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Dr. Jonathan Maldonado

Charge: 
Department of Biology
E-mail: 
jonathan.maldonado@usach.cl
Biography: 

Dr. Maldonado holds a degree in Molecular Biotechnology from the University of Chile (2009) after defending his thesis entitled "Identification of metabolic pathways involved in the synthesis of compounds with aromatic properties in Fragaria chiloensis (white strawberry)". In 2012, he obtained a CONICYT National Doctoral Scholarship and completed his doctoral thesis at the Institute of Nutrition and Food Technology of the University of Chile (INTA) within the Doctorate program in sciences, majoring in Molecular, Cellular Biology and Neurosciences of the Faculty of Sciences, University of Chile (BMCN). In 2017, he obtained his Doctorate defending his thesis "Reconstruction of soil bacterial genomes by analyzing abundance changes between two pH conditions to demonstrate taxa-specific pH adaptation mechanisms." He completed a postdoctoral fellowship at the FONDAP Center of Excellence "Center for Genome Regulation (CRG)" with Dr. Mauricio González Canales of INTA-UChile (2018-2019).
He subsequently completed an ANID-FONDECYT postdoctoral fellowship in the laboratory of Dr. Rodrigo Gutiérrez at the Pontifical Catholic University of Chile entitled “Contribution of the rhizospheric microbiome to the tolerance of Hoffmannseggia doellii to changes in nitrogen availability” (2019-2021).
Dr. Maldonado was hired in 2022 through an ANID-SIA competition by the University of Santiago de Chile as a Researcher and Assistant Professor in the Department of Biology, Faculty of Chemistry and Biology, where he currently directs the Plant Multiomics and Bioinformatics Laboratory and is a member of the faculty of the Doctorate program in Biotechnology. He is also a Young Researcher at the Millennium Institute of Integrative Biology (iBio).
With over 10 years of experience in biotechnology and bioinformatics, he has planned and executed national and international collaborative projects with FONDECYT, CORFO, FONDAP, FIA, and Núcleos Milenio.

Research Area: 

During his scientific career, he has mainly discussed two lines of research: On the one hand, together with Dr. Herman Silva (University of Chile), Dr. Lee Meisel (University of Chile), Dr. Karina Ruiz (UAP), Dr. Nathalie Kuhn (Catholic University of Valparaíso), Dr. Talía del Pozo (University Mayor), Dr. Giovanna Sotil (UNMSM, Peru), among others, he has explored different biological phenomena that are associated with production and post-harvest problems in fruit trees, other plants of economic interest and fish. These works have included the study of the transcriptomic response of different species to water and/or saline stress, application of hormones, nutrient deficiencies, among others, and post-harvest problems such as cherry splitting and peach softening. On the other hand, together with Dr. Mauricio González (University of Chile), Dr. Dinka Mandakovic (University Mayor), Dr. Francisco Cubillos (USACH), Dr. Gil Eshel (NYU, USA), Dr. Giovanna Sotil (UNMSM, Peru), and Dr. Patricia Águila (University Austral), among others, he has explored the taxonomic and functional properties of microbial communities (bacteria and fungi) that grow in extreme areas of Chile and Peru, their ecology at different scales and the possible interactions with the flora of these areas. He is currently investigating in the laboratory whether native plants of the Atacama Desert can modulate the soil microbiome under favorable conditions under the hypothesis that this microbiome contains favorable or enhanced functional elements for plant development under nutrient deficit conditions and adverse environmental conditions.

