Dr. Rafael J. L. Morcillo graduated in Environmental Sciences from University of Granada in 2007. He completed his PhD thesis focused on the study of the role of plant hormones during the establishment of the arbuscular mycorrhizal symbiosis, under the supervision of Dr. José Manuel García Garrido at the Estación Experimental del Zaidín (Granada). Thereafter, he joined the laboratory of Dr. Huiming Zhang at the Shanghai Center for Plant Stress Biology (PSC; Chinese Academy of Sciences) as a postdoc to study the effect of microbial volatiles compounds in plant growth and health. In 2018, he joined the laboratory of Dr. Alberto Macho at PSC to investigate the molecular mechanisms governing infection processes of host plants by Ralstonia solanaceraum. In 2019, he returned to University of Granada (Spain) as postdoc to investigate the PGPR application to recover dry lands. Currently, he is working as a Senior Postdoc in The Institute for Mediterranean and Subtropical Horticulture "La Mayor
EDUCATION
Degree in Environmental Science by University of Granada (Spain).
PhD at "Estacion Experimental del Zaidin", Spanish National Research Council (Spain).
RESEARCH INTERESTS
Basis of plant biostimulation through interactions with microbes. I am interesting in getting a holistic view on the regulatory, biochemical and molecular mechanisms involved in the response of plants to microbial volatile compounds and the impact of these responses in the rhizosphere microbiota.
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Scopus Publications
Scopus Publications
Multimodal learning reveals plants’ hidden sensory integration logic Kelly L. Vomo-Donfack, Rafael Jorge León Morcillo, Grégory Ginot, Verónica G. Doblas, Ian Morilla BMC Genomics, 2026 Plants integrate complex environmental signals through interconnected molecular networks, yet the fundamental rules governing this sensory integration remain unknown. Studying tomato roots interacting with fungal symbionts, we discovered how microbial effectors systematically reprogram plant sensory systems by coordinating transcriptional, metabolic, and phenotypic responses. Our multimodal analysis not only confirmed prior experimental findings through purely computational means, but also revealed novel integration hubs where sensory pathways converge. This dual validation approach revealed two key mechanisms: first, the rewiring of iron homeostasis through citrate-mediated redox control, and second, the targeted suppression of jasmonate defences. Furthermore, we demonstrate how nuclear splicing programs are isolated from metabolic noise. These findings establish a new paradigm for understanding plant-microbe communication by showing how symbionts exploit latent hubs where sensory pathways converge. The discovered integration logic provides both fundamental insights into plant perception and concrete targets for engineering stress-resilient crops.
Perception of a bacterial quorum sensing signal activates a tripartite plant immune strategy Danxia He, Yang Zhou, Meng Li, Miao Wang, Wenjia Yu, Chuyang Shao, Sunil Kumar Singh, Meijiao Gu, Yuhua Wang, Jianlong Yuan, Xiaoxuan Wu, Shuai Zheng, Yi Xie, Lixian Chen, Rafael J. L. Morcillo, Yu Yang, Juan Ignacio Vílchez, Jin-Lin Zhang, Yansong Miao, Alberto P. Macho, Huiming Zhang Proceedings of the National Academy of Sciences of the United States of America, 2026 Bacterial quorum sensing (QS) signals an increasing threat during pathogenesis. How plants deploy timely defenses through QS perception is poorly understood. Here, we report that Arabidopsis thaliana perceives 2’-aminoacetophenone (2’-AA), a volatile QS signal from Pseudomonas aeruginosa , and mounts a multilayered defense. This response comprises BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-dependent intracellular immunity, extracellular quorum quenching through the release of acetic acid, and ecological remodeling of the root microbiome to suppress Pseudomonas . Our findings demonstrate that plants can translate the detection of a specific bacterial QS molecule into a coordinated, preemptive disease resistance strategy.
