Over the past century, advances in agronomy and breeding have doubled crop yields, primarily through increased use of water, fertilizers, pesticides, and improved genetics. However, with the global population projected to double by 2050 and rising demand for renewable resources, we now face the challenge of increasing productivity with fewer inputs, developing an eco-friendly and sustainable agriculture. The plant root system is crucial for anchoring, nutrient and water uptake and symbiotic interactions, playing a key role in plant growth, yield, and resilience to abiotic and biotic stresses.

 

We focus on uncovering the molecular and physiological mechanisms that underpin these adaptive responses, with the goal of supporting long-term crop performance under suboptimal growing conditions.

 

Our main research areas are:

 

1. Discovery of new compounds that enhance root system development and plant growth.
2. Study of root and shoot responses to phosphate (Pi) starvation and heat stress and the molecular mechanisms underlying stress responses (DNA methylation, gene transcription, and miRNA activity).
3. Identification of beneficial bacteria and fungi that improve plant tolerance to combined heat stress and low Pi and study of the molecular mechanisms underlying this enhanced resilience (DNA methylation, gene transcription, and miRNA activity).

 

Novel plant growth regulators:

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Natural compounds play a key role in sustainable agriculture by promoting plant growth and resilience without relying on synthetic chemicals, thus reducing environmental impact.

 

• We have identified a new metabolite, BiAux, which specifically increases the number of lateral roots by modulating auxin receptor sensitivity via TIR1 and AFB2 co-receptors.
• Additionally, we are characterizing a compound that may mediate root responses to heat stress, using mutants and transcriptomic analyses.
• We will screen a library of natural compounds to identify those that promote root growth and enhance beneficial microbiome interactions.
  
  

Responses to phosphate starvation

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Using the D-Root device, we found that root responses to Pi starvation differ significantly from previous reports. The transcriptional response of specific root cell layers during Pi starvation is not well understood and may involve specialized genetic changes.

 

• We are analyzing cell-type-specific gene expression and alternative splicing to reconstruct functional adaptation networks and identify key regulators for sustained growth and Pi uptake.

 

The Dark-Root (D-Root) device allows to grow Arabidopsis seedlings in vitro with the root system in the darkness while exposing the shoot to the light.

Graphic representation of the D-Root device.

(b) The petri dish is inserted into the methacrylate box. Arrow points to the methacrylate combo used to block partially the light coming from the top.

(c) D-Root device adaptation to illuminate roots with different light wavelengths using led technology or a UV- lamp.

(d) Phenotype of  12 day old Arabidopsis seedling grown with root in presence of light (LGR- Light Grown Roots) or in darkness (DGR-Dark Grown Roots). B) Root growth quantification in A. (low Pi corresponds to 5 µM of Pi).

 

Responses to combined phosphate starvation and heat stress

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Extreme heat waves and nutrient deficiencies threaten crop productivity and food security. Our research shows a correlation between heat stress responses and Pi deficiency. Using the D-Root system and the TGRooZ device (which creates a natural temperature gradient in the root zone), we found that root heat responses differ from previous findings, suggesting new genes and pathways can be identified.

 

• We are evaluating plant responses to combined stresses (Pi starvation plus heat) through transcriptomics, ionomics and hormonomics.
  
  

The TGRooZ device generates a temperature gradient like the natural soil and affects the root and shoot growth of Arabidopsis in response to heat.

(A) Optical (top) and thermal pictures (bottom) of 12x12 cm plates containing agar cultivated at 22ºC, or 32ºC homogenously (22SR,  32SR) or 32TGRooZ.

(B) In the right side, is shown optical (top) and thermal pictures (bottom) of 3.5L pots containing soil that were cultivated at 24ºC, or 36ºC homogenously (24SR, 36SR) or 36TGRooZ.Colors indicate the different temperatures found along the plate or the pots.

(C) Phenotype of Arabidopsis plants that were grown in homogeneous temperature in root and shoot (22SR for 22ºC or 32SR for 32ºC) or at 32TGRooZ; 32ºC in the aerial part and a decreasing gradient in the root system. 

(D) Confocal images of root meristems of 22RS, 32SR or 32TGRooZ seedlings grown for 6 days after transplanting. White arrowheads indicate the QC and arrows indicate the final of the meristem. Scale bar corresponds to 50 µm.

