1. Team

    – Principal Investigator:

    Bernardo González Ojeda

    – Associate researchers:

    María Josefina Poupin Swinburn

    Thomas Ledger Hermosilla

    Gonzalo Ruz Heredia

    Cedric Little Orellana

    Juan Rivadeneira Hurtado

    – Postdoctoral associates:



– International collaborators:

– Dietmar H. Pieper. Helmholtz-Zentrum für Infektionsforschung, HZI, Braunschweig, Alemania

– Ramon Rosselló-Móra. Instituto Mediterráneo de Estudios Avanzados, IMEDEA, CSIC. Mallorca, España

– José Eduardo González-Pastor. Centro de Astrobiología. INTA. Madrid, España


Microorganisms are an essential biological component in the functioning of our planet. Although there is still a great deal of ignorance about types, characteristics and microbial processes, which if known today is that there is tremendous potential in microorganisms conducive to improving productivity, innovation and protect the environment. It is in the effective implementation of this potential, among other initiatives, where the “Center of Applied Ecology and Sustainability” (CAPES) focuses on both the generation and transfer of original knowledge, the formation of advanced human capital in order to allow development sustainable in Chile. Examples of this are the research and develop technology transfer in areas such as design of agrochemicals or biocides based on beneficial microorganisms; the application of bio strategies and phytoremediation to clean petroleum-contaminated environments, mining waste or other pollutants; or monitoring and control of the activity of microorganisms that produce undesirable effects such as acid mine drainage, biocorrosion or biofouling; in addition to studying the microbial production of materials such as cellulose and calcite. For this traditional and modern approaches such as synthetic biology, the (meta) transcriptomics, data mining and bioinformatics, among others are used.


1) Using last generation approaches to the study of microbial processes of environmental relevance (massive sequencing, (meta) transcriptomics and (meta) genomics, computational tools of high capacity data mining, modeling and prediction).

2) Contribute to fundamental research in areas that have inexplicably received less attention (microbial mechanisms promoting plant growth under normal and stressful conditions; molecular and physiological responses of plants to microorganisms, mechanisms of biofilm growth monitoring; bases that evaluate effectiveness of strategies in bio (phyto) remediation geomicrobiology acid mine drainage, etc.).

3) Integrate Engineering and Computer Science researchers to facilitate the resolution of real problems where they are involved microbial processes through the acquisition, preprocessing, modeling and analysis of the data generated in the laboratory.

4) Dissemination of the importance of microbial functions in multiple technological and environmental aspects, and fundamental and applied research conducted at different actors in society issues.

5) Establishment of synergistic interactions with other CAPES lines that address relevant problems in ecophysiology, Ecotoxicology, Environmental Management, Ecology of Populations, among others, which have a microbial component to consider in its resolution or study.

Actual research lines:

1) Study the microbial molecular mechanisms involved inplant growth promotion.

2) Characterize the molecular and physiological responses involved in plant responses to microorganisms in normal growth conditions or stress.

3) Study the factors involved in chemical signaling between plants and microorganisms.

4) Evaluate bio strategies involved in (phyto) remediation of petroleum contaminated sites, chloroaromatic pesticides or metals.

5) Evaluate microbial component in the potential for acid mine drainage.

6) Develop algorithms to construct gene regulatory networks using gene expression data.

7) Study robustness of biological networks through neutral space.

8) Study microbial strategies involved in the production of cellulose and precipitation of calcite, regulation and metabolic requirements.

Projections and challenges:

1) Design of genetic circuits using synthetic biology tools for the development of growth-promoting agents, screening tools, and / or academic teaching of molecular genetic resources.

2) Contribute to the effective resolution of environmental problems in Chile.

3) Develop agricultural chemicals that reduce the environmental impact of agriculture, which does not allow the use of arable land and / or improve the productivity of the industry.

4) Generate high impact scientific knowledge in the fundamental areas of Environmental Microbiology and Plant Biology, and with specific applications in relevant activities at the national level, such as agriculture, mining, waste treatment, etc.

5) Incorporate mathematical modeling and computer simulations to study environmental problems as well as see the effect they could have proposed solutions.

6) Train new scientists with ability to apply basic knowledge of Microbiology, Plant Biology and Environmental Biotechnology, among others, to solve real problems.

7) Establish genuine links between different actors (companies, government, NGOs, etc.) that allow efficiently translate research carried out in our laboratories in environmentally sustainable development strategies.



1) Gacitúa MA, González B, Majone M & Aulenta F (2014) Boosting the electrocatalytic activity of Desulfovibrio paquesii biocathodes with magnetite nanoparticles. Int J Hydrog Energ. doi: 10.1016/j.ijhydene.2014.07.057. PDF: Gazitua et al. 2014

2) Lardies MA, Arias MB, Poupin M & Bacigalupe L (2014). Heritability of hsp70 expression in the beetle Tenebrio molitor: Ontogenetic and environmental effects. Journal of Insect Physiology 67:70-75 . PDF: Lardies et al. 2014

3) Lardies MA, Arias MB, Poupin MJ, Manríquez P, Torres R, Vargas C, Navarro J & Lagos N. (2014).Differential response to ocean acidification in physiological traits of Concholepas concholepas. Journal of Sea Research 90:127-134. PDF: Lardies et al. 2014b

4) Ruz GA, Timmermann T, Barrera J, Goles E (2014) Neutral space analysis for a Boolean network model of the fission yeast cell cycle network. Biological Research 47(1):64. doi:10.1186/0717-6287-47-64. PDF: Ruz et al. 2014