Molecular changes promoted by long-term water deficit in tomato can be largely mitigated by a fungal biostimulant Lidia López-Serrano, Alberto Férez-Gómez, Remedios Romero-Aranda, Emilio Jaime-Fernández, Jesús Leal-López, Edurne Baroja-Férnandez, Goizeder Almagro, Karel Doležal, Ondrej Novak, Luis Díaz, Rocío Bautista, Alicia Talavera, Noé Fernández-Pozo, Rafael Jorge León Morcillo, Javier Pozueta-Romero Plant Stress, 2026 • Fungal culture filtrates improve tomato performance and fruit yield under water deficit • The biostimulant attenuates a large portion of drought-induced molecular responses • The biostimulant reduces stress perception, making plants less sensitive to drought • Plant responses to the biostimulant depend on water status • The mode of action of this biostimulant differs from that reported for others The use of cell-free microbial culture filtrates (CF) as biostimulants is emerging as a safe and ecologically sound approach to improve crop performance while reducing anthropogenic pressure. However, the mechanisms underlying their biological activity remain poorly understood. We previously identified volatile organic compounds as major bioactive constituents of fungal CF. Here, we show that foliar application of cell-free CF derived from Trichoderma harzianum enhanced fruit yield, root growth, photosynthetic performance and agronomic water use efficiency in a commercial tomato cultivar grown in Mediterranean greenhouses under long-term water deficit conditions. To elucidate the biochemical and molecular bases of this phenomenon, we adopted an integrative approach to characterize plants grown under optimal and suboptimal irrigation conditions (OIC and SOIC, respectively) with or without the fungal CF treatment. Water deficit induced extensive changes in drought stress-related signaling molecules and in the leaf transcriptome, which accounted for many of the physiochemical differences recorded between OIC- and SOIC-grown plants. Notably, many of these changes were largely alleviated by foliar application of fungal CF to SOIC-grown plants, including those affecting the expression of approximately 50% of water deficit-responsive genes. These genes did not respond to CF in OIC-grown plants, indicating that the transcriptomic response to CF is strongly dependent on plant water status. Taken together, our results indicate that foliar application of fungal CF enhances tomato tolerance to long-term water deficit primarily by attenuating a substantial fraction of drought-induced metabolic and transcriptional responses rather than by inducing new ones, thereby reducing plant sensitivity to water stress.
The Highly Conserved Cys95 Residue of Fructose-1,6-Bisphosphatase 1 Mediates the pH-Driven Structure and Activity of the Enzyme and Photosynthesis Samuel Gámez‐Arcas, Edurne Baroja‐Fernández, Francisco José Muñoz, Antonio J. Serrato, Mónica Balsera, Ángela María Sánchez‐López, Abdellatif Bahaji, Jesús Leal‐López, Rafael Jorge León Morcillo, Javier Pozueta‐Romero Plant Cell and Environment, 2025 In Arabidopsis, exposure to microbial volatile compounds promotes thiol reduction of the Cys95 residue of the photosynthetic enzyme fructose‐1,6‐bisphosphatase (cFBP1). Although highly conserved in plants, the Cys95 function still remains unknown. We characterised recombinant wild‐type (WT) cFBP1 and a variant (C95S) in which the Cys95 residue was replaced by serine. Furthermore, we characterised cFBP1‐lacking cfbp1 transgenic plants expressing WT or C95S cFBP1. Cys95 replacement by serine reduced cFBP1 activity and its Mg2+ binding affinity and cooperativity. Although it is widely assumed that active cFBP1 is strictly homotetrameric, WT and C95S cFBP1 were present as inactive tetramers at pH 7.0 and active dimers at pH 8.3. At pH 7.8, WT and C95S cFBP1 were predominantly present as dimers and tetramers, respectively. WT cFBP1 expression totally reverted to WT the reduced photosynthetic activity of cfbp1 plants grown in the absence or presence of microbial volatiles, but that of C95S cFBP1 only partially did it. Artificial intelligence‐based AlphaFold protein structure analyses predicted that the replacement of Cys95 by serine promotes cFBP1 conformational changes. We conclude that (i) active cFBP1 is strictly dimeric at pH values occurring in illuminated chloroplasts and (ii) Cys95 is an important determinant of the stromal pH‐driven structure and activity of cFBP1 and photosynthesis.