Projects: 
  • Principal researcher of the ANID project, Grant for Installation at the Academy SIA-2022/SA77210103, entitled: “Strengthening research and teaching of the Doctorate in Biotechnology at the Faculty of Chemistry and Biology of the University of Santiago deChile, with an emphasis on the Plant area and on scientific-academic collaboration through omics”. (2022-2024)
  • Co-Researcher in ANID-FONDECYT project N° 1231491 titled: “Temporal Network Analysis of Sweet Cherry Fruit Ripening: using plant growth regulators to unravel the cross-talk between developmental and environmental cues”. Principal Researcher Dr. Lee Meisel. (2023-2026)
  • Collaborator on the FIA PYT-2023-0671 project entitled: "Development, validation, and implementation of an efficient identification technique for Cytospora and Pseudomona in cherry trees." Principal Researcher: Dr. Talía del Pozo. (2023-2026)
  • Collaborator in ANID-FONDECYT Initiation project N°11221186 entitled: “Participation of the auxin-gibberellin negative regulatory module during the fruit ripening initiation in the non-climacteric sweet cherry: Towards a seed-fruit interaction multiscale model”. Principal researcher: Dr. Nathalie Kuhn. (2022-2024)
  • Principal Researcher of ANID-FONDECYT Postdoctoral Project No. 3190194 entitled: "Contribution of the rhizospheric microbiome to the tolerance of Hoffmannseggia doellii to changes in nitrogen availability." Sponsoring Institution: Pontifical Catholic University of Chile. Sponsoring Researcher: Dr. Rodrigo Gutiérrez. (2019-2021)
Latest Publications: 
1. Núñez, D., Jiménez, P., Cortez-San Martin, M., Cortes, C., Cárdenas, M., Michelson, S., Garay, T., Vecchiola, M., Céspedes, A., Maldonado, J. E., & Vásquez-Martínez, Y. (2024). Molecular and Phylogenomic Analysis of a Vancomycin Intermediate Resistance USA300LV Strain in Chile. Microorganisms, 12(7).
 
2. Copier, C., Osorio-Navarro, C., Maldonado, J. E., Auger, J., Silva, H., & Esterio, M. (2024). A Conservative Mutant Version of the Mrr1 Transcription Factor Correlates with Reduced Sensitivity to Fludioxonil in Botrytis cinerea. Pathogens, 13(5). 
https://doi.org/10.3390/10.3390/pathogens13050374
 
3. Kobayashi, S., Maldonado, J. E., Gaete, A., Araya, I., Aguado-Norese, C., Cumplido, N., Díaz, S., Espinoza, A., Fernández, E., Gajardo, F., González-Ordenes, F., Hauyon, K., Maldonado, P., Maldonado, R., Pochet, I., . . . School Earwig Genome, Consortium. (2023). DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species. Biological Research, 56(1), 6.
 
4. Mandakovic, D., Aguado-Norese, C., García-Jiménez, B., Hodar, C., Maldonado, J. E., Gaete, A., Latorre, M., Wilkinson, M. D., Gutiérrez, R. A., Cavieres, L. A., Medina, J., Cambiazo, V., & Gonzalez, M. (2023). Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert. Environmental Microbiome, 18(1), 24.
 
5. Ormeño, M. A., Maldonado, J. E., González, M., Silva, H., & Covarrubias, J. I. (2023). Evaluation of a Red Grape Marc Extract as a Natural Nitrification Inhibitor and its Effect on Soil Bacterial Community. Journal of Soil Science and Plant Nutrition, 23(2), 2708-2722.
 
6. Aguila-Torres, P., Gonzalez, M., Maldonado, J. E., Miranda, R., Zhang, L., Gonzalez-Stegmaier, R., Rojas, L. A., & Gaete, A. (2022). Associations between bacterial communities and microplastics from surface seawater of the Northern Patagonian area of Chile. Environmental Pollution, 306, 119313.
 
7. Battistoni, B., Salazar, J., Vega, W., Valderrama-Soto, D., Jiménez-Muñoz, P., Sepúlveda-González, A., Ahumada, S., Cho, I., Gardana, C. S., Morales, H., Peña-Neira, Á., Silva, H., Maldonado, J., González, M., Infante, R., . . . Pacheco, I. (2022). An Upgraded, Highly Saturated Linkage Map of Japanese Plum (Prunus salicina
Lindl.), and Identification of a New Major Locus Controlling the Flavan-3-ol Composition in Fruits. Frontiers in Plant Science, 13.
 
8. Carrasco, B., Arévalo, B., Perez-Diaz, R., Rodríguez-Alvarez, Y., Gebauer, M., Maldonado, J. E., García-Gonzáles, R., Chong-Pérez, B., Pico-Mendoza, J., Meisel, L. A., Ming, R., & Silva, H. (2022). Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea
chilensis) Using GBS Tools. Plants, 11(16), 2151.
 
9. Díaz-Silva, M., Maldonado, J., Veloso, P., Delgado, N., Silva, H., & Gallardo, J. A. (2022). RNA-seq analysis and transcriptome assembly of Salicornia neei reveals a powerful system for ammonium detoxification. Electronic Journal of Biotechnology, 58, 70-81.
 
