Main research lines:

  1. Phytoremediation of persistent organic pollutants
  2. Improving tree biomass production, from management to molecular technology
  3. Defining novel mechanisms for heat- and water-stress tolerance in forest plantations
  4. Functional genomics (trees, including non-model species and hybrids)


We are interested in applied problems where trees play significant roles. One major goal is to exploit the natural ability of trees to clean up soil pollution (phytoremediation). We focus mainly on persistent organic pollutants, such as polychlorinated biphenyls, pentachlorophenol or hydrocarbons derived from fossil fuels. Molecular technologies are applied here to uncover novel metabolic pathways and define the roles of relevant components. We also apply these technologies to study natural responses in heavily polluted sites, under field conditions. Another major goal is improving yields in forest plantations, especially for bioenergy (biomass production). Our studies range from culture management to molecular analysis, both under controlled conditions and in commercial settings. As before, the goal is to identify key components and evaluate their applied interest using a biotechnological approach.

1) Tree biomass and stress tolerance

Environmental stress causes vast losses in the forest sector, with drought and heat episodes being the foremost drivers. We use different approaches to dissect natural tolerance mechanisms in species and hybrids of economic relevance, mostly poplar, walnut and chestnut. Over the last years we have identified some key genes and evaluated their applied potential through a biotechnological scheme. It covers from genetic studies in model species to research under field conditions. Our results bolster the feasibility of improving valuable genotypes for plantation forestry, an increasingly important field where in vitro recalcitrance, long breeding cycles and other practical factors constrain conventional breeding.

For example, we have obtained the first poplar lines with a substantial and durable increase in thermotolerance. Specifically, these lines accumulate a major cytosolic sHSP with convenient features. Experimental evidence was obtained linking the unique biochemical activity of such protein with protective effects under stressful conditions. Moreover, significant positive correlations were found between phenotype strength and protein accumulation. The remarkable sHSP baseline levels of our poplar lines have not been previously reported, even in model plants stressed under controlled conditions. They are not matched either in poplar populations growing under field conditions, as judged by quantitative real-time PCR and immunodetection analysis. It is noteworthy that no pleiotropic effects were found in our lines that might decrease yields in commercial plantations. Such lines also outperformed controls under other stressful conditions, including in vitro micropropagation, i.e., shoot production and ex vitro survival. The applied interest of these findings was highlighted in the On the inside section of the journal Plant Physiology.

Effects of acute heat stress on control and engineered Populus plants. Control and HSP-lines grown in soil were suddenly exposed to 45ºC for 2.5 h, transferred to 25ºC for recovery, and documented at the times indicated.

Drought tolerance provides another good example. By combining proteomics, genetic analysis and controlled stress treatments, we have identified major responsive components in poplar trees. Besides well-known protective proteins, such as dehydrins, molecular chaperones or enzymes that attenuate oxidative stress (SOD, APX, GR and others), novel components have been pinpointed (unpublished results). Detailed characterization of several enzymes is under way. Whereas their families are widely distributed in plants and other organisms, no previous connections have been reported with drought tolerance. Our efforts are now focused on their biochemical activity and regulation under different stresses and hormone treatments as well as under field conditions. The integration of functional and phylogenetic studies suggests that at least some of these enzymes have suffered a recent process of diversification and neo-functionalization.

Compared to control plants (ColO), engineered Arabidopsis lines expressing a drought-inducible poplar enzyme (L4, L6, L8, L10) show a significant increase in water-stress tolerance.


2) Phytoremediation and metabolic engineering

Environmental pollution is a first-rate problem and traditional cleanup methods are too expensive and inefficient. Phytoremediation, the use of plants and their associated microbiota, has recently emerged as an ecological and cost-effective alternative. Arguably, trees are ideal organisms for soil and water clean-up.

In situ phytoremediation performed by our research group as part of the LIFE11 ENV/ES/000505 project. Over two thousand trees were planted in a highly-polluted fuel plant near “Bahía de Cádiz” Natural Park.

We are currently interested in exploring the potential of commercial poplar varieties (Populus spp.) for in situ degradation of relevant pollutants, especially aromatic and aliphatic hydrocarbons derived from the fuel industry. We are also interested in halogenated compounds listed in the Stockholm's Convention on Persistent Organic Pollutants, such as polychlorinated biphehyls, pentachlorophenol and dioxins.

3D structure of a poplar enzyme identified by us which is involved in natural PCB degradation (biphenyl moieties). Its biochemical activity is complemented by additional poplar enzymes, leading to pollutant degradation under field conditions.

Our group has received several grants to conduct these studies, including recent European LIFE+ funding to evaluate different remediation technologies at field scale. Among other partners, this project involved Spain's Department of Defense, which provided a heavily-polluted petrol plant in the naval base of San Fernando, Cádiz. We have planted there over two thousand trees, from local species previously-selected by us, to analyze their influence on the evolution of the pollution plume. At the same time, we have used molecular technology to analyze their natural response to various treatments and levels of petrol-derived hydrocarbons under field conditions. Besides qRT-PCR and biochemical studies, different omics approaches are under way in collaboration with the University of Malaga and its Supercomputing and Bioinformatics Center. These include (1) transcriptomic analyses of relevant genes involved in the uptake, accumulation and/or degradation of hydrocarbons and (2) metagenomic analysis of the root-associated microbiota during the remediation process.


