Rodrigo da Silva Costa (5917-D500-D251)

Curriculum Vitae

Rodrigo da Silva Costa

Rodrigo Costa is an Associate Professor (since 2020) at the Department of Bioengineering (DBE) of Instituto Superior Técnico (IST), University of Lisbon. He graduated in Biological Sciences at the Federal University of Rio de Janeiro, Brazil, in 1998 and obtained his M.Sc. degree in Ecology from this same University in 2001. He acquired his Ph.D. degree in Life Sciences from the Technical University of Braunschweig, Germany, in 2006, and was a post-doctoral fellow at the University of Groningen, The Netherlands, from 2006 to 2008. He was then awarded the Research Scientist contracts Ciência (2008) and FCT Investigator (2015) from the Portuguese Foundation for Science and Technology (FCT). During this period, he founded and led the Microbial Ecology and Evolution Research Group (MicroEcoEvo) at the Centre of Marine Sciences (CCMar), Algarve University, Portugal, where he built a novel molecular microbiology laboratory acquired through extramural funding. Prof. Rodrigo Costa was an invited affiliate (Research Scientist) of the Lawrence Berkeley National Laboratory (LBNL), University of California at Berkeley, USA (March 2019-August 2021), and of CCMAR from 2016 to 2021. He holds the position (by invitation) of Ambassador of the International Society for Microbial Ecology (ISME) in Portugal, is an invited member of the Editorial Board of Scientific Reports, and member of three academic societies. In 2019, he chaired the International Symposium on Bacterial Genetics and Ecology (BAGECO) in Lisbon, Portugal, and since then is a member of the steering scientific committee of the symposium. Prof. Costa has authored > 100 scientific publications encompassing original research articles in international journals, book chapters, and theses. His published work has been cited c. 7,400 times, featuring an h-index of 45, an i-10 index of 70, and studies published in top-ranked, multidisciplinary journals such as Microbiomes, The ISME Journal, Nature Communications, Nature Microbiology, Science of the Total Environment, mSystems, and Environmental Microbiology, among others. Prof. Costa participated in over 220 communications (> 80 oral) in scientific conferences, workshops, and colloquia. Since 2010, he supervised several post-doctoral fellows, Ph.D., M.Sc., and undergraduate students - in the framework of 19 R&D projects (10 as PI / Co-PI), leading six PhD thesis (five ongoing) and 28 Master thesis (eight ongoing) completions, and securing > 2 MEuros extramural research funding in the last five years. Prof. Rodrigo Costa is the coordinator of the course units Fundamentals of Ecology and Microbiomes at IST/ULisbon, being awarded by students with the Excellence in Teaching prize in several disciplines across the years. His research addresses the diversity and function of microorganisms in natural and fabricated biomes - with emphasis on Eukaryote-Prokaryote symbioses studied with metagenomics approaches -, their implications to host/ecosystem health and climate regulation, and potential use as renewable sources of innovative biotechnological appliances. Current research projects focus on harnessing the metabolism of bacterial symbionts of marine organisms and developing microbiome engineering approaches to (i) suppress microbial diseases and mitigate climate change stressors in aquaculture and coral reef ecosystems, and (ii) design marine-based bioproducts of application across multiple sectors (e.g., health, environment, food, and feed) to leverage the circular blue bioeconomy. Prof. Costa belongs to the group of fifteen specialists invited by the Portuguese Government in 2023 to propose a package of legislative, financial, and scientific competitive measures for the development of the Blue Biotechnology Sector in Portugal. Full CV: https://drive.google.com/file/d/1TEj7hpMElFkqLhJSL9OEMzBqmafYvVGC/view?usp=sharing

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Identification

Personal identification

Full name: Rodrigo da Silva Costa

Citation names

Costa, Rodrigo

Author identifiers

Ciência ID: 5917-D500-D251
ORCID iD: 0000-0002-5932-4101

Email addresses

rodrigoscosta@tecnico.ulisboa.pt (Professional)

Telephones

Telephone

218417339 Ext.: 1339 (Professional)

Addresses

Av Rovisco Pais 1, Instituto Superior Técnico, Dep. de Bioengenharia, Alameda Campus, 1049-001, Lisbon, Lisbon, Portugal (Professional)

Websites

https://scholar.google.pt/citations?user=poZe7rwAAAAJ&hl=en (Professional)
http://orcid.org/0000-0002-5932-4101 (Professional)
www.facebook.com/MicroEcoEvo/ (Social media)
https://www.instagram.com/microecoevo/ (Social media)
https://www.linkedin.com/in/rodrigo-costa-82124b17/ (Social media)

Knowledge fields

Natural sciences - Biological Sciences - Biology

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
Portuguese (Mother tongue)
English	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)
German	Advanced (C1)	Advanced (C1)	Advanced (C1)	Advanced (C1)

Education

	Degree	Classification
2002 - 2006 Concluded	Natural Sciences (Doctor) Technische Universität Braunschweig, Germany	Magna cum laude
1999 - 2001 Concluded	Ecology (Master) Universidade Federal do Rio de Janeiro, Brazil	Summa cum laude
1995 - 1998 Concluded	Biological Sciences (Bachelor) Major in Ecology Universidade Federal do Rio de Janeiro, Brazil	Cum laude (8.4 in 10)

Affiliation

Science

	Category Host institution	Employer
2016 - Current	Principal Investigator (Research)	Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal

2019/03 - 2021/08	Invited Principal Investigator (Research)	E O Lawrence Berkeley National Laboratory, United States

2014/10 - 2020/03	Principal Investigator (Research)	Centro de Ciências do Mar, Portugal
	Centro de Ciências do Mar, Portugal
2008/10 - 2013/09	Auxiliary Researcher (Research)	Centro de Ciências do Mar, Portugal
	Centro de Ciências do Mar, Portugal
2006/08 - 2008/09	Postdoc (Research)	Rijksuniversiteit Groningen, Netherlands
	Rijksuniversiteit Groningen, Netherlands

Teaching in Higher Education

	Category Host institution	Employer
2020/08/01 - Current	Associate Professor (University Teacher)	Universidade de Lisboa Instituto Superior Técnico, Portugal

2016/04 - Current	Assistant Professor (University Teacher)	Universidade de Lisboa Instituto Superior Técnico, Portugal
	Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal

Projects

Grant

	Designation	Funders
2006/08/01 - 2008/07/31	Evolution of bacterial antibiotic-encoding genes and their role in soil microbial community diversity Soil Biotechnology Foundation Post-doc Fellow Rijksuniversiteit Groningen, Netherlands	Concluded
2002/04/01 - 2006/06/05	Microbial community structure and function in the rhizosphere of crop plants DAAD Grant PhD Student Fellow Technische Universität Braunschweig, Germany
1999 - 2001	Genetic diversity and variability of bacterial communities associated with the maize rhizosphere in an arable land in Rio de Janeiro, Brazil CAPES Grant Master Student Fellow Universidade Federal do Estado do Rio de Janeiro, Brazil	Concluded

