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I am currently an Assistant Researcher at University of Minho, a position granted by FCT in the 1st ed. of the national contest Individual Call to Scientific Employment Stimulus. I am an integral member of the ME-Barcode group at CBMA and ARNET, where my research focus on the description and interpretation of the biological diversity of natural populations in aquatic ecosystems, exposed to different environmental pressures under global change. I have assisted almost from the beginning, in the establishment of the line Biodiversity research and monitoring through (e)DNA (meta)barcoding, at the ME-Barcode group._During my early years and PhD (2003-2008), I have investigated the impacts of anthropogenic stress on plant-litter decomposition and associated microbiota in streams at UMinho, UAveiro (Portugal), and UPaul Sabatier (France). In my 1st post-doc (2009-2015), I developed molecular tools to assess fungal diversity in freshwaters at UMinho and Mount Allison University (Canada). During this period, I successfully secured funding for my research - FunDiver project (2011-2014). This project contributed to several key achievements, such as disentangling inter- and intra-specific relationships and phylogeographic patterns among aquatic fungi, and assessing total and active fungal diversity in environmental samples using innovative tools (DNA (meta)barcoding), marking pioneering contributions to this research area._In 2016, I shifted my research to coastal and marine ecosystems by embracing a 2nd post-doc in collaboration with UGuelph (Canada) and UVigo (Spain). During this time, I focused on using (e)DNA (meta)barcoding to characterize estuarine benthic communities and study spatial and temporal patterns, as well as responses to environmental gradients. Since 2019, I established my research line - implementation of high throughput sequencing tools for the early detection and monitoring of non-indigenous and invasive species, in coastal ecosystems - and secured funding for my research - NIS-DNA project (2018-2022). In the scope of this project, we have successfully detected several NIS in recreational marinas along the Portuguese coast, some of which appear to be 1st records, highlighting the high potential of these tools in the early detection of nuisance species._I have been actively involved in various projects (>100M Euros), as PI (FunDiver, NIS-DNA), co-PI (A-Fish-DNA-Scan), Task leader (River2Ocean) or team member, most of them related with the development and implementation of innovative tools for biodiversity assessment. I have co-authored 74 publications (scientific papers, book chapters and abstracts in conference proceedings), most of them in highly recognized journals in the areas of Marine & Freshwater Biology, Ecology and Environmental Sciences, and I was the 1st or last author in >50%, with a co-author network of 150 researchers from 50 countries. I was invited to gave many talks in scientific events, including one plenary and co-authored several communications in conferences. I have been also a proficient reviewer for 38 journals (88 verified reviews, WoS), reviewed projects for 4 international funding agencies (e.g. BIODIVERSA+) and I serve as editor for 3 scientific journals. I have been/am involved in the supervision 2 PhD (ongoing), 5 MSc (3 concluded), 15 BSc (all concluded) and 5 research fellows (all concluded). Beyond research, I am committed to education, having been involved in lecturing activities (>100 h) and publication of pedagogical manuals, to BSc and MSc courses, and advanced courses. I have also organized several outreach activities, contributing to science dissemination to students, professors, and the broader society (e.g. EcologyDay, European researcher's night, Visits Program of UMinho School of Sciences). Currently, I serve as technical representative of UMinho in the support structure for the co-management commission of Litoral Norte Nature Park, a protected area in the North of Portugal.
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Identification

Personal identification

Full name
Sofia Alexandra Ferreira Duarte

Citation names

  • Duarte, Sofia
  • Duarte, S

Author identifiers

Ciência ID
731A-6C00-0352
ORCID iD
0000-0002-0181-0676
Google Scholar ID
https://scholar.google.pt/citations?user=CONCcGQAAAAJ&hl=pt-PT&oi=aoorg/0000-0002-0181-0676
Researcher Id
H-3323-2013
Scopus Author Id
23088270700

Email addresses

  • sduarte@bio.uminho.pt (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Biodiversity Conservation

Languages

Language Speaking Reading Writing Listening Peer-review
English Intermediate (B1) Advanced (C1) Advanced (C1) Intermediate (B1)
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2019/09/26 - 2019/09/28
Concluded
 Science communication to non-scientific public (18 hours) (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2017/01/16 - 2017/02/07
Concluded
 Basic concepts of programming with R (18 hours) (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2016/07/03 - 2016/07/03
Concluded
 Introduction to Meta-analysis in Ecology (5.5 hours) (Postgraduate Certificate)
Universitat Rovira i Virgili, Spain
2013/06/30 - 2013/06/30
Concluded
 From genes to ecosystems: hands on bioinformatics of metagenomics data (8 hours) (Curso de Especialização Tecnológica)
Westfalische Wilhelms-Universität Münster Institut für Evolution und Biodiversität, Germany
2011/07/04 - 2011/07/08
Concluded
 River restoration: principles and practices (30 hours) (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2011/05/14 - 2011/05/16
Concluded
 Biofilm transcriptomics (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2011/05/09 - 2011/05/13
Concluded
 Global change and biodiversity: implications for ecosystem services (30 hours) (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2010/07/19 - 2010/07/23
Concluded
 Assessment of freshwater ecosystem condition (40 hours) (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2010/07/14 - 2010/07/16
Concluded
 Ecotoxicology and environmental risk assessment in aquatic ecosystems (20 hours) (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2003/11/01 - 2008/07/21
Concluded
 Ph. D. in Sciences (Doutoramento)
Major in Biology
Universidade do Minho Escola de Ciências, Portugal
"Biodiversity and activity of microbial decomposers of leaf litter in streams under anthropogenic stress" (THESIS/DISSERTATION)
 Approved by unanimity
2007/07/17 - 2007/07/20
Concluded
 Interactions of fungi with toxic metals (38 hours) (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2007/06/12 - 2007/06/13
Concluded
 Real time PCR "From food industry to genetic expression - applications", ministered by BioPortugal and Applied Biosystems (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2007/05/20 - 2007/05/20
Concluded
 How to best conduct and report aquatic ecotoxicity tests according to International Guidelines (8 hours), ministered by Ecotoxsolutions.com (Curso de Especialização Tecnológica)
Universidade do Porto, Portugal
2005/09/05 - 2005/09/09
Concluded
 Combining morphological and molecular approaches for studying the diversity and phylogenetic relationships of freshwater fungi (38 hours) (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2004/02/16 - 2004/02/20
Concluded
 Methods for ecotoxicological assessment in terrestrial environments (38 hours) (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
2003/06/30 - 2003/07/04
Concluded
 Molecular methods in the identification and typing of microorganisms (38 hours) (Curso de Especialização Tecnológica)
Universidade do Minho, Portugal
1998/10/01 - 2002/10/22
Concluded
 Applied Biology (Licenciatura)
Universidade do Minho Escola de Ciências, Portugal
"Effects of zinc on Alnus glutinosa leaf decomposition by aquatic hyphomycetes – studies in streams and microcosms" (THESIS/DISSERTATION)
 16/20
Affiliation

Science

Category
Host institution 		Employer
2019/05/01 - Current Auxiliary Researcher (Research) Universidade do Minho, Portugal
Universidade do Minho, Portugal
2016/03/01 - 2019/04/30 Postdoc (Research) Universidade do Minho, Portugal
2009/07/01 - 2015/06/30 Postdoc (Research) Universidade do Minho, Portugal
2002/11/01 - 2003/09/30 Researcher (Research) Universidade do Minho, Portugal
2002/02/16 - 2002/10/22 Research Trainee (Research) Universidade do Minho, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2021/03 - 2022/07 Invited Assistant Professor (University Teacher) Universidade do Minho, Portugal
2019/02 - 2019/02 Invited Assistant Professor (University Teacher) Universidade do Minho, Portugal
2008/10/01 - 2009/06/30 Invited Assistant Professor (University Teacher) Universidade do Minho, Portugal

Others

Category
Host institution 		Employer
2022/10 - Current Section Board Editor of "Marine Ecology" of "Marine Science and Engineering" journal MDPI AG, Switzerland
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2022/07 - Current Associate Editor of "Frontiers in Environmental Science" journal Frontiers Media SA, Switzerland
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2017 - Current Subject editor for the journal "Metabarcoding & Metagenomics" journal Pensoft Publishers, Bulgaria
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2017/02 - 2017/03 Short-term scientific mission under the scope of the COST action CA15219 DNAqua-net European Cooperation in Science and Technology, Belgium
AZTI-Tecnalia Sukarrieta, Spain
(...)
2015/05 - 2015/06 Development of research work at Mount Allison University in Canada under the scope of post-doc project (SFRH/BPD/47574/2008) Fundação para a Ciência e a Tecnologia, Portugal
Mount Allison University, Canada
2007/09 - 2007/09 Development of research work at EcoLab from University Paul Sabatier in France under the scope of PhD project (SFRH/BD/13482/2003) Fundação para a Ciência e a Tecnologia, Portugal
Laboratoire Écologie Fonctionnelle et Environnement, France
2005/05 - 2005/06 Development of research work at the Department of Biology from University of Aveiro in Portugal under the scope of PhD project (SFRH/BD/13482/2003) Fundação para a Ciência e a Tecnologia, Portugal
Universidade de Aveiro Departamento de Biologia, Portugal
Projects

Grant

Designation Funders
2021/02/01 - 2024/01/31 Exploring the use of environmental DNA to monitor the ichthyofauna and provide data to assist fish stock assessment in the Atlantic
CIRCNA/BRB/0156/2019
Supervisor
Universidade do Minho, Portugal
Ongoing
2020 - 2024 Optimization of DNA metabarcoding for the early detection and improved monitoring of non-indigenous species (NIS) in Portuguese coastal ecosystems
UI/BD/150871/2021
Supervisor
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia - FCT
Ongoing
2016/03/01 - 2019/04/30 Metabarcoding of meio­ and macrobenthic estuarine communities: performance assessment and implementation in monitoring programmes
SFRH/BPD/109842/2015
Post-doc Fellow
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia - FCT
Concluded
2009/07/01 - 2015/06/30 Development of DNA barcoding for aquatic fungi
SFRH/BPD/47574/2008
Post-doc Fellow
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia - FCT
Concluded
2003/11/01 - 2007/10/31 Biodiversity and activity of microbial decomposers in streams under anthropogenic stress
SFRH/BD/13482/2003
PhD Student Fellow
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia - FCT
Concluded
2002/11/01 - 2003/10/31 Effect of pollution on leaf decomposition by aquatic hyphomycetes: analysis of their sensitivity/resistance to metal ions and acidic environments
POCTI/BSE/34024/2000
Scientific Initiation Fellow
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia - FCT
Concluded

Contract

Designation Funders
2023 - Current eDNAqua-plan: A Plan towards an eDNA reference library and data repository for Aquatic Organisms, navigating Europe towards the next generation biodiversity monitoring
project ID 101112800
Researcher
Ongoing
2021/01/01 - 2025/12/31 Rede de Infraestruturas em Investigação Aquática
LA/P/0069/2020
10.54499/LA/P/0069/2020
Universidade do Minho, Portugal

Universidade do Algarve, Portugal

Instituto Politécnico de Leiria, Portugal

Instituto Universitário de Ciências Psicológicas Sociais e da Vida, Portugal

Associação para a Inovação e Desenvolvimento da FCT, Portugal

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal

Universidade de Coimbra, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal

Universidade de Évora, Portugal

Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Portugal

Centro de Ciências do Mar e do Ambiente, Portugal

Universidade NOVA de Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2022/01/16 - 2025/01/15 Fish-DNA-Monitor: Supporting monitoring and management of fisheries resources in Guinea-Bissau through capacity-building on cutting-edge DNA-based approaches
FCT AGA-KHAN /541703280/2019
Researcher
Universidade do Minho, Portugal
 Aga Khan Development Network

Associação para a Inovação e Desenvolvimento da FCT
Ongoing
2020/01/01 - 2023/12/31 CENTRO DE BIOLOGIA MOLECULAR E AMBIENTAL
UIDB/04050/2020
10.54499/UIDB/04050/2020
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal

Universidade do Minho, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2021 - 2023 RIVER2OCEAN: Socio-ecological and biotechnological solutions for the conservation and valorization of aquatic biodiversity in the Minho Region (Task leader)
NORTE-01-0145-FEDER-000068
Researcher
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
Ongoing
2020 - 2023 A-Fish-DNA-Scan: Cutting-edge DNA-based approaches for improved monitoring and management of fisheries resources along Magellan-Elcano's Atlantic route (co-PI)
CIRCNA/BRB/0156/2019
Researcher
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
Ongoing
2020 - 2023 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
Researcher
Ongoing
2018/10/01 - 2021/09/30 NIS-DNA: Early detection and monitoring of non-indigenous species (NIS) in coastal ecosystems based on high-throughput sequencing tools (PI)
PTDC/BIA-BMA/29754/2017
Principal investigator
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia - FCT
Ongoing
2019 - 2021 URBIFUN: Urbanization effects on the relationship between microbial biodiversity and ecosystem functioning
URBIFUN
Researcher
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 Iberian Association of Limnology (AIL)
Ongoing
2017 - 2020 THE NEXTSEA: Next generation monitoring of coastal ecosystems in a scenario of global change
NORTE-01-0145-FEDER-0000032
Other
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
Ongoing
2019/01/01 - 2019/12/31 CENTRO DE BIOLOGIA MOLECULAR E AMBIENTAL
UID/BIA/04050/2019
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal

Universidade do Minho, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016 - 2018 AGRHYDROM: A timely look at effects of agriculture on fluvial dissolved organic matter: the role of hydrology
AGRYDHROM
Researcher
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 Iberian Association of Limnology (AIL)
Concluded
2013/07/01 - 2015 Molecular profiling of taxonomic, functional and genetic diversity of aquatic fungi along a pollution gradient
info:eu-repo/grantAgreement/FCT/COMPETE/130477/PT
Researcher
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2012/04/30 - 2015 FreshBioFun: Biodiversity and the functioning of detritus food-webs in freshwaters
info:eu-repo/grantAgreement/FCT/COMPETE/117068/PT
Researcher
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2011/03/01 - 2014/08/31 FunDiver: Development of molecular tools for assessing fungal diversity and activity in freshwaters (PI)
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/113746/PT
Principal investigator
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia - FCT
Concluded
2011/10/01 - 2014/03/31 Networking Primary Science Educators as a means to provide training and professional development in Inquiry Based Teaching
info:eu-repo/grantAgreement/EC/FP7/266647/EU
Researcher
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 European Commission
Concluded
2011/10/01 - 2014/03/31 Creative Little Scientists: Enabling Creativity through Science and Mathematics in Preschool and First Years of Primary Education
info:eu-repo/grantAgreement/EC/FP7/289081/EU
Researcher
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 European Commission
Concluded
2011/01/01 - 2013/12/31 Projecto Estratégico - UI 4050 - 2011-2012
PEst-C/BIA/UI4050/2011
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal

Universidade do Minho, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2008/06/01 - 2012 Predicting the effect of global warming on stream ecosystems
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/67180/PT
Other
Fundação para a Ciência e a Tecnologia - FCT
Concluded

Other

Designation Funders
2016 - 2020 DNAqua-net: Developing new genetic tools for bioassessment of aquatic ecosystems in Europe Management
EU-COST ACTION DNAqua-Net CA15219
Researcher
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
 European Cooperation in Science and Technology
Ongoing
Outputs