RAPID ALKALINIZATION FACTOR 22 is a key modulator of the root hair growth responses to fungal ethylene emissions in Arabidopsis Rafael Jorge León Morcillo, Jesús Leal-López, Alberto Férez-Gómez, Lidia López-Serrano, Edurne Baroja-Fernández, Samuel Gámez-Arcas, Germán Tortosa, Leonel E López, José Manuel Estevez, Verónica G Doblas, Laura Frías-España, María Dolores García-Pedrajas, Jorge Sarmiento-Villamil, Javier Pozueta-Romero Plant Physiology, 2024 In Arabidopsis (Arabidopsis thaliana (L.) Heynh), exposure to volatile compounds (VCs) emitted by Penicillium aurantiogriseum promotes root hair (RH) proliferation and hyper-elongation through mechanisms involving ethylene, auxin, and photosynthesis signaling. In addition, this treatment enhances the levels of the small signaling peptide RAPID ALKALINIZATION FACTOR 22 (RALF22). Here, we used genetics to address the role of RALF22 in fungal VC-promoted RH growth and to identify the bioactive fungal VC. We found that RHs of ralf22 and feronia (fer-4) plants impaired in the expression of RALF22 and its receptor FERONIA, respectively, responded weakly to fungal VCs. Unlike in wild-type roots, fungal VC exposure did not enhance RALF22 transcript levels in roots of fer-4 and ethylene- and auxin-insensitive mutants. In ralf22 and fer-4 roots, this treatment did not enhance the levels of ERS2 transcripts encoding one member of the ethylene receptor family and those of some RH-related genes. RHs of ers2-1 and the rsl2rsl4 double mutants impaired in the expression of ERS2 and the ethylene- and auxin-responsive ROOT HAIR DEFECTIVE 6-LIKE 2 and 4 transcription factors, respectively, weakly responded to fungal VCs. Moreover, roots of plants defective in photosynthetic responsiveness to VCs exhibited weak RALF22 expression and RH growth responses to fungal VCs. VCs of ΔefeA strains of P. aurantiogriseum cultures impaired in ethylene synthesis weakly promoted RH proliferation and elongation in exposed plants. We conclude that RALF22 simultaneously functions as a transcriptionally regulated signaling molecule that participates in the ethylene, auxin, and photosynthesis signaling-mediated RH growth response to fungal ethylene emissions and regulation of ethylene perception in RHs.
Dynamic population changes during a bioaugmented sewage sludge composting process: Improvement of pharmaceutical active compounds degradation and conversion into an organic soil amendment G. Angeles-de Paz, R. León-Morcillo, A. Štovícek, M. Sagova-Mareckova, T. Robledo-Mahón, C. Calvo, E. Aranda Journal of Environmental Chemical Engineering, 2024 Bioaugmentation has resulted in an interesting tool to improve composting technologies. However, the structure and dynamic of native populations might be affected, hence, the whole process performance. Here, we aimed to identify and evaluate the fungal and bacterial dynamic changes produced by the bioaugmentation with an exogenous inoculant: Penicillium oxalicum XD 3.1 and an endogenous natural consortia obtained from enrichment: enriched culture during a sewage sludge composting process (applied and designed for the improvement of pharmaceutical active compounds degradation, under real conditions). To do so, microbial structure of the enriched culture was first described and then, the microbial dynamic population into the composite samples were studied. Microbial DNA was obtained from the enriched culture (before and after the enrichment) and from the compost (at key stages of the process: inoculation, thermophilic and maturation). The amplicon sequencing of 16 S rRNA genes and internal transcribed spacer (ITS) region for bacteria and fungi was then performed using an Illumina Platform. Results showed that fungal and bacterial α-diversity in bioaugmented piles was significantly changed during inoculation and thermophilic stages. The inoculation and the fluctuation of the physicochemical parameters, altered by the bioaugmentation, explained the microbial diversity changes. Temperature, mineral matter, conductivity, dry matter, and total solids were the significant explanatory variables for diversity, dominance and ASVs counts. Redundancy analyses of β-diversity revealed the asynchronous interaction with all physicochemical parameters that varied according to the composting stage. In general, these outcomes lead to a deeper understanding of the promising combined bioaugmentation-composting mechanism.