Contract

	Designation	Funders
2023/03 - Current	Blue Bioeconomy Pact C632741873-00467082 Principal investigator Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal	Agência para a Competitividade e Inovação IP Ongoing
2022/01/01 - Current	ChicoBionts - Harnessing the catalyst power of host-microbe interactions: a quest for novel chitinases from octocoral symbionts EXPL/BIA-MIC/0286/2021 Researcher	Fundação para a Ciência e a Tecnologia Ongoing
2019/03 - 2026/02	GEBA - Genomic Encyclopeadia of Bacteria and Archaea GEBA - Genomic Encyclopeadia of Bacteria and Archaea Researcher DOE Joint Genome Institute, United States	DOE Joint Genome Institute Ongoing
2021/01/01 - 2025/12/31	Institute for Health and Bioeconomy LA/P/0140/2020 10.54499/LA/P/0140/2020 Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal Universidade Nova de Lisboa, Portugal INESC Microsistemas e Nanotecnologias, Portugal Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal Unidade de Ciências Biomoleculares Aplicadas, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2020/08 - 2022/07	Aquatic Symbiosis Genomics Project Aquatic Symbiosis Genomics Project Researcher Wellcome Sanger Institute, United Kingdom	Wellcome Sanger Institute Ongoing
2019/10 - 2021/09	SymbioReactor: sustainable production of bioactive metabolites from microbial symbionts of marine sponges and corals FA_05_2017_032 Principal investigator Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal Universidade de Lisboa Instituto Superior Técnico, Portugal	Direção-Geral de Política do Mar - Ministério do Mar Ongoing
2018/08 - 2021/07	MicroControl: Exploiting the healing capacity of nature´s microbiomes for improved fish larviculture" 031996 Principal investigator Universidade de Lisboa Instituto Superior Técnico, Portugal Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal	Portuguese Foundation for Science and Technology Concluded
2016/07 - 2020/06	Harnessing the power of the microbial metamobilome: using marine sponges as models to uncover novel biotechnological appliances from symbiont communities Provided by PTCRIS: 140172 Principal investigator Universidade de Lisboa Instituto Superior Técnico, Portugal Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal	Fundação para a Ciência e a Tecnologia
2016/03/01 - 2020/05/31	Harnessing the power of host-microbe interactions: diversity, function and biotechnology of marine symbioses in a changing climate IF/01076/2014/CP1268/CT0001 Universidade de Lisboa Instituto Superior Técnico, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2019/01/01 - 2019/12/31	Centre of Marine Sciences UID/Multi/04326/2019 Centro de Ciências do Mar, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2019/01/01 - 2019/12/31	Institute for Bioengineering and Biosciences UID/BIO/04565/2019 Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2015/06/01 - 2016/02/29	Harnessing the power of host-microbe interactions: diversity, function and biotechnology of marine symbioses in a changing climate IF/01076/2014/CP1217/CT0003 Centro de Ciências do Mar, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2015/01 - 2015/12	Functional and taxonomic profiling of microbial communities in caves of the Algarve, Southern Portugal Not applicable Supervisor	National Speleological Foundation
2014/08 - 2015/08	Deciphering the codes of communication between marine sponges and their symbionts: an integrative metabolomics-transcriptomics approach (additional support for Europe) 810402 Researcher	VolkswagenStiftung Concluded
2014/03 - 2015/08	Illuminating the metabolism of foundational and elusive microbial symbionts in benthic ecosystems: a cultivation-independent quest for Hahellaceae (Gammaproteobacteria, Oceanospirillales) genomes EXPL/MAR-EST/1664/2013 Supervisor Centro de Ciências do Mar, Portugal	Portuguese Foundation for Science and Technology (FCT) Concluded
2013/06 - 2015/05	Single cell genomics and metagenomics-aided cultivation of the unculturable: uncovering the function and metabolic features of Acidobacteria symbionts of marine sponges Provided by PTCRIS: 130434 130434 Principal investigator Centro de Ciências do Mar, Portugal	Associação para a Inovação e Desenvolvimento da FCT Concluded
2012 - 2015	Sponge Microbiomes in Times of Global Change - A Contribution to the Earth Microbiome Project DE-AC02-06CH11357 Researcher Centro de Ciências do Mar, Portugal	Concluded
2011/06 - 2014/12	Waterborne seaweed metabolites as a green solution for antimicrobial therapy in aquaculture 112792 Researcher	Portuguese Foundation for Science and Technology (FCT)
2014/06 - 2014/08	Will an increase in extreme temperature anomalies limit the ability of marine organisms to adapt to long-term climate change AdaptChange Supervisor	Research Executive Agency Concluded
2012/01 - 2013/12	Rules of attraction: unveiling bacterial behavior in a host-driven chemical sphere daad130764425719792 Principal investigator	Portuguese Foundation for Science and Technology (FCT)
2010/04 - 2013/10	Global climate change and pollution: a synergy designed for disaster? 107916 Provided by PTCRIS: 107916 Researcher	Universidade de Coimbra Concluded
2011/09 - 2013/08	SEAWEED AD: anaerobic digestion of seaweed for biofuels 274373 Researcher	Research Executive Agency
2010/01 - 2013/06	Unlocking the bacterial diversity encrypted in the metagenomes of marine sponges 101431 Provided by PTCRIS: 101431 Principal investigator Centro de Ciências do Mar, Portugal	Universidade de Coimbra
2011/01/01 - 2012/12/31	Strategic Project - LA 15 - 2011-2012 PEst-C/MAR/LA0015/2011 Centro de Investigação Marinha e Ambiental, Portugal Universidade do Porto Faculdade de Desporto, Portugal Centro de Ciências do Mar, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Outputs

