Compost-associated microbiota modulates root transcriptional responses and enhances tomato drought resilience

Compost is a promising sustainable alternative to mineral fertilization because it supplies nutrients and organic matter while hosting diverse microbial communities. However, even if its application to plants has been proven to alleviate different biotic and abiotic stresses, it remains unclear whether its benefits arise from its physico-chemical properties, its associated microbiota, or both. In this study, we compared the impact of compost, sterile compost and an NPK treatment providing equivalent macronutrient inputs on tomato plants cv. Micro-Tom. After assessing physiological parameters of the leaves and molecular responses of the roots under optimal conditions, we performed a drought stress experiment under the three fertilization treatments, complementing the analysis with the investigation of substrate water-retention properties. Although all fertilized treatments improved plant performance relative to nutrient-poor soil, RNA sequencing revealed distinct root transcriptional profiles among compost, sterile compost and NPK, with the compost treatment upregulating several pathways related to plant growth and health, such as hormone signaling, nutrient metabolism, and stress responses. When subjected to severe water stress, compost-treated plants retained the highest photosynthetic efficiency and compost showed the highest available water content compared to the other treatments. These findings suggest that compost may enhance tomato drought resilience through combined effects of substrate water availability and compost-associated microbiota.