1) Goles E, Ruz GA (2015) Dynamics of neural networks over undirected graphs Neural Networks 63: 156-16.  PDF: Goles& Ruz_2015

2) Mora-Ruiz M, Font-Verdera F, Díaz-Gil C, Urdiain M, Rodríguez-Valdecantos G, González B, Orfila A & Rosselló-Móra R (2015) Moderate halophilic bacteria colonizing the phylloplane of halophytes of the subfamily Salicornioideae (Amaranthaceae). Systematic and Applied Microbiology 38 (6):406-416. PDF

3) Moraga F & Aquea F (2015) Composition of the SAGA complex in plants and its role in controlling gene expression in response to abiotic stresses. Front Plant Sci. 6:865. PDF

4) Pérez-Pantoja D, Leiva-Novoa P, Donoso RA, Little C, Godoy M, Pieper DH & González B (2015) Hierarchy of carbon source utilization in soil bacteria: Hegemonic preference for benzoate in complex aromatic compound mixtures degraded by Cupriavidus pinatubonensis Appl Environ Microbiol.  PDF: Pérez-Pantoja et al. 2015

5) Pinedo I, Ledger T, Greve M & Poupin MJ (2015) Burkholderia phytofirmans PsJN induces long-term metabolic and transcriptional changes involved in Arabidopsis thaliana salt tolerance. Front Plant Sci. 23(6):466. PDF

6) Viver T, Cifuentes A, Díaz S, Rodríguez-Valdecantos G, González B, Antón J, Rosselló-Móra R (2015) Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: Evidence that unexplored sites constitute sources of cultivable novelty. Systematic and Applied Microbiology 38(4):266-275. PDF: Viver et al. 2015


1) Aguilera V, Vargas CA, Lardies MA & Poupin MJ (2016) Adaptive variability to low-pH river discharges in Acartia tonsa and stress responses to high PCO2 conditions. Marine Ecology 37: 215–226. PDF

2) Ledger T, Rojas S, Timmermann T, Pinedo I, Poupin MJ, Garrido T, Richter P, Tamayo J & Donoso R (2016) Volatile-Mediated Effects Predominate in Paraburkholderia phytofirmans Growth Promotion and Salt Stress Tolerance of Arabidopsis thaliana. Front. Microbiol. 7:1838. doi: 10.3389/fmicb.2016.01838. PDF.

3) Loyola R, Herrera D, Mas A, Chern Jan Wong D, Höll J, Cavallini E, Amato A, Azuma A, Ziegler T, Aquea F, Castellarin SD, Bogs J, Tornielli GB, Peña-Neira A, Czemmel S, Alcalde JA, Matus JT & Arce-Johnson P (2016) The photomorphogenic factors UV-B receptor 1, elongated hypocotyl 5, and hy5 homologue are part of the UV-B signalling pathway in grapevine and mediate flavonol accumulation in response to the environment. Journal of Experimental Botany 67(18): 5429–5445. https://doi.org/10.1093/jxb/erw307. PDF

4) Poupin MJ, Greve M, Carmona V & Pinedo I (2016) A Complex Molecular Interplay of Auxin and Ethylene Signaling Pathways Is Involved in Arabidopsis Growth Promotion by Burkholderia phytofirmans PsJN. Front Plant Sci. 12(7):492. PDF

5) Tapia JE, González B, Goulitquer S, Potin P & Correa JA (2016) Microbiota Influences Morphology and Reproduction of the Brown Alga Ectocarpus sp. Front Microbiol 24 (7): 197. PDF


1) Aquea F, Timmermann T & Herrera-Vásquez A (2017) Chemical inhibition of the histone acetyltransferase activity in Arabidopsis thaliana. Biochemical and Biophysical Research Communications. 483(1): 664-668. https://doi.org/10.1016/j.bbrc.2016.12.086. PDF

2) Donoso R, Leiva-Novoa P, Zúñiga A, Timmermann T, Recabarren-Gajardo G & González B (2017) Biochemical and genetic bases of indole-3-acetic acid (auxin phytohormone) degradation by the plantgrowth-promoting rhizobacterium Paraburkholderia phytofirmans PsJN. Appl Environ Microbiol 83:e01991-16. https://doi.org/10.1128/AEM.01991-16. PDF

3) Filker S, Forster D, Weinisch L, Mora-Ruiz M, González B, Farías ME, Rosselló-Móra R & Stoeck T. (2017 in press) Transition boundaries for protistan species turnover in hypersaline waters of different biogeographic regions. Environmental Microbiology. DOI: 10.1111/1462-2920.13805. PDF

4) Henríquez PA & Ruz GA (2017) Extreme learning machine with a deterministic assignment of hidden weights in two parallel layers. Neurocomputing 226: 109-116. http://dx.doi.org/10.1016/j.neucom.2016.11.040. PDF

5) Menares F,  Carrasco MA,  González B, Fuentes I & Casanova M (2017) Phytostabilization ability of Baccharis linearis and its relation to properties of a tailings-derived technosol. Water Air Soil Pollut (2017) 228: 182. DOI 10.1007/s11270-017-3348-y. PDF.

6) Osores SJA, Lagos NA, San Martín V, Manríquez PA, Vargas CA, Torres R, Navarro JM, Poupin MJ, Saldías GS & Lardies MA (2017) Plasticity and inter-population variability in physiological and life-history traits of the mussel : A reciprocal transplant experiment, Journal of Experimental Marine Biology and Ecology. 490: 1-12, http://dx.doi.org/10.1016/j.jembe.2017.02.005. PDF