Publications

Book chapter	Couceiro, J.F.; Costa, R., Keller-Costa, T.. "Beyond restoration: coral microbiome biotechnology". In Coral Reef Microbiome. Springer, 2024. Accepted Couceiro, Joana; Costa, Rodrigo; Keller-Costa, Tina. Corresponding author: Keller-Costa, Tina. "Chapter 16. Beyond restoration: Coral Microbiome Biotechnology". In Coral Reef Microbiome, edited by Peixoto, Raquel; Voolstra, Christian. Springer, 2024. Under revision Costa, R., Kimes, N.E., Nunes da Rocha, U., López-Pérez, M., Esteves, A.I.S., Mizuno, C.M.. "Marine Microbial Diversity". In Molecular Diversity of Environmental Prokaryotes, 57-85. CRC Press, 2016. Published • 10.1201/9781315381909-4 Gomes, Newton C. M.; Costa, Rodrigo; Smalia, Kornelia. "Section 1 update: Rapid simultaneous extraction of DNA and RNA from bulk and rhizophere soil". In Molecular Microbial Ecology Manual, 2061-2071. Springer Netherlands, 2008. 10.1007/978-1-4020-2177-0_112 Van Elsas, J.D.; Costa, R.. "Molecular assessment of soil microbial communities with potential for plant disease suppression". In Biotechnology and Plant Disease Management, 498-517. 2007. Published Oros-Sichler M.; Costa, Rodrigo; Heuer, H.; Smalla, K.. "Molecular fingerprinting techniques of microbial communities". In Book Chapter. Oros-Sichler, M., Costa, R. §, Heuer, H. & Smalla, K. Molecular fingerprinting techniques of microbial communities. In: Modern Soil Microbiology II (J.D. van Elsas, J.T. Trevors and J.K. Jansson Eds.), CRC Press, Boca Raton USA (2007). Boca Raton, United States, 2007. Published Gomes, Newton; Costa, Rodrigo; Smalla, Kornelia. "Rapid simultaneous extraction of DNA and RNA from bulk and rhizosphere soil". In Molecular Microbial Ecology Manual, 159-170. Netherlands: Kluwer Academic Publishers, 2004. Published
Conference abstract	Costa, R.. "The list below is non-exhaustive. Please find the full list of communications in scientific conferences at https://drive.google.com/file/d/1phpycFhuNGNBslQXL50EjJfzYWayDVvf/view?usp=sharing". 2024. Louro, Catarina; Zilhão, Henrique; Dias, Rodrigo; Gomes, Susana Sousa; Araujo, MF; Araujo, F; Araujo, M; Vieira, Gonçalo; Cesário, Rute; Costa, Rodrigo; Canário, João. "Assessing Availability and Potential Toxicity of Trace-element Contaminants in Permafrost Soils from two Antarctic Ecosystems (Deception and Livingston Islands)". Paper presented in SCAR Open Science Conference, Pucón, 2023. Submitted Costa, R.. "O microbioma marinho para um oceano saudável e uma bioeconomia sustentável". Paper presented in Microrganismos e Desenvolvimento Sustentável - Dia Internacional do Microrganismo, Lisbon, 2022. Pires, Francisco R.; Hardoim, Cristiane C.P.; Costa, Rodrigo; Xavier, Joana R.. "A new species of Spongia (Dictyoceratida, Spongiidae) from the Azores [poster]". Paper presented in 9th World Sponge Conference, Perth, 2013. Published Lago-Lestón M.A.; Hardoim, Cristiane C.P.; Pires, Francisco R.; Gonçalves, Jorge M.S.; Cox, Cymon J.; Xavier, Joana R.; Costa, Rodrigo. "Unravelling the structure of the marine sponge microbiome across biogeographical gradients [poster]". Paper presented in 9th World Sponge Conference, Perth, 2013. Hardoim, Cristiane C.P.; Cardinale, Massimiliano; Cúcio, Ana C. B.; Xavier, Joana R.; Cox, Cymon J.; Costa, Rodrigo. "Degrees of host specificity, effects of sample handling, and extent of cultivation bias elucidated for bacterial communities in closely related marine sponges [oral presentation]". Paper presented in 9th World Sponge Conference, Perth, 2013. Published Esteves, Ana I.S.; Hardoim, Cristiane C.P.; Xavier, Joana R.; Gonçalves, Jorge M.S.; Costa, Rodrigo. "Diversity of bacteria cultured from Irciniidae sponges [oral presentation]". Paper presented in 9th World Sponge Conference, Perth, 2013. Published Costa, Rodrigo; Hardoim, Cristiane C.P.; Esteves, Ana I.S.; Lago-Lestón M.A.; Cox, Cymon J.; Xavier, Joana R.. "Challenging the specificity of the marine sponge microbiome - a biogeographical approach". Paper presented in 9th World Sponge Conference, Perth, 2013. Published
Conference paper	Costa, Rodrigo. "Tackling the specificity of the marine sponge microbiome: a biogeographical approach". Paper presented in 2nd International Conference on Microbial Diversity: Microbial Interactions in Complex Ecosystems, 2013. Published Wichard, T.; Costa, Rodrigo; Grueneberg, J.; Engelen, A.. "Chemosphere of the marine green alga Ulva: induction of algal morphogenesis by bacterial compounds". 2011. Berg, G., Opelt, K., Zachow, C., Götz, M. Costa, R. & Smalla, K.. "Molecular ecology of fungal and bacterial Verticillium antagonists in/on different host plants and soils". 2007. Published Costa, Rodrigo. "Monitoring gfp-tagged bacterial antagonists in the rhizosphere of tomato plants". Paper presented in Multitrophic Interactions in Soil and Integrated Control, 2003. Published
Conference poster	Costa, R.. "The list below in non-exhaustive. Please find the full list of communications in scientific conferences at https://drive.google.com/file/d/1phpycFhuNGNBslQXL50EjJfzYWayDVvf/view?usp=sharing". 2024. 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. Pascoal, Francisco; Costa, Rodrigo; Branco, Paula; Torgo, Luis; Assmy, Philipp; Magalhães, Catarina. "Construction of a long-term dataset of prokaryotic diversity from two transects of the MOSJ program". Paper presented in XV Conferência Portuguesa de Ciências Polares, 2023. Pascoal, Francisco; Branco, Paula; Costa, Rodrigo; Magalhães, Catarina. "Unsupervised learning based definition of the microbial rare biosphere". Paper presented in BTC - Blue Think Conference, 2023. Couceiro, Joana F.; Costa, Rodrigo; Keller-Costa, Tina. "Pharmaceutical and Biotechnological Applications of the Coral Microbiome". Paper presented in MIT Portugal Annual Conference, 2023. Pascoal, Francisco; Costa, Rodrigo; Torgo, Luis; Duarte, Pedro; Assmy, Philipp; Magalhães, Catarina. "Full-length 16S rRNA gene sequencing combined with GTDB database improved the description of microbial communities from marine polar environments". Paper presented in BAGECO - Bacterial Genomics and Ecology, 2023. Marques, Matilde; Santos, Elsa; Baylina, Núria; Raquel Peixoto; Keller-Costa, Tina; Costa, Rodrigo. "Insights into the culturable bacterial community of long-term aquarium tropical octocorals". Paper presented in Bacterial Genetics and Ecology, 2023. Almeida, João F.; Costa, Rodrigo; Keller-Costa, Tina. "From chitin degradation to antibiotics production: leveraging the marine bacterial genus Aquimarina for the blue circular economy". Paper presented in SymbNET Metabolomics Workshop for Biologists: Metabolite-data driven stories on Host-Microbe Symbioses 2023, Lausanne, Switzerland, 2023. 