Publications

Book chapter
  1. Duarte, Sofia; Wurzbacher, Christian; Seena, Sahadevan. "Metabarcoding of Litter-Associated Fungi and Bacteria". In Methods to Study Litter Decomposition, 339-346. Springer International Publishing, 2020.
    10.1007/978-3-030-30515-4_37
  2. Seena Sahadevan; Duarte, Sofia; Wurzbacher, Christian. "A Bioinformatics Primer for the Analysis of Illumina MiSeq Data of Litter-Associated Fungi and Bacteria". In Methods to Study Litter Decomposition, 573-582. Springer International Publishing, 2020.
    Published • 10.1007/978-3-030-30515-4_62
  3. Seena, Sahadevan; Duarte, Sofia; Cássio, Fernanda; Sobral, Olímpia. "Chapter 5. Fungi and Bacteria". edited by Ferreira, Verónica; Feio, Maria-João. Coimbra, Portugal: Imprensa da Universidade de Coimbra, 2019.
    Published • 10.14195/978-989-26-1624-7
  4. Leese, Florian; Bouchez, Agnès; Abarenkov, Kessy; Altermatt, Florian; Borja, Ángel; Bruce, Kat; Ekrem, Torbjørn; et al. "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". In Next Generation Biomonitoring: Part 1, 63-99. Elsevier, 2018.
    10.1016/bs.aecr.2018.01.001
  5. Duarte, Sofia; Cassio, Fernanda; Pascoal, Claudia. "Denaturing Gradient Gel Electrophoresis (DGGE) in Microbial Ecology - Insights from Freshwaters". In Gel Electrophoresis - Principles and Basics. InTech, 2012.
    10.5772/38177
Conference abstract
  1. Weigand, H; Beermann, AJ; Ciampor, F; Costa, FO; Csabai, Z; Duarte, S; et al.. "A barcode gap-analysis for aquatic biomonitoring in Europe". 2019.
    10.1139/gen-2019-0097
  2. Fais, M; Duarte, S; Vieira, PE; Sousa, R; Hajibabaei, M; Canchaya, C; Costa, FO. "Small-scale spatial variation of meiofaunal communities in Rio Lima estuary (NW Portugal) assessed through metabarcoding". 2019.
    10.1139/gen-2019-0097
  3. Duarte, Sofia; Rodríguez-Ezpeleta, Naiara; Borja, Ángel; Costa, Filipe Oliveira. "Species gap-analysis in DNA barcode reference libraries of macrobenthic fauna from transition and coastal waters along the western European Atlantic coast". Paper presented in 7th International Barcode of Life conference (iBOL7), Krueger National Park, 2017.
    Published • 10.1139/gen-2017-0178
  4. Fais, Maria; Duarte, Sofia; Sousa, Ronaldo; Hajibabaei, Mehrdad; Canchaya, Carlos Alberto; Costa, Filipe Oliveira. "Surveying estuarine meiofauna through DNA metabarcoding: optimization of sampling and molecular protocols". Paper presented in 7th International Barcode of Life conference (iBOL7), Krueger National Park, 2017.
    Published • 10.1139/gen-2017-0178
Conference poster
  1. Moutinho, J; Carreira-Flores, D; Gomes, PT; Costa, FO; Duarte, S. "Assessing seasonal and spatial dynamics of zooplankton communities in a temperate estuary through DNA metabarcoding". Paper presented in I CBMA OPEN DAY & II PhD|Bio SYMPOSIUM, 2024.
  2. Ferreira, AO; Azevedo, OM; Barroso, C; Duarte, S; Egas, C; Fontes, JT; Ré, P; Piecho-Santos, AM; Costa, FO. "DNA Metabarcoding as a tool to identify fish species in zooplankton samples: a proof-of-concept study on the Portuguese coast". Paper presented in I CBMA OPEN DAY & II PhD|Bio SYMPOSIUM, 2024.
  3. Lavrador, AS; Amaral, FG; Moutinho, J; Vieira, PE; Costa, FO; Duarte, S. "Detection of non-indigenous invertebrate species in recreational marinas of North of Portugal using DNA metabarcoding: impact of season and sample type". Paper presented in I CBMA OPEN DAY & II PhD|Bio SYMPOSIUM, 2024.
  4. Moutinho, J.; Carreira-Flores, Diego; Gomes, P.T.; Costa, F.O.; Duarte, S. "Assessing seasonal and spatial dynamics of zooplankton communities in a temperate estuary through DNA metabarcoding". Paper presented in IV International Meeting of the Portuguese Society of Genetics (IMPSG), 2023.
  5. Machado, C.; Azevedo, O.M.; Barroso, C.; Duarte, S; Egas, C.; Fontes, J.T.; Oliveira, C.; Piecho-Santos, A.M.; Costa, F.O.. "A comparison of eDNA metabarcoding and morphological analyses for detecting ichthyoplankton in the Guadiana estuary". Paper presented in IV International Meeting of the Portuguese Society of Genetics (IMPSG), 2023.
  6. Ferreira, A.O.; Azevedo, O.M.; Barroso, C.; Duarte, S; Egas, C.; Fontes, J.T.; Ré, P.; Piecho-Santos, A.M.; Costa, F.O.. "DNA Metabarcoding as a tool to identify fish species in zooplankton samples: a proof-of-concept study on the Portuguese coast". Paper presented in IV International Meeting of the Portuguese Society of Genetics (IMPSG), 2023.
  7. Azevedo, M.M.; Saraiva, E.; Duarte, Sofia. "Deteção precoce de espécies invasoras em ecossistemas costeiros através de ferramentas baseadas em DNA Barcoding. Atividade com alunos do Ensino Básico.". Paper presented in Encontro de Ciência 2023, 2023.
  8. Azevedo, OM; Cruz, J; Ré, P; Machado, C; Teodósio, A; Duarte, S; Costa, FO; Piecho-Santos, A. M.. "Old meets new: 1. Morphological analyses of Guadiana ichthyoplankton as a basis for DNA-based approaches". Paper presented in 46th Larval fish conference, 2023.
  9. Machado, C; Azevedo , OM; Barroso, C; Duarte, S; Egas, C; Fontes, JT; Oliveira, C; Piecho-Santos, A. M.; Costa, FO. "Old meets new: 2. eDNA metabarcoding vs morphological analyses for detecting ichthyoplankton in the Guadiana estuary". Paper presented in 46th Larval fish conference, 2023.
  10. Ferreira, AO; Barroso, C; Cruz, J; Duarte, S; Egas, C; Gomes, P; Oliveira, C; et al. "Testing COI primers for ichthyoplankton metabarcoding and their capability to assess local mesozooplankton communities". Paper presented in I PhD | Bio SYMPOSIUM, 2023.
  11. Lavrador, AS; Fontes, JT; Vieira, PE; Costa, FO; Duarte, S. "Compilation, revision, and annotation of DNA barcodes of marine invertebrate non-indigenous species (NIS) occurring in European coastal regions". Paper presented in I PhD | Bio SYMPOSIUM, 2023.
  12. Duarte, S; Costa, FO. "Current status on the use of eDNA-based tools for the targeted detection of endangered and rare species". Paper presented in XVIII Encontro Nacional de Biologia Evolutiva (ENBE), 2022.
  13. Moutinho, J; Lavrador, AS; Vieira, PE; Costa, FO; Duarte, S. "Assessing the seasonal dynamics of zooplankton in a recreational marina of the northwest of Portugal through multi-marker DNA metabarcoding". Paper presented in XVIII Encontro Nacional de Biologia Evolutiva (ENBE), 2022.
  14. Machado, C; Barroso, C; Baylina, N; Duarte, S; Egas, C; Fernandes, M; Oliveira, C; et al. "Environmental DNA for detecting marine fish species: testing the volume of sampled water, markers and primers in a public oceanarium". Paper presented in XVIII Encontro Nacional de Biologia Evolutiva (ENBE), 2022.
  15. Ferreira, AO; Barroso, C; Cruz, J; Duarte, S; Egas, C; Gomes, P; Oliveira, C; Piecho-Santos, AM; Costa, FO. "COI metabarcoding of mesozooplankton communities: the impact of OTU versus ASV-based pipelines on recovered diversity". Paper presented in XVIII Encontro Nacional de Biologia Evolutiva (ENBE), 2022.
  16. Lavrador, AS; Amaral, FG; Moutinho, J; Vieira, PE; Costa, FO; Duarte, S. "Detection and monitoring of non-indigenous invertebrate species in recreational marinas through DNA metabarcoding of zooplankton communities in the North of Portugal". Paper presented in ICES Annual Science Conference 2022, SCOR MetaZooGene Symposium 2022, 2022.
  17. Machado, C; Barroso, C; Baylina, N; Duarte, S; Egas, C; Fernandes, M; Oliveira, C; et al. "Testing the efficiency of environmental DNA metabarcoding for detecting marine fish species using a public aquarium". Paper presented in ICES Annual Science Conference 2022, Growing together: prospects and opportunities for environmental DNA and fisheries sciences, 2022.
  18. Amaral, FG; Lavrador, AS; Vieira, PE; Costa, FO; Duarte, S. "Detection and monitoring of invertebrate non-indigenous species through DNA metabarcoding in a recreational marina of the Northwest of Portugal". Paper presented in International Conference on DNA Barcoding and Biodiversity (ICDBB), 2022.
  19. Moutinho, J; Lavrador, AS; Vieira, PE; Costa, FO; Duarte, S. "Assessing the seasonal dynamics of zooplankton in a recreational marina of the northwest of Portugal through multi-marker DNA metabarcoding". Paper presented in International Conference on DNA Barcoding and Biodiversity (ICDBB), 2022.
  20. Ferreira, AO; Barroso, C; Cruz, J; Duarte, S; Egas, C; Gomes, P; Oliveira, C; et al. "Testing COI primers for ichthyoplankton metabarcoding and their capability to assess local mesozooplankton communities". Paper presented in International Conference on DNA Barcoding and Biodiversity (ICDBB), 2022.
  21. Lavrador, AS; Amaral, FG; Vieira, PE; Duarte, Sofia; Costa, FO. "Surveillance of non-indigenous invertebrate species through DNA metabarcoding in recreational marinas in the North and Center of Portugal". Paper presented in 1st DNAQUA International Conference, 2021.
  22. Vieira, PE; Lavrador, Ana S.; Parente, Manuela; Parretti, P; Costa, AC; Costa, FO; Duarte, Sofia. "Current status of DNA barcode reference libraries for marine invertebrates from Macaronesia". Paper presented in XIX Encontro Nacional de Ecologia, 2020.
  23. Colls, Miriam; Romero, F; Chonova, T; Álvarez, I; Antunes, I; Aranguren-Gassis, M; Argudo, M; et al. "The URBIFUN project - Urbanization effects on the relationship between microbial diversity and ecosystem functioning". Paper presented in 2nd International Conference on Microbial Ecotoxicology (EcotoxicoMic 2020), 2020.
  24. Duarte, Sofia; Parente, MI; Costa, AC; Costa, FO. "Species gap analysis in DNA barcode reference libraries of marine non-indigenous species in the Azores archipelago". Paper presented in Iberian Symposium on Marine Biology Studies (XX SIEBM), 2019.
  25. Duarte, S; Vieira, PE; Costa, FO. "Current status of the DNA barcode reference library of non-indigenous marine species occurring in European coastal regions". Paper presented in 20th Iberian Symposium on Marine Biology Studies (XX SIEBM), 2019.
  26. Fais, M; Duarte, S; Vieira, PE; Sousa, Ronaldo; Hajibabaei, M; Chanchaya, C; Costa, FO. "Small-scale spatial variation of meiofaunal communities in Rio Lima estuary (NW Portugal) assessed through metabarcoding)". Paper presented in 8th International Barcode of Life Conference (iBOL8), 2019.
  27. Weigand, H; Beermann, AJ; Ciampor, F; Costa, FO; Csabai, Zoltán; Duarte, S; Geiger, MF; et al. "A barcode gap-analysis for aquatic biomonitoring in Europe". Paper presented in 8th International Barcode of Life Conference (iBOL8), 2019.
  28. Duarte, S; Rodríguez-Ezpeleta, N; Borja, A; Costa, FO. "Species gap analysis in DNA barcode reference libraries of macrobenthic fauna from transition and coastal waters along the western European Atlantic coast". Paper presented in 7th International Barcode of Life conference (iBOL7), 2017.
  29. Fais, M; Duarte, S; Sousa, Ronaldo; Hajibabaei, M; Canchaya, CA; Costa, FO. "Surveying estuarine meiofauna through DNA metabarcoding: optimization of sampling and molecular protocols". Paper presented in 7th International Barcode of Life conference (iBOL7), 2017.
  30. Estévez, E; Abril, M; Alirangues, MM; Arenas-Sánchez, A; Arias del Real, R; Arranz, I; Bruno, D; et al. "A timely to look at effects of agricultural on fluvial DOM: the role of hydrology. AGRHYDROM, 2nd Young collaborative project from the Iberian Association of Limnology". Paper presented in Symposium for European Freshwater Sciences (SEFS 10), 2017.
  31. Fais, Maria; Duarte, Sofia; Sousa, Ronaldo; Hajibabaei, Mehrdad; Canchaya, Carlos; Costa, FO. "DNA metabarcoding on estuarine meiofauna: testing the effect of sample’s amount and primer pair". Paper presented in DNAqua-net Kick-off conference, 2017.
  32. Vieira, Pedro; Lobo, Jorge; Fais, Maria; Duarte, Sofia; Queiroga, Henrique; Costa, FO. "Compiling a DNA barcode reference library for macrobenthic invertebrate fauna from the southern European Atlantic coast". Paper presented in Campus do Mar International Science Conference 2016 (CdM ISC’16), 2016.
  33. Fais, Maria; Hollatz, C; Lobo, Jorge; Duarte, Sofia; Borges, LMS; Costa, FO. "Compiling a DNA barcode reference library for benthic molluscs of the Southern European Atlantic coast". Paper presented in XIX Iberian Symposium on Marine Biology Studies (SIEBM), 2016.
  34. Ferreira, Verónica; Koricheva, J; Duarte, Sofia; Niyogi, D; Guérold, F. "A meta-analysis on the effects of heavy metal contamination on litter decomposition in streams". Paper presented in 4º Iberian Ecological Congress, 2015.
  35. Duarte, Sofia; Mora-Gómez, J; Romaní, A; Cássio, F; Pascoal, Cláudia. "Eutrophication alters responses of stream-dwelling microbial decomposers to drought". Paper presented in Detrital Dynamics Conference, 2014.
  36. Lima-Fernandes, E; Sousa, Mafalda; Duarte, Sofia; Cássio, F; Pascoal, Cláudia. "Nutrient enrichment affects microbial decomposition and invertebrate feeding activity more than fungal diversity". Paper presented in Detrital Dynamics Conference, 2014.
  37. Fernandes, Isabel; Pereira, Ana; Trabulo, J; Pascoal, Cláudia; Cássio, F; Duarte, Sofia. "A case of using traditional and molecular approaches to assess the effects of season and eutrophication on fungal communities on plant litter decomposing in streams". Paper presented in XVII Congress of the Iberian Association of Limnology, 2014.
  38. Duarte, Sofia; Ferreira, Verónica; Canhoto, C; Pascoal, Cláudia; Cássio, F. "Seasonal variability overwhelms effects of global warming on microbial decomposers in streams". Paper presented in 11th INTECOL Congress, Ecology: Into the next 100 years, 2013.
  39. Batista, Daniela; Pascoal, Cláudia; Cássio, F; Duarte, Sofia. "Is intraspecific diversity of aquatic hyphomycetes on decomposing leaves in streams related to season?". Paper presented in Symposium for European Freshwater Sciences (SEFS 8), 2013.
  40. Pascoal, Cláudia; Batista, Daniela; Cássio, F; Duarte, Sofia. "New DNA barcodes for 8 aquatic hyphomycete species". Paper presented in Symposium for European Freshwater Sciences (SEFS 8), 2013.
  41. Mora-Gómez, J; Romaní, AM; Boix, D; Duarte, Sofia; Cássio, F; Pascoal, Cláudia. "Can summer drought affect leaf decomposition when the water flow returns to the stream?". Paper presented in Symposium for European Freshwater Sciences (SEFS 8), 2013.
  42. Antunes, B; Trabulo, J; Duarte, Sofia; Seena, S; Cássio, F; Pascoal, Cláudia. "Intraspecific diversity affects plant-litter decomposition in freshwaters". Paper presented in XVI Congress of the Iberian Association of Limnology (AIL), 2012.
  43. Seena, S; Duarte, Sofia; Pascoal, Cláudia; Cássio, F. "An ubiquitous perspective of the intraspecific diversity of the aquatic fungus Articulospora tetracladia". Paper presented in XVI Congress of the Iberian Association of Limnology (AIL), 2012.
  44. Fernandes, Isabel; Duarte, Sofia; Pascoal, Cláudia; Cássio, F. "Long-term effects of riparian-plant diversity loss on a stream invertebrate shredder". Paper presented in XVI Congress of the Iberian Association of Limnology (AIL), 2012.
  45. Antunes, B; Trabulo, J; Duarte, Sofia; Seena, S; Cássio, F; Pascoal, Cláudia. "Intraspecific diversity affects plant-litter decomposition in freshwaters". Paper presented in XIV Jornadas de Biologia Aplicada – BioPercursos no século XXI, 2012.
  46. Duarte, Sofia; Fernandes, Isabel; Nogueira, M-J; Pinheiro, André; Cássio, F; Pascoal, Cláudia. "Temperature changes interspecific relationships among aquatic hyphomycetes". Paper presented in Symposium for European Freshwater Sciences (SEFS 7), 2011.
  47. Seena, S; Duarte, Sofia; Pascoal, Cláudia; Cássio, F. "ITS barcodes as unambiguous discriminators of strains of Articulospora tetracladia". Paper presented in 2nd conference of the European Consortium for the Barcode of Life (ECBOL2), 2010.
  48. Duarte, Sofia; Pascoal, Cláudia; Cássio, F. "Can microbial decomposers of plant litter be used as bioindicators of anthropogenic stress in streams?". Paper presented in III International Conference on Environmental, Industrial and Applied Microbiology - BioMicroWorld 2009, 2009.
  49. Sridhar, KR; Duarte, Sofia; Cássio, F; Pascoal, Cláudia. "Fungal communities in sediments from streams with contrasting water chemistry". Paper presented in III International Conference on Environmental, Industrial and Applied Microbiology - BioMicroWorld 2009, 2009.
  50. Duarte, Sofia; Pascoal, Cláudia; Cássio, F. "High diversity of fungi may mitigate the impact of pollution on plant litter decomposition in streams". Paper presented in SETAC Europe 19th Annual Meeting, 2009.
