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Plants interact with diverse microorganisms, particularly around their roots, in a zone called the rhizosphere. These microbial communities, i.e. microbiomes, play an important role in plant health and growth, and therefore in the overal yield of the crop. Understanding how these microbiomes form and function, and developing strategies to manipulate them—for example, by introducing a desired function beneficial to the plant—could help increase crop productivity while reducing reliance on harmful chemical pesticides and herbicides.
In the Garrido-Sanz group, our research focuses on three main areas: (1) Rhizosphere microbiome assembly, (2) Plant microbiome manipulation, and (3) Rhizosphere bacterial interactions.
Root of wheat (Triticum aestivum) being colonized by Pseudomonas protegens CHA0 constitutively tagged with gfp2 (green spots)
Rhizosphere microbiome assembly
We study how plants support the assembly of their microbiome through selection of soil bacteria and bacteria vertically inherited from seeds. Our work focuses on ecological processes such as priority effects [1], where early colonizers influence microbiome assembly; niche preemption and facilitation; and competition among microbes for the abundant resources found in the rhizosphere. These processes are key to understanding how plant microbiomes are assemble and function.
Plant microbiome manipulation
Our research explores targeted strategies to manipulate the rhizosphere microbiome of crop plants. In particular, we study how plant-beneficial bacterial inoculants interact with native microbiomes [2, 3], aiming to promote plant health. Additionally, we investigate the targeted removal of unwanted microbial members using specific bacteriophages, providing a precise and environmentally friendly approach to microbiome engineering.
Rhizosphere bacterial interactions
We examine the interaction mechanisms used by bacteria to competitively colonize the rhizosphere. By isolating and characterizing bacteria from crop plants, we aim to uncover novel microbial diversity [4]. Our research explores bacterial weapon systems, such as antimicrobial production, and resource sharing mechanisms that facilitate coexistence, providing insights into the ecological principles governing rhizosphere dynamics.
[1] Garrido-Sanz D, Keel C. 2025. Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation. Nature Microbiology. DOI: 10.1038/s41564-025-01973-1
[2] Garrido-Sanz D, Čaušević S, Vacheron J, Heiman CM, Sentchilo V, van der Meer JR, Keel C. 2023. Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere. Microbiome, 11(1):214. DOI: 10.1186/s40168-023-01660-5
[3] Harmsen N, Vesga P, Glauser G, Klötzli F, Heiman CM, Altenried A, Vacheron J, Muller D, Moënne-Loccoz Y, Steinger R, Keel C, Garrido-Sanz D. 2024. Natural plant disease suppressiveness in soils extends to insect pest control. Microbiome, 12(1):127. DOI: 10.1186/s40168-024-01841-w
[4] Poli N, Keel CJ, Garrido-Sanz D. 2024. Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties. Frontiers in Microbiology, 15: 1440341. DOI: 10.3389/fmicb.2024.1440341
Our approach
Our lab combines cutting-edge experimental and computational techniques to unravel the ecology of plant-associated microbiomes.
On the experimental side, we use a variety of classical microbiology methods, from isolating and culturing bacteria to studying their growth and interaction dynamics. We delve into molecular microbiology by engineering bacterial mutants to disrupt or enhance gene function and tagging strains with fluorescent markers such as GFP to visualize and track their behavior. These tools are complemented by plant growth experiments that allow us to study microbe-plant interactions in controlled microcosms.
On the computational side, we explore microbiomes using amplicon sequencing, metagenomics, and other high-throughput -omic approaches to uncover microbial diversity, functions and interactions. These techniques allow us to explore microbial communities and their roles in the rhizosphere with a comprehensive and integrative perspective.
Our lab is a space for innovation and discovery, offering opportunities to address emerging questions in microbiome ecology using flexible, multidisciplinary approaches. Whether you're a postdoc, PhD student, master's student, or technical specialist, joining us means contributing to an open-ended research journey characterized by curiosity, collaboration, and scientific exploration.
Our funders
Our research is financed by
César Nombela Program for Talent Attraction of the Community of Madrid (2024-T1/BIO-31220).
Financed by the European Union
NextGenerationEU
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