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. Silva, Sandra G. ; Keller-Costa, Tina; Costa, Rodrigo. "Genome-wide and phenotypic assays reveal versatile secondary metabolite biosynthesis capacities and antimicrobial activities by Aquimarina species. Poster Prize Winner - First author Sandra Silva was my PhD student.". Paper presented in 2nd iBB workshop 2022, Lisbon, Portugal, 2022. Couceiro, Joana F.; Keller-Costa, Tina; Costa, Rodrigo. "Aquimarina aquimarinae sp. nov. and Aquimarina spinosulus sp. nov., new bacterial species with versatile natural product biosynthesis potential isolated from marine sponges. Short-listed for Poster Award - First author Joana Couceiro is my PhD student.". Paper presented in MIT Portugal 2022 Annual Conference, Aveiro, Portugal, 2022. 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. Meunier, Laurence; Costa, Rodrigo; Keller-Costa, Tina; George, Isabelle. "Artificial selection of chitin degrading bacterial communities from natural marine habitats". Paper presented in ISME18 - International Symposium on Microbial Ecology, Lausanne, Switzerland, 2022. 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. Marques, Matilde; Keller-Costa, Tina; Lago-Lestón, Asunción; Ulisses Nunes da Rocha; Kyrpides, Nikos C.; Páez-Espino, David; Costa, Rodrigo. "Functional and comparative metagenomics of viral communities in healthy and diseased octocoral tissue and seawater". Paper presented in Microbiotec21, 2021. Almeida, João; Marques, Matilde; Oliveira, Vanessa; Egas, Conceição; Mil-Homens, Dalila; Fialho, Arsénio; Teixeira, Miguel Cacho; et al. "Marine host-associated bacteria show versatile secondary metabolite biosynthesis capacities and antimicrobial activities.". Paper presented in MicroBiotec 21, 2021. Marques, Matilde; Almeida, João; Mil-Homens, Dalila; Fialho, Arsénio; Oliveira, Vanessa; Gomes, Newton; Costa, Rodrigo; Keller-Costa, Tina. "Bioprospecting bacterial symbionts of marine animals: sponge and coralassociated Gammaproteobacteria inhibit growth of notorious human and aquaculture pathogens.". Paper presented in MicroBiotec 21, 2021. 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. Marques, Matilde; Keller-Costa, Tina; Raquel Peixoto; Costa, Rodrigo. "Microbiome therapy for improved octocoral health and reef resilience". Paper presented in MIT Portugal Annual Conference, 2021. Pascoal, Francisco; Costa, Rodrigo; Magalhãe, Catarina. "The types of prokaryotic rarity in the Arctic ocean". Paper presented in Arctic Science Summit Week, 2021. 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. Pascoal, Francisco; Costa, Rodrigo; Magalhães, Catarina. "The prokaryotic rare biosphere is sensible to environmental heterogeinity in the Arctic ocean". Paper presented in Portuguese Polar Sciences Conference, 2020. Marques, Matilde; Silva, Sandra G.; Bernardes, Nuno; Keller-Costa, Tina; Fialho, Arsénio; Costa, Rodrigo. "Extracellular metabolites from Aquimarina (Bacteroidetes) species possess promising anticancer activity". Paper presented in Congresso de Microbiologia e Biotecnologia, 2019. Pascoal, Francisco; Magalhães, Catarina; Costa, Rodrigo. "Thinking microbial rarity". Paper presented in Halifax Mini Symposium on marine microbiology, 2019. Raimundo, Inês; Silva, Rúben; Meunier, Laurence; Keller-Costa, Tina; Costa, Rodrigo. "Chitin degradation capacity of sponge and octocoral microbiomes". Paper presented in BAGECO 15, 2019. Raimundo, Inês; Keller-Costa, Tina; Silva, Rúben; Meunier, Laurence; Costa, Rodrigo. "Multi-omics and laboratory-assisted evaluation of chitin-degrading capacities in sponge and coral microbiomes". Paper presented in ISME 17, 2018. Raimundo, Inês; Silva, Rúben; Keller-Costa, Tina; Costa, Rodrigo; Pereira, Cátia. "Multi-omics and laboratory-assisted evaluation of the chitin-degrading capacities of gorgonian coral-associated bacteria". Paper presented in Microbiotec 17, 2017. Karimi, E.; Ramos, Miguel J. N.; Franco, Telma; Rocha, U. N.; Gonçalves, J.; Reis, M. P.; Costa, Rodrigo. "Uncovering the life-style of the unculturabe: genomics and metagenomics aided cultivation of marine sponge symbionts". Paper presented in Exploiting Metagenomics Approach in Life Science Research, 2015.
Journal article	Pascoal, Francisco; Duarte, Pedro; Assmy, Philipp; Costa, Rodrigo; Magalhães, Catarina. "Full-length 16S rRNA gene sequencing combined with adequate database selection improves the description of Arctic marine prokaryotic communities". Annals of Microbiology 74 1 (2024): http://dx.doi.org/10.1186/s13213-024-01767-6. 10.1186/s13213-024-01767-6 Joana F. Couceiro; Matilde Marques; Sandra G. Silva; Tina Keller-Costa; Rodrigo Costa. "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 (2024): https://doi.org/10.1099/ijsem.0.006228. 10.1099/ijsem.0.006228 Sandra Godinho Silva; Masun Nabhan Homsi; Tina Keller-Costa; Ulisses Rocha; Rodrigo Costa; Marnix Medema. "Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon". mSystems (2023): https://doi.org/10.1128/msystems.00643-23. 10.1128/msystems.00643-23 Rocha, Ulisses; Coelho Kasmanas, Jonas; Kallies, René; Saraiva, Joao Pedro; Toscan, Rodolfo Brizola; Štefanic, Polonca; Bicalho, Marcos Fleming; et al. "MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy". Molecular Ecology Resources 24 2 (2023): http://dx.doi.org/10.1111/1755-0998.13904. Published • 10.1111/1755-0998.13904 Rocha, Ulisses; Coelho Kasmanas, Jonas; Kallies, René; Saraiva, Joao Pedro; Toscan, Rodolfo Brizola; Štefanic, Polonca; Bicalho, Marcos Fleming; et al. "MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy". Molecular Ecology Resources 24 2 (2023): http://dx.doi.org/10.1111/1755-0998.13904. 10.1111/1755-0998.13904 Rocha, Ulisses; Coelho Kasmanas, Jonas; Kallies, René; Saraiva, Joao Pedro; Toscan, Rodolfo Brizola; Štefanic, Polonca; Bicalho, Marcos Fleming; et al. "MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy". Molecular Ecology Resources 24 2 (2023): http://dx.doi.org/10.1111/1755-0998.13904. 10.1111/1755-0998.13904 Daniela M. G. da Silva; Filipa R. Pedrosa; M. Ângela Taipa; Rodrigo Costa; Tina Keller-Costa. "Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos". ISME Communications (2023): https://doi.org/10.1038/s43705-023-00316-7. 10.1038/s43705-023-00316-7 Pascoal, Francisco; Tomasino, Maria Paola; Piredda, Roberta; Quero, Grazia Marina; Torgo, Luís; Poulain, Julie; Galand, Pierre E.; et al. "Inter-comparison of marine microbiome sampling protocols". ISME Communications 3 1 (2023): http://dx.doi.org/10.1038/s43705-023-00278-w. 10.1038/s43705-023-00278-w 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. Published • 10.1016/j.zool.2023.126091 João Fragoso Almeida; Matilde Marques; Vanessa Oliveira; Conceição Egas; Dalila Mil-Homens; Romeu Viana; Daniel F. R. Cleary; et al. "Marine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities Against Human Pathogens". Marine Drugs (2022): https://www.mdpi.com/1660-3397/21/1/34. 