  51. Sridhar, KR; Duarte, Sofia; Cássio, F; Pascoal, Cláudia. "The role of early colonizers in leaf-litter decomposition in streams". Paper presented in 5th International Meeting on Plant Litter Processing in Freshwaters (PLPF), 2008.
  52. Fernandes, Isabel; Duarte, Sofia; Cássio, F; Pascoal, Cláudia. "Mixtures of zinc and phosphate affect leaf litter decomposition by aquatic fungi". Paper presented in SETAC Europe 17th Annual Meeting, 2007.
  53. Medeiros, A; Duarte, Sofia; Pascoal, Cláudia; Cássio, F; Graça, MAS. "Effects of heavy metals on leaf litter breakdown by aquatic fungi: a microcosm study". Paper presented in SETAC Europe 17th Annual Meeting, 2007.
  54. Duarte, Sofia; Alves, A.; Pascoal, Cláudia; Correia, A; Cássio, F. "Diversity and activity of fungi and bacteria on decomposing leaves in a low-order stream". Paper presented in 11th International Symposium on Microbial Ecology (ISME-11), 2006.
  55. Duarte, Sofia; Pascoal, Cláudia; Alves, A.; Correia, A; Cássio, F. "Effects of copper and zinc mixtures on leaf decomposition by freshwater fungi and bacteria". Paper presented in 11th International Symposium on Microbial Ecology (ISME-11), 2006.
  56. Borges, F; Duarte, Sofia; Pascoal, Cláudia; Cássio, F. "Assessment of fungal biomass based on Denaturing Gradient Gel Electrophoresis band intensities". Paper presented in 11th International Symposium on Microbial Ecology (ISME-11), 2006.
  57. Duarte, Sofia; Pascoal, Cláudia; Cássio, F. "Fungal diversity may be more sensitive to pollution than fungal biomass and leaf decomposition in streams". Paper presented in XIII Congress of the Iberian Association of Limnology (AIL), 2006.
Journal article
  1. Lavrador, Ana S.; Amaral, Fábio G.; Moutinho, Jorge; Vieira, Pedro E.; Costa, Filipe O.; Duarte, Sofia. "Comprehensive DNA metabarcoding-based detection of non-indigenous invertebrates in recreational marinas through a multi-substrate approach". Marine Environmental Research 200 (2024): 106660. http://dx.doi.org/10.1016/j.marenvres.2024.106660.
    10.1016/j.marenvres.2024.106660
  2. Ferreira, André O.; Azevedo, Olga M.; Barroso, Cristina; Duarte, Sofia; Egas, Conceição; Fontes, João T.; Ré, Pedro; Santos, A. Miguel P.; Costa, Filipe O.. "Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples". Scientific Reports 14 1 (2024): http://dx.doi.org/10.1038/s41598-024-69963-7.
    10.1038/s41598-024-69963-7
  3. Moutinho, Jorge; Carreira-Flores, Diego; Gomes, Pedro T.; Costa, Filipe O.; Duarte, Sofia. "Assessing the Seasonal and Spatial Dynamics of Zooplankton through DNA Metabarcoding in a Temperate Estuary". Animals 13 24 (2023): 3876. http://dx.doi.org/10.3390/ani13243876.
    10.3390/ani13243876
  4. Duarte, Sofia; Simões, Luara; Costa, Filipe O.. "Current status and topical issues on the use of eDNA-based targeted detection of rare animal species". Science of The Total Environment 904 (2023): 166675. http://dx.doi.org/10.1016/j.scitotenv.2023.166675.
    10.1016/j.scitotenv.2023.166675
  5. Carvalho, Susana; Shchepanik, Hailey; Aylagas, Eva; Berumen, Michael L; Costa, Filipe O; Costello, Mark John; Duarte, Sofia; et al. "Hurdles and opportunities in implementing marine biosecurity systems in data-poor regions". BioScience 73 7 (2023): 494-512. http://dx.doi.org/10.1093/biosci/biad056.
    10.1093/biosci/biad056
  6. Colls, Miriam; Viza, Aida; Zufiarre, Aitziber; Camacho-Santamans, Alba; Laini, Alex; González-Ferreras, Alexia Maria; Filipe, Ana Filipa; et al. "Impacts of diffuse urban stressors on stream benthic communities and ecosystem functioning: A review". Limnetica 43 1 (2023): 1. http://dx.doi.org/10.23818/limn.43.07.
    10.23818/limn.43.07
  7. Leite, Barbara R.; Duarte, Sofia; Troncoso, Jesús S.; Costa, Filipe O.. "Artificial Seaweed Substrates Complement ARMS in DNA Metabarcoding-Based Monitoring of Temperate Coastal Macrozoobenthos". Diversity 15 5 (2023): 657. http://dx.doi.org/10.3390/d15050657.
    10.3390/d15050657
  8. Duarte, Sofia; Vieira, Pedro E.; Leite, Barbara R.; Teixeira, Marcos A.L.; Neto, João M.; Costa, Filipe O.. "Macrozoobenthos monitoring in Portuguese transitional waters in the scope of the water framework directive using morphology and DNA metabarcoding". Estuarine, Coastal and Shelf Science 281 (2023): 108207. http://dx.doi.org/10.1016/j.ecss.2022.108207.
    10.1016/j.ecss.2022.108207
  9. Lavrador, Ana S.; Fontes, João T.; Vieira, Pedro E.; Costa, Filipe O.; Duarte, Sofia. "Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions". Diversity 15 2 (2023): 174. http://dx.doi.org/10.3390/d15020174.
    10.3390/d15020174
  10. Ferreira, André O.; Barroso, Cristina; Cruz, Joana; Duarte, Sofia; Egas, Conceição; Gomes, Pedro; Oliveira, Cláudio; et al. "Testing COI primers for ichthyoplankton metabarcoding and their capability to assess local mesozooplankton communities". ARPHA Conference Abstracts 5 (2022): http://dx.doi.org/10.3897/aca.5.e87495.
    10.3897/aca.5.e87495
  11. Moutinho, Jorge; Lavrador, Ana S.; Vieira, Pedro E.; Costa, Filipe O.; Duarte, Sofia. "Assessing the seasonal dynamics of zooplankton in a recreational marina of the northwest of Portugal through multi-marker DNA metabarcoding". ARPHA Conference Abstracts 5 (2022): http://dx.doi.org/10.3897/aca.5.e87492.
    10.3897/aca.5.e87492
  12. Amaral, Fábio; Lavrador, Ana Sofia; Duarte, Sofia; Costa, Filipe; Vieira, Pedro. "Detection and monitoring of invertebrate non-indigenous species through DNA metabarcoding in a recreational marina of the Northwest of Portugal". ARPHA Conference Abstracts 5 (2022): http://dx.doi.org/10.3897/aca.5.e87557.
    10.3897/aca.5.e87557
  13. Pawlowski, J.; Bruce, K.; Panksep, K.; Aguirre, F.I.; Amalfitano, S.; Apothéloz-Perret-Gentil, L.; Baussant, T.; et al. "Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods". Science of The Total Environment (2022): 151783. http://dx.doi.org/10.1016/j.scitotenv.2021.151783.
    10.1016/j.scitotenv.2021.151783
  14. Adriana E. Radulovici; Pedro E. Vieira; Sofia Duarte; Marcos A. L. Teixeira; Luisa M. S. Borges; Bruce E. Deagle; Sanna Majaneva; et al. "Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon". Metabarcoding and Metagenomics (2021): https://doi.org/10.3897/mbmg.5.67862.
    10.3897/mbmg.5.67862
  15. Bellisario, Bruno; Fais, Maria; Duarte, Sofia; Vieira, Pedro E.; Canchaya, Carlos; Costa, Filipe O.. "The network structure of intertidal meiofaunal communities from environmental DNA metabarcoding surveys in Northwest Iberia". Aquatic Sciences 83 4 (2021): http://dx.doi.org/10.1007/s00027-021-00828-1.
    10.1007/s00027-021-00828-1
  16. Vieira, Pedro E.; Lavrador, Ana S.; Parente, Manuela I.; Parretti, Paola; Costa, Ana C.; Costa, Filipe O.; Duarte, Sofia. "Gaps in DNA sequence libraries for Macaronesian marine macroinvertebrates imply decades till completion and robust monitoring". Diversity and Distributions (2021): http://dx.doi.org/10.1111/ddi.13305.
    Published • 10.1111/ddi.13305
  17. Lavrador, Ana; Amaral, Fábio; Vieira, Pedro E.; Costa, Filipe; Duarte, Sofia. "Surveillance of non-indigenous invertebrate species through DNA metabarcoding in recreational marinas in the North and Center of Portugal". ARPHA Conference Abstracts 4 (2021): http://dx.doi.org/10.3897/aca.4.e64900.
    10.3897/aca.4.e64900
  18. Duarte, Sofia; Vieira, Pedro E.; Lavrador, Ana S.; Costa, Filipe O.. "Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding". Science of The Total Environment (2021): 141729. http://dx.doi.org/10.1016/j.scitotenv.2020.141729.
    Published • 10.1016/j.scitotenv.2020.141729
  19. Duarte, Sofia; Leite, Barbara R.; Feio, Maria João; Costa, Filipe O.; Filipe, Ana Filipa. "Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates". Water 13 3 (2021): 331. http://dx.doi.org/10.3390/w13030331.
    Published • 10.3390/w13030331
  20. Duarte, Sofia; Vieira, Pedro E.; Costa, Filipe O.. "Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions". Metabarcoding and Metagenomics 4 (2020): http://dx.doi.org/10.3897/mbmg.4.55162.
    10.3897/mbmg.4.55162
  21. Mora-Gómez, J; Boix, D; Duarte, Sofia; Cássio, F; Pascoal, C; Elosegi, A; Romaní, AM. "Legacy of Summer Drought on Autumnal Leaf Litter Processing in a Temporary Mediterranean Stream". Ecosystems 23 (2020): 989-1003. http://dx.doi.org/10.1007/s10021-019-00451-0.
    10.1007/s10021-019-00451-0
  22. Fais, Maria; Bellisario, Bruno; Duarte, Sofia; Vieira, Pedro Emanuel; Sousa, Ronaldo; Canchaya, Carlos; Costa, Filipe Oliveira. "Meiofauna metabarcoding in Lima estuary (Portugal) suggests high taxon replacement within a background of network stability". Regional Studies in Marine Science 38 (2020): 101341. http://dx.doi.org/10.1016/j.rsma.2020.101341.
    10.1016/j.rsma.2020.101341
  23. Leite, B.R.; Vieira, P.E.; Teixeira, M.A.L.; Lobo-Arteaga, J.; Hollatz, C.; Borges, L.M.S.; Duarte, S.; Troncoso, J.S.; Costa, F.O.. "Gap-analysis and annotated reference library for supporting macroinvertebrate metabarcoding in Atlantic Iberia". Regional Studies in Marine Science (2020): 101307. http://dx.doi.org/10.1016/j.rsma.2020.101307.
    10.1016/j.rsma.2020.101307
  24. Fais, M; Duarte, Sofia; Vieira, P; Hajibabaei, M; Canchaya, CA; Costa, FO. "Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding". Estuarine, Coastal and Shelf Science (2020): 106683. http://dx.doi.org/10.1016/j.ecss.2020.106683.
    10.1016/j.ecss.2020.106683
  25. Feio, M-J; Filipe, AF; Garcia-Raventós, A; Ardura, A; Calapez, AR; Pujante, AM; Mortágua, A; et al. "Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems". Limnetica (2020): http://doi.org/10.23818/limn.39.27.
    10.23818/limn.39.27
  26. Duarte, Sofia; Antunes, B; Trabulo, J; Seena, S; Cássio, F; Pascoal, C. "Intraspecific diversity affects stress response and the ecological performance of a cosmopolitan aquatic fungus". Fungal Ecology 41 (2019): 218-223. http://dx.doi.org/10.1016/j.funeco.2019.06.001.
    10.1016/j.funeco.2019.06.001
  27. Weigand, H; Beermann, AJ; Ciampor, F; Costa, FO; Csabai, Z; Duarte, Sofia; Geiger, MF; et al. "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 (2019): 499-524. http://dx.doi.org/10.1016/j.scitotenv.2019.04.247.
    10.1016/j.scitotenv.2019.04.247
  28. Duarte, Sofia; Vieira, Pedro; Costa, Filipe. "Current status of the DNA barcode reference library of non-indigenous marine species occurring in European coastal regions". Frontiers in Marine Science 6 (2019): http://dx.doi.org/10.3389/conf.fmars.2019.08.00169.
    10.3389/conf.fmars.2019.08.00169
  29. Duarte, Sofia; Parente, Manuela; Costa, Ana; Costa, Filipe. "Species gap analysis in DNA barcode reference libraries of marine non-indigenous species in the Azores archipelago". Frontiers in Marine Science 6 (2019): http://dx.doi.org/10.3389/conf.fmars.2019.08.00170.
    10.3389/conf.fmars.2019.08.00170
  30. Fais, Maria; Duarte, Sofia; Vieira, Pedro; Sousa, Ronaldo; Hajibabaei, Mehrdad; Canchaya, Carlos; Costa, Filipe. "Patterns of spatial and temporal variation in estuarine meiofaunal communities assessed through DNA metabarcoding: a case study in the Lima estuary (NW Portugal)". Frontiers in Marine Science 6 (2019): http://dx.doi.org/10.3389/conf.fmars.2019.08.00060.
    10.3389/conf.fmars.2019.08.00060
  31. Mora-Gómez, Juanita; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Romaní, Anna M.. "Microbial decomposition is highly sensitive to leaf litter emersion in a permanent temperate stream". Science of The Total Environment 621 (2018): 486-496. http://dx.doi.org/10.1016/j.scitotenv.2017.11.055.
    10.1016/j.scitotenv.2017.11.055
  32. Azevedo, Maria-Manuel; Duarte, Sofia. "Continuous Enhancement of Science Teachers’ Knowledge and Skills through Scientific Lecturing". Frontiers in Public Health 6 (2018): http://dx.doi.org/10.3389/fpubh.2018.00041.
    10.3389/fpubh.2018.00041
  33. Duarte, Sofia; Mora-Gómez, Juanita; Romaní, Anna M.; Cássio, Fernanda; Pascoal, Cláudia. "Responses of microbial decomposers to drought in streams may depend on the environmental context". Environmental Microbiology Reports 9 6 (2017): 756-765. http://dx.doi.org/10.1111/1758-2229.12592.
    10.1111/1758-2229.12592
  34. Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Bärlocher, Felix. "Taxa-area relationship of aquatic fungi on deciduous leaves". PLOS ONE 12 7 (2017): e0181545. http://dx.doi.org/10.1371/journal.pone.0181545.
    10.1371/journal.pone.0181545
  35. Duarte, S.; Cássio, F.; Pascoal, C.. "Environmental drivers are more important for structuring fungal decomposer communities than the geographic distance between streams". Limnetica 36 2 (2017): 491-506. http://www.scopus.com/inward/record.url?eid=2-s2.0-85024480917&partnerID=MN8TOARS.
    10.23818/limn.36.17
  36. Leese, Florian; Altermatt, Florian; Bouchez, Agnès; Ekrem, Torbjørn; Hering, Daniel; Meissner, Kristian; Mergen, Patricia; et al. "DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe". Research Ideas and Outcomes 2 (2016): e11321. http://dx.doi.org/10.3897/rio.2.e11321.
    10.3897/rio.2.e11321
  37. Mora-Gómez, Juanita; Elosegi, Arturo; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Romaní, Anna M.. "Differences in the sensitivity of fungi and bacteria to season and invertebrates affect leaf litter decomposition in a Mediterranean stream". FEMS Microbiology Ecology 92 8 (2016): fiw121. http://dx.doi.org/10.1093/femsec/fiw121.
    10.1093/femsec/fiw121
  38. Pereira, Ana; Trabulo, José; Fernandes, Isabel; Pascoal, Cláudia; Cássio, Fernanda; Duarte, Sofia. "Spring stimulates leaf decomposition in moderately eutrophic streams". Aquatic Sciences 79 1 (2016): 197-207. http://dx.doi.org/10.1007/s00027-016-0490-3.
    10.1007/s00027-016-0490-3
  39. Duarte, Sofia; Cássio, Fernanda; Ferreira, Verónica; Canhoto, Cristina; Pascoal, Cláudia. "Seasonal Variability May Affect Microbial Decomposers and Leaf Decomposition More Than Warming in Streams". Microbial Ecology 72 2 (2016): 263-276. http://dx.doi.org/10.1007/s00248-016-0780-2.
    10.1007/s00248-016-0780-2
  40. Fernández, Diego; Tummala, Mallikarjun; Schreiner, Verena C.; Duarte, Sofia; Pascoal, Cláudia; Winkelmann, Carola; Mewes, Daniela; Muñoz, Katherine; Schäfer, Ralf B.. "Does nutrient enrichment compensate fungicide effects on litter decomposition and decomposer communities in streams?". Aquatic Toxicology 174 (2016): 169-178. http://dx.doi.org/10.1016/j.aquatox.2016.02.019.
    10.1016/j.aquatox.2016.02.019
  41. Ferreira, Verónica; Koricheva, Julia; Duarte, Sofia; Niyogi, Dev K.; Guérold, François. "Effects of anthropogenic heavy metal contamination on litter decomposition in streams: A meta-analysis". Environmental Pollution 210 (2016): 261-270. http://dx.doi.org/10.1016/j.envpol.2015.12.060.
    10.1016/j.envpol.2015.12.060
  42. Duarte, Sofia; Bärlocher, Felix; Pascoal, Cláudia; Cássio, Fernanda. "Biogeography of aquatic hyphomycetes: Current knowledge and future perspectives". Fungal Ecology 19 (2016): 169-181. http://dx.doi.org/10.1016/j.funeco.2015.06.002.
    10.1016/j.funeco.2015.06.002
  43. Maria, Fais; Claudia, Hollatz; Jorge, Lobo; Sofia, Duarte; Luisa, Borges; Filipe, Costa. "Compiling a DNA barcode reference library for benthic molluscs of the Southern European Atlantic coast.". Frontiers in Marine Science 3 (2016): http://dx.doi.org/10.3389/conf.fmars.2016.05.00132.
    10.3389/conf.fmars.2016.05.00132
  44. Fernandes, Isabel; Pereira, Ana; Trabulo, José; Pascoal, Cláudia; Cássio, Fernanda; Duarte, Sofia. "Microscopy- or DNA-based analyses: Which methodology gives a truer picture of stream-dwelling decomposer fungal diversity?". Fungal Ecology 18 (2015): 130-134. http://dx.doi.org/10.1016/j.funeco.2015.08.005.
    10.1016/j.funeco.2015.08.005
  45. Duarte, Sofia; Batista, Daniela; Bärlocher, Felix; Cássio, Fernanda; Pascoal, Cláudia. "Some new DNA barcodes of aquatic hyphomycete species". Mycoscience 56 1 (2015): 102-108. http://dx.doi.org/10.1016/j.myc.2014.04.002.
    10.1016/j.myc.2014.04.002
  46. Fernandes, Isabel; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia. "Plant litter diversity affects invertebrate shredder activity and the quality of fine particulate organic matter in streams". Marine and Freshwater Research 66 5 (2015): 449. http://dx.doi.org/10.1071/mf14089.
    10.1071/mf14089
