Francesco Mercati

Plant–microbe interactions can modulate the production of bioactive compounds involved in plant growth-promoting activity. This study investigates the metabolic reprogramming of the actinomycete model strain Streptomyces coelicolor M145 during co-cultivation with Citrus aurantium and Citrus limon seeds, used as defined plant-derived chemical inputs, under contrasting nutritional conditions with or without L-tryptophan (Trp) supplementation. Untargeted metabolome profiling revealed medium- and Citrus seed-dependent metabolic shifts in co-cultures compared with corresponding Citrus seed and S. coelicolor single cultures used as controls. Under R2YE production conditions, co-cultivation with C. limon resulted in 27 extracellular metabolites, compared with 11 detected in the TSB vegetative medium; similar trends were observed for C. aurantium. Multivariate analyses confirmed that growth medium, Citrus species, and Trp significantly shaped S. coelicolor extracellular metabolic profiles, mainly in quantitative terms. Production conditions, particularly with Trp supplementation, promoted metabolites associated with antimicrobial activity and iron acquisition, whereas vegetative conditions promoted primary metabolism and biotransformation of Citrus-derived compounds. Spent medium bioassays on Solanum lycopersicum showed that these metabolic differences were correlated with distinct biological responses. Overall, these findings demonstrate that defined plant-derived inputs modulate S. coelicolor specialized metabolism in a context-dependent manner, generating metabolomic signatures associated with differential plant growth responses compared to single cultures.

Key message: Gene expression analyses reveal tissue-specific and temporally regulated networks driving Posidonia oceanica development, and identify key hub genes that coordinate root, leaf, and seed maturation. Seagrasses are marine angiosperms that form extensive underwater meadows, providing habitat, stabilising sediments, storing carbon, and protecting coastlines. Posidonia oceanica is the endemic foundation seagrass of the Mediterranean Sea, yet its meadows are rapidly declining. Despite its ecological importance, the molecular basis of P. oceanica development is still poorly understood. Here, we analysed gene expression in roots, leaves, and seeds across four developmental stages, revealing strong tissue-specific patterns and temporally regulated expression dynamics. Leaves exhibited active regulation of photosynthesis-related processes, while roots were enriched in pathways related to carbohydrate metabolism and cell wall biogenesis, supporting primary root growth and anchoring. The seeds retained metabolic activity, with glycolytic enzymes indicating readiness for germination. Temporal analyses identified a major transcriptional shift, with distinct gene sets sequentially activated during early establishment and late maturation in tissues. Weighted Gene Co-expression Network Analysis (WGCNA) identified modules strongly associated with specific tissues and developmental transitions, highlighting key hub genes involved in photosynthesis, metabolism, cell wall remodelling, and protein synthesis. Together, these results reveal complex, temporally coordinated regulatory networks underlying P. oceanica development .

The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enables the investigation of molecular dynamics occurring at the earliest stages of sex chromosome evolution. With two independently young origins of dioecy, Asparagus is a model genus for studying the genetics of sex-determination and sex chromosome evolution. Dioecy first evolved in Asparagus ∼3 to 4 million years ago (Ma) in the ancestor of a now widespread Eurasian clade including garden asparagus (Asparagus officinalis). A second origin occurred in a smaller, geographically restricted, Mediterranean Basin clade, including Asparagus horridus. New haplotype-resolved reference genomes for garden asparagus and A. horridus, elucidate contrasting first steps in the origin of the sex chromosomes of the Eurasian and Mediterranean Basin clade ancestors. Analysis of the A. horridus genome revealed an XY system derived from a different ancestral pair of autosomes with different sex-determining genes than have been characterized for garden asparagus. We estimate that proto-XY chromosomes evolved 1 to 2 Ma in the Mediterranean Basin clade, following a ∼2.1-megabase inversion that now distinguishes the X and Y chromosomes. Recombination suppression and LTR retrotransposon accumulation drove the expansion of the male-specific region on the Y (MSY) that reaches ∼9.6-megabases in A. horridus. The garden asparagus genome revealed an MSY spanning ∼1.9-megabases. A segmental duplication and neofunctionalization of one duplicated gene (SOFF) drove the origin of dioecy in the Eurasian clade. These findings support previous inference based on phylogeographic analysis revealing two recent origins of dioecy in Asparagus and establish the genus as a model for investigating sex chromosome evolution.

BACKGROUND: Plant interactions with beneficial microbes can modulate defense responses against insect herbivores, yet the mechanisms remain poorly understood for herbivorous stink bugs. This study evaluated the impact of the plant growth‐promoting fungus, Trichoderma harzianum T22, on direct and indirect defenses of tomato plants challenged by the invasive stink bug Halyomorpha halys . RESULTS: Inoculation of tomato plants with T. harzianum T22 reduced the relative growth rate of H. halys nymphs, accompanied by enhanced expression of defense‐related genes involved in the jasmonic acid and salicylic acid pathways, notably ToPIN2 , ToLOXD and ToPR1 . Behavioral assays revealed that females of the egg parasitoid Trissolcus japonicus, one of the main natural enemies of H. halys, were more strongly attracted to volatiles emitted from inoculated plants induced by stink bug feeding and oviposition. However, no effect of fungal inoculation was detected in the chemical composition of plant volatiles. CONCLUSION: These findings demonstrate that T. harzianum T22 enhances tomato responses against H. halys by strengthening defense signaling pathways and modulating indirect defenses that facilitate natural enemy recruitment. Overall, these results suggest that using plant‐growth‐promoting fungi to enhance plant defenses is a promising crop protection strategy for controlling stink bug pests. © 2025 Society of Chemical Industry.