10.3390/md21010034 Oliveira, Vanessa; Polónia, Ana R.M.; Cleary, Daniel F.R.; Huang, Yusheng M.; de Voogd, Nicole J.; Keller-Costa, Tina; Costa, Rodrigo; Gomes, Newton C.M.. "Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts". Microbiological Research 265 (2022): 127183. http://dx.doi.org/10.1016/j.micres.2022.127183. 10.1016/j.micres.2022.127183 Nata’ala, Muhammad Kabiru; Avila Santos, Anderson P.; Coelho Kasmanas, Jonas; Bartholomäus, Alexander; Saraiva, João Pedro; Godinho Silva, Sandra; Keller-Costa, Tina; et al. "MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes". Environmental Microbiome 17 1 (2022): http://dx.doi.org/10.1186/s40793-022-00449-7. Published • 10.1186/s40793-022-00449-7 Joana Fernandes Couceiro; Tina Keller-Costa; Nikos C. Kyrpides; Tanja Woyke; William B. Whitman; Rodrigo Costa; Frank J. Stewart. "Genome Sequencing Suggests Diverse Secondary Metabolism in Coral-Associated Aquimarina megaterium". Microbiology Resource Announcements (2022): https://doi.org/10.1128/mra.00620-22. 10.1128/mra.00620-22 Keller-Costa, Tina; Kozma, Lydia; Silva, Sandra G.; Toscan, Rodolfo; Gonçalves, Jorge; Lago-Lestón, Asunción; Kyrpides, Nikos C.; Nunes da Rocha, Ulisses; Costa, Rodrigo. "Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome". Microbiome 10 1 (2022): http://dx.doi.org/10.1186/s40168-022-01343-7. Published • 10.1186/s40168-022-01343-7 Lígia F. Coelho; Marie-Amélie Blais; Alex Matveev; Tina Keller-Costa; Warwick F. Vincent; Rodrigo Costa; Zita Martins; João Canário. "Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus". Scientific Reports (2022): https://doi.org/10.1038/s41598-022-16370-5. 10.1038/s41598-022-16370-5 Sanches-Fernandes, Gracinda M. M.; Sá-Correia, Isabel; Costa, Rodrigo. "Vibriosis Outbreaks in Aquaculture: Addressing Environmental and Public Health Concerns and Preventive Therapies Using Gilthead Seabream Farming as a Model System". Frontiers in Microbiology 13 (2022): http://dx.doi.org/10.3389/fmicb.2022.904815. Published • 10.3389/fmicb.2022.904815 Sandra Godinho Silva; Patrícia Paula; José Paulo da Silva; Dalila Mil-Homens; Miguel Cacho Teixeira; Arsénio Mendes Fialho; Rodrigo Costa; Tina Keller-Costa. "Insights into the Antimicrobial Activities and Metabolomes of Aquimarina (Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere". Marine Drugs 20 7 (2022): 423-423. https://doi.org/10.3390/md20070423. 10.3390/md20070423 Coelho, Lígia Fonseca; Couceiro, Joana Fernandes; Keller-Costa, Tina; Valente, Sara Martinez; Ramalho, Tiago Pereirinha; Carneiro, Joana; Comte, Jérôme; et al. Corresponding author: Costa, Rodrigo. "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 Gracinda M. M. Sanches-Fernandes; Gianmaria Califano; Sara Castanho; Florbela Soares; Laura Ribeiro; Pedro Pousão-Ferreira; Leonardo Mata; Rodrigo Costa. "Effects of live feed manipulation with algal-derived antimicrobial metabolites on fish larvae microbiome assembly: A molecular-based assessment". Aquaculture Research (2022): https://doi.org/10.1111/are.15648. 10.1111/are.15648 "Peixoto, R., Voolstra, C.V., Sweet, M., Duarte, C.M., Carvalho, S., Villela, H., Lunshof, J.E., Walter, J., Woodhams, D.C., Walke, J.B., Gram, L., Roik, A., Hentschel, U., Thurber, R.V., Daisley, B., Ushijima, B., Daffonchio, D., Costa, R., Keller-Costa, T., et al. Implementing microbiome stewardship in rapidly declining ecosystems.". Nature Microbiology (2022): Accepted Dieterich, Cora L.; Probst, Silke I.; Ueoka, Reiko; Sandu, Ioana; Schäfle, Daniel; Molin, Michael Dal; Minas, Hannah A.; et al. "Aquimarins, Peptide Antibiotics with Amino-Modified C-Termini from a Sponge-Derived Aquimarina sp. Bacterium". Angewandte Chemie 134 8 (2021): http://dx.doi.org/10.1002/ange.202115802. 10.1002/ange.202115802 Coelho, Lígia F.; Madden, Jack; Kaltenegger, Lisa; Zinder, Stephen; Philpot, William; Esquível, M. Glória; Canário, João; et al. "Color Catalogue of Life in Ice: Surface Biosignatures on Icy Worlds". Astrobiology (2021): http://dx.doi.org/10.1089/ast.2021.0008. 10.1089/ast.2021.0008 I. Raimundo; R. Silva; L. Meunier; S. M. Valente; A. Lago-Lestón; T. Keller-Costa; R. Costa. "Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes". Microbiome 9 1 (2021): https://doi.org/10.1186/s40168-020-00970-2. 10.1186/s40168-020-00970-2 Gracinda M. M. Sanches-Fernandes; Gianmaria Califano; Tina Keller-Costa; Sara Castanho; Florbela Soares; Laura Ribeiro; Pedro Pousão-Ferreira; et al. "Draft Genome Sequence of Vibrio jasicida 20LP, an Opportunistic Bacterium Isolated from Fish Larvae". Microbiology Resource Announcements 10 44 (2021): https://doi.org/10.1128/MRA.00813-21. 10.1128/MRA.00813-21 Gracinda M. M. Sanches-Fernandes; Gianmaria Califano; Tina Keller-Costa; Sara Castanho; Florbela Soares; Laura Ribeiro; Pedro Pousão-Ferreira; et al. "Draft Genome Sequence of Vibrio chagasii 18LP, Isolated from Gilthead Seabream (Sparus aurata) Larvae Reared in Aquaculture". Microbiology Resource Announcements (2021): https://doi.org/10.1128/MRA.00658-21. 10.1128/MRA.00658-21 Joana Fernandes Couceiro; Tina Keller-Costa; Matilde Marques; Nikos C. Kyrpides; Tanja Woyke; William B. Whitman; Rodrigo Costa; J. Cameron Thrash. "The Roseibium album (Labrenzia alba) Genome Possesses Multiple Symbiosis Factors Possibly Underpinning Host-Microbe Relationships in the Marine Benthos". Microbiology Resource Announcements (2021): https://doi.org/10.1128/MRA.00320-21. 10.1128/MRA.00320-21 Pascoal, Francisco; Costa, Rodrigo; Assmy, Philipp; Duarte, Pedro; Magalhães, Catarina. "Exploration of the Types of Rarity in the Arctic Ocean from the Perspective of Multiple Methodologies". Microbial Ecology (2021): http://dx.doi.org/10.1007/s00248-021-01821-9. 10.1007/s00248-021-01821-9 Michael Sweet; Helena Villela; Tina Keller-Costa; Rodrigo Costa; Stefano Romano; David G. Bourne; Anny Cárdenas; et al. "Insights into the Cultured Bacterial Fraction of Corals". mSystems 6 3 (2021): https://doi.org/10.1128/mSystems.01249-20. 10.1128/mSystems.01249-20 Keller-Costa, T.; Lago-Lestón, A.; Saraiva, J. P.; Toscan, R.; Silva, S. G.; Gonçalves, J.; Cox, C. J.; et al. Corresponding author: Keller-Costa, T.. "Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals". Microbiome 9 1 (2021): http://dx.doi.org/10.1186/s40168-021-01031-y. Open access • 10.1186/s40168-021-01031-y Borges, Nuno; Keller-Costa, Tina; Sanches-Fernandes, Gracinda M.M.; Louvado, António; Gomes, Newton C.M.; Costa, Rodrigo. "Bacteriome Structure, Function, and Probiotics in Fish Larviculture: The Good, the Bad, and the Gaps". Annual Review of Animal Biosciences 9 1 (2021): 423-452. http://dx.doi.org/10.1146/annurev-animal-062920-113114. 