  47. Duarte, Sofia; Bärlocher, Felix; Trabulo, José; Cássio, Fernanda; Pascoal, Cláudia. "Stream-dwelling fungal decomposer communities along a gradient of eutrophication unraveled by 454 pyrosequencing". Fungal Diversity 70 1 (2014): 127-148. http://dx.doi.org/10.1007/s13225-014-0300-y.
    10.1007/s13225-014-0300-y
  48. Duarte, Sofia; Bärlocher, Felix; Cássio, Fernanda; Pascoal, Cláudia. "Current status of DNA barcoding of aquatic hyphomycetes". Sydowia 66 2 (2014): 191-202. http://www.scopus.com/inward/record.url?eid=2-s2.0-84922561871&partnerID=MN8TOARS.
    10.12905/0380.sydowia66(2)2014-0191
  49. Fernandes, Isabel; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia. "Effects of Riparian Plant Diversity Loss on Aquatic Microbial Decomposers Become More Pronounced with Increasing Time". Microbial Ecology 66 4 (2013): 763-772. http://dx.doi.org/10.1007/s00248-013-0278-0.
    10.1007/s00248-013-0278-0
  50. Duarte, Sofia; Fernandes, Isabel; Nogueira, Maria João; Cássio, Fernanda; Pascoal, Cláudia. "Temperature alters interspecific relationships among aquatic fungi". Fungal Ecology 6 3 (2013): 187-191. http://dx.doi.org/10.1016/j.funeco.2013.02.001.
    10.1016/j.funeco.2013.02.001
  51. Duarte, Sofia; Seena, Sahadevan; Bärlocher, Felix; Pascoal, Cláudia; Cássio, Fernanda. "A decade's perspective on the impact of DNA sequencing on aquatic hyphomycete research". Fungal Biology Reviews 27 1 (2013): 19-24. http://dx.doi.org/10.1016/j.fbr.2013.02.003.
    10.1016/j.fbr.2013.02.003
  52. Duarte, Sofia; Seena, Sahadevan; Bärlocher, Felix; Cássio, Fernanda; Pascoal, Cláudia. "Preliminary Insights into the Phylogeography of Six Aquatic Hyphomycete Species". PLoS ONE 7 9 (2012): e45289. http://dx.doi.org/10.1371/journal.pone.0045289.
    10.1371/journal.pone.0045289
  53. Seena, Sahadevan; Duarte, Sofia; Pascoal, Cláudia; Cássio, Fernanda. "Intraspecific Variation of the Aquatic Fungus Articulospora tetracladia: An Ubiquitous Perspective". PLoS ONE 7 4 (2012): e35884. http://dx.doi.org/10.1371/journal.pone.0035884.
    10.1371/journal.pone.0035884
  54. Duarte, Sofia; Fidalgo, Maria Leonor; Pascoal, Cláudia; Cássio, Fernanda. "The role of the freshwater shrimp Atyaephyra desmarestii in leaf litter breakdown in streams". Hydrobiologia 680 1 (2011): 149-157. http://dx.doi.org/10.1007/s10750-011-0912-0.
    10.1007/s10750-011-0912-0
  55. Moreirinha, Catarina; Duarte, Sofia; Pascoal, Cláudia; Cássio, Fernanda. "Effects of Cadmium and Phenanthrene Mixtures on Aquatic Fungi and Microbially Mediated Leaf Litter Decomposition". Archives of Environmental Contamination and Toxicology 61 2 (2010): 211-219. http://dx.doi.org/10.1007/s00244-010-9610-6.
    10.1007/s00244-010-9610-6
  56. Duarte, Sofia; Pascoal, Cláudia; Alves, Artur; Correia, António; Cássio, Fernanda. "Assessing the dynamic of microbial communities during leaf decomposition in a low-order stream by microscopic and molecular techniques". Microbiological Research 165 5 (2010): 351-362. http://dx.doi.org/10.1016/j.micres.2009.06.002.
    10.1016/j.micres.2009.06.002
  57. Medeiros, Adriana; Duarte, Sofia; Pascoal, Cláudia; Cássio, Fernanda; Graça, Manuel. "Effects of Zn, Fe and Mn on Leaf Litter Breakdown by Aquatic Fungi: a Microcosm Study". International Review of Hydrobiology 95 1 (2010): 12-26. http://dx.doi.org/10.1002/iroh.200911182.
    10.1002/iroh.200911182
  58. Sridhar, K. R.; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia. "The Role of Early Fungal Colonizers in Leaf-Litter Decomposition in Portuguese Streams Impacted by Agricultural Runoff". International Review of Hydrobiology 94 4 (2009): 399-409. http://dx.doi.org/10.1002/iroh.200811154.
    10.1002/iroh.200811154
  59. Duarte, Sofia; Pascoal, Cláudia; Cássio, Fernanda. "Functional stability of stream-dwelling microbial decomposers exposed to copper and zinc stress". Freshwater Biology 54 8 (2009): 1683-1691. http://dx.doi.org/10.1111/j.1365-2427.2009.02217.x.
    10.1111/j.1365-2427.2009.02217.x
  60. Duarte, Sofia; Pascoal, Cláudia; Garabétian, Frédérique; Cássio, Fernanda; Charcosset, Jean-Yves. "Microbial Decomposer Communities Are Mainly Structured by Trophic Status in Circumneutral and Alkaline Streams". Applied and Environmental Microbiology 75 19 (2009): 6211-6221. http://dx.doi.org/10.1128/aem.00971-09.
    10.1128/aem.00971-09
  61. Fernandes, Isabel; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia. "Mixtures of zinc and phosphate affect leaf litter decomposition by aquatic fungi in streams". Science of The Total Environment 407 14 (2009): 4283-4288. http://dx.doi.org/10.1016/j.scitotenv.2009.04.007.
    10.1016/j.scitotenv.2009.04.007
  62. Duarte, Sofia; Pascoal, Cláudia; Cássio, Fernanda. "High Diversity of Fungi may Mitigate the Impact of Pollution on Plant Litter Decomposition in Streams". Microbial Ecology 56 4 (2008): 688-695. http://dx.doi.org/10.1007/s00248-008-9388-5.
    10.1007/s00248-008-9388-5
  63. DUARTE, SOFIA; PASCOAL, CLÁUDIA; ALVES, ARTUR; CORREIA, ANTÓNIO; CÁSSIO, FERNANDA. "Copper and zinc mixtures induce shifts in microbial communities and reduce leaf litter decomposition in streams". Freshwater Biology 0 0 (2007): 070908014237001-???. http://dx.doi.org/10.1111/j.1365-2427.2007.01869.x.
    10.1111/j.1365-2427.2007.01869.x
  64. Duarte, Sofia; Pascoal, Cláudia; Cássio, Fernanda; Bärlocher, Felix. "Aquatic hyphomycete diversity and identity affect leaf litter decomposition in microcosms". Oecologia 147 4 (2006): 658-666. http://dx.doi.org/10.1007/s00442-005-0300-4.
    10.1007/s00442-005-0300-4
  65. Duarte, S.; Pascoal, C.; Cássio, F.. "Effects of Zinc on Leaf Decomposition by Fungi in Streams: Studies in Microcosms". Microbial Ecology 48 3 (2004): 366-374. http://dx.doi.org/10.1007/s00248-003-2032-5.
    10.1007/s00248-003-2032-5
Manual
  1. Duarte, S. Manual of the Teoretical-practical classes of Eye Pharmacology. University of Minho, Braga, Portugal. 2022.
    Published
  2. Pascoal, Cláudia; Aguiar, Cristina; Costa, Manuela; Varela, Paulo; Paiva, Sandra; Duarte, Sofia. Science from 3 to 11 - Experimental activities in Biology and Environment. University of Minho, Braga, Portugal. 2013.
    Published
  3. Duarte, Sofia; Paiva, Sandra. Pharmacology - Theoretical-practical exercises. University of Minho, Braga, Portugal. 2011.
  4. Azevedo, Maria-Manuel; Duarte, Sofia; Paiva, Sandra. Physiological systems: from theory to practice. University of Minho, Braga, Portugal. 2011.
    Published
Newspaper article
  1. Duarte, Sofia. "Ingold's journey in the discovery of aquatic hyphomycetes: the main agents of organic matter recycling in rivers", Correio do Minho, 2013
Online resource
  1. Fernandes, Isabel; Batista, Daniela; Pereira, Ana; Cássio, Fernanda; Pascoal, Cláudia; Duarte, Sofia. GenBank Accession numbers: KF952606-KF952741 (136 ITS sequences), under the project "DNA barcoding of aquatic fungi". 2013.
  2. Duarte, S; Batista, Daniela; Cássio, Fernanda; Pascoal, Cláudia. GenBank Accession numbers: KF730795-KF730849 (55 ITS sequences), under the project "New DNA barcodes for 9 aquatic hyphomycete species". 2013.
  3. Duarte, S; Seena, Sahadevan; Pascoal, Cláudia; Cássio, Fernanda. GenBank Accession numbers: JX089461-JX089572 (111 ITS sequences), under the project "Preliminary insights into the phylogeography of six aquatic hyphomycete species". 2012.
  4. Seena, Sahadevan; Duarte, S; Pascoal, Cláudia; Cássio, Fernanda. GenBank Accession numbers: JF895397-JF895437 (41 ITS sequences), under the project "Intraspecific variation of the aquatic fungus Articulospora tetracladia: an ubiquitous perspective". 2012.
Preprint
  1. Lavrador, Ana S.; Amaral, Fábio G.; Moutinho, Jorge; Vieira, Pedro E.; Costa, Filipe O.; Duarte, Sofia. "DNA metabarcoding-based detection of non-indigenous invertebrates in recreational marinas: influence of sample type and seasonal variation". 2024. http://dx.doi.org/10.1101/2024.01.25.577180.
    10.1101/2024.01.25.577180
  2. Ferreira, André O.; Azevedo, Olga M.; Barroso, Cristina; Duarte, Sofia; Egas, Conceição; Fontes, João T.; Ré, Pedro; Piecho-Santos, A. Miguel; Costa, Filipe O.. "Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples: a proof-of-concept study". 2024. http://dx.doi.org/10.21203/rs.3.rs-4600568/v1.
    10.21203/rs.3.rs-4600568/v1
  3. Duarte, Sofia; Simões, Luara; Costa, Filipe O.. "Catch me if you can: current status and topical issues on the use of eDNA-based targeted detection of rare and endangered animal species". 2023. http://dx.doi.org/10.1101/2023.06.13.544783.
    10.1101/2023.06.13.544783
  4. Duarte, Sofia; Vieira, Pedro E.; Leite, Barbara R.; Teixeira, Marcos A.L.; Neto, João M.; Costa, Filipe O.. "Comparing DNA metabarcoding with morphology in the assessment of macrozoobenthos in Portuguese transitional waters in the scope of the Water Framework Directive monitoring". 2022. http://dx.doi.org/10.1101/2022.05.10.491303.
    10.1101/2022.05.10.491303
  5. Bellisario, Bruno; Fais, Maria; Duarte, Sofia; Vieira, Pedro E.; Canchaya, Carlos; Costa, Filipe O.. "The spatial network structure of intertidal meiofaunal communities derived from environmental DNA metabarcoding surveys in Northwest Iberia". 2021. http://dx.doi.org/10.1101/2021.03.16.435605.
    10.1101/2021.03.16.435605
  6. Radulovici, Adriana E.; Vieira, Pedro E.; Duarte, Sofia; Teixeira, Marcos A. L.; Borges, Luisa M. S.; Deagle, Bruce; Majaneva, Sanna; et al. "Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon". 2021. http://dx.doi.org/10.1101/2021.03.07.434272.
    10.1101/2021.03.07.434272
  7. Duarte, Sofia; Vieira, Pedro E.; Lavrador, Ana S.; Costa, Filipe O.. "Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding". 2020. http://dx.doi.org/10.1101/2020.05.25.114280.
    10.1101/2020.05.25.114280
  8. Weigand, Hannah; Beermann, Arne J.; Ciampor, Fedor; Costa, Filipe O.; Csabai, Zoltán; Duarte, Sofia; Geiger, Matthias F.; et al. "DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work". 2019. http://dx.doi.org/10.1101/576553.
    10.1101/576553
Thesis / Dissertation
  1. Duarte, S. "Biodiversity and activity of microbial decomposers in streams under anthropogenic stress". PhD, Universidade do Minho Escola de Ciências, 2008.
  2. Duarte, S. "Effects of zinc on Alnus glutinosa litter decomposition by aquatic hyphomycetes: studies in stream and microcosms". Degree, Universidade do Minho Departamento de Biologia, 2002.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/10/20 Seasonal variation of non-indigenous invertebrate species in recreational marinas in the Northwest of Portugal using DNA metabarcoding: impact of sample type IV International Meeting of the Portuguese Society of Genetics (IMPSG)
Portuguese Society of Genetics (IMPSG) (Braga, Portugal)
2023/09/11 Seasonal variation of non-indigenous invertebrate species in recreational marinas in the north of Portugal using DNA metabarcoding: impact of substrate selection ICES Annual Science Conference 2023
AZTI (Bilbao, Spain)
2023/07/19 Developing and implementing DNA-based tools for detecting and monitoring non-indigenous species (NIS) in Portuguese coastal ecosystems Workshop Monitoring marine non-indigenous species through introduction sites
Central Fisheries Research Institute (Trabzon, Turkey)
2023/05/07 A proof-of-concept study to use DNA metabarcoding as a tool for species identification in ichthyoplankton samples 46th Larval fish conference
Early Life History Section of the American Fisheries Society (Lisbon, Portugal)
2021/11/26 Developing and implementing DNA-based tools for detection and monitoring of non-indigenous species (NIS) in Portuguese coastal ecosystems Marine biodiversity unravelled by DNA: from polychaetes and crustaceans to non-indigenous species
Advanced Topics in Biodiversity, Ecology and Global Change (Beagle)
2021/09/03 A matter of DNA...of marine exotic species Piquenique no Jardim
Planetário-Centro Ciência Viva de Braga (Braga)
2021/06/15 DNA-based monitoring of non-indigenous species in Portuguese coastal ecosystems Workshop Biological Invasions in the Red Sea: emerging challenges and opportunities
KAUST university (Saudi Arabia)
2021/06 Urbanization effects on river biofilm metabolism along a European gradient Symposium for European Freshwater Sciences (SEFS 12)
2021/02/11 Monitoring in the marine environment: molecular approaches for exotic species detection Mar de Conversas
FPAS (Portugal)
2021/02/08 Detection and monitoring of non-indigenous species in coastal ecosystems through DNA-based tools: are we ready? Science on the Screen
CBMA (Portugal)
2020/12/09 Monitoring non-indigenous species in marine and coastal ecosystems through molecular tools: are we ready? XIX Encontro Nacional de Ecologia
Sociedade Portuguesa de Ecologia (Portugal)
2020/12/09 Detection of non-indigenous invertebrate species in the marina of Viana do Castelo through DNA metabarcoding XIX Encontro Nacional de Ecologia
Sociedade Portuguesa de Ecologia (Portugal)
2020/12/09 Surveillance of non-indigenous invertebrate species in recreational marinas in the North and Center of Portugal through DNA metabarcoding TiBE | Metabarcoding and Metagenomics
CIBIO-InBIO (Vila do Conde, Portugal)
2020/11/27 A barcode for all exotic marine species Pint of Science - European Researchers’ Night Special Edition
(Portugal)
2020/10/26 Are we ready to monitor non-indigenous species in aquatic ecosystems through DNA metabarcoding? XX congress of the Iberian Association of Limnology (AIL)
Iberian Association of Limnology (AIL) (Spain)
2020/02/19 A barcode for all the species Os Investigadores voltam às escolas
Escola Secundária Rocha Peixoto (Póvoa de Varzim, Portugal)
2020/02/11 Genetic barcodes and exotic species Dia internacional das Mulheres e Meninas na Ciência
Planetário-Centro Ciência Viva de Braga (Braga, Portugal)
2019/11/20 A barcode for all the species Os investigadores voltam às escolas
Escola Secundária Alcaides de Faria (Barcelos, Portugal)
2019/11/07 NIS-DNA: Early detection and monitoring of non-indigenous species in Portuguese coastal ecosystems based on DNA-based tools Master in Ecology (Molecular Ecology class)
Department of Biology, University of Minho (Braga, Portugal)
2019/09/12 Patterns of spatial and temporal variation in estuarine meiofaunal communities assessed through DNA metabarcoding: a case study in the Lima estuary (NW Portugal) 20th Iberian Symposium on Marine Biology Studies (XX SIEBM)
University of Minho (Braga, Portugal)
2019/06/10 Assessing the diversity of meiofaunal communities in estuarine sediments through metabarcoding WG2-3 Workshop: Sedimentary DNA – sampling preservation and extraction
DNAqua-Net (Roma, Italy)
2019/05/24 NIS-DNA: Early detection and monitoring of non-indigenous species in Portuguese coastal ecosystems based on DNA-based tools Spring Seminar BIOISLES
CIBIO-InBIO, University of Açores (Ponta Delgada, Portugal)
2019/04/02 Detection of non-indigenous species in coastal and marine ecosystems through DNA Os investigadores voltam às escolas
Colégio Nova Encosta (Paços de Ferreira, Portugal)
2018/11/22 The use of metabarcoding to assess the diversity of estuarine/marine communities: the case of meiofauna and non-indigenous species Master in Ecology (Molecular Ecology class)
Department of Biology, University of Minho (Braga, Portugal)
2018/07 Surveying estuarine meiobenthos through DNA metabarcoding: a pilot study in the Lima estuary (NW Portugal) 3rd Central European Symposium for Aquatic Macroinvertebrate Research
University of Lodz (Lódz, Poland)
2018/06 Metabarcoding of meiobenthic estuarine communities: optimization of protocols XIX congress of the Iberian Association of Limnology (AIL)
University of Coimbra (Coimbra, Portugal)
2018/06 A timely look at effects of agriculture on fluvial DOM: the role of hydrology XIX congress of the Iberian Association of Limnology (AIL)
University of Coimbra (Coimbra, Portugal)
2017/02/24 Biogeography of aquatic fungi: insights from freshwater and marine ecosystems
AZTI-Tecnalia (Pasaia, Spain)
2016/10 Microscopy- or DNA-based analyses: which methodology gives a truer picture of decomposer fungal diversity in streams? Conference community Ecology for the 21st century – from genes to ecosystems
CIBIO-InBIO (Portugal)
2016/07/12 The impact of next generation sequencing on Microbial Ecology: insights from aquatic ecosystems Advanced course in Genomics Metagenomics and Bioinformatics
Department of Biology, University of Minho (Braga, Portugal)
