Centro de Biologia Molecular e Ambiental

Centre of Molecular and Environmental Biology


Biodiversity and Functional Ecology Group

The Biodiversity and Functional Ecology research group develops theoretical, empirical and observational approaches to understand the role of biodiversity in ecosystem functioning and to propose actions towards ecological sustainability under the ongoing global climate change.

The research group joins expertise on marine and freshwater biology, ecology, ecotoxicology, microbiology, genetics, and mathematics. The application of diversified tools (e.g. omics and modelling) to address questions on the ecology and biodiversity of wild populations allows the design of strategies for the management and conservation of ecosystems and populations.

The research group has developed complementary research in Molecular and Functional Ecology, Modelling and Conservation Biology to: 



Develop new tools for assessing and monitoring ecosystems' biodiversity

The group strives to reveal the biological and ecological basis of the diversity of natural populations and species over space and time. Several projects with a large taxonomic scope, including aquatic fungi, marine macroinvertebrates and fishes, have been developed to assess i) molecular biodiversity - DNA barcoding related research, ii) phylogeography at regional and global scales, and iii) population genetics. 


Assess impacts of biodiversity on ecosystem processes under global change

The high rates of species extinctions have motivated our research to ascertain how increasingly fewer species are able to maintain ecological processes. The research group has used aquatic detritus food-webs as a model system to address the relationships between biodiversity and ecosystem functioning. Impacts of biodiversity loss have being addressed across multitrophic levels, through a range of spatial and temporal scales and along gradients of anthropogenic and climate stress. Particular attention has been given to global warming as well as to the effects of priority and emerging contaminants at the community, population and cellular level. Addressing impacts within and across different levels of biological organization pave the way to identify sensitive organisms, potential biomarkers, and to elucidate the action mechanism of contaminants in aquatic organisms, ultimately contributing to ecological risk assessment.


Apply modeling to describe the dynamics of complex ecological processes

A unifying approach, inspired by mathematical methods and techniques, was developed to study the dynamics of ecological processes and to understand the evolution of cooperation. Similar mathematical techniques have been employed to deal with the problem of avoiding dangerous climate change outcomes, viewed as a tragedy of the commons.

Main achievements

The Biodiversity and Functional Ecology group develops research to promote the conservation of species/ecosystems and the sustainable use of natural resources. Results from the research group showed the suitability of DNA barcodes for the identification of a wide range of organisms (fungi, crustacea, fishes) and contributed to i) create a comprehensive reference library of DNA barcodes of marine specimens [1,2]; ii) improve tools to assist fisheries management in EU [3]; and iii) improve monitoring tools for quality assessment following the EU Water Framework Directive. 

The research group used aquatic detritus foodwebs to address how different components of biodiversity affect ecosystem functioning [4,5]. Data showed that biodiversity helps to buffer environmental variability and to maintain ecological processes, because different species, phenotypes or genotypes respond differently to environmental changes leading to functional compensations [6]. We found that anthropogenic stressors, such as metals [7], nanoparticles [8] and eutrophication [9], are threatening biodiversity and functional ecosystem integrity. Exposure to multiple stressors led to synergistic, additive or antagonistic effects: effects of metals in mixtures were mainly additive [4], but warming potentiated metal toxicity [10]. Survival of aquatic organisms in metal-stressed environments was associated with their ability to initiate an efficient antioxidant defense system and to undergo programmed cell death [11].

Modelling of complex population dynamical processes was applied to i) disentangle the contribution of species richness and replacement to beta-diversity at small and large scales [12], ii) understand the evolution of cooperation at different levels of biological organization [13,14], iii) solve problems of collective action as those related to Greenhouse Gas Emissions [15], iv) predict the comparative performance of bottom-up vs top-down approaches in managing the Climate Change problem [16], and v) characterize the spatio-temporal layout of urban areas to identify (and even predict) areas requiring the most proximate planning and regulation.

Key Publications (last 5 years)

1. Costa FO, Landi M, Martins R, Costa MH, Costa ME, Carneiro M, Alves MJ, Steinke D, Carvalho GR. (2012). A ranking system for reference libraries of DNA barcodes: Application to marine fish species from Portugal. PLoS ONE, 7: e35858.

2. Lobo J, Costa PM, Teixeira MAL, Ferreira MS, Costa MH, Costa FO. (2013). Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans. BMC Ecology 13: 34.

3. Riccioni G, Landi M, Ferrara G, Milano I, Cariani A, Zane L, Sella M, Barbujani G, Tinti F. (2010). Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic Bluefin tuna of the Mediterranean Sea. Proceedings of the National Academy of Sciences USA, 107: 2102-2107.

4. Reiss J, Bailey RA, Cassio F, Woodward G, Pascoal C. (2010). Assessing the Contribution of Micro-Organisms and Macrofauna to Biodiversity–Ecosystem Functioning Relationships in Freshwater Microcosms. Advances in Ecological Research, 43: 151-176.

5. Fernandes I, Duarte S, Cássio F, Pascoal C. (2013). Effects of riparian plant diversity loss on aquatic microbial decomposers become more pronounced with increasing time. Microbial Ecology, 66:763-772. 3.2

6. Fernandes I,  Pascoal C, Cássio. (2011). Intraespecific traits change biodiversity effects on ecosystem functioning under metal stress. Oecologia 166: 1019-1028.

7. Duarte S, Pascoal C, Alves A, Correia A, Cássio F. (2008). Copper and zinc mixtures induce shifts in microbial communities and reduce leaf litter decomposition in streams. Freshwater Biology, 53: 91-102

8. Pradhan A, Seena S, Pascoal C, Cássio F. (2011). Can metal nanoparticles be a threat to microbial decomposers of plant litter in streams?. Microbial ecology, 62: 58-68.

9. Duarte S, Pascoal C, Garabetian F, Cássio F, Charcosset J-Y. (2009). Microbial decomposer communities are mainly structured by trophic status in circumneutral and alkaline streams. Applied and Environmental Microbiology 75: 6211-6221.

10. Batista D, Pascoal C, Cássio F. (2012). Impacts of warming on freshwater decomposers along a gradient of cadmium stress. Environmental Pollution, 169: 35-41.

11. Azevedo M-M, Almeida B, Ludovico P, Cássio F. (2009). Metal stress induces programmed cell death in aquatic fungi. Aquatic Toxicology 92: 264–270.

12. Carvalho JC, Cardoso P, Gomes P. (2012). Determining the relative roles of species turnover and species richness differences in generating beta-diversity patterns. Global Ecology and Biogeography, 21: 760-771.

13. Pacheco JM, Pinheiro FL, Santos FC. (2009). Population structure induces a symmetry breaking favoring the emergence of cooperation. PLoS-Computational Biology 5(12) e1000596.

14. Santos FC, Santos MD, Pacheco JM. (2008). Social diversity promotes the emergence of cooperation in public goods games. Nature 454: 213-216.

15. Santos FC, Pacheco JM. (2011). Risk of collective failure provides an escape from the tragedy of the commons. Proceedings of the National Academy of Sciences (USA) 108: 10421-10425.

16. Vasconcelos VV, Santos FC, Pacheco JM. (2013) A bottom-up institutional approach to cooperative governance of risky commons. Nature Climate Change 3 797–801.











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