10.1146/annurev-animal-062920-113114 Pascoal, Francisco; Costa, Rodrigo; Magalhães, Catarina. "The microbial rare biosphere: current concepts, methods and ecological principles". FEMS Microbiology Ecology 97 1 (2020): http://dx.doi.org/10.1093/femsec/fiaa227. 10.1093/femsec/fiaa227 Marques, Matilde; Borges, Nuno; Silva, Sandra Godinho; da Rocha, Ulisses Nunes; Lago-Lestón, Asunción; Keller-Costa, Tina; Costa, Rodrigo. "Metagenome-Assembled Genome Sequences of Three Uncultured Planktomarina sp. Strains from the Northeast Atlantic Ocean". Microbiology Resource Announcements 9 12 (2020): http://dx.doi.org/10.1128/mra.00127-20. 10.1128/mra.00127-20 Pascoal, Francisco; Magalhães, Catarina; Costa, Rodrigo. "The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential". Frontiers in Microbiology 11 (2020): http://dx.doi.org/10.3389/fmicb.2020.00231. Accepted • 10.3389/fmicb.2020.00231 Califano, Gianmaria; Kwantes, Michiel; Abreu, Maria Helena; Costa, Rodrigo; Wichard, Thomas. "Cultivating the Macroalgal Holobiont: Effects of Integrated Multi-Trophic Aquaculture on the Microbiome of Ulva rigida (Chlorophyta)". Frontiers in Marine Science 7 (2020): http://dx.doi.org/10.3389/fmars.2020.00052. Published • 10.3389/fmars.2020.00052 Elham Karimi; Tina Keller-Costa; Beate M. Slaby; Cymon J. Cox; Ulisses N. da Rocha; Ute Hentschel; Rodrigo Costa. "Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria". Scientific Reports 9 1 (2019): https://doi.org/10.1038/s41598-019-38737-x. 10.1038/s41598-019-38737-x Sandra G. Silva; Jochen Blom; Tina Keller-Costa; Rodrigo Costa. "Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host-associated and free-living Aquimarina ( Bacteroidetes, Flavobacteriaceae ) species". Environmental Microbiology 21 11 (2019): 4002-4019. https://doi.org/10.1111/1462-2920.14747. Published • 10.1111/1462-2920.14747 Eric J. N. Helfrich; Reiko Ueoka; Alon Dolev; Michael Rust; Roy A. Meoded; Agneya Bhushan; Gianmaria Califano; et al. "Automated structure prediction of trans-acyltransferase polyketide synthase products". Nature Chemical Biology (2019): https://doi.org/10.1038/s41589-019-0313-7. Published • 10.1038/s41589-019-0313-7 Inês Raimundo; Sandra Godinho Silva; Rodrigo Costa; Tina Keller Costa. "Bioactive Secondary Metabolites from Octocoral-Associated Microbes—New Chances for Blue Growth". Marine Drugs (2018): http://www.mdpi.com/1660-3397/16/12/485. Open access • 10.3390/md16120485 Cristina Díez-Vives; Ana I. S. Esteves; Rodrigo Costa; Shaun Nielsen; Torsten Thomas. "Detecting signatures of a sponge-associated lifestyle in bacterial genomes". Environmental Microbiology Reports (2018): https://doi.org/10.1111%2F1758-2229.12655. 10.1111/1758-2229.12655 Elham Karimi; Beate M Slaby; André R Soares; Jochen Blom; Ute Hentschel; Rodrigo Costa. "Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges". FEMS Microbiology Ecology 94 6 (2018): https://doi.org/10.1093%2Ffemsec%2Ffiy074. 10.1093/femsec/fiy074 Gisele Nunes Rodrigues; Asunción Lago-Lestón; Rodrigo Costa; Tina Keller-Costa. "Draft Genome Sequence of Labrenzia sp. Strain EL143, a Coral-Associated Alphaproteobacterium with Versatile Symbiotic Living Capability and Strong Halogen Degradation Potential". Genome Announcements 6 10 (2018): https://doi.org/10.1128/genomeA.00132-18. 10.1128/genomeA.00132-18 Sandra Godinho Silva; Asunción Lago-Lestón; Rodrigo Costa; Tina Keller-Costa. "Draft Genome Sequence of Sphingorhabdus sp. Strain EL138, a Metabolically Versatile Alphaproteobacterium Isolated from the Gorgonian Coral Eunicella labiata". Genome Announcements 6 9 (2018): https://doi.org/10.1128/genomeA.00142-18. 10.1128/genomeA.00142-18 Costa, Rodrigo; Castanho, Sara; Califano, Gianmaria; Soares, F.; Costa, Rodrigo; Mata, L.; Pousao-Ferreira, P.; Ribeiro, L.; Gianmaria Califano. "The effect of live feeds bathed with the red seaweed Asparagopsis armata on the survival, growth and physiology status of Sparus aurata larvae.". Fish Physiology and Biochemistry 43 4 (2017): 1043-1054. http://hdl.handle.net/10400.1/13056. 10.1007/s10695-017-0351-6. Costa, Rodrigo. "Morphogenesis of Ulva mutabilis (Chlorophyta) induced by Maribacter species (Bacteroidetes, Flavobacteriaceae).". (2017): 10.1515/bot-2016-0083 Califano, Gianmaria; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Cox, Cymon J.; Mata, Leonardo; Costa, Rodrigo. "Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (Sparus aurata) Hatchery". Frontiers in Microbiology 8 (2017): http://dx.doi.org/10.3389/fmicb.2017.00204. Published • 10.3389/fmicb.2017.00204 Elham Karimi; Jorge M. S. Gonçalves; Margarida Reis; Rodrigo Costa. "Draft Genome Sequence of Microbacterium sp. Strain Alg239_V18, an Actinobacterium Retrieved from the Marine Sponge Spongia sp". Genome Announcements 5 3 (2017): https://doi.org/10.1128/genomeA.01457-16. 10.1128/genomeA.01457-16 Costa, Rodrigo. "Ecophysiological plasticity and bacteriome shift in the seagrass Halophila stipulacea along a depth gradient in the Northern Red Sea.". (2017): 10.3389/fpls.2016.02015 Elham Karimi; Miguel Ramos; Jorge M. S. Gonçalves; Joana R. Xavier; Margarida P. Reis; Rodrigo Costa. "Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium". Frontiers in Microbiology 8 (2017): https://doi.org/10.3389%2Ffmicb.2017.02499. 10.3389/fmicb.2017.02499 Costa, Rodrigo. "The sponge microbiome project". GigaScience (2017): 10.1093/gigascience/gix077 Costa, Rodrigo. "The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation". (2017): doi.org/10.1093/femsec/fix143 Francisco J. R. C. Coelho; Daniel F. R. Cleary; Rodrigo Costa; Marina Ferreira; Ana R. M. Polónia; Artur M. S. Silva; Mário M. Q. Simões; Vanessa Oliveira; Newton C. M. Gomes. "Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution". Molecular Ecology (2016): http://dx.doi.org/10.1111/mec.13779. 10.1111/mec.13779 Tina Keller-Costa; Rúben Silva; Asunción Lago-Lestón; Rodrigo Costa. "Genomic Insights into Aquimarina sp. Strain EL33, a Bacterial Symbiont of the Gorgonian Coral Eunicella labiata". Genome Announcements 4 4 (2016): https://doi.org/10.1128%2Fgenomea.00855-16. 10.1128/genomea.00855-16 Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Björk, Johannes R.; Easson, Cole; Astudillo-García, Carmen; Olson, Julie B.; et al. "Diversity, structure and convergent evolution of the global sponge microbiome". Nature Communications 7 1 (2016): http://dx.doi.org/10.1038/ncomms11870. Published • 10.1038/ncomms11870 Cúcio, Catarina; Engelen, Aschwin H.; Costa, Rodrigo; Muyzer, Gerard. "Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific". Frontiers in Microbiology 7 (2016): http://dx.doi.org/10.3389/fmicb.2016.00440. 