2016/07/07 Biogeography of stream-dwelling decomposer fungi: current knowledge and future perspectives XVIII Congress of the Iberian Association of Limnology (AIL)
Iberian Association of Limnology (Tortosa, Spain)
2016/07 Effects of anthropogenic heavy metal contamination on litter decomposition in streams: a meta-analysis XVIII Congress of the Iberian Association of Limnology (AIL)
Iberian Association of Limnology (AIL) (Tortosa, Spain)
2015/08 Sensitivity of fungal and bacterial assemblages to seasonality and invertebrates results in differential leaf litter decomposition Second EMBO Conference on Aquatic Microbial Ecology: SAME-14
(Uppsala, Sweden)
2015/07/09 Assessing diversity of decomposer fungal communities in streams by 454 pyrosequencing Advanced course in next generation sequencing
Department of Biology, University of Minho (Braga, Portugal)
2015/05 Effects of fungicides on decomposer communities and leaf decomposition in streams SETAC Europe 25th Annual Meeting
(Barcelona, Spain)
2015/02 Drought duration affects microbial processing of plant-litter in a temperate stream Aquatic Sciences Meeting (ASLO)
(Granada, Spain)
2015/01/27 Diversity and activity of leaf-decomposing fungi in streams IV Ciclo de Conferências Científicas 2015
Escola Secundária Camilo Castelo Branco (Vila Nova de Famalicão, Portugal)
2014/07 Diversity of stream-dwelling fungal decomposer communities unravelled by 454 pyrosequencing XVII Congress of the Iberian Association of Limnology (AIL)
Iberian Association of Limnology (AIL) (Santander, Spain)
2014/07 Seasonal effects of eutrophication on litter decomposition and associated fungal and invertebrate communities XVII Congress of the Iberian Association of Limnology (AIL)
Iberian Association of Limnology (AIL) (Santander, Spain)
2013/07/18 The impact of DNA barcoding on aquatic hyphomycete research: preliminary studies Advanced course on Microbial diversity: methods and applications
Department of Biology, University of Aveiro (Aveiro, Portugal)
2013/07 A decade's perspective on the impact of DNA sequencing on aquatic hyphomycete research Symposium for European Freshwater Sciences (SEFS 8)
(Münster, Germany)
2013/07 Effects of riparian plant diversity loss on detritus food webs become more pronounced at longer times Symposium for European Freshwater Sciences (SEFS 8)
(Girona, Spain)
2013/04/10 The impact of DNA barcoding on aquatic hyphomycete research: preliminary studies DBio Seminars
Department of Biology, University of Minho (Braga, Portugal)
2013/02 Diversity and activity of leaf-decomposer fungi in streams: traditional and molecular approaches XIV Jornadas de Biologia Aplicada – BioPercursos no século XXI
Department of Biology, University of Minho (Braga, Portugal)
2012/07/09 Food preferences of the freshwater shrimp Atyaephyra desmarestii XV Congress of the Iberian Association of Limnology
Iberian Association of Limnology (Ponta Delgada, Portugal)
2012/07/05 Biogeography of aquatic fungi: preliminary conclusions XVI Congress of the Iberian Association of Limnology (AIL)
University of Minho (Guimarães, Portugal)
2011/11/23 Awakening for Science
Escola E. B. 2, 3 D. Maria II, Portugal (Vila Nova de Famalicão, Portugal)
2011/07 Long-term effects of riparian vegetation diversity on stream-dwelling microbes and litter decomposition Symposium for European Freshwater Sciences (SEFS 7)
University of Girona (Girona, Spain)
2010/06/16 Food preferences of the freshwater shrimp Atyaephyra desmarestii DBio Seminars
Department of Biology, University of Minho (Braga, Portugal)
2009/05/20 Effects of eutrophication on microbial decomposers of submerged leaf litter in streams DBio Seminars
Department of Biology, University of Minho (Braga, Portugal)
2008/07/24 Effects of eutrophication on microbial decomposers of submerged leaf litter 5th International Meeting on Plant Litter Processing in Freshwaters (PLPF 5)
University of Coimbra (Coimbra, Portugal)
2008/07 Effects of cadmium and phenantrene mixtures on leaf-litter decomposition by fungi in streams 5th International Meeting on Plant Litter Processing in Freshwaters (PLPF 5)
University of Coimbra (Coimbra, Portugal)
2007/05 Functional stability of microbial decomposers to stress induced by copper and zinc in streams SETAC Europe 17th Annual Meeting
Society of Environmental Toxicology and Chemistry (SETAC) (Porto, Portugal)
2005/12 Effects of species loss on the functioning of freshwater ecosystems Micro’05-Biotec’05
(Póvoa de Varzim, Portugal)
2005/11 Effects of aquatic hyphomycete species richness and identity on leaf mass loss, fungal biomass and conidium production The IX International Marine and Freshwater Mycology Symposium (IMFMS)
(Chiang Mae, Thailand)
2004/07/08 Effects of zinc on leaf decomposition by fungi in streams XII Congress of the Iberian Association of Limnology (AIL)
Iberian Association of Limnology (Porto, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2021/01/01 - Current Optimization of DNA metabarcoding for the early detection and improved monitoring of non-indigenous species (NIS) in Portuguese coastal ecosystems (UI/BD/150871/2021)
Supervisor
 Programa Doutoral em Biologia Molecular e Ambiental (PhD)
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2024 - 2025 Creating a DNA barcoding reference library of non-indigenous species in Portuguese marine and coastal ecosystems
Supervisor
 Genética Molecular (Master)
Universidade do Minho, Portugal
2021/02/01 - 2024/01/31 Exploring the use of environmental DNA to monitor the ichthyofauna and provide data to assist fish stock assessment in the Atlantic
Co-supervisor
 Doutoramento em Ciências, Área de conhecimento Biologia (PhD)
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2023/04 - 2024 Prevalence and genetic characterization of pathogenic mycobacteria in fish
Co-supervisor
 Genética Molecular (Master)
Universidade do Minho, Portugal
2023/04/01 - 2023/06/30 Development of an eDNA-based method for the detection and sustainable management of fish with commercial importance in the Minho region
Supervisor
 Research fellow (Other)
Universidade do Minho, Portugal
2023/04 - 2023/06 Estaremos preparados para monitorizar a biodiversidade de peixes da região do Minho através de DNA ambiental?
Supervisor
 Biologia Aplicada (Degree)
Universidade do Minho, Portugal
2021/07 - 2022/11/29 DNA metabarcoding monitoring of zooplankton for the detection of non-indigenous species (NIS): a seasonal study in a recreational marina of the northwest of Portugal
Supervisor
 Biodiversidade, Ecologia e Alterações Globais (Master)
Universidade do Minho, Portugal
2020/09/01 - 2022/02/11 Optimization of molecular tools for non-indigenous species monitoring in coastal regions in the North of Portugal
Supervisor
 Ecologia (Master)
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2022 - 2022 Comparison of diversity indices and occurrence patterns of marine invertebrate species
Co-supervisor
 Estatística Aplicada (Degree)
Universidade do Minho, Portugal
2021/05 - 2021/06 The use of bioinformatic tools to audit a reference library of DNA barcodes of invasive species occurring in coastal and marine European regions
Supervisor
 Biologia Aplicada (Degree)
Universidade do Minho, Portugal
2021/05 - 2021/06 The use of DNA metabarcoding to detect and monitor exotic species in coastal and marine ecosystems
Supervisor
 Biologia Aplicada (Degree)
Universidade do Minho, Portugal
2020/03 - 2020/12 Early detection and monitoring of non-indigenous species (NIS) in coastal ecosystems based on high-throughput sequencing tools
Supervisor
 Research fellow (Other)
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2020/04 - 2020/07 Compilation of a reference library of DNA barcodes for non-indigenous invertebrate species with high impact in marine and coastal ecosystems from Europe
Supervisor
 Licenciatura Biologia Aplicada (Degree)
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2019/04 - 2019/07 Compilation of a reference library of DNA barcodes for non-indigenous invertebrate species occurring in Azores coastal regions
Supervisor
 Biologia Aplicada (Degree)
Universidade do Minho, Portugal
2019/04 - 2019/07 Compilation of a reference library of DNA barcodes for non-indigenous invertebrate species occurring in Madeira coastal regions
Supervisor
 Bioquímica (Degree)
Universidade do Minho Departamento de Biologia, Portugal
2017/04 - 2017/07 The use of environmental DNA in biomonitoring and ecological research
Co-supervisor
 Biologia Aplicada (Degree)
Universidade do Minho Departamento de Biologia, Portugal
2017/04 - 2017/04 Exploring the potential of DNA barcoding and metabarcoding for the identification and monitoring of aquatic communities
Co-supervisor
 Biologia Aplicada (Degree)
Universidade do Minho Departamento de Biologia, Portugal
2016/04 - 2016/04 Compilation and analysis of macrozoobenthic organisms checklists in coastal regions from Portugal continental
Co-supervisor
 Biologia Aplicada (Degree)
Universidade do Minho Departamento de Biologia, Portugal
2013/03 - 2014/05 Development of molecular tools for assessing fungal diversity and activity in freshwaters
Supervisor
 Research fellow (Other)
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2014/04 - 2014/04 Biodiversity and Biogeography of aquatic fungi
Co-supervisor
 Biologia Aplicada (Degree)
Universidade do Minho Departamento de Biologia, Portugal
2013/02 - 2014/04 Development of molecular tools for assessing fungal diversity and activity in freshwaters
Supervisor
 Research fellow (Other)
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2012/10 - 2013/12 Effects of eutrophication on stream-dwelling decomposers of plant-litter
Supervisor
 Ecologia (Master)
Universidade do Minho Escola de Ciências, Portugal
2013/04 - 2013/07 Effects of temperature and genetic diversity of aquatic hyphomycetes on leaf-litter decomposition in streams
Supervisor
 Biologia Aplicada (Degree)
Universidade do Minho Departamento de Biologia, Portugal
2013/04 - 2013/07 Effects of aquatic hyphomycete diversity and eutrophication on leaf-litter decomposition in streams
Supervisor
 Biologia Aplicada (Degree)
Universidade do Minho Departamento de Biologia, Portugal
2013/04 - 2013/07 Does intraspecific diversity of aquatic fungi affects riparian vegetation decomposition under cadmium stress?
Supervisor
 Biologia Aplicada (Degree)
Universidade do Minho Departamento de Biologia, Portugal
2012/03 - 2013/02 Development of molecular tools for assessing fungal diversity and activity in freshwaters
Supervisor
 Research fellow (Other)
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2010/04 - 2010/04 Interspecific relationships among aquatic fungi under cadmium stress
Supervisor
 Biologia Aplicada (Degree)
Universidade do Minho Departamento de Biologia, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2023/09/21 - 2023/09/25 Co-organization of the outreach Activity: Missão Invisível - A Vida Secreta dos Micróbios/Mission Impossible: the secret life of the microbes, preparatory activity in the scope of European Researchers Nigh (NEI). (2023/09/21 - 2023/09/25)
Workshop (Co-organisor)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2023/02/06 - 2023/05/04 Outreach Activity "Códigos de barras de ADN: à procura de espécies invasoras no mar"/"DNA barcodes: finding invasive species in the sea", delivered to up to 100 secondary school students from 3 different schools as part of the "Programa de Visitas, Escola de Ciências da Universidade do Minho", in 4 different occasions (2023/02/06 - 2023/05/04)
Workshop
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2022/05/12 - 2022/05/12 Outreach Activity "Códigos de barras de ADN: à procura de espécies invasoras no oceano"/"DNA barcodes: finding invasive species in the ocean", to the 9th grade of the secondary school students in the scope of "Concurso dos Clubes Europeus - Os Oceanos" (2022/05/12 - 2022/05/12)
Workshop (Member of the Organising Committee)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2022/03/25 - 2022/04/06 Outreach Activity "Será que os códigos de barras só existem nos supermercados?"/"Do barcodes only exist in supermarkets?", to 8th grade secondary school students (2022/03/25 - 2022/04/06)
Workshop (Member of the Organising Committee)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2021/09/14 - 2021/09/14 Outreach activity "Can you detect invasive species through its DNA in the ports and marinas of Portugal?", in the scope of the Ecology Day (2021/09/14 - 2021/09/14)
Workshop (Member of the Organising Committee)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2021/01/25 - 2021/03/11 First DNAQUA International Conference (2021/03/09 - 2021/03/11)
Conference (Member of the Scientific Committee)
2020/11/27 - 2020/11/27 Outreach activity "Can you detect invasive species through its DNA in the ports of Portugal?", in the scope of the European Researchers night (2020/11/27 - 2020/11/27)
Workshop (Member of the Organising Committee)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2020/06/22 - 2020/06/26 Co-organization and chair of the session "DNA barcoding, (e)DNA metabarcoding and metagenomics to address ecological and evolutionary questions in aquatic ecosystems" to be held in the "XX Congress of the Iberian Association of Limnology (2020/06/22 - 2020/06/26)
Congress (Co-organisor)
 Iberian Association of Limnology (AIL), Spain
2019/09/09 - 2019/09/12 Chair of the session of "Global Change, Invasive Species and Conservation", in the 20th Iberian Symposium on Marine Biology Studies (XX SIEBM) (2019/09/09 - 2019/09/12)
Symposium (Co-organisor)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2013/07/01 - 2013/07/05 Co-chair of the session "Phylogeny, molecular biodiversity and biogeography" in the 8th Symposium for European Freshwater Sciences (SEFS 8) (2013/07/01 - 2013/07/05)
Symposium (Co-organisor)
 Universität Münster, Germany
2013/02/16 - 2013/03/09 "Science from 3 to 11: Experimental activities in Biology and Environment", Pri-Sci-Net course for training preschool and 1st and 2nd cycle basic grade school professors (2013/02/16 - 2013/03/09)
Other (Member of the Organising Committee)
 Universidade do Minho Departamento de Biologia, Portugal
2012/07/02 - 2012/07/06 XVI Congress of the Iberian Association of Limnology (2012/07/02 - 2012/07/06)
Congress (Member of the Organising Committee)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2012/07/02 - 2012/07/06 Co-chair of the session "Biodiversity and biogeography", in the XVI Congress of the Iberian Association of Limnology (2012/07/02 - 2012/07/02)
Congress (Co-organisor)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2011/02/05 - 2011/02/12 Course "Physiological systems: from theoretical to practical classes" for basic school professors (2011/02/05 - 2011/02/12)
Other (Member of the Organising Committee)
 Universidade do Minho Departamento de Biologia, Portugal
2010/07/23 - 2010/07/23 Workshop "River restoration and management" (2010/07/23 - 2010/07/23)
Workshop (Member of the Organising Committee)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2010/07/19 - 2010/07/23 Advanced course "Assessment of freshwater ecosystem condition" (2010/07/19 - 2010/07/23)
Other (Member of the Organising Committee)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2010/07/14 - 2010/07/16 Advanced course "Ecotoxicology and environmental risk assessment in aquatic ecosystems" (2010/07/14 - 2010/07/16)
Other (Member of the Organising Committee)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2010/06/02 - 2010/06/04 2nd conference of the European Consortium for the Barcode of Life (ECBOL2) (2010/06/02 - 2010/06/04)
Conference (Member of the Organising Committee)
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2004/02/16 - 2004/02/20 Advanced course "Methods for ecotoxicological assessment in terrestrial environments" (2004/02/16 - 2004/02/20)
Other (Member of the Organising Committee)
 Universidade do Minho Departamento de Biologia, Portugal
2001/11/12 - 2001/11/13 III Jornadas de Biologia Aplicada (2001/11/12 - 2001/11/13)
Meeting (Member of the Organising Committee)
 Universidade do Minho, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2024/09 - 2024/09 Co-chair in the 13th International Conference on Biological Invasions
Conference
 13th International Conference on Biological Invasions (Neobiota)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Évora, Portugal

