Environmental Microbiology and Toxicogenomics

Team Isabel Sá-Correia, Cristina A. Viegas, Miguel C. Teixeira, Jorge H. Leitão, Arsénio M. Fialho, Sílvia A. Sousa, Paulo J Dias 


The activities of the BSRG in Environmental  Microbiology and Toxicogenomics aim: i) to explore the catabolic ability of selected Pseudomonas and Arthrobacter aurescens strains envisaging biodegradation of s-triazine herbicides in contaminated environments, ii) to characterize the microbial diversity and the population dynamics inside sludge bed reactors used for wastewater treatment, and iii) to get mechanistic insights into the toxicity of, and the adaptive responses to, xenobiotic compounds, in particular pesticides and other environmental pollutants. The eukaryotic model Saccharomyces cerevisiae and environmental bacteria of the Pseudomonas genus are at the centre of our studies. Global approaches are being used to identify potential toxicity biomarkers and to gain insights into the mechanisms of adaptation to these stress inducers.


Research Topics

1 - Environmental Microbiology

Strategies to accelerate biodegradation of s-triazine herbicides in contaminated soils - studies aiming the optimization of bioaugmentation and biostimulation treatments that may accelerate the biodegradation of atrazine and terbuthylazine to contribute to the cleanup of contaminated soils, are underway. These studies are focused on the understanding of factors that may influence survival and activity of specific biodegrading bacteria in soil microcosms spiked with formulations of these herbicides simulating worst-case scenarios ( e.g. mix-load or accidental spills). The efficacy of potential bioremediation treatments, either at laboratory or semi-field scales, is being followed at the ecotoxicological level (collaboration with IMAR-Univ. Coimbra) in order to obtain a more realistic insight into cleanup efficacy.

Yeast- and Caenorhabditis elegans-based toxicity testing - the single-cell eukaryotic model S. cerevisiae (endpoints: growth inhibition; modification of the expression of selected gene biomarkers) and the simple animal model C. elegans (endpoint: inhibition of reproduction) are being exploited for the assessment of the potential toxicity of xenobiotics ( e.g. pesticides and synthetic dyes).


Elucidation of the role of MDR transporters in pesticide resistance in yeast - The role of Drug-H + Antiporters in yeast resistance to xenobiotic compounds is being examined. The extrapolation of the gathered knowledge on the MDR phenomenon in yeast to more complex eukaryotes, in particular focusing Arabidopsis thaliana resistance to the herbicide 2,4-D, is being pursued.


Molecular characterization of microbial communities in UASB reactors - The molecular characterization of microbial populations thriving inside UASB 
reactors (collaboration with CESAM and DEP - Univ. Aveiro), is being performed based on a set of oligonucleotide primers targeting the 16S rRNA gene sequences of the Archaeal phyla 
Euryarchaeota or Crenarchaeota, and the Eubacterial phyla FirmicutesBacteroidetes
ChloroflexiProteobacteriaDeferibacteres or Spirochaetes. The microbial population dynamics associated with changes in the reactors´ operational parameters is being assessed based on FISH 


2 - Environmental Toxicogenomics

Toxicogenomics is an emerging field that allies genome-wide approaches to classical toxicology to increase our understanding of mechanisms of toxicity and resistance to xenobiotics, including pharmaceuticals and pesticides. This research area is further expected to increase the ability to predict the toxicological outcome of xenobiotic exposure, which is a key aspect in the risk assessment of pesticides and other environmental toxicants, and, eventually, be able to establish suitable biomarkers of contamination, of value as hazard indicators.

In this field, yeast is explored to gain mechanistic insights into the toxicity of, and tolerance to, the widely used agricultural fungicide mancozeb, linked to the development of Parkinson disease and cancer as the result of environmental exposure, by using toxicoproteomics and chemogenomics approaches. It is expected that the findings resulting from this research work focused on the eukaryotic model S. cerevisiae will represent a step forward in the understanding of the molecular mechanisms governing pesticide toxicity in humans and pesticide resistance in other fungi and plants.

A combination of molecular biology approaches and expression proteomic analysis is also being used to elucidate the regulatory networks underlying adaptation to phenol and its efficient catabolism in Pseudomonas. A previous study involving quantitative proteomics of the sequenced strain P. putida KT2440 and focused on soluble proteins was extended to membrane proteins.

DNA microarrays are being used to identify biomarkers for the biomonitoring of the toxicity of pesticides (chloroacetoanilide, phenylurea, chlorophenoxyacetic acid, carbamate and anylopirimidine families) in environmental samples.


Selected Publications

- Gil, F.N., Moreira-Santos, M., Chelinho, S., Pereira, C., Feliciano, J.R., Leitão, J.H., Sousa, J.P., Ribeiro, R., Viegas, C.A. “Suitability of a Saccharomyces cerevisiae-based assay to assess the toxicity of pyrimethanil sprayed soils via surface runoff: Comparison with standard aquatic and soil toxicity assays”, Science of the Total Environment, 505: 161-171, 2015.

- dos Santos, S.C., Sá-Correia, I., "Yeast toxicogenomics: lessons from a eukaryotic cell model and cell factory", Current Opinion in Biotechnology 33:183–191, 2015.

- Gil, F.N., Becker, J.D., Viegas, C.A. 2014. "Potential Mechanisms Underlying Response to Effects of the Fungicide Pyrimethanil from Gene Expression Profiling in Saccharomyces cerevisiae, Journal of Agricultural and Food Chemistry. (DOI: 10.1021/jf5007775)

- Nadais, H., Barbosa, M., Capela, I., Arroja, L., Ramos, C.G., Grilo, A., Sousa, S.A., Leitão, J.H., "Enhancing wastewater degradation and biogas production by intermittent operation of UASB reactors", Energy , 36: 2164-2168, 2011

- Chelinho, - S., Moreira-Santos, M., Lima, D., Silva, C., Viana, P., André, S., Lopes, I., Ribeiro, R., Fialho, A.M., Viegas, C.A., Sousa, J.P., "Cleanup of atrazine-contaminated soils: ecotoxicological study on the efficacy of a bioremediation tool with Pseudomonas sp. ADP", Journal of Soils and Sediments , 10:568-578, 2010.

- Ramos, C.G., Grilo, A.M., Sousa, S.A., Barbosa, M.L., Nadais, H., Leitão, J.H., "A new methodology combining PCR, cloning, and sequencing of clones discriminated by RFLP for the study of microbial populations: application to an UASB reactor sample",Applied Microbiology and Biotechnology , 85: 801-806, 2010.

- Roma-Rodrigues, C., Santos, P.M., Benndorf, D., Rapp, E., Sá-Correia, I., "Response of Pseudomonas putida KT2440 to phenol at the level of membrane proteome", Journal of PROTEOMICS , 73(8): 1461-1478, 2010.

- Lima, D., Viana, P., André, S., Chelinho, S., Costa, C., Ribeiro, R., Sousa, J.P., Fialho, A.M., Viegas, C.A., "Evaluating a bioremediation tool for atrazine contamination soils in open soil microcosmos: the effectiveness of bioaugmentation and biostimulation approaches", Chemosphere , 74, 187, 2009.

- Santos, P.M., Simões, T., Sá-Correia, I., "Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach", PROTEOMICS , 19, 657-670, 2009.

- Teixeira, M.C., Duque, P., Sá-Correia, I., "Environmental Genomics: mechanistic insights into toxicity of and resistance to the herbicide 2,4-D", Trends in Biotechnology , 25: 363-370, 2007.