Biology subjects

Garcia-Molina, A.

Publications and source records attributed to Garcia-Molina, A..

6 recordsLinked to original sources

bioRxiv2026

Elevated CO2 enhances tomato tolerance to Botrytis cinerea through transcriptional and metabolic defence reprogramming

Atmospheric CO2 concentration is projected to rise substantially over the coming decades, yet its impact on the molecular mechanisms governing plant immunity remains poorly understood. Here, we investigated how elevated CO2 (eCO2; 650 ppm) combined with increased temperature (+5 {degrees}C) influences tomato responses to Botrytis cinerea through integrated phenotypic, metabolomic, transcriptomic, and gene regulatory network (GRN) analyses across eight cultivars. Although cultivars displayed contrasting susceptibility under ambient conditions, eCO2 consistently enhanced tolerance across all genetic backgrounds. Multi-omics analyses revealed a partial uncoupling between transcriptional and metabolic responses during infection, with repression of photosynthesis- and carbon metabolism- related genes contrasting with the accumulation of carbon- and amino acid-derived metabolites. Under eCO2, this metabolic disruption was attenuated, preserving metabolic homeostasis during infection. GRN reconstruction identified a conserved WRKY-ERF regulatory module underlying the growth-defence trade-off, while functional perturbation demonstrated that its contribution to resistance depends on both genotype and environmental context, highlighting the importance of basal defence mechanisms. Targeted metabolomics further revealed that eCO2 promotes a metabolically primed state characterized by reinforcement of structural and chemical defence barriers rather than stronger activation of inducible immune responses. Together, our findings show that enhanced tolerance under eCO2 emerges from coordinated reorganization across regulatory and metabolic networks, providing a systems- level framework for understanding plant immunity and improving crop resilience under future climate scenarios.

plant biology↗

bioRxiv2026

Integrative genomic and regulatory network analysis reveals adaptive mechanisms to salt-alkalinity stress in Brassica fruticulosa

Salinity poses a widespread and increasing threat to plant fitness, ultimately constraining agricultural productivity worldwide. An inherent roadblock to understanding the precise physiological impacts of high-salinity soils is the frequent co-occurrence of multiple stressors. In calcareous soils, salinity typically coincides with alkalinity. To address this realistic combinatorial stress scenario, we deconstructed the enhanced performance of the coastally distributed, salt-tolerant Brassica fruticulosa under salt-alkaline conditions using comparative physiological, transcriptomic, and genomic analyses across major brassica crops. First, to gain a high-resolution genomic view, we generated phased, chromosome-level genome assemblies of B. fruticulosa and performed cross-species comparisons of transcriptome-derived Gene Regulatory Networks (GRNs) among important related crop models with contrasting salt tolerances. These results revealed that B. fruticulosa mounts predominantly root-centered transcriptional responses to cope with high salinity, whereas salt-sensitive species rely largely on shoot-level mechanisms to mitigate salt toxicity. Consistently, regulatory modules within GRNs diverged substantially between organs and among species, reflecting distinct adaptive programmes of varying efficacy. Functional categorisation of transcription factors with high centrality in B. fruticulosa shoot GRNs highlighted processes related to iron (Fe) homeostasis, suggesting that effective maintenance of Fe allocation to aerial tissues supports biomass retention under combined salt and alkalinity stress. Collectively, these findings establish B. fruticulosa as a valuable new model for dissecting adaptation to salinity in natural environments and provide mechanistic insight into the regulatory architecture underlying salt-alkaline tolerance.

plant biology↗

bioRxiv2026

Molecular basis of delayed leaf senescence induced by short-term treatment with low phosphate in rice

Leaf senescence is a programmed plant developmental process that can also be regulated by environmental factors, like nutrient availability. Although phosphorus is an essential element determining plants growth and productivity, mechanisms underlying adaptation to phosphorus availability in plants are not well understood. In this study, we combined physiological, biochemical and molecular approaches to investigate the effect of phosphate supply on leaf senescence in rice. We show that short-term treatment of rice seedlings with low phosphate increases photosynthetic pigments content, confers tolerance to methyl viologen-induced oxidative stress in chloroplasts, and increases antioxidant enzyme activities. Leaves from low-Pi-treated plants also showed a reduction in membrane lipid peroxidation and electrolyte leakage. Opposite trends were observed in seedlings under high Pi supply, in which accelerated leaf senescence occurs. Further analyses indicated that CRISPR/Cas9-mediated editing of MIR827, and subsequent reduction in Pi content, promotes delayed leaf senescence, while Pi accumulation in MIR827 or MIR399 overexpressing plants accelerates senescence. These findings strongly support that short treatment with low phosphate delays rice leaf senescence. Transcriptomic analysis demonstrated multiple biological processes underlying adaptation of rice plants to low phosphate, including senescence-associated and metabolic processes. These findings provide novel insights into leaf senescence potentially contributing to sustainable rice production.

plant biology↗

bioRxiv2026

Phosphite, an analog of phosphate, counteracts Phosphate Induced Susceptibility of rice to the blast fungus Magnaporthe oryzae

