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Joana Couceiro is a PhD student, enrolled in the PhD program in Biotechnology and Biosciences from Instituto Superior Técnico (IST), University of Lisbon (UL), since 2022. She is funded by an individual PhD scholarship from the highly competitive MIT Portugal program, and her dissertation focuses on the sustainable production of secondary metabolites from bacterial symbionts of octocorals. In the scope of her PhD, Joana described two novel marine bacterial species in the genus Aquimarina, A. aquimarini sp. nov. and A. spinulae sp. nov., published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). She also wrote a book chapter on bioactive natural products and biotechnological applications of the coral microbiome for the Springer book titled 'Coral Reef Microbiome', currently in press. Joana has also developed experimental work where she applies metabolomics and transcriptomics to test if co-cultures of sympatric marine bacteria enhances secondary metabolite production in the peptide antibiotic producing bacterium Aquimarina aquimarini, and a manuscript is currently in preparation. In her current experimental work, Joana is establishing a culture collection of bacteria associated with the temperate octocoral Leptogorgia sarmentosa. The collection encompasses ca. 400 isolates from three different oxygen conditions (aerobic, microaerophilic and anaerobic) which will later be tested for their antimicrobial and antifouling capacities. The prokaryotic diversity hosted by this octocoral will further be explored employing 16S rRNA amplicon sequencing. Joana obtained her Integrated Master's degree in Biological Engineering from IST-UL in January 2021. Her Master thesis at the Institute for Bioengineering and Biosciences (iBB/IST) focused on the diversity and structure of bacterioplankton communities in ice and water samples from the Subarctic, using metagenomics tools, and was rated excellent (18 on a 0-20 scale). Her MSc thesis work contributed to a research article published in the Journal "Science of the Total Environment" and an iPoster presented at the World Microbe Forum (ASM/FEMS). Between her Master and PhD studies, Joana was hired as research assistant on the R&D project SymbioReactor, funded through the FundoAzul program of the Portuguese Ministry of the Sea (DPGM). Here she acquired scientific training in marine genomics, annotating symbiosis-related genes and secondary metabolite biosynthesis gene clusters on the genomes of Roseibium album (Alphaproteobacteria) and Aquimarina megaterium (Flavobacteriia) strains isolated from octocorals. This work was published in two articles in the ASM journal "Microbiology Resource Announcements", both with Joana as first author. During her time as a Bachelor student, in summer 2017, Joana performed an internship in Microbial Biotechnology at the Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, Beja, investigating bacterial tolerance to inhibitors derived from plant biomass hydrolysis. From August 2018 to January 2019, she gained international experience as an Erasmus exchange student at the KTH Royal Institute of Technology, in Stockholm, Sweden, taking courses on Drug Development and Microbial Cultivation in Bioreactors. From 2019 to the beginning of 2020, Joana was part of a student team developing a design project which won the 3rd ESBES-BIOT Biotechnical Design Competition, with a project entitled 'Continuous production of lentivirus for use in gene and/or cell therapy products'. So far, Joana has authored/co-authored five research articles and presented her work in over 10 poster and oral presentations in multiple national and international conferences.
Identification

Personal identification

Full name
Joana Andreia Fernandes Couceiro

Citation names

  • Couceiro, Joana F.

Author identifiers

Ciência ID
8D1E-D651-4AAC
ORCID iD
0000-0003-1824-5017
Google Scholar ID
uiBfPXoAAAAJ

Email addresses

  • joana.couceiro@tecnico.ulisboa.pt (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Microbiology
  • Engineering and Technology - Industrial Biotechnology - Bioprocessing Technologies
  • Natural sciences - Biological Sciences - Biochemistry

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2022/05/11 - 2026/05
Ongoing
PhD program in Biotechnology and Biosciences (Doutoramento)
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2015/09/11 - 2021/01
Concluded
Engenharia Biológica (Mestrado integrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Discovering the polar microbiome: structure and diversity of prokaryotic communities in ice and seawater along a salinity gradient in the Subarctic " (THESIS/DISSERTATION)
15 (Bachelor 15, Master 16)
Affiliation