PGI1-mediated vascular oxidative pentose phosphate pathway modulates photosynthesis via long-distance cytokinin signaling Ángela María Sánchez-López, Abdellatif Bahaji, Samuel Gámez-Arcas, Nuria De Diego, Ondřej Vrobel, Petr Tarkowski, Edurne Baroja-Fernández, Francisco José Muñoz, Goizeder Almagro, Jose María Seguí-Simarro, Mercedes Tabernero-Mendoza, Lidia López-Serrano, Rafael J.L. Morcillo, Javier Pozueta-Romero Plant Physiology and Biochemistry, 2024 In Arabidopsis, the plastidial isoform of phosphoglucose isomerase, PGI1, mediates growth and photosynthesis, likely due to its involvement in the vascular production of cytokinins (CK). To examine this hypothesis, we characterized pgi1-2 knockout plants impaired in PGI1 and pgi1-2 plants specifically expressing PGI1 in root tips and vascular tissues. Moreover, to investigate whether the phenotype of pgi1-2 plants is due to impairments in the plastidial oxidative pentose phosphate pathway (OPPP) or the glycolytic pathway, we characterized pgl3-1 plants with reduced OPPP and pfk4pfk5 knockout plants impaired in plastidial glycolysis. Compared with wild-type (WT) leaves, pgi1-2 leaves exhibited weaker expression of photosynthesis- and 2-C-methyl-D-erythritol 4-P (MEP) pathway-related proteins, and stronger expression of oxidative stress protection-related enzymes. Consistently, pgi1-2 leaves accumulated lower levels of chlorophyll, and higher levels of tocopherols, flavonols and anthocyanins than the WT. Vascular- and root tip-specific PGI1 expression countered the reduced photosynthesis, low MEP pathway-derived CK content, dwarf phenotype and the metabolic characteristics of pgi1-2 plants, reverting them to WT-like levels. Moreover, pgl3-1, but not pfk4pfk5 plants phenocopied pgi1-2. Histochemical analyses of plants expressing GUS under the control of promoter regions of genes encoding plastidial OPPP enzymes exhibited strong GUS activity in root tips and vascular tissues. Overall, our findings show that root tip and vascular PGI1-mediated plastidial OPPP activity affects photosynthesis and growth through mechanisms involving long-distance modulation of the leaf proteome by MEP pathway-derived CKs.
Pharmaceutical active compounds in sewage sludge: Degradation improvement and conversion into an organic amendment by bioaugmentation-composting processes G. Angeles-de Paz, R. León-Morcillo, S. Guzmán, T. Robledo-Mahón, C. Pozo, C. Calvo, E. Aranda Waste Management, 2023 • Bioaugmentation and composting have been combined for emerging pollutants removal. • Physicochemical features during composting were improved under bioaugmentation. • Bioaugmentation yields to a more stable, mature and sanitized final compost. • Penicillium improved metals immobilization and the pharmaceuticals degradation. • Toxicity in sewage sludge was reduced after bioaugmentation with Penicillium. Around 143,000 chemicals find their fate in wastewater treatment plants in the European Union. Low efficiency on their removal at lab-based studies and even poorer performance at large scale experiments have been reported. Here, a coupled biological technology (bioaugmentation and composting) is proposed and proved for pharmaceutical active compounds degradation and toxicity reduction. The optimization was conducted through in situ inoculation of Penicillium oxalicum XD 3.1 and an enriched consortium (obtained from non-digested sewage sludge), into pilot scale piles of sewage sludge under real conditions. This bioaugmentation-composting system allowed a better performance of micropollutants degradation (21 % from the total pharmaceuticals detected at the beginning of the experiment) than a traditional composting process. Particularly, inoculation with P. oxalicum allowed the degradation of some recalcitrant compounds like carbamazepine, cotinine and methadone, and also produced better stabilization features in the mature compost (significant passivation of copper and zinc, higher macronutrients value, adequate physicochemical conditions for soil direct application and less toxic effect on germination) compared to the control and the enriched culture. These findings provide a feasible, alternative strategy to obtain a safer mature compost and a better removal of micropollutants performance at large scale.