Phosphate (Pi) and phosphite (Phi), a non-metabolizable analogue of Pi, are taken up by plant roots through the same transport system. Whereas Pi is an essential nutrient for plants, Phi might function as a biostimulant and in protection against pathogens. However, how Phi mechanistically exerts beneficial effects on plants remains unsolved. We examined the impact of Phi and Pi on Arabidopsis thaliana and rice growth and upon pathogen infection. Phi inhibited the in vitro growth of Plectosphaerella cucumerina and Fusarium fujikuroi in a dose-dependent manner, whereas Magnaporthe oryzae growth was largely unaffected. Phis effect on plant growth was dependent on the plant species, the basal Pi level in the plant, and the ratio Pi to Phi. In Arabidopsis, Phi enhanced resistance to P. cucumerina by triggering a hypersensitive response-like cell death. Notably, Phi reversed Pi-induced susceptibility to blast (M. oryzae) and bakanae (F. fujikuroi) diseases in rice. Transcriptomic analysis revealed that Phi triggered extensive reprogramming in rice under high Pi, including the activation of signaling pathways enriched in phosphorylation-dependent processes, while attenuating induction of carbon metabolism. Phi acts as a multifaceted agent, promotes balanced metabolic state, improved plant performance, and reduced Pi-induced disease susceptibility when applied under appropriate Pi conditions. HighlightPhosphite application confers protection against fungal pathogens in Arabidopsis and rice plants by regulating signaling pathways depending on phosphorylation processes.

plant biology↗

bioRxiv2026

Decoding microbial diversity in roots of rice plants under flooded conditions: influence of the host genotype, root compartment and mycorrhizal association

BackgroundThe root microbiome plays a critical role in nutrient acquisition, stress tolerance and overall plant health. Rice, a staple food for more than half of the worlds population, is commonly cultivated under flooded conditions. Despite its agronomical importance, our current understanding of root-associated microbiomes in rice grown under flooded conditions is limited. On the other hand, nitrogen (N) and phosphorus (P) fertilizers are routinely applied to maximize rice yield. It is also well known that root colonization by arbuscular mycorrhizal (AM) fungi enhances mineral nutrition in plants, but whether mycorrhizal associations influence the composition of the rice root microbiome remains poorly understood. In this study, shotgun metagenomic sequencing was used to characterize the root endosphere and rhizosphere microbiomes in two temperate japonica rice varieties (cv. Bomba and JSendra) grown under flooded conditions. The impact of colonization by the AM fungus Rhizophagus irregularis on the root microbiome was investigated. ResultsRoot-associated compartments harbour distinct microbial communities in rice with bacterial taxa comprising approximately 95% of the total microbia in rice roots. At the Phylum level, the root bacteriome was primarily composed of Pseudomonadota (Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria) followed by Actinomycetota. The fungal microbiome was dominated by Ascomycota (Sordariomycetes, Eurotiomycetes and Dothideomycetes) and Basidiomycota. Not only the root compartment, but also the host genotype can shape the root microbiome. Recruitment of specific microorganism mainly occurs at the species level. Genotype-specific and compartment-specific associations of microbial species in mycorrhizal rice roots were also observed supporting that root colonization by an AM fungus contributes to variations in the root microbiome. Further, key microbial species primarily associated to methane production and nutrient cycling (e.g. Phosphate Solubilizing Bacteria and Nitrogen cycling bacteria) colonizing root compartments in each rice genotype and mycorrhizal condition are described. ConclusionsThe rice genotype, root compartment and mycorrhizal condition markedly influence the microbiome in roots of rice plants growing in flooded rice fields. These findings illustrate the potential of the plant to shape its associated root microbiome, thus, offering valuable insights for the development of microbiome-based strategies to improve growth and performance in rice plants under flooded conditions.

microbiology↗

bioRxiv2023

At the core of salinity: convergent and divergent transcriptome response pathways to neutral and alkaline salinity in natural populations of Arabidopsis thaliana

More than 70% of lands cultivated area is affected by alkaline salinity stress. As 98% of plants are glycophytes - unable to successfully reproduce under salinity - our previous research focused on comparative studies of Arabidopsis thaliana demes with differential performance under neutral and alkaline salinity (neuSAL and alkSAL) due to local adaptation processes. Here, an integrated analysis on leaf tissue was performed, including physiological indicators, nutritional status, endogenous phytohormonal concentration and transcriptome profiling, to further understand differences in molecular mechanisms underlying neuSAL and alkSAL responses. The results support that alkSAL is more detrimental to plant performance than neuSAL and indicate higher sensitivity to alkSAL in demes locally adapted to coastal siliceous soils. A decreased internal Fe use efficiency in coastal demes under alkSAL is proposed to be the driver of their enhanced sensitivity, and sequence variation at {beta}-CA1 and -CA1 locus is hypothesized to contribute to the imbalance of Fe homeostasis. Dissection on the down-regulated transcripts shared by neuSAL and alkSAL confirmed enhanced inhibition of central features on primary and secondary metabolism in coastal individuals under alkSAL. The cell wall and vacuolar {beta}-galactosidase BGAL4 was revealed as a candidate for conferring tolerance to neuSAL by favoring stress-regulated cell wall rearrangement, but not to alkSAL, probably due to pH-restricted enzymatic activity. In addition, differential modulation of endogenous phytohormonal cues was reported among salinity types and demes, by which higher alteration of the auxinic, ethylene and jasmonic acid signaling pathways was exerted by alkSAL but sustained ABA biosynthesis was detected only in coastal plants under neuSAL. Weighted correlation network analysis (WGCNA) confirmed the involvement of the identified candidate genes in co-expression modules significantly correlating with favorable responses to neuSAL and alkSAL. Overall, the present study provides useful insights into key targets for breeding improvement in alkaline saline soils.

molecular biology↗