  1. LIFE11 ENV/ES/000505. New approach to soil remediation by combining biological and chemical oxidation processes. EU LIFE+ Programme
  2. BIO2013-46076-R. Studying gibberellin signaling to improve seed germination and resistance to stress. MINECO-RETOS
  3. BIO2016-77840-R. Genes que regulan la germinacion de las semillas y el crecimiento de Arabidopsis como herramientas para mejorar la produccion de biomasa y el rendimiento de las cosechas. MINECO-Ret


Representative Publications

Contreras, Á., Merino, I., Álvarez, E., Bolonio, D., Ortiz, J.-E., Oñate-Sánchez, L., Gómez, L. 2021. A poplar short-chain dehydrogenase reductase plays a potential key role in biphenyl detoxification. Proceedings of the National Academy of Sciences USA 118, e2103378118. DOI: 10.1073/pnas.2103378118

Llebrés, M.T., Pascual, M.B., Valle, C., de la Torre, F.N., Valderrama-Martin, J.M., Gómez, L., Avila, C., Cánovas, F.M. 2020. Structural and Functional Characteristics of Two Molecular Variants of the Nitrogen Sensor PII in Maritime Pine. Frontiers in Plant Science 11, 823. DOI: 10.3389/fpls.2020.00823

Carrera-Castaño, G., Calleja-Cabrera, J., Pernas, M., Gómez, L., Oñate-Sánchez, L. 2020. An Updated Overview on the Regulation of Seed Germination. Plants 9, 703. DOI: 10.3390/plants9060703

Sánchez-Montesino, R.; Bouza-Morcillo, L.; Marquez, J.; Ghita, M.; Duran-Nebreda, S.; Gómez, L.; Holdsworth, M.J.; Bassel, G.; Oñate-Sánchez, L. 2019. "A regulatory module controlling GA-mediated endosperm cell expansion is critical for seed germination in Arabidopsis". Molecular Plant. DOI: 10.1016/j.molp.2018.10.009.

Gomez, L., Contreras, A., Bolonio, D., Quintana, J., Oñate-Sanchez, L., Merino, I. 2019. Phytoremediation with trees, in: Advances in Botanical Research. Academic Press. DOI: 10.1016/bs.abr.2018.11.010

Seoane, P.; Espigares, M.; Carmona, R.; Polonio, Á.; Quintana, J.; Cretazzo, E.; Bota, J.; Pérez-García, A.; Dios Alché, J. de; Gómez, L.; Claros, M.G. 2018. "TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms". BMC Bioinformatics 19, 416. DOI: 10.1186/s12859-018-2384-y

Espigares, M. Seoane, P. Bautista, R. Quintana, J. Gómez, L. Claros, M.G. 2017. "Obtaining the most accurate de novo transcriptomes for non-model organisms: the case of Castanea sativa. In: Rojas I., Ortuño F. (eds) Bioinformatics and Biomedical Engineering". pp. 489-499. Springer International Publishing, ISBN: 978-3-319-56153-0. DOI: 10.1007/978-3-319-56154-7_44

Bolonio, D. Llamas, A. Rodríguez-Fernández, J. Al-Lal, AM. Canoira, L. Lapuerta, M. Gómez, L. 2015. "Estimation of cold flow performance and oxidation stability of bacterial fatty acid ethyl esters". Mendez-Vilas, A (ed.), Materials and Technologies for Energy Efficiency, pp. 12–16. Brown Walker Press, Boca Raton, Florida, USA, ISBN-10: 1-62734-559-0.

Quintana, J. Contreras, A. Merino, I. Vinuesa, A. Orozco, G. Ovalle, F. Gomez, L. 2015. "Genetic characterization of chestnut (Castanea sativa Mill.) orchards and traditional nut varieties in El Bierzo, a glacial refuge and major cultivation site in northwestern Spain". Tree Genetics and Genomes. DOI: 10.1007/s11295-014-0826-x

Licea-Moreno, RJ; Contreras, A; Morales, AV; Urban, I; Daquinta, M; Gomez, L. 2015. "Improved walnut mass micropropagation through the combined use of phloroglucinol and FeEDDHA". Plant Cell, Tissue and Organ Culture. DOI: 10.1007/s11240-015-0822-3".

Bolonio, D; Llamas, A; Rodríguez-Fernández, J; Al-Lal, AM; Canoira, L; Lapuerta, M; Gómez, L. 2015. "Estimation of cold flow performance and oxidation stability of fatty acid ethyl esters from lipids obtained from Escherichia coli". Energy & Fuels. DOI: 10.1021/acs.energyfuels.5b00141".

Merino, I; Contreras, A; Jing, Z-P; Gallardo, F; Cánovas, FM; Gómez, L. 2014. "Plantation forestry under global warming: hybrid poplars with improved thermotolerance provide new insights on the in vivo function of small heat shock protein chaperones". Plant Physiology. DOI: 10.1104/pp.113.225730".