10.3389/fmicb.2016.00440 Telma Franco; Gianmaria Califano; Ana C. S. Gonçalves; Catarina Cúcio; Rodrigo Costa. "Draft Genome Sequence of Vibrio sp. Strain Evh12, a Bacterium Retrieved from the Gorgonian Coral Eunicella verrucosa". Genome Announcements 4 1 (2016): e01729-15. https://doi.org/10.1128/genomeA.01729-15. 10.1128/genomeA.01729-15 Grueneberg, Jan; Engelen, Aschwin H.; Costa, Rodrigo; Wichard, Thomas. "Macroalgal Morphogenesis Induced by Waterborne Compounds and Bacteria in Coastal Seawater". Plos One 11 1 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000367815600037&KeyUID=WOS:000367815600037. 10.1371/journal.pone.0146307 Goncalves, Ana C. S.; Franco, Telma; Califano, Gianmaria; Dowd, Scot E.; Pohnert, Georg; Costa, Rodrigo; Ana C S Gonçalves; et al. "Draft Genome Sequence of Vibrio sp. Strain Vb278, an Antagonistic Bacterium Isolated from the Marine Sponge Sarcotragus spinosulus". Genome announcements 3 3 (2015): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:26021918&KeyUID=MEDLINE:26021918. 10.1128/genomeA.00521-15 Coelho, Francisco J. R. C.; Cleary, Daniel F. R.; Rocha, Rui J. M.; Calado, Ricardo; Castanheira, Jose M.; Rocha, Silvia M.; Silva, Artur M. S.; et al. "Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities". Global Change Biology 21 5 (2015): 1871-1886. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000353220500011&KeyUID=WOS:000353220500011. 10.1111/gcb.12801 Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-Guerra, Antonio; et al. "The ocean sampling day consortium". GigaScience 4 (2015): 27-27. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:26097697&KeyUID=MEDLINE:26097697. 10.1186/s13742-015-0066-5 Califano, Gianmaria; Franco, Telma; Goncalves, Ana C. S.; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Mata, Leonardo; et al. "Draft Genome Sequence of Aliivibrio fischeri Strain 5LC, a Bacterium Retrieved from Gilthead Sea Bream (Sparus aurata) Larvae Reared in Aquaculture". Genome announcements 3 3 (2015): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:26044435&KeyUID=MEDLINE:26044435. 10.1128/genomeA.00593-15 Hardoim, Cristiane; Costa, Rodrigo. "Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review". Marine Drugs 12 10 (2014): 5089-5122. http://dx.doi.org/10.3390/md12105089. Published • 10.3390/md12105089 Keller-Costa, Tina; Jousset, Alexandre; van Overbeek, Leo; van Elsas, Jan Dirk; Costa, Rodrigo. "The Freshwater Sponge Ephydatia fluviatilis Harbours Diverse Pseudomonas Species (Gammaproteobacteria, Pseudomonadales) with Broad-Spectrum Antimicrobial Activity". PLoS ONE 9 2 (2014): e88429. http://dx.doi.org/10.1371/journal.pone.0088429. 10.1371/journal.pone.0088429 Hardoim, Cristiane C. P.; Cardinale, Massimiliano; Cucio, Ana C. B.; Esteves, Ana I. S.; Berg, Gabriele; Xavier, Joana R.; Cox, Cymon J.; Costa, Rodrigo. "Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges". Frontiers in Microbiology 5 (2014): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000345747500001&KeyUID=WOS:000345747500001. 10.3389/fmicb.2014.00611 Alexandrino, Maria; Costa, Rodrigo; Canario, Adelino V. M.; Costa, Maria C.. "Clostridia Initiate Heavy Metal Bioremoval in Mixed Sulfidogenic Cultures". Environmental Science & Technology 48 6 (2014): 3378-3385. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000333776000036&KeyUID=WOS:000333776000036. 10.1021/es4052044 Hardoim, Cristiane C. P.; Costa, Rodrigo. "Temporal dynamics of prokaryotic communities in the marine sponge Sarcotragus spinosulus". Molecular Ecology 23 12 (2014): 3097-3112. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000337610600016&KeyUID=WOS:000337610600016. 10.1111/mec.12789 Costa, R.; Keller-Costa, T.; Gomes, N.C.M.; da Rocha, U.N.; van Overbeek, L.; van Elsas, J.D.. "Evidence for Selective Bacterial Community Structuring in the Freshwater Sponge Ephydatia fluviatilis". Microbial Ecology 65 1 (2013): 232-244. http://www.scopus.com/inward/record.url?eid=2-s2.0-84872340581&partnerID=MN8TOARS. 10.1007/s00248-012-0102-2 Coelho, F.J.R.C.; Rocha, R.J.M.; Pires, A.C.C.; Ladeiro, B.; Castanheira, J.M.; Costa, R.; Almeida, A.; et al. "Development and validation of an experimental life support system for assessing the effects of global climate change and environmental contamination on estuarine and coastal marine benthic communities". Global Change Biology 19 8 (2013): 2584-2595. http://www.scopus.com/inward/record.url?eid=2-s2.0-84880132597&partnerID=MN8TOARS. 10.1111/gcb.12227 Hardoim, C.C.P.; Cox, C.J.; Peixoto, R.S.; Rosado, A.S.; Costa, R.; van Elsas, J.D.. "Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulva". Brazilian Journal of Microbiology 44 1 (2013): 329-334. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879150283&partnerID=MN8TOARS. 10.1590/S1517-83822013000100048 Silva, Y.J.; Manco, S.; Costa, R.; Rodrigues, V.; Dias, J.; Ferreira, H.; Pousão-Ferreira, P.; et al. "Effect of different culture conditions on the structural diversity of prokaryote communities in the sediment of earth ponds stocked with gilthead seabream Sparus aurata (Linnaeus, 1758)". Aquaculture Research (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84889044428&partnerID=MN8TOARS. 10.1111/are.12336 Esteves, A.I.S.; Hardoim, C.C.P.; Xavier, J.R.; Gonçalves, J.M.S.; Costa, R.. "Molecular richness and biotechnological potential of bacteria cultured from Irciniidae sponges in the north-east Atlantic". FEMS Microbiology Ecology 85 3 (2013): 519-536. http://www.scopus.com/inward/record.url?eid=2-s2.0-84881556290&partnerID=MN8TOARS. 10.1111/1574-6941.12140 Hardoim, C.C.P.; Esteves, A.I.S.; Pires, F.R.; Gonçalves, J.M.S.; Cox, C.J.; Xavier, J.R.; Costa, R.. "Phylogenetically and Spatially Close Marine Sponges Harbour Divergent Bacterial Communities". PLoS ONE 7 12 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84871657844&partnerID=MN8TOARS. 10.1371/journal.pone.0053029 Gomes NC; Cleary DF; Calado R; Costa R. "Mangrove bacterial richness.". (2011): http://europepmc.org/abstract/med/21966560. 10.4161/cib.4.4.15253 Van Elsas, J.D.; Semenov, A.V.; Costa, R.; Trevors, J.T.. "Survival of Escherichia coli in the environment: Fundamental and public health aspects". ISME Journal 5 2 (2011): 173-183. http://www.scopus.com/inward/record.url?eid=2-s2.0-78149408759&partnerID=MN8TOARS. 10.1038/ismej.2010.80 Alexandrino, M.; Macías, F.; Costa, R.; Gomes, N.C.M.; Canário, A.V.M.; Costa, M.C.. "A bacterial consortium isolated from an Icelandic fumarole displays exceptionally high levels of sulfate reduction and metals resistance". Journal of Hazardous Materials 187 1-3 (2011): 362-370. http://www.scopus.com/inward/record.url?eid=2-s2.0-79951853200&partnerID=MN8TOARS. 