Centro de Ciências do Mar e do Ambiente, Portugal
2023/07/15 - 2023/07/15 Monitor in the "Bioblitz Braga: quantas espécies conseguimos identificar na ecovia do Rio Este num só dia"/"Bioblitz Braga: how many species can we identify in the Este River ecoroute in only one day?", Build Up activity in the European Researchers' Night initiative
Workshop
Universidade do Minho, Portugal
2022/08/08 - 2022/08/08 Participation in the podcast "Uma gota no Oceano" in the episode "Episódio 12: Espécies Invasoras Marinhas (Especial Dia da Juventude)"
2022 - 2022 Interview to Jovens Repórteres para o Ambiente about "ADN ambiental: Invasoras em investigação". 1st prize (category 15-18 years old) attributed to Diogo Martins in the national contest JRA 2022

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2024/07 Metagenomics reveal taxonomic diversity of microbial communities along gradients of environmental stress in river basins of North Portugal
(Thesis) Main arguer
 Pedro Alexandre Cunha Senra Bogas Gonçalves (Master)
Universidade do Minho, Portugal
2023/12/18 A seca e o enriquecimento em nutrientes afetam mais a diversidade do que as funções das comunidades decompositoras nos rios
(Thesis) Main arguer
 Eduardo Joaquim Marinho da Silva (Master)
Universidade do Minho Departamento de Biologia, Portugal
2023/06 Estaremos preparados para monitorizar a biodiversidade de peixes da região do Minho através de DNA ambiental?
Supervisor
 Guilherme Pereira Vieira (Other)
Universidade do Minho Departamento de Biologia, Portugal
2022/02/11 Optimization of molecular tools for monitoring non-indigenous species (NIS) in coastal regions of the North of Portugal
Supervisor
 Fábio Gouveia Amaral (Master)
Universidade do Minho, Portugal
2022 Comparison of diversity indices and occurrence patterns of marine invertebrate species
Supervisor
 António Miguel Martinho (Other)
Universidade do Minho, Portugal
2022 DNA metabarcoding monitoring of zooplankton for the detection of non-indigenous species (NIS): a seasonal study in a recreational marina of the northwest of Portugal
Supervisor
 Jorge Moutinho (Master)
Universidade do Minho, Portugal
2022 Phyllodocida (Annelida, Polychaeta) of the North East Atlantic as a model for the investigation of cryptic species
(Thesis) Arguer
 Marcos André Machado Lima Teixeira (PhD)
2021 Analysis of functional genes diversity in aquatic fungal species
(Thesis) Main arguer
 Joana Mariz (Master)
Universidade do Minho, Portugal
2021 Use of bioinformatic tools for auditing a reference library of DNA barcodes for European marine invasive species
Supervisor
 Nuno Faria (Other)
Universidade do Minho, Portugal
2021 The use of DNA metabarcoding for detecting and monitoring exotic species in coastal and marine ecosystems
Supervisor
 Pedro Batista (Other)
Universidade do Minho, Portugal
2019/07 Compilation of a reference library of DNA barcodes for non-indigenous invertebrate species occurring in Azores coastal regions
Supervisor
 Cidália Manuela Lopes Pereira (Other)
Universidade do Minho Escola de Ciências, Portugal
2019/07 Compilation of a reference library of DNA barcodes for non-indigenous invertebrate species occurring in Madeira coastal regions
Supervisor
 Miguel André Rocha Dias (Other)
Universidade do Minho Escola de Ciências, Portugal
2018/12/12 Genetic studies of mitochondrial DNA in Saccharomyces cerevisiae
(Thesis) Main arguer
 Soraia Joana Almeida Aires Esteves (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2018/07/30 Margaritifera margaritifera in Portugal: main threats to its conservation
(Thesis) Main arguer
 André Luís Oliveira Ferreira (Master)
Universidade do Minho Escola de Ciências, Portugal
2017/07 The use of environmental DNA in biomonitoring and ecological research
Supervisor
 Maria Beatriz Magalhães Cardoso Queirós (Other)
Universidade do Minho Escola de Ciências, Portugal
2017/07 Exploring the potential of DNA barcoding and metabarcoding for the identification and monitoring of aquatic communities
Supervisor
 Vanessa Silveira Carvalho (Other)
Universidade do Minho Escola de Ciências, Portugal
2016/12/16 DNA barcodes of marine fishes from Europe: compilation of a curated reference library and study of genetic divergence patterns
(Thesis) Main arguer
 Luís Manuel Coelho Oliveira (Master)
Universidade do Minho Escola de Ciências, Portugal
2013/07 Effects of temperature and genetic diversity of aquatic hyphomycetes on leaf-litter decomposition in streams
Supervisor
 Ilisa Daniela Costa Antunes (Other)
Universidade do Minho Escola de Ciências, Portugal
2013/07 Effects of aquatic hyphomycete diversity and eutrophication on leaf-litter decomposition in streams
Supervisor
 Mafalda Sofia Alves de Sousa (Other)
Universidade do Minho Escola de Ciências, Portugal
2011/07 Does intraspecific identity of aquatic fungi affect riparian vegetation decomposition under cadmium stress?
Supervisor
 José Miguel Castro Trabulo (Other)
Universidade do Minho Escola de Ciências, Portugal
2011/07 Effects of intraspecific diversity of aquatic fungi on the decomposition of leaf-litter detritus exposed to cadmium
(Thesis) Arguer
 Bruno Ricardo Campos Antunes (Other)
Universidade do Minho Escola de Ciências, Portugal
2011 The role of aquatic fungal genetic diversity in organic matter decomposition in streams: a microcosm experiment
(Thesis) Main arguer
 Ricardo Sarmento Andrade (Master)
Universidade do Minho Escola de Ciências, Portugal
2011 Does the riparian stand age affect ecosystem functioning in streams?
(Thesis) Arguer
 Francisco André Costa Carvalho (Other)
Universidade do Minho, Portugal
2010/07 Effects of fungal diversity and nanoparticles pollution on alder litter degradation in streams
(Thesis) Main arguer
 Hugo Sá Lemos Sotto-Mayor Loureiro (Other)
Universidade do Minho Escola de Ciências, Portugal
2010 Interspecific relationships among aquatic fungi under cadmium stress
Supervisor
 André Filipe Linhares Pinheiro (Other)
Universidade do Minho Escola de Ciências, Portugal
2008 Effects of fungal diversity and temperature increase on leaf-litter decomposition in streams
(Thesis) Main arguer
 Paulo Jorge Passos Geraldes (Other)
Universidade do Minho Escola de Ciências, Portugal

