iPlantMicro Lab
ITQB NOVA (Oeiras, PT)
Other members
André Sousa
PhD Student
Millia McQuade
PhD Student
Kusum Niraula
PhD Student
Daniel Silva
MSc Student
Luana Silva
MSc Student
Joana Gomes
MSc Student
Overview
At iPlantMicro Lab we work to understand communication systems in beneficial plant–microbe interactions, with the aim of using them to support more sustainable agricultural management.
Context and challenge
Agriculture feeds a continuously growing global population, but climate change, soil degradation (salinization, desertification), and the decline of soil health threaten agricultural productivity. The rhizosphere microbiota determines soil fertility and health and exerts a strong influence on plant growth and development. Among these microbes, many beneficial strains promote nutrient availability and plant tolerance to environmental stress.
Research lines
Identify the relationship between plant responses to environmental stresses and their associated microbiome.
Decode the signaling pathways required for beneficial plant–microbe relationships, as well as their regulatory mechanisms.
Apply signaling models to new formulations in biofertilizers and biocontrol agents to enhance crop development and productivity.
Study the transgenerational inheritance of microbiomes and the role of epigenetic regulation in this phenomenon.
Representative publications
Vílchez J.I., Yang Y., He D., et al. (2020). DNA demethylases are required for myo-inositol-mediated mutualism between plants and beneficial rhizobacteria. Nature Plants 6(8): 983-995.
Romão I.R., do Carmo Gomes J., Silva D., & Vílchez J.I. (2025) The seed microbiota from an application perspective: an underexplored frontier in plant–microbe interactions. Crop Health 3, 12.
Morcillo R.J.L., Singh S.K., He D., An G., Vílchez J.I. (2020). Rhizobacterium-derived diacetyl modulates plant immunity in a phosphate-dependent manner. The EMBO Journal 39:e102602.
Niza-Costa M., Rodríguez-dos Santos A.S., Rebelo-Romão I., Ferrer M.V., Sequero López C., Vílchez J.I. (2022). Geographically disperse, culturable seed-associated microbiota in forage plants of alfalfa (Medicago sativa L.) and pitch clover (Bituminaria bituminosa L.): characterization of beneficial inherited strains as plant stress-tolerance enhancers. Biology 11(12): 1838.
Vílchez J.I., Niehaus K., Dowling D.N., González-López J., Manzanera M. (2018). Protection of pepper plants from drought by Microbacterium sp. 3J1 by modulation of the plant’s glutamine and α-ketoglutarate content: a comparative metabolomics approach. Frontiers in Microbiology 9:284.
Gil T., Rebelo Romão I., do Carmo Gomes J., Vergara-Diaz O., Amoroso Lopes de Carvalho L., Sousa A., Kasa F., Teixeira R., Mateus S., Katamadze A., Pinheiro D.G., Vicente R., Vílchez J.I. (2024). Comparing native and non-native seed-isolated strains for drought resilience in maize (Zea mays L.). Plant Stress 12: 100462.
Vílchez J.I., Navas A., González-López J., Arcos S.C., Manzanera M. (2016). Biosafety test for plant growth-promoting bacteria: proposed Environmental and Human Safety Index (EHSI) protocol. Frontiers in Microbiology 6:1514.
Projects
SaltBiome: study of the microbiota of hyper–salt-tolerant and halophilic varieties to improve salt stress tolerance in sensitive rice.
Exudome: evaluation of stress-induced exudate changes as mechanisms for selective recruitment of beneficial microbiota.
InheritME: characterization of seed microbiota and mechanisms of directed microbial inheritance for biotechnological use.
MaizeSurvivor: analysis of maize seed microbiota for drought treatments, from laboratory to field scale.
FireBiome: search for microbial solutions to accelerate soil recovery after wildfires, using a case study in Los Guájares (Granada, Spain).
Key methods
The group has a broad range of modern and advanced methods. Below is a list you can incorporate:
Multi-omics approach: metagenomics, transcriptomics, metabolomics, epigenomics + plant phenotyping.
Studies under different conditions: laboratory, greenhouse, and field.
Rhizosphere and seed microbiota analysis: culturomics and high-throughput sequencing to characterize microbial communities.
Root exudate studies / plant-to-microbiome signaling: for example, exudate metabolomics to understand microbial recruitment.
Fluorescent labeling / tracking of microbial colonization “in planta”, molecular fingerprints to monitor vertical transmission / inheritance of beneficial microbiomes.
Stress tolerance assays (for example, drought, salinity) in plants with microbial inoculation and analysis of plant metabolic content (glutamine, α-keto acids, etc.).
Development of biofertilizer or biocontrol products based on signaling and microbiome knowledge.
Approach
To address these challenges, we employ a multi-omics approach (metagenomics, metabolomics, transcriptomics, epigenomics, phenotyping), combined with laboratory, greenhouse, and field studies. We also develop in vitro / in planta treatments that include tracking with fluorescent markers and molecular fingerprints to monitor the (vertical) transmission and inheritance of beneficial microbiota to future crop generations.
Models and study species
We use model plants from the Fabaceae and Solanaceae families (and other crops of interest such as maize or rice) to evaluate the effectiveness of the designed strategies.
Future vision
Our goal is to generate microbial tools and microbiome engineering strategies that reduce the use of chemical inputs, improve crop resilience to stress, and contribute to more sustainable, profitable, and environmentally friendly agriculture.