10. Gaete, A., Andreani-Gerard, C., Maldonado, J. E., Munoz-Torres, P. A., Sepulveda- Chavera, G. F., & Gonzalez, M. (2022). Bioprospecting of Plant Growth-Promoting Traits of Pseudomonas sp. Strain C3 Isolated from the Atacama Desert: Molecular and Culture-Based Analysis. Diversity, 14(5).
 
11. Maldonado, J. E., Gaete, A., Mandakovic, D., Aguado-Norese, C., Aguilar, M., Gutiérrez, R. A., & González, M. (2022). Partners to survive: Hoffmannseggia doellii root-associated microbiome at the Atacama Desert. New Phytologist, 234(6), 2126-2139.
 
12. Santibáñez, P., Romalde, J., Maldonado, J., Fuentes, D., & Figueroa, J. (2022). First characterization of the gut microbiome associated with Mytilus chilensis collected at a mussel farm and from a natural environment in Chile. Aquaculture, 548, 737644.
https://doi.org/10.1016/j.aquaculture.2021.737644
 
13. Eshel, G., Araus, V., Undurraga, S., Soto, D. C., Moraga, C., Montecinos, A., Moyano, T., Maldonado, J., Díaz, F. P., Varala, K., Nelson, C. W., Contreras-López, O., Pal-Gabor, H., Kraiser, T., Carrasco-Puga, G., . . . Gutiérrez, R. A. (2021). Plant ecological genomics at the limits of life in the Atacama Desert. Proceedings of the National
Academy of Sciences, 118(46), e2101177118.
 
14. Gaete, A., Pulgar, R., Maldonado, J. E., Hodar Quiroga, C., Zamorano, D., Pavez, L., Pastenes, C., González, M., & Mandakovic, D. (2021). Tomato cultivars with variable tolerances to water deficit differentially modulate the composition and interaction patterns of their rhizosphere microbial communities. Frontiers in Plant Science,12(1361).
 
15. Kuhn, N., Maldonado, J., Ponce, C., Arellano, M., Time, A., Multari, S., Martens, S., Carrera, E., Donoso, J. M., Sagredo, B., & Meisel, L. A. (2021). RNAseq reveals different transcriptomic responses to GA3 in early and midseason varieties before ripening initiation in sweet cherry fruits. Scientific Reports, 11(1), 13075.
 
16. Ortiz-Severín, J., Stuardo, C. J., Jiménez, N. E., Palma, R., Cortés, M. P., Maldonado, J., Maass, A., & Cambiazo, V. (2021). Nutrient Scarcity in a New Defined Medium Reveals Metabolic Resistance to Antibiotics in the Fish Pathogen Piscirickettsia salmonis. Frontiers in Microbiology, 12(2973).
 
17. Aguila-Torres, P., Maldonado, J., Gaete, A., Figueroa, J., Gonzalez, A., Miranda, R., Gonzalez-Stegmaier, R., Martin, C., & Gonzalez, M. (2020). Biochemical and Genomic Characterization of the Cypermethrin-Degrading and Biosurfactant-Producing Bacterial Strains Isolated from Marine Sediments of the Chilean Northern Patagonia. Marine Drugs, 18(5).
 
18. Arias, D., Maldonado, J., Silva, H., & Stange, C. (2020). A de novo transcriptome analysis revealed that photomorphogenic genes are required for carotenoid synthesis in the dark-grown carrot taproot. Molecular Genetics Genomics, 295(6), 1379-1392.
https://doi.org/10.1007/s00438-020-01707-4
 
19. Mandakovic, D., Pulgar, R., Maldonado, J., Mardones, W., González, M., Cubillos, F. A., & Cambiazo, V. (2020). Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures. Microorganisms, 8(6).
 
20. Mandakovic, D., Cintolesi, A., Maldonado, J., Mendoza, S. N., Aite, M., Gaete, A., Saitua, F., Allende, M., Cambiazo, V., Siegel, A., Maass, A., Gonzalez, M., & Latorre, M. (2020). Genome-scale metabolic models of Microbacterium species isolated from a high-altitude desert environment. Scientific Reports, 10(1), 5560.
 
21. Miranda, R. M., Águila‐Torres, P., Aranda, C. P., Maldonado, J., & Casado, A. (2020). Taxonomy and diversity of bacterial communities associated with marine sediments from Chilean salmonid farms. Aquaculture Research, 52(4), 1605-1620.
https://doi.org/10.1111/are.15014