Cell-free microbial culture filtrates as candidate biostimulants to enhance plant growth and yield and activate soil- and plant-associated beneficial microbiota Rafael Jorge León Morcillo, Edurne Baroja-Fernández, Lidia López-Serrano, Jesús Leal-López, Francisco José Muñoz, Abdellatif Bahaji, Alberto Férez-Gómez, Javier Pozueta-Romero Frontiers in Plant Science, 2022 In this work we compiled information on current and emerging microbial-based fertilization practices, especially the use of cell-free microbial culture filtrates (CFs), to promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identified limitations to bring microbial CFs to the market as biostimulants. In nature, plants act as metaorganisms, hosting microorganisms that communicate with the plants by exchanging semiochemicals through the phytosphere. Such symbiotic interactions are of high importance not only for plant yield and quality, but also for functioning of the soil microbiota. One environmentally sustainable practice to increasing crop productivity and/or protecting plants from (a)biotic stresses while reducing the excessive and inappropriate application of agrochemicals is based on the use of inoculants of beneficial microorganisms. However, this technology has a number of limitations, including inconsistencies in the field, specific growth requirements and host compatibility. Beneficial microorganisms release diffusible substances that promote plant growth and enhance yield and stress tolerance. Recently, evidence has been provided that this capacity also extends to phytopathogens. Consistently, soil application of microbial cell-free culture filtrates (CFs) has been found to promote growth and enhance the yield of horticultural crops. Recent studies have shown that the response of plants to soil application of microbial CFs is associated with strong proliferation of the resident beneficial soil microbiota. Therefore, the use of microbial CFs to enhance both crop yield and stress tolerance, and to activate beneficial soil microbiota could be a safe, efficient and environmentally friendly approach to minimize shortfalls related to the technology of microbial inoculation. In this review, we compile information on microbial CFs and the main constituents (especially volatile compounds) that promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identify challenges and limitations for their use as biostimulants to bring them to the market and we propose remedial actions and give suggestions for future work.
Glucose-6-P/phosphate translocator2 mediates the phosphoglucose-isomerase1-independent response to microbial volatiles Samuel Gámez-Arcas, Francisco José Muñoz, Adriana Ricarte-Bermejo, Ángela María Sánchez-López, Marouane Baslam, Edurne Baroja-Fernández, Abdellatif Bahaji, Goizeder Almagro, Nuria De Diego, Karel Doležal, Ondřej Novák, Jesús Leal-López, Rafael Jorge León Morcillo, Araceli G Castillo, Javier Pozueta-Romero Plant Physiology, 2022 In Arabidopsis (Arabidopsis thaliana), the plastidial isoform of phosphoglucose isomerase (PGI1) mediates photosynthesis, metabolism, and development, probably due to its involvement in the synthesis of isoprenoid-derived signals in vascular tissues. Microbial volatile compounds (VCs) with molecular masses of <45 Da promote photosynthesis, growth, and starch overaccumulation in leaves through PGI1-independent mechanisms. Exposure to these compounds in leaves enhances the levels of GLUCOSE-6-PHOSPHATE/PHOSPHATE TRANSLOCATOR2 (GPT2) transcripts. We hypothesized that the PGI1-independent response to microbial volatile emissions involves GPT2 action. To test this hypothesis, we characterized the responses of wild-type (WT), GPT2-null gpt2-1, PGI1-null pgi1-2, and pgi1-2gpt2-1 plants to small fungal VCs. In addition, we characterized the responses of pgi1-2gpt2-1 plants expressing GPT2 under the control of a vascular tissue- and root tip-specific promoter to small fungal VCs. Fungal VCs promoted increases in growth, starch content, and photosynthesis in WT and gpt2-1 plants. These changes were substantially weaker in VC-exposed pgi1-2gpt2-1 plants but reverted to WT levels with vascular and root tip-specific GPT2 expression. Proteomic analyses did not detect enhanced levels of GPT2 protein in VC-exposed leaves and showed that knocking out GPT2 reduced the expression of photosynthesis-related proteins in pgi1-2 plants. Histochemical analyses of GUS activity in plants expressing GPT2-GUS under the control of the GPT2 promoter showed that GPT2 is mainly expressed in root tips and vascular tissues around hydathodes. Overall, the data indicated that the PGI1-independent response to microbial VCs involves resetting of the photosynthesis-related proteome in leaves through long-distance GPT2 action.