Beneficial fungi reprogram tree metabolism toward growth and stress-associated pathways

ABSTRACT Beneficial fungi are increasingly recognized as key modulators of plant growth and stress resilience, yet their functional roles in woody tree species remain poorly understood. Here, we examined the physiological, nutritional, and metabolic responses of sengon ( Falcataria moluccana ) to two plant growth-promoting fungi, Penicillium olsonii TLL1 and Aspergillus aculeatus TLL1, during a 6-month greenhouse experiment. Inoculation with A. aculeatus significantly enhanced leaf number, and shoot and root biomass compared with uninoculated controls, whereas P. olsonii showed more limited growth effects. Fungal inoculation led to a marked increase in root nutrient accumulation, including nitrogen (~2.5-fold), phosphorus (~1.5-fold), magnesium (~1.75-fold), and zinc (~2.5-fold), relative to controls, indicating improved nutrient acquisition. Untargeted metabolomic profiling revealed extensive metabolic reprogramming, with over 1,600 metabolites detected in negative ion mode and 2,800 metabolites in positive ion mode. Comparative analysis identified 367 and 206 differentially regulated metabolites in P. olsonii- and A. aculeatus -treated plants, respectively. Notably, enhanced nutrient status was accompanied by coordinated shifts in hormone-associated and secondary metabolic pathways, including phenylpropanoid-, lignin-, and terpenoid-related metabolites, consistent with a defense-primed metabolic state rather than constitutive defense activation. Together, these findings demonstrate that beneficial fungi reprogram tree metabolism by coupling improved nutrient acquisition with metabolic allocation toward growth and inducible defense, highlighting their potential role in sustainable forestry systems with tangible yield benefits. IMPORTANCE Fast-growing tropical trees are central to reforestation and sustainable forestry, yet their productivity is often constrained by nutrient availability and vulnerability to pests and diseases. While beneficial microbes are widely used in annual crops, their functional impact on long-lived woody plants remains largely unexplored. This study shows that plant growth-promoting fungi do more than stimulate tree growth—they quantitatively enhance root nutrient acquisition and translate this nutritional advantage into systemic metabolic reprogramming. By integrating long-term growth measurements, elemental profiling, and metabolomics, we reveal that fungal colonization increases the bioavailability of key macro- and micronutrients in roots and supports the allocation of metabolic resources toward lignification, secondary metabolism, and inducible defense without compromising biomass accumulation. These findings provide mechanistic insight into how nutrient status and metabolism are coordinated in tree-microbe interactions and support the rational use of beneficial fungi in forestry and agroforestry applications.