Science

Category
Host institution
Employer
2022/01/01 - 2022/05/11 Research Assistant (Research) Universidade de Lisboa Instituto Superior Técnico, Portugal
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2020/02 - 2021 Research Trainee (Research) Universidade de Lisboa Instituto Superior Técnico, Portugal
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2017/07/03 - 2017/09/15 Research Trainee (Research) Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, Portugal

Others

Category
Host institution
Employer
2022/05/11 - Current PhD Student Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2018/08 - 2019/01 Erasmus Exchange Student Kungliga Tekniska Högskolan, Sweden
Kungliga Tekniska Högskolan, Sweden
Projects

Grant

Designation Funders
2023/02/01 - Current Blue Bioeconomy Pack (PBA) - Recovery and Resilience Plan (PRR); Active on Work Package WP9 - Portuguese Blue Biobank
C632741873-00467082
PhD Student Fellow
Ongoing
2022/05 - 2022/12 Symbioreactor - Sustainable production of bioactive metabolites from microbial symbionts of marine sponges and corals
FA05-2017-032
PhD Student Fellow
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
Concluded
2022/01 - 2022/05 Symbioreactor - Sustainable production of bioactive metabolites from microbial symbionts of marine sponges and corals
FA05-2017-032
Research Technician Fellow
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
Concluded
Outputs

Publications

Book chapter
  1. Couceiro, Joana F.; Costa, Rodrigo; Keller-Costa, Tina. "Chapter 16 - Beyond Restauration: Coral Microbiome Biotechnology". In Coral Reef Microbiome, edited by Raquel Peixoto; Christian R. Voolstra. Springer, 2024.
    In press
Conference poster
  1. Couceiro, Joana F.; Costa, Rodrigo; Keller-Costa, Tina. "Pharmaceutical and Biotechnological Applications of the Coral Microbiome". Paper presented in MICROBIOTEC'23 - Congress of Microbiology and Biotechnology, 2023.
  2. Fernandes, Ana M.; Couceiro, Joana F.; Keller-Costa, Tina; Costa, Rodrigo. "Exploring the potential of co-cultures to enhance secondary metabolites production in the marine bacterium Aquimarina sp. Aq135". Paper presented in MICROBIOTEC'23 - Congress of Microbiology and Biotechnology, 2023.
  3. Couceiro, Joana F.; Costa, Rodrigo; Keller-Costa, Tina. "Pharmaceutical and Biotechnological Applications of the Coral Microbiome". Paper presented in 3rd iBB workshop, 2023.
  4. Couceiro, Joana F.; Costa, Rodrigo; Keller-Costa, Tina. "Pharmaceutical and Biotechnological Applications of the Coral Microbiome". Paper presented in 2nd Microbiome Summit, 2023.
  5. Couceiro, Joana F.; Costa, Rodrigo; Keller-Costa, Tina. "Pharmaceutical and Biotechnological Applications of the Coral Microbiome". Paper presented in MIT Portugal Annual Conference, 2023.
  6. Couceiro, Joana F.; Marques, Matilde; Silva, Sandra G.; Keller-Costa, Tina; Costa, Rodrigo. "Aquimarina aquimarinae sp. nov. and Aquimarina spinosulus sp. nov., new bacterial species with versatile natural product biosynthesis potential". Paper presented in 16th Symposium on Bacterial Genetics and Ecology, 2023.
  7. Couceiro, Joana F.; Costa, Rodrigo; Keller-Costa, Tina. "Sustainable Production of Bioactive Metabolites from Octocoral Symbionts". Paper presented in SymbNET Metabolomics Workshop for Biologists, 2023.
  8. Couceiro, Joana F.; Marques, Matilde; Silva, Sandra G.; Keller-Costa, Tina; Costa, Rodrigo. "Aquimarina aquimarinae sp. nov. and Aquimarina spinosulus sp. nov., new bacterial species with versatile natural product biosynthesis potential". Paper presented in MIT Portugal Annual Conference, 2022.
  9. Roveta, Camilla; Annibaldi, Anna; Calcinai, Barbara; Coppari, M; Di Camillo, C.G; Girolametti, Federico; Puce, S.; et al. "Heavy meals for a light sponge. Mercury bioaccumulation in the sponge Chondrosia reniformis Nardo, 1847 and its prokaryotic community". Paper presented in 11th World Sponge Conference, Leiden, The Netherlands, 2022.
  10. Couceiro, Joana F.; Keller-Costa, Tina; Marques, Matilde; Kyrpides, Nikos C.; Woyke, Tanja; Whitman, William B.; Costa, Rodrigo. "The Roseibium album (Labrenzia alba) pangenome reveals multiple symbiosis factors likely underpinning host-microbe relationships in the marine benthos". Paper presented in MICROBIOTEC'21 - Congress of Microbiology and Biotechnology, 2021.
  11. Coelho, Lígia F.; Couceiro, Joana F.; Keller-Costa, Tina; Valente, Sara; Ramalho, Tiago; Carneiro, Joana; Comte, Jerôme; et al. "Structural shifts revealed for seawater and ice microbiomes across a salinity gradient in the high Subarctic". Paper presented in World Microbe Forum, 2021.
Journal article
  1. Couceiro, Joana F.; Fernandes, Ana S.; Costa, Rodrigo; Keller-Costa, Tina. "Co-cultivation of bacterial competitors enhances secondary metabolite biosynthesis in the marine bacterium Aquimarina aquimarini.". FEMS Microbiology Ecology (2025):
  2. Couceiro, Joana F.; Marques, Matilde; Silva, Sandra G.; Keller-Costa, Tina; Costa, Rodrigo. "Aquimarina aquimarini sp. nov. and Aquimarina spinulae sp. nov., novel bacterial species with versatile natural product biosynthesis potential isolated from marine sponges". International Journal of Systematic and Evolutionary Microbiology 74 1 (2024): http://dx.doi.org/10.1099/ijsem.0.006228.
    10.1099/ijsem.0.006228
  3. Roveta, Camilla; Calcinai, Barbara; Girolametti, Federico; Fernandes Couceiro, Joana; Puce, Stefania; Annibaldi, Anna; Costa, Rodrigo. "The prokaryotic community of Chondrosia reniformis Nardo, 1847: from diversity to mercury detection". Zoology 158 (2023): 126091. http://dx.doi.org/10.1016/j.zool.2023.126091.
    10.1016/j.zool.2023.126091
  4. Couceiro, Joana Fernandes; Keller-Costa, Tina; Kyrpides, Nikos C.; Woyke, Tanja; Whitman, William B.; Costa, Rodrigo. "Genome Sequencing Suggests Diverse Secondary Metabolism in Coral-Associated Aquimarina megaterium". Microbiology Resource Announcements 11 11 (2022): http://dx.doi.org/10.1128/mra.00620-22.
    10.1128/mra.00620-22
  5. Coelho, Lígia Fonseca; Couceiro, Joana Fernandes; Keller-Costa, Tina; Valente, Sara Martinez; Ramalho, Tiago Pereirinha; Carneiro, Joana; Comte, Jérôme; et al. "Structural shifts in sea ice prokaryotic communities across a salinity gradient in the subarctic". Science of The Total Environment 827 (2022): 154286. http://dx.doi.org/10.1016/j.scitotenv.2022.154286.
    10.1016/j.scitotenv.2022.154286
  6. Couceiro, Joana Fernandes; Keller-Costa, Tina; Marques, Matilde; Kyrpides, Nikos C.; Woyke, Tanja; Whitman, William B.; Costa, Rodrigo. "The Roseibium album (Labrenzia alba) Genome Possesses Multiple Symbiosis Factors Possibly Underpinning Host-Microbe Relationships in the Marine Benthos". Microbiology Resource Announcements 10 34 (2021): http://dx.doi.org/10.1128/mra.00320-21.
    Open access • 10.1128/mra.00320-21
Thesis / Dissertation
  1. Couceiro, Joana F.. "Discovering the polar microbiome: structure and diversity of prokaryotic communities in ice and seawater along a salinity gradient in the Subarctic". Master, Universidade de Lisboa Instituto Superior Técnico, 2021.
Translation
  1. Marques, Matilde; Couceiro, Joana F.; Keller-Costa, Tina. Coral Heroes. SECORE. 2023.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022/10/18 Aquimarina aquimarinae sp. nov. e Aquimarina spinosulus sp. nov., novas espécies bacterianas com potencial biossintético de produtos naturais Microbiologia 2022
Sociedade Portuguesa de Microbiologia (SPM)

