management and ensuring sustainable crop production.

Soil salinity has a serious impact on plant growth and agricultural yield. Inoculation of crop plants with fungal endophytes is a cost-effective way to improve salt tolerance. We used metabolomics to study how Trichoderma harzianum T-22 alleviates NaCl-induced stress in two barley (Hordeum vulgare L.) cultivars, Gairdner and Vlamingh, with contrasting salinity tolerance. GC-MS was used to analyse polar metabolites and LC-MS to analyse lipids in roots during the early stages of interaction with Trichoderma. Inoculation reversed the severe effects of salt on root length in sensitive cv. Gairdner and, to a lesser extent, improved root growth in more tolerance cv. Vlamingh. Biochemical changes showed a similar pattern in inoculated roots after salt treatment. Sugars increased in both cultivars, with ribulose, ribose, and rhamnose specifically increased by inoculation. Salt stress caused large changes in lipids in roots but inoculation with fungus greatly reduced the extent of these changes. Many of the metabolic changes in inoculated cv. Gairdner after salt treatment mirror the response of uninoculated cv. Vlamingh, but there are some metabolites that changed in both cultivars only after fungal inoculation. Further study is required to determine how these metabolic changes are induced by fungal inoculation.

One of the most important environmental factors impacting crop plant productivity is soil salinity. Fungal endophytes have been characterised as biocontrol agents that help in plant productivity and induce resistance responses to several abiotic stresses, including salinity. In the salt-tolerant cereal crop barley (Hordeum vulgare L.), there is limited information about the metabolites and lipids that change in response to inoculation with fungal endophytes in saline conditions. In this study, gas chromatography coupled to mass spectrometry (GC–MS) and LC–electrospray ionisation (ESI)–quadrupole–quadrupole time of flight (QqTOF)-MS were used to determine the metabolite and lipid changes in two fungal inoculated barley genotypes with differing tolerance levels to saline conditions. The more salt-tolerant cultivar was Vlamingh and less salt tolerant was Gairdner. Trichoderma harzianum strain T-22 was used to treat these plants grown in soil under control and saline (200 mM NaCl) conditions. For both genotypes, fungus-colonised plants exposed to NaCl had greater root and shoot biomass, and better chlorophyll content than non-colonised plants, with colonised-Vlamingh performing better than uninoculated control plants. The metabolome dataset using GC–MS consisted of a total of 93 metabolites of which 74 were identified in roots of both barley genotypes as organic acids, sugars, sugar acids, sugar alcohols, amino acids, amines, and a small number of fatty acids. LC-QqTOF-MS analysis resulted in the detection of 186 lipid molecular species, classified into three major lipid classes—glycerophospholipids, glycerolipids, and sphingolipids, from roots of both genotypes. In Cultivar Vlamingh both metabolites and lipids increased with fungus and salt treatment while in Gairdner they decreased. The results from this study suggest that the metabolic pathways by which the fungus imparts salt tolerance is different for the different genotypes.