The early stages of plant–microbe interaction are critical for establishing beneficial symbioses. We investigated how the endophytic fungus Fusarium solani strain FsK modulates tomato (Solanum lycopersicum) development and hormone pathways during in vitro co-cultivation. Seedlings were sampled at three early interaction stages (pre-contact, T1; initial contact, T2, 3 days post-contact, T3). Root traits and root and leaf transcripts for abscisic acid (ABA) and ethylene (ET) pathways were quantified, alongside fungal ET-biosynthesis genes. FsK altered root system architecture, increasing root area, lateral root number, root-hair length, and fresh biomass. These morphological changes coincided with tissue- and time-specific shifts. In leaves, FsK broadly affected ABA biosynthetic and homeostasis genes (ZEP1, NCED1, ABA2, AAO1, ABA-GT, BG1), indicating reduced de novo synthesis with enhanced deconjugation of stored ABA. ET biosynthesis was curtailed in leaves via down-regulation of ACC oxidase (ACO1–3), with isoform-specific changes in ACC synthase (ACS). The ET receptor ETR1 was transiently expressed early (T1–T2). FsK itself showed staged activation of fungal ET-biosynthesis genes. These results reveal coordinated fungal–plant hormone control at the transcriptional level that promotes root development during early interaction and support FsK’s potential as a biostimulant.

Fusarium solani strain K (FsK) is a beneficial root-residing fungal endophyte previously shown to enhance tomato resilience to biotic stresses. Here, we evaluated whether FsK also improves drought tolerance and investigated the underlying molecular and metabolic mechanisms. Tomato plants were inoculated with FsK or mock-treated and subjected to either well-watered or reduced-irrigation conditions. Physiological measurements, transcriptome profiling (RNA-seq), targeted hormone quantification, and untargeted metabolomic analyses were performed on leaf tissues to assess systemic plant responses. FsK-colonized plants exhibited enhanced drought tolerance, displaying higher relative water content and biomass accumulation compared with non-inoculated stressed plants. RNA-seq analysis revealed differential regulation of genes associated with abscisic acid (ABA) and jasmonic acid (JA) signaling, WRKY transcription factors, mitogen-activated protein kinase (MAPK) signaling MAPK pathways, and stress-responsive regulators, including several transcripts showing priming-type expression patterns. Metabolomic profiling showed a strong effect of FsK on leaf metabolic composition, with significant increases in ABA, JA, and specific metabolites such as kaempferol derivatives, D-glucosamine, and malic acid. Overall, our findings demonstrate that FsK primes tomato plants for drought tolerance through coordinated modulation of hormonal signaling, transcriptional regulation, and metabolic adjustment, providing insight into systemic mechanisms underlying endophyte-mediated stress resilience.

Bioponics is a promising agricultural system designed to integrate circular economy principles by recovering nutrients from organic waste. In this context we implemented a tri-trophic circular system, where insect larvae fed on crop residues and fruits were processed into insect meal for fish feed. The water used in fish rearing then irrigated tomato crops in an aquaponic setup, closing the nutritional loop. Tomato was cultivated in this system with the aim of thoroughly evaluating its applicability via assessing the dynamics of growth, yield, and functional responses of the crop across three treatments: coupled aquaponics (CAP), decoupled aquaponics (DCAP), and hydroponics (HP, as control). DCAP matched HP in all parameters assessed and even outperformed it in fertilizer use efficiency by 31%. In contrast, CAP showed reduced growth and yield (by 38%) and limitations in photochemical efficiency and photosynthetic performance, likely due to significant deficiencies in potassium and phosphorus (9-fold and 2-fold lower than in HP, respectively). DCAP demonstrated strong potential to achieve similar crop outcomes to conventional hydroponics with enhanced resource efficiency. Overall, adopting the DCAP variant of aquaponics in this circular nutrition system is a promising alternative to conventional hydroponics, supporting a transition toward more environmentally resilient farming practices.

A circular tri-trophic system integrating aquaponics, i.e., combined cultivation of crops and fish, with insect rearing is presented for lettuce cultivation. The nutrition cycle among crops, insects and fish turns waste into resource, thereby increasing the sustainability of this food production system. A comprehensive evaluation of the system’s efficiency was performed, including the growth, functional and resource use efficiency traits of lettuce, the dynamics of which were followed in a pilot-scale aquaponics greenhouse, under three treatments: conventional hydroponics (HP) as the control, coupled aquaponics (CAP) with crops irrigated with fish-derived water, and decoupled aquaponics (DCAP), where fish-derived water was amended with fertilizers to reach the HP target. The main findings indicate comparable physiological performance between DCAP and HP, despite the slightly lower yield observed in the former. The CAP treatment exhibited a significant decrease in biomass accumulation and functional impairments, which were attributed to reduced nutrient levels in lettuce leaves. The DCAP treatment exhibited a 180% increase in fertilizer use efficiency compared to the HP treatment. We conclude that the tri-trophic cropping system with the implementation of DCAP variant is an effective system that enables the combined production of crops and fish, the latter being fed with sustainably derived insect protein. The tri-trophic system improves the environmental impact and sustainability of lettuce production, while making circularity feasible.