10.1016/j.jhazmat.2011.01.035 Dini-Andreote, F.; Andreote, F.D.; Costa, R.; Taketani, R.G.; van Elsas, J.D.; Araújo, W.L.. "Bacterial soil community in a Brazilian sugarcane field". Plant and Soil 336 1 (2010): 337-349. http://www.scopus.com/inward/record.url?eid=2-s2.0-78049275323&partnerID=MN8TOARS. 10.1007/s11104-010-0486-z Gomes, N.C.; Flocco, C.G.; Costa, R.; Junca, H.; Vilchez, R.; Pieper, D.H.; Krögerrecklenfort, E.; et al. "Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia". FEMS Microbiology Ecology 74 2 (2010): 276-290. http://www.scopus.com/inward/record.url?eid=2-s2.0-78649383108&partnerID=MN8TOARS. 10.1111/j.1574-6941.2010.00962.x Costa, R.; Van Aarle, I.M.; Mendes, R.; Van Elsas, J.D.. "Genomics of pyrrolnitrin biosynthetic loci: Evidence for conservation and whole-operon mobility within Gram-negative bacteria". Environmental Microbiology 11 1 (2009): 159-175. http://www.scopus.com/inward/record.url?eid=2-s2.0-58149242718&partnerID=MN8TOARS. 10.1111/j.1462-2920.2008.01750.x Hardoim, C.C.P.; Costa, R.; V.araújo, F.; Hajdu, E.; Peixoto, R.; Lins, U.; Rosado, A.S.; Van, J.D.E.. "Diversity of bacteria in the marine sponge aplysina fulva in brazilian coastal waters". Applied and Environmental Microbiology 75 10 (2009): 3331-3343. http://www.scopus.com/inward/record.url?eid=2-s2.0-66249094562&partnerID=MN8TOARS. 10.1128/AEM.02101-08 van Elsas, J.D.; Costa, R.; Jansson, J.; Sjöling, S.; Bailey, M.; Nalin, R.; Vogel, T.M.; van Overbeek, L.. "The metagenomics of disease-suppressive soils - experiences from the METACONTROL project". Trends in Biotechnology 26 11 (2008): 591-601. http://www.scopus.com/inward/record.url?eid=2-s2.0-53949095625&partnerID=MN8TOARS. 10.1016/j.tibtech.2008.07.004 Costa, R.; Gomes, N.C.M.; Krögerrecklenfort, E.; Opelt, K.; Berg, G.; Smalla, K.. "Pseudomonas community structure and antagonistic potential in the rhizosphere: Insights gained by combining phylogenetic and functional gene-based analyses". Environmental Microbiology 9 9 (2007): 2260-2273. http://www.scopus.com/inward/record.url?eid=2-s2.0-34547686154&partnerID=MN8TOARS. 10.1111/j.1462-2920.2007.01340.x Adesina, M.F.; Lembke, A.; Costa, R.; Speksnijder, A.; Smalla, K.. "Screening of bacterial isolates from various European soils for in vitro antagonistic activity towards Rhizoctonia solani and Fusarium oxysporum: Site-dependent composition and diversity revealed". Soil Biology and Biochemistry 39 11 (2007): 2818-2828. http://www.scopus.com/inward/record.url?eid=2-s2.0-34547730211&partnerID=MN8TOARS. 10.1016/j.soilbio.2007.06.004 Costa, R.; Götz, M.; Mrotzek, N.; Lottmann, J.; Berg, G.; Smalla, K.. "Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds". FEMS Microbiology Ecology 56 2 (2006): 236-249. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645977196&partnerID=MN8TOARS. 10.1111/j.1574-6941.2005.00026.x Götz, M.; Gomes, N.C.M.; Dratwinski, A.; Costa, R.; Berg, G.; Peixoto, R.; Mendonça-Hagler, L.; Smalla, K.. "Survival of gfp-tagged antagonistic bacteria in the rhizosphere of tomato plants and their effects on the indigenous bacterial community". FEMS Microbiology Ecology 56 2 (2006): 207-218. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646014149&partnerID=MN8TOARS. 10.1111/j.1574-6941.2006.00093.x Berg, G.; Opelt, K.; Zachow, C.; Lottmann, J.; Götz, M.; Costa, R.; Smalla, K.. "The rhizosphere effect on bacteria antagonistic towards the pathogenic fungus Verticillium differs depending on plant species and site". FEMS Microbiology Ecology 56 2 (2006): 250-261. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646003568&partnerID=MN8TOARS. 10.1111/j.1574-6941.2005.00025.x Costa, R.; Salles, J.F.; Berg, G.; Smalla, K.. "Cultivation-independent analysis of Pseudomonas species in soil and in the rhizosphere of field-grown Verticillium dahliae host plants". Environmental Microbiology 8 12 (2006): 2136-2149. http://www.scopus.com/inward/record.url?eid=2-s2.0-33750919098&partnerID=MN8TOARS. 10.1111/j.1462-2920.2006.01096.x Costa, R.; Gomes, N.C.M.; Peixoto, R.S.; Rumjanek, N.; Berg, G.; Mendonça-Hagler, L.C.S.; Smalla, K.. "Diversity and antagonistic potential of Pseudomonas spp. associated to the rhizosphere of maize grown in a subtropical organic farm". Soil Biology and Biochemistry 38 8 (2006): 2434-2447. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746863682&partnerID=MN8TOARS. 10.1016/j.soilbio.2006.03.003 Meier, J.; Costa, R.; Smalla, K.; Boehrer, B.; Wendt-Potthoff, K.. "Temperature dependence of Fe(III) and sulfate reduction rates and its effect on growth and composition of bacterial enrichments from an acidic pit lake neutralization experiment". Geobiology 3 4 (2005): 261-274. http://www.scopus.com/inward/record.url?eid=2-s2.0-33644826898&partnerID=MN8TOARS. 10.1111/j.1472-4669.2006.00065.x Berg, G.; Zachow, C.; Lottmann, J.; Götz, M.; Costa, R.; Smalla, K.. "Impact of plant species and site on rhizosphere-associated fungi antagonistic to Verticillium dahliae Kleb.". Applied and Environmental Microbiology 71 8 (2005): 4203-4213. http://www.scopus.com/inward/record.url?eid=2-s2.0-23744446235&partnerID=MN8TOARS. 10.1128/AEM.71.8.4203-4213.2005 Costa, R.; Gomes, N.C.M.; Milling, A.; Smalla, K.. "An optimized protocol for simultaneous extraction of DNA and RNA from soils". Brazilian Journal of Microbiology 35 3 (2004): 230-234. http://www.scopus.com/inward/record.url?eid=2-s2.0-19944409539&partnerID=MN8TOARS. Published Marcial Gomes, N.C.; Fagbola, O.; Costa, R.; Gouvea Rumjanek, N.; Buchner, A.; Mendona-Hagler, L.; Smalla, K.. "Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics". Applied and Environmental Microbiology 69 7 (2003): 3758-3766. http://www.scopus.com/inward/record.url?eid=2-s2.0-0038493638&partnerID=MN8TOARS. 10.1128/AEM.69.7.3758-3766.2003 Gomes, N.C.M.; Heuer, H.; Schönfeld, J.; Costa, R.; Mendonça-Hagler, L.; Smalla, K.. "Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil studied by temperature gradient gel electrophoresis". Plant and Soil 232 1-2 (2001): 167-180. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034948012&partnerID=MN8TOARS. 10.1023/A:1010350406708
Magazine article	Costa, Rodrigo. "Esponjas marinhas: do mar à farmácia", Boletim de Biotecnologia, 2014, http://www.forumoceano.pt/files/6_Comunicacao/61_artigos/Boletim_SPBT_julh2014.pdf?d=37fr.
Newspaper article	Costa, Rodrigo; Isabel Sá-Correia. "Microbiologia Azul: Pilar da Bioeconomia do mar, Jornal i online, artigo de opinião de 11 de Janeiro de 2022", 2022, https://ionline.sapo.pt/artigo/758885/microbiologia-azul-pilar-da-bioeconomia-do-mar?seccao=Opiniao_ihttps://ionline.sapo.pt/artigo/758885/microbiologia-azul-pilar-da-bioeconomia-do-mar?seccao=Opiniao_i.
Online resource	Pascoal, F., Branco, P., Torgo, L