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Plant-Microbiome Interactions



J. Ignacio Vílchez
PhD in Fundamental and Systems Biology 2016
University of Granada

Phone (+351) 214469647
Extension 1647


Research Interests

Considering a continuously growing population, necessity to ensure food requirements may be jeopardized due to the difficulty to increase the productivity of farmlands. Moreover, future productivity range is threatened by progressive soil degradation or desertification, the spread of increasingly resistant pathogens or the effects of climate change. In this context, the use of biotechnological tools linked to the management of beneficial microorganisms supposes a reliable alternative. However, application of this technology still requires a deeper knowledge of the plant-microorganism interactions, the associated microbiomes and their management under different conditions. 

Under this view, our group seek to address these challenges in a comprehensive manner. In this way, the main objectives of the group are: (i) identifying the relationship between plant responses to environmental stresses and their associated microbiomes, (ii) identifying the signaling pathways necessary for beneficial relationships and their regulatory mechanisms, and (iii) applying the signaling models to new formula in biofertilizer and biocontroller products in order to enhance crops development and production. Additionally, we want to study transgenerational inheritance of microbiomes and the epigenetic regulation role behind this phenomenon.

Throughout application of multiomics analyses (metagenomics, metabolomics, transcriptomics, epigenomics and phenotyping) and applying lab, greenhouse and field-based studies, will aim to provide new bioengineering tools in sustainable agriculture. With this, we aim to enhance agricultural management by reducing water costs, soil degradation and boosting local beneficial interactions.


Group Members

  • Inês Rebelo Romão, MSc Student
  • Ana Sofia Rodrigues dos Santos, MSc Student
  • Eva María Lopes Dias, Bsc Student
  • Marla Niza Costa, BSc Student
  • João Pedro Nunes Carrilho, BSc Student
  • Horácio Manuel Mixão de Jesus, BSc Student


Selected Publications

  1. Kaushal, R., Peng, L., Singh, S.K., Zhang, M., Zhang, X., Vílchez, J.I., et al. Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation. 2021. Microbiome 9, 57.

  2. Vílchez, J.I., Yang, Y., He, D., et al. DNA demethylases are required for myo-inositol-mediated mutualism between plants and beneficial rhizobacteria. 2020. Nature Plants 6(8): 983-995.

  3. Morcillo, R.J.L., Singh, S.K., He, D., An, G., Vílchez, J.I., * Rhizobacterium‐derived diacetyl modulates plant immunity in a phosphate‐dependent manner. 2020. The EMBO Journal. 39: e102602.

  4. Vílchez, J.I., Niehaus, K., Dowling, D.N., González-López, J., Manzanera, M. 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. 2018. Frontiers in Microbiology. 9, 284. doi: 10.3389/fmicb.2018.00284

  5. Vílchez, J.I., Navas, A., González-López, J., Arcos, S.C., Manzanera, M. Biosafety test for plant growth-promoting bacteria: proposed Environmental and Human Safety Index (EHSI) protocol. 2016. Frontiers in Microbiology. 6, 1514.

  6. Vílchez, J.I., García-Fontana, C., Román-Naranjo, D., González-López, J., Manzanera, M. Plant drought tolerance enhancement by trehalose production of desiccation tolerant microorganisms. 2016. Frontiers in Microbiology. 7,1577. doi: 10.3389/fmicb.2016.01577

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