Sofia Duarte

People Detail

Address : 2Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar 4710-057 Braga Portugal

Research Area : Biodiversity

Position : Integrated members


Assistant Researcher at CBMA since 2019, under the project “Early detection and monitoring of non-indigenous species (NIS) in coastal ecosystems based on high-throughput sequencing tools”. Post-doc researcher at CBMA between 2009 and 2015, under the project “Barcoding of aquatic fungi” and between 2016 and 2019, under the project “Metabarcoding of meio­ and macrobenthic estuarine communities: performance assessment and implementation in monitoring programmes”. Invited Assistant Professor at Departamento de Biologia da Universidade do Minho, between 2008 and 2009. PhD (2008) in Sciences (Freshwater Ecology) at Departamento de Biologia da Universidade do Minho. Visiting PhD student at Departamento de Biologia da Universidade de Aveiro (2005) and EcoLab at the Université Paul Sabatier (2007). Visiting post-doc researcher at Mount Allison University (2015) and AZTI Tecnalia (2017).


The objective of her research is to develop and optimize DNA-based tools for the early detection and monitoring of non-indigenous species (NIS) in coastal Ecosystems.

Ongoing Projects

1. ATLANTIDA: Platform for the monitoring of the North Atlantic Ocean and tools for the sustainable exploitation of the marine resources (NORTE-01-0145-FEDER-000040), funded by Programa Operacional Regional do Norte (NORTE2020). Team member since 2020.

2. A-Fish-DNA-Scan: Cutting-edge DNA-based approaches for improved monitoring and management of fisheries resources along Magellan-Elcano´s Atlantic route (CIRCNA/BRB/0156/2019), funded by FCT. Co-Principal Investigator since 2020.

3. URBIFUN: Urbanization effects on the relationship between microbial biodiversity and ecosystem functioning. Young researcher’s collaborative project funded by the Iberian Association of Limnology (AIL). Team member since 2019.

4. NIS-DNA: Early detection and monitoring of non-indigenous species (NIS) in coastal ecosystems based on high-throughput sequencing tools (PTDC/BIA-BMA/29754/2017), funded by FCT. Principal Investigator since 2018.

5. THE NEXTSEA: Next generation monitoring of coastal ecosystems in a scenario of global change (operação NORTE-01-0145-FEDER-0000032). Collaborator since 2016.

6. EU-COST ACTION DNAqua-Net CA15219 “Developing new genetic tools for bioassessment of aquatic ecosystems in Europe Management”. Management committee substitute from Portugal since 2016.

Concluded Projects

1. AGRHYDROM: A timely look at effects of agriculture on fluvial dissolved organic matter: the role of hydrology. Young researcher’s collaborative project funded by the Iberian Association of Limnology (AIL) (2016-2018). Team member.

2. DIVERSEAQUAFUN: Molecular profiling of taxonomic, functional and genetic diversity of aquatic fungi along a pollution gradient (PTDC/AAG-GLO/3896/2012), funded by FCT (2013-2015). Team member.

3. FRESHBIOFUN: Biodiversity and functioning of detritus foodwebs in freshwaters (PTDC/AAC-AMB/117068/2010), funded by FCT (2012-2015). Team member.

4. Creative Little Scientists. FP7-Science-in-Society-2011-1 / SiS.2011. (2012-2014). Team member.

5. Networking Primary Science Educators as a means to provide training and professional development in Inquiry Based Teaching (Pri-Sci-Net). FP7-SCIENCE-IN-SOCIETY-2010-1 / SiS-2010- (2012-2014). Team member.

6. FUNDIVER: Development of molecular tools for assessing fungal diversity and activity in freshwaters (PTDC/AAC-AMB/113746/2009), funded by FCT (2011-2014). Principal Investigator.

7. Predicting the effect of global warming on stream ecosystems (PTDC/CLI/67180/2006) funded by FCT, (2009-2012). Collaborator.

8. Effect of pollution on leaf decomposition by aquatic hyphomycetes: analysis of their sensitivity/resistance to metal ions and acidic environments (POCTI/BSE/34024/2000), funded by FCT (2002-2003). Team member.


Co-supervision of:
- 3 MSc student
- 4 research fellows
- 11 undergraduate students


Selected publications:
1. Duarte S, Vieira PE, Lavrador AS, Costa FO. 2021. Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding. Science of the Total Environment 751: 141729.

2. Duarte S, Vieira PE, Costa FO. 2020. Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions. Metabarcoding and Metagenomics 4: e55162.

3. Leite B, Vieira PE, Teixeira MAL, Lobo-Arteaga J, Hollatz C, Borges LMS, Duarte S, Troncoso JS, Costa FO. 2020. Gap-analysis and annotated reference library for supporting macroinvertebrate metabarcoding in Atlantic Iberia. Regional Studies in Marine Science 36: 101307.

4. Feio MJ, Filipe AF, Garcia-Raventós A, Ardura A, Calapez AR, Pujante AM, Mortágua A, Múrria C, Diaz-de-Quijano D, Martins FMS, Duarte S et al. 2020. Advances on the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems. Limnetica 39: 419-440.

5. Fais M, Duarte S, Vieira PE, Sousa R, Hajibabaei M, Canchaya C, Costa FO. 2020. Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding. Estuarine, Coastal and Shelf Science 238: 106683.

6. Weigand H, Beermann AJ, Čiampor F, Costa FO, Csabai Z, Duarte S, et al. 2019. DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. Science of the Total Environment 678: 499-524.

7. Leese F, Bouchez A, Abarenkov K, Altermatt F, Borja Á, Bruce K, Ekrem T, Čiampor Jr F, Čiamporová-Zaťovičová Z, Costa FO, Duarte S, et al. 2018. Chapter 2 - Why we need sustainable networks bridging countries, disciplines, cultures and generations for aquatic biomonitoring 2.0: A perspective derived from the DNAqua-Net COST Action. Advances in Ecological Research 58: 63-99.

8. Duarte S, Cássio F, Pascoal C, Bärlocher F. 2017. Taxa-area relationship of aquatic fungi on deciduous leaves. PLoS ONE 12(7): e0181545.

9. Leese F, Altermatt F, Bouchez A, Ekrem T, Hering D, Meissner K, Mergen P, Pawlowski J, Piggott JJ, Rimet F, Steinke D, Taberlet P, Weigand AM, Abarenkov K, Beja P, Bervoets L, Björnsdóttir S, Boets P, Boggero A, Bones AM, Borja Á, Bruce K, Bursić V, Carlsson J, Čiampor F, Čiamporová-Zatovičová Z, Coissac E, Costa F, Costache M, Creer S, Csabai Z, Deiner K, DelValls Á, Drakare S, Duarte S, et al. 2016. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. Research Ideas and Outcomes 2: e11321.

10. Duarte S, Bärlocher F, Pascoal C, Cássio F. 2016. Biogeography of aquatic hyphomycetes: current knowledge and future perspectives. Fungal Ecology 19: 169-181.

11. Duarte S, Bärlocher F, Trabulo J, Cássio F, Pascoal C. 2015. Stream-dwelling fungal decomposer communities along a gradient of eutrophication unraveled by 454 pyrosequencing. Fungal Diversity 70: 127-148.

12. Duarte S, Seena S, Bärlocher F, Pascoal C, Cássio F. 2013. A decade´s perspective on the impact of DNA sequencing on aquatic hyphomycete research. Fungal Biology Reviews 27:19-24.

Full list of publications at: