Our main research interest is to understand the underlying mechanisms of plant protection against (a)biotic stresses mediated by microorganisms. Our group is specialized in the development of new multidisciplinary approaches to systematically correlate microbial genes and biosynthetic gene clusters (BGCs) to their functions in plants under stress. In addition, in our research programs also focus on the diversity, dynamics and beneficial functions of microorganisms associated with plants. In our team we study the functions and mechanisms of these microbes for plant protection to (a)biotic stresses, such as fungal pathogens or drought.

Our Projects:

bacLIFE: Prediction of bacterial lifestyle and lifestyle-associated genes

Utilizing next-generation sequencing (NGS) technologies, I employ advanced bioinformatic tools to delve into the genomic features of previously unidentified microorganisms. NGS has transformed data generation, providing profound insights, yet the current challenge is deciphering meaningful information from extensive datasets. Microorganisms, crucial to all ecosystems, exhibit niche versatility and diverse phylogenetic profiles. Within the same genus, bacteria can adopt pathogenic or commensal lifestyles, complicating environmental role assignments. Microbes play integral roles in biochemical cycles, impacting animal and plant development, growth, and diversification. Despite their positive contributions, they can also be pathogenic, influencing plant development and crop production. Mutually beneficial plant-microbe interactions enhance stress tolerance and dispersion. Understanding bacterial lifestyles is pivotal for discerning potential applications or threats in fields such as plant engineering and managing abiotic stresses. Leveraging bioinformatics, I navigate the complexities of NGS data to address these critical questions.

Contact: Guillermo Guerrero Egido

Bacterial functions enriched in plants under pathogen attack

Endophytic bacteria colonize and thrive within plant tissues and can act as a second layer of defense against pathogen infection. Here we aim to identify functional traits in the endophytic microbiome and decipher how specific bacterial genes involved in plant defense are activated by metabolites released from plant roots upon fungal infection. In previous studies (Carrion et al., 2019; Science), we established a large collection of endophytic bacterial strains that harbor various biosynthetic gene clusters (BGCs) with unknown functions. More specifically, we focus on endophytic Flavobacterium and Chitinophaga that act synergistically in protection against the fungal root pathogen Rhizoctonia solani via the expression of BGC298 and chitinase genes, respectively. By integrating molecular and multi-omics techniques, we study and highlight the potential of endophytic bacteria in plant protection against biotic stresses.

Contact: Xinya Pan

Halophytes as a source of microorganisms for salt stress alleviation

Salinity is one of most threatening stress that plants face nowadays. Climate change together with the salinization of agricultural soils due to the abuse of chemical fertilizers are risking the food supply worldwide in the coming decades. Most plants are sensitive to salt stress and their yield is comprised under these harsh conditions. Nevertheless, halophytes are salt-tolerant plants which can complete their life cycles in soil containing more than 3 g Na+/Kg through several known mechanisms. By its side, little is known about the role of the microorganisms living in tight relation with these plants either in the rhizosphere or the endosphere. This project aims to analyze the halophytes microbiomes and study the potential of these communities for salt stress alleviation in crop plants.

Contact: Miguel Rodríguez González

MicroRes: Microbial Resilience to Drought Stress

In the past decade, yields of major food crops worldwide have decreased due to drought. Over the past years, it has become evident that microorganisms associated with plants can enhance drought tolerance, allowing sustainable crop growth under abiotic stress conditions. However, the mechanisms by which plant-associated bacteria enhance drought tolerance are largely unknown. To successfully implement beneficial bacteria, agriculture requires a fundamental understanding of the complex molecular and chemical interplay between bacteria and plants. The prime aim of the MicroRes project is to identify bacterial and plant genes as well as signaling molecules governing drought tolerance of plants by root-associated bacteria.

Contact: Pascal Nuijten

Avocado microbiome as a source of biocontrol agents

Diseases affecting the avocado crop in Spain, such as white root rot and dieback of avocado branches caused by the fungal pathogens Rosellinia necatrix and Botryosphaeriaceae group, respectively, are the focus of this project. Due to limited knowledge in combating these diseases, the project focuses on mechanistic studies for biological solutions. It explores the microbial biodiversity in both healthy and diseased avocado plants, utilizing advanced sequencing techniques like metagenomics, metatranscriptomics, and metaproteomics to analyze microbial communities under diverse phytopathological conditions. Following data analysis, the identification of microorganisms with relevant activities will be assessed through the screening of culturable samples. Selected microorganisms will then be evaluated as potential biological control agents in agriculture. Additionally, the project aims to develop a platform for efficiently identifying bacteria producing novel NRPS and PKS with antifungal properties and isolating potential antifungal compounds with additional activities.

Contact: Marcos Pedraza


The MicroGRICE project’s primary goal is to reduce methane emissions from rice paddies through bacteria. Within this project I work on the development of a synthetic bacterial community that can improve rice growth and yield. In addition, I study the role of microbiomes and bacteria in alleviating salt stress on rice plants. My overarching research goal is the development of microbe-centered strategies that will improve the sustainability of rice cultivation.

Contact: Kevin Bretscher

microTRIAS: Microbiome training towards improving agricultural sustainability

Microbes are essential for plants to grow in good health, and we already know it. What we also know is how some of the microbes help plants and how others don’t (diseases). In our project we want to get what’s the best for crops from the hidden pool of soil microbes. In principle, we will shape the complex communities of microbes on demand to magnify the beneficial potential of any soil. The soil beneath our feet is not just a medium for growing plants; it’s a thriving ecosystem of microorganisms that play a crucial role in nutrient cycling, plant health, and overall ecosystem stability. We believe that the key to a more sustainable and resilient agricultural future lies beneath our feet: in the rich and complex world of soil microbiomes.

Contact: Adam Ossowicki