Plant-derived nanovesicles (PDNVs) are emerging as a novel class of biological messengers, capable of crossing biological barriers and transferring bioactive molecules to human cells. We have previously isolated and characterized nanovesicles from lemon juice (LNVs) that interact with human cells, modulating the mechanisms of oxidative stress and inflammation. However, the mechanisms through which LNVs exert their effect are still poorly understood. Extensive researches have been conducted on the microRNA content of PDNVs, however the profile and role of long noncoding RNAs (lncRNAs) within the vesicles remain unexplored still. In the present study, the lncRNA cargo of LNVs and its role was investigated; highly conserved lncRNAs among Citrus species was highlighted, with a notable enrichment of LM_XLOC_013494 within the vesicles. The lncRNA was successfully transferred to human hepatic (THLE-2) and intestinal (CACO-2) cells treated with LNVs, as confirmed by RT-qPCR and RNA in situ hybridization. Bioinformatic prediction analyses coupled with experimental validation revealed that the isolated lncRNA acts as a molecular sponge, specifically targeting human miR-181b-3p and miR-4420. Importantly, LNV-treated cells showed a statistically significant downregulation of these miRNAs (p ≤ 0.05), suggesting a cross-kingdom regulatory role for the plant lncRNA in modulating human gene expression. Overall, to our knowledge, this study provides novel insights into the trans-kingdom transfer of plant-derived lncRNAs, expanding upon previous findings and offering new experimental evidence.

The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enable investigation of molecular dynamics occurring at the earliest stages of sex chromosome evolution. With two independently young origins of dioecy in the genus, Asparagus is a model taxon for studying genetic sex-determination and sex chromosome evolution. Dioecy first evolved in Asparagus ~3-4 million years ago (Ma) in the ancestor of a now widespread Eurasian clade that includes garden asparagus ( Asparagus officinalis ), while the second origin occurred in a smaller, geographically restricted, Mediterranean Basin clade including Asparagus horridus . The XY sex chromosomes and sex-determination genes in garden asparagus have been well characterized, but the genetics underlying dioecy in the Mediterranean Basin clade are unknown. We generated new haplotype-resolved reference genomes for garden asparagus and A. horridus , to elucidate the sex chromosomes of A. horridus and explore how dioecy evolved between these two closely related lineages. Analysis of the A. horridus genome revealed an independently evolved XY system derived from different ancestral autosomes (chromosome 3) with different sex-determining genes than documented for garden asparagus (on chromosome 1). We estimate that proto-XY chromosomes evolved around 1-2 Ma in the Mediterranean Basin clade, following an ~2.1-megabase inversion between the ancestral pair. Recombination suppression and LTR retrotransposon accumulation drove the establishment and expansion of the Y-linked sex-determination region (Y-SDR) that now reaches ~9.6-megabases in A. horridus . The new garden asparagus genome revealed a Y-SDR that spans ~1.9-megabases with ten hemizygous genes. Our results evoke hemizygosity as the most probable mechanism responsible for the origin of proto-XY recombination suppression in the Eurasian clade, and that neofunctionalization of one duplicated gene ( SOFF ) drove the origin of dioecy. These findings support previous inference based on phylogeographic analysis revealing two recent origins of dioecy in Asparagus . Moreover, this work implicates alternative molecular mechanisms for two separate shifts to dioecy in a model taxon important for investigating young sex chromosome evolution.

SUMMARY: In recent years, the ongoing climate changes have made it crucial to rethink agriculture in a more sustainable way. This includes reducing and optimizing the use of resources, including water, through the identification and selection of genotypes more tolerant to abiotic stresses. Although considered a xerophytic species, the olive tree requires an adequate water supply to ensure both quantity and quality production. Drought‐tolerant olive cultivars have been identified through breeding programs; however, the key molecular mechanisms involved in this tolerance remain largely unknown. To investigate in depth the plant responses to drought, six cultivars of different genetic backgrounds were grown in controlled conditions and exposed to water stress as well as inoculated with arbuscular mycorrhizal fungi (AMF). The physiological responses to drought stress varied among cultivars, as expected, showing complementary and/or alternative strategies, even according to AMF inoculation. This approach allowed us to identify two contrasting olive tree cultivars in response to drought stress (“Frantoio” and “Arbequina” as susceptible and tolerant, respectively). Transcriptomic profiles comparison of these cultivars enabled us to identify differentially expressed genes (DEG) with key roles in the regulation of metabolic pathways involved in drought tolerance, useful to support future olive tree breeding programs. Interestingly, the AMF inoculum was able to alleviate water stress damages mainly in the susceptible cultivar; this effect involved the more important plant physiological responses.