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Fernando Puente Sánchez

Fernando Puente Sanchez
Marie Curie fellow at the Department of Aquatic Sciences and Assessment


My area of expertise is the study of microbial ecosystems using metagenomics, metatranscriptomics and 16S rRNA gene profiling. I have worked in several settings (deep-subsurface, acidic rivers, ocean, lakes...), and I strive to find common patterns in the way that microorganisms interact between themselves and with the environment.

To achieve this, I apply (and if necessary, develop) bioinformatics methods in order to integrate the vast amount of information generated by modern approaches (large-scale spatial and temporal series comprised of functional, taxonomic and physicochemical profiles) and form a coherent picture of what drives the behaviour of the community. Ultimately, I want to find interesting and hopefully useful stories about how microbes and ecosystems work.


At SLU, I study the diversification trajectories of freshwater microorganisms, their relationship with environmental constraints, and the internal structure of the resulting microbial species.

Are freshwater microbial species delimited by well-defined boundaries, or is there a fuzzy continuum of genotypes capable of exchanging genetic information? Do phylogenetically unrelated microorganisms follow parallel diversification trajectories when subjected  to similar pressures? Does this diversification lead to an increase in community stability? I aim to answer these questions by combining metagenomics, metatranscriptomics and enrichment cultures over a set of more than 200 lake samples, and studying the dynamics of individual genomes in space, time, and over the niche landscape.


Marie Curie fellow    Spring 2021 - Ongoing

Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden

Causes and consequences of diversification in freshwater microorganisms

Juan de la Cierva fellow   2020-2021

Systems Biology Department, Spanish National Centre for Biotechnology (CSIC), Madrid, Spain

Abundance and expression dynamics of iron acquisition genes in marine microbial communities during the Arctic spring

Post-doc positions    2016-2019

Systems Biology Department, Spanish National Centre for Biotechnology (CSIC), Madrid, Spain

Study of cross-biome microbial community structure at different taxonomic resolutions

Ph. D in Microbiology    2010-2016

Molecular Ecology Department, Spanish Astrobiology Center (INTA-CSIC), Torrejón de Ardoz, Spain

Thesis Title: Microbial Ecology of the Iberian Pyrite Belt Deep Subsurface

M. Sc in Microbiology    2009-2010

Autonomous University of Madrid, Madrid, Spain

Thesis Title: Optimization of protocols for the extraction of RNA in iron/sulfur-rich environments

B. Sc in Biotechnology    2004-2009

University of Salamanca, Salamanca, Spain


- Natalia García García (M. Sc, 2018): Network Analysis of Microbial Ecosystems at Multiple Taxonomic Resolutions

- Luis Alberto Macías Pérez (M. Sc, 2018): Identification of clusters co-varying microbial functions across a time-series of Arctic Ocean samples

- Natalia García-García (Ph. D, Ongoing, Co-Supervised): Study of microdiversity and its influence in microbial community structure and functioning in marine ecosystems

Selected publications

- Puente-Sánchez, F., García-García, N., & Tamames, J. (2020). SQMtools: automated processing and visual analysis of’omics data with R and anvi’o. BMC bioinformatics, 21(1), 1-11.

- García-García, N., Tamames, J., Linz, A. M., Pedrós-Alió, C., & Puente-Sánchez, F. (2019). Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions. The ISME journal, 13(12), 2969-2983.

- Blanco, Y., Rivas, L. A., González-Toril, E., Ruiz-Bermejo, M., Moreno-Paz, M., Parro, V., ... & Puente-Sánchez, F. (2019). Environmental parameters, and not phylogeny, determine the composition of extracellular polymeric substances in microbial mats from extreme environments. Science of the Total Environment, 650, 384-393.

- Tamames, J., & Puente-Sánchez, F. (2019). SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline. Frontiers in microbiology, 9, 3349.

- Puente-Sánchez, F., Arce-Rodríguez, A., Oggerin, M., García-Villadangos, M., Moreno-Paz, M., Blanco, Y., ... & Parro, V. (2018). Viable cyanobacteria in the deep continental subsurface. Proceedings of the National Academy of Sciences, 115(42), 10702-10707.

- Puente-Sánchez, F., Díaz, S., Penacho, V., Aguilera, A., & Olsson, S. (2018). Basis of genetic adaptation to heavy metal stress in the acidophilic green alga Chlamydomonas acidophila. Aquatic Toxicology, 200, 62-72.

- Puente-Sánchez, F., Aguirre, J., & Parro, V. (2016). A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies. Nucleic acids research, 44(4), e40-e40.

- Puente-Sánchez, F., Sanchez-Roman, M., Amils, R., & Parro, V. (2014). Tessaracoccus lapidicaptus sp. nov., an actinobacterium isolated from the deep subsurface of the Iberian pyrite belt. International journal of systematic and evolutionary microbiology, 64(10), 3546-3552.

- Puente‐Sánchez, F., Moreno‐Paz, M., Rivas, L. A., Cruz‐Gil, P., García‐Villadangos, M., Gómez, M. J., ... & Parro, V. (2014). Deep subsurface sulfate reduction and methanogenesis in the Iberian Pyrite Belt revealed through geochemistry and molecular biomarkers. Geobiology, 12(1), 34-47.