Event organisation

Event name
Type of event (Role)
Institution / Organization
2016 - 2019 Collaborator at the Bioengineering Department Open Labs (2016, 2018, 2019) (2016)
Exhibition (Member of the Organising Committee)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2018 Collaborator at the Chemical Engineering Department Open Labs (2018) (2018)
Exhibition (Member of the Organising Committee)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Event participation

Activity description
Type of event
Event name
Institution / Organization
2024/02/06 - 2024/02/06 Workshop on the use and application of cluster computing systems for Big Data.
Workshop
Course on Computational Biosciences using HPC systems
Unidade de Ciências Biomoleculares Aplicadas, Portugal
2021/09/17 - 2023/09/17 International Microorganism Day - IMD, yearly since 2021 exhibitor
Exhibition
International Microorganism Day
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/06/06 - 2023/06/08 Application of metabolomics to the study of host-microbiome interactions.
Workshop
SymbNET Metabolomics Workshop for Biologists
Université de Lausanne, Switzerland

Instituto Gulbenkian de Ciência, Portugal
2021/05/23 - 2023/05/23 Dia do Técnico exhibitor; yearly since 2021 engagement with the public and school classes, showcasing 'The wonderful world of marine bacteria' 'The symbionts of corals and sponges' and 'Life in a drop of water'
Exhibition
Dia do Técnico / Técnico Open Day
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/05 - 2023/05 Introduction to R utilization in Biological sciences (WS1 – introduction to R, WS2 – biostatistical basis in R and WS4 – single cell) Olissipo | EMBL training Introduction and computation with R
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2022/04/04 - 2022/04/08 Overview of Python and R languages with an emphasis on biology related practical problem solving, focused on data plotting and reproducibility.
Workshop
Introduction to R and Python for Biologists
Wellcome Sanger Institute, United Kingdom
2021/09/06 - 2021/09/10 35 hours of theoretical and field training on environmental sampling techniques commonly used for water, sediments, soils and biological samples
Workshop
1st course of environmental sampling
Universidade de Lisboa Centro de Química Estrutural, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal

Association member

Society Organization name Role
2021 - Current SPM - Sociedade Portuguesa de Microbiologia Member
2017 - 2020 Tuna Feminina do Instituto Superior Técnico Member (2017-2019) and President (2020)
2017 - 2018 Núcleo de Engenharia Biológica do Instituto Superior Técnico Collaborator

Mentoring / Tutoring

Topic Student name
2016 - 2018 IST Mentoring program (2016-2018) First Year Students
Distinctions

Award

2021 ESBES-BIOT Biotechnical Design Competition winner with the project 'Continuous production of lentivirus for use in gene and/or cell therapy products'
American Chemical Society, United States

Other distinction

2022 Honorable mention - oral presentation at Microbiologia'22
Sociedade Portuguesa de Microbiologia, Portugal
2022 Poster shortlisting - 25 best posters at MIT Portugal Annual Conference 2022
Massachusetts Institute of Technology MIT Portugal Program, Portugal