First Tetraploa Genome and Multi‐Omics Analysis Reveal Key Plant‐Microbe‐Soil Interactions for Salt Tolerance and Yield Improvement of Wheat

Salinity is a major threat to global agricultural productivity of staple crops such as wheat. Although microbial-based solutions hold promise for alleviating salinity stress, practical implementation is hindered by insufficient mechanistic characterization of bioinoculants and their interactions with plants. Here, we assembled the first complete reference genome of a halotolerant strain within the genus Tetraploa-the endophytic fungus Tetraploa sp. E00680. This novel genomic resource serves as a foundation for exploring previously uncharacterised salt tolerance mechanisms in this potential fungal inoculant. Our research demonstrates that E00680 enhances wheat yield under both controlled and field saline conditions. We found that E00680 systematically modulates the plant-microbe-soil interactions by optimizing rhizosphere microbial communities, increasing nutrient bioavailability, and triggering coordinated transcriptional and metabolic reprogramming in wheat. Notably, E00680 expands tryptophan metabolism to synergistically boost auxin biosynthesis in wheat by supplying precursors and activating relevant metabolic pathways. This cross-kingdom metabolic coupling facilitates better growth and salt tolerance in wheat plants. Our findings offer multi-omics and rhizosphere-level insights that can guide the development of microbial inoculants to enhance climate-resilient and sustainable crop production.