Association member

Society Organization name Role
2012 - Current Iberian Association of Limnology (AIL) Member associate
2002 - 2009 Associação Juvenil Aventura da Saúde Member associate and supplementary vowel
2002 - 2004 Sociedade Portuguesa de Bioquímica Member associate

Committee member

Activity description
Role 		Institution / Organization
2022/09 - Current Technical representative of University of Minho in the support structure of the commission of co-management of the North Littoral Natural Park (PNLN)
Member
2014 - 2015 CBMA newsletter editorial team
Member
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2013 - 2013 Electoral commission of the Molecular and Environmental Biology Centre (CBMA) director elections
Member
 Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal

Conference scientific committee

Conference name Conference host
2020/06/22 - 2020/06/26 XX Congress of the Iberian Association of Limnology Murcia (Spain)
2015/11/26 - 2015/11/26 III Conference of the Doctoral Program in Molecular and Environmental Biology Braga (Portugal)
2014/11/27 - 2014/11/27 II Conference of the Doctoral Program in Molecular and Environmental Biology Braga (Portugal)
2014/07/06 - 2014/07/11 XVII Congress of the Iberian Association of Limnology Santander (Espanha)

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2023/03/23 - 2023/03/23 Catch me if you can: the use of environmental DNA-based tools for the detection and monitoring of invasive species Advanced course on Biological Invasions (Mestrado) Universidade do Minho, Portugal
2021/03 - 2022/07 Eye Pharmacology (theoretical-practical classes) Optometria e Ciências da Visão (Licenciatura) Universidade do Minho, Portugal
2022/06/27 - 2022/06/27 Catch me if you can: the use of eDNA-based tools to detect rare species Advanced course on Next Generation Sequencing in Environmental Monitoring (Mestrado) Universidade do Minho, Portugal
2021/02/05 - 2021/02/05 DNA metabarcoding on plankton: an efficient approach to detect early the presence of non-indigenous species in coastal ecosystems Advanced course "Plankton in a changing world" (Pós-Graduação) Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal
2020/02 - 2020/02 "Biodiversity databases" in the scope of "Biodiversity and global changes" curricular unit (theoretical-practical classes) Biologia Aplicada, Biologia e Geologia e Ciências do Ambiente (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal
2019/02 - 2019/06 Cell and Molecular Biology (theoretical-practical classes) Engenharia Biológica (Mestrado integrado) Universidade do Minho Departamento de Biologia, Portugal
2019/02 - 2019/06 Molecular and Cell Biology (theoretical-practical classes) Engenharia Biomédica (Mestrado integrado) Universidade do Minho Departamento de Biologia, Portugal
2017/04 - 2017/04 "Genetic databases" in the scope of "Biodiversity and global changes" curricular unit (theoretical-practical classes) Biologia Aplicada, Biologia e Geologia, Ciências do Ambiente (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal
2016/07/18 - 2016/07/20 Module "Molecular Biodiversity: a barcode for all the species" in the scope of the internship "Biodiversity evaluation in a changing world" (theoretical and practical classes) Ciência viva no laboratório 2016 (Outros) Universidade do Minho Departamento de Biologia, Portugal
2015/04 - 2015/04 "DGGE for assessing fungal diversity on decomposing plant material in streams" and "Software tools for gel analysis and cluster and ordination analyses of aquatic fungal communities" in the "Intensive course in Methods in Litter Decomposition" (theoretical-practical classes) Intensive course in methods in litter decomposition (Postgraduate Certificate) Universidade de Coimbra, Portugal
2013 - 2013 Animal Biology and Stream Ecology classes (practical classes) Ciência dos 3 aos 11 : Actividades experimentais de Biologia e Ambiente (Outros) Universidade do Minho Departamento de Biologia, Portugal
2004 - 2013 Microbiology (practical classes) Biologia Aplicada e Biologia e Geologia (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal
2011 - 2011 "Human physiological systems" in the course "Physiological systems: from theoretical to practical classes" (practical classes) Sistemas Fisiológicos: da teoria à prática (Outros) Universidade do Minho Departamento de Biologia, Portugal
2011 - 2011 "Ergosterol extraction from decomposing leaf litter" in the scope of "Biodiversity and Functional Ecology" curricular unit (practical classes) Ecologia (Mestrado) Universidade do Minho Departamento de Biologia, Portugal
2010 - 2010 "DGGE for assessing fungal diversity on decomposing plant material in streams" and "Software tools for gel analysis and cluster and ordination analyses of aquatic fungal communities" in the advanced course "Litter decomposition in streams" Advanced course Litter decomposition in streams (Postgraduate Certificate) Universidade de Coimbra, Portugal
2010 - 2010 "Statistical analyses with Statistica" in the scope of "Biodiversity and Functional Ecology" curricular unit (practical classes) Ecologia (Mestrado) Universidade do Minho Departamento de Biologia, Portugal
2009/02 - 2009/06 Differentiation and Development Biology (practical classes) Biologia Aplicada (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal
2009/02 - 2009/06 General Histology and Physiology (theoretical-practical classes) Optometria e Ciências da Visão (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal
2009/02 - 2009/06 Microbiology (practical classes) Biologia e Geologia (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal
2008/10 - 2009/02 Human Biology (practical classes) Psicologia (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal
2008/10 - 2009/02 Pharmacology (theoretical-practical classes) Optometria e Ciências da Visão (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal
2008/10 - 2009/02 Cell Biochemistry and Physiology (practical classes) Optometria e Ciências da Visão (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal
2009 - 2009 Circulatory and Respiratory physiological systems (practical classes) Ciências Naturais (9º ano) (Ensino básico 3º ciclo) Escola E. B. 2, 3 D. Maria II, Portugal
2008 - 2008 Genetic Diversity, Global Change and Ecosystems Sustainability (practical classes) Genética Molecular (Mestrado) Universidade do Minho Departamento de Biologia, Portugal
2006 - 2006 "Ergosterol extraction from decomposing leaf-litter" in the scope of "Eco-physiology of Aquatic Fungi" curricular unit (practical classes) Biologia Aplicada (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal
2005 - 2005 "Ergosterol extraction from decomposing leaf-litter" in the scope of "Eco-physiology of Aquatic Fungi" curricular unit (practical classes) Biologia Aplicada (Licenciatura) Universidade do Minho Departamento de Biologia, Portugal

Interview (tv / radio show)

Program Topic
2021/01/13 - 2021/01/13 UM & ID NIS-DNA: Early detection and monitoring of non-indigenous species (NIS) in coastal ecosystems based on high-throughput sequencing tools
2020/12/14 - 2020/12/14 90 segundos de Ciência NIS-DNA: Early detection and monitoring of non-indigenous species (NIS) in coastal ecosystems based on high-throughput sequencing tools

Journal scientific committee

Journal title (ISSN) Publisher
2022 - Current Mediterranean Marine Science Elsevier
2021 - Current Diversity MDPI
2021 - Current Environmental Microbiology Wiley
2021 - Current Marine Pollution Bulletin Elsevier
2021 - Current Phytobiomes APS publications
2020 - Current Environment International (0160-4120) Elsevier
2020 - Current Biodiversity Data Journal Pensoft
2020 - Current Environmental Sciences Europe Springer
2019 - Current Ecological Indicators (1470-160X) Elsevier
2019 - Current Limnology and Oceanography (0024-3590) Wiley (Blackwell Publishing)
2019 - Current Frontiers in Ecology and Evolution (2296-701X) Frontiers Media SA
2019 - Current Genome (1480-3321) Canadian Science Publishing
2018 - Current Peer J
2017 - Current FEMS Microbiology Ecology (1574-6941) Oxford University Press
2016 - Current Journal of Biogeography (1365-2699) Wiley (Blackwell Publishing)
2016 - Current Freshwater Biology (1365-2427) Wiley (Blackwell Publishing)
2016 - Current Water Air & Soil Pollution (1573-2932) Springer-Verlag
2016 - Current International Review of Hydrobiology (1522-2632) Wiley (John Wiley & Sons)
2016 - Current African Journal of Microbiology Research (1996-0808) Academic Journals
2015 - Current Environmental Science and Pollution Research (1614-7499) Springer-Verlag
2015 - Current Limnologica (0075-9511) Elsevier
2015 - Current Mycology: An International Journal of Fungal Biology
2015 - Current The Science of The Total Environment (0048-9697) Elsevier
2015 - Current MycoKeys (1314-4049) Pensoft Publishers
2015 - Current The ISME Journal (1751-7370) Springer Science and Business Media LLC
2015 - Current PLoS ONE (1932-6203) Public Library of Science
2015 - Current Scientific Reports (2045-2322) Springer Science and Business Media LLC
2015 - Current Fungal Ecology (1754-5048) Elsevier
2015 - Current Biological Procedures Online (1480-9222) Springer (Biomed Central Ltd.)
2014 - Current Limnetica
2014 - Current Journal of Applied Ecology (1365-2664) Wiley (Blackwell Publishing)
2013 - Current Soil Use and Management (1475-2743) Wiley (Blackwell Publishing)
2013 - Current Ecotoxicology (1573-3017) Springer-Verlag
2011 - Current Microbial Ecology (1432-184X) Springer-Verlag
2011 - Current Education Research Journal
2010 - Current Fundamental and Applied Limnology / Archiv für Hydrobiologie (1863-9135) Schweizerbart
2010 - Current Hydrobiologia (1573-5117) Springer-Verlag
2022 - 2022 Marine Science and Engineering MDPI

Other jury / evaluation

Activity description Institution / Organization
2022 - 2022 Evaluation of Research proposals in the scope of the 2021-2022 BiodivERsA Call on "Supporting the protection of Biodiversity and Ecosystems across land and sea"
2022 - 2022 Evaluation of Research proposals for the "National Science Centre Poland"
2021/06 - 2021/06/21 Evaluation of research proposals in the scope of the 2020-2021 BiodivERsA and Water JPI Joint Call on "Conservation and restoration of degraded ecosystems and their biodiversity, including a focus on aquatic systems"
2016 - 2019 Evaluation of Research proposals for the "Estonian Research Council"
2015 - 2015 Evaluation of Research proposals for the "Research Foundation – Flanders"
Distinctions

Award

2024 Prize for 3rd best poster in the I CBMA OPEN DAY & II Phd|Bio SYMPOSIUM
2017 Grant for conducting a short term scientific mission (STSM) in AZTI-Tecnalia, Spain (February-March 2017)
2012 3rd best poster presentation in the XVI Congress of the Iberian Association of Limnology
2007 Poster spotlight in the SETAC Europe 17th Annual Meeting
2003 Prize "Universidade do Minho" for finishing the graduation in Applied Biology with the best classification in 2002
Universidade do Minho, Portugal
2002 Merit scholar prize for obtaining a classification equal or higher to 14/20 during the 3rd year of graduation in Applied Biology
Universidade do Minho, Portugal
2002 Merit scholarship for finishing the graduation in Applied Biology with the best classification in 2002
2001 Merit scholar prize for obtaining a classification equal or higher to 14/20 during the 2nd year of graduation in Applied Biology
Universidade do Minho, Portugal
2000 Merit scholar prize for obtaining a classification equal or higher to 14/20 during the 1st year of graduation in Applied Biology
Universidade do Minho, Portugal