(E) Confocal images of a z-stack PI-stained root apical meristems from 22SR, 32SR or 32TGRooZ CYCB1;1:CYCB1;1-GFP seedlings grown for 6 days after transplanting. White arrows indicate the end of the meristem. Scale bar corresponds to 50 µm.

Effect of TGRooZ in tomato seedlings. Heat also reduced root and shoot growth in tomato plants, reduction that is recovered by the use of TGRooZ.

(A) Optical and thermal pictures of tomato seedlings cultivated on germination paper at 26ºC, or 36ºC homogenous in shoot and root (26SR,  36SR) or 36TGRooZ. The thermal picture shows the homogeneous temperature or the gradient formed. Right photographs correspond to representative pictures of tomato seedling grown in those conditions.

Representative pictures of tomato plants grown in the TGRooZ-pots system for 3 weeks. Note that heat on root (36SR) severely reduces shoot growth.

 

Role of Epigenetic and Chromatin Dynamics in stress adaptation

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We investigate how plants respond to abiotic stresses such as heat and Pi deficiency, or the combination of both, by characterizing changes in DNA methylation. A particularly novel aspect of our work is the analysis of combined stress conditions, where we have uncovered unique epigenetic responses that differ from those triggered by individual stresses. By integrating DNA methylation data with transcriptional and chromatin accessibility profiles, we aim to unravel the complex regulatory networks that drive plant adaptation and stress memory.

Role of microRNAs in stress adaptation

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In a complementary line of research, we study how plants integrate multiple environmental signals through the regulation of microRNAs (miRNAs). miRNAs are particularly intriguing because they not only regulate gene expression but also serve as key mediators of inter-organ communication within the plant and inter-organisms between kingdoms. Using small RNA sequencing, we have identified novel drivers of miRNAs responses in stress conditions. These miRNAs appear to orchestrate gene expression programs that enable plants to cope with complex and overlapping stress cues. Our goal is to uncover the molecular logic behind stress integration and identify regulatory nodes relevant for plant resilience.

 

Epigenetics role in stress adaptation. DNA methylation and miRNAs are important regulators of plant resilience to abiotic stress.

(A) DNA methylation levels in centromeres (cent) and arms (arm) of stressed plants’ shoots and roots.

(B) Metaplot showing TE CHH methylation levels in stressed plants.

(C) Example of CHH methylation level in ONSEN2 heat-responsive TE.

(D) Photograph showing barley plants from stressed and not stressed parentals growing in rizotrons to measure their differences in root development.

(E) Venn diagram showing the number of upregulated miRNAs in shoots and roots of stressed plants.

 

Role of microbes in stress adaptation:

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Beneficial microbes enhance plant growth and improve stress tolerance by promoting nutrient uptake, supporting root development, and helping plants adapt to challenging environmental conditions.

 

• We are screening an endophytic fungi collection to identify strains that enhance plant growth under low Pi. Our rapid screening method, in collaboration with Tradecorp (Rovensa Next), has identified two promising isolates, now field-tested and intellectually protected.
• We are now using single-cell RNA sequencing to gain deeper insight into the cellular interactions between this fungus and Arabidopsis, allowing us to unravel their communication and functional dynamics at unprecedented resolution.
• Using TGRooZ, we have also developed a collection of bacteria and fungi that may increase plant tolerance to combined heat and Pi stress. So far, we have identified one bacterium and one fungus that enhance thermotolerance, and we are investigating the molecular and physiological mechanisms involved.
• We study the mechanisms by which plant growth-promoting microorganisms (PGPMs) alleviate the effects of abiotic stress. For one fungal isolate, we have found evidence suggesting that its beneficial effects are mediated through the modulation of plant DNA methylation patterns. These findings point to a microbial influence on host epigenetic regulation, opening new avenues for sustainable strategies to improve crop stress tolerance.

 

 

TGRooZ generates a temperature gradient similar to that found in natural soils, which is essential for establishing proper root–soil–microbiota interactions. This gradient is also crucial for an appropriate heat stress response in the aerial parts of the plant, helping to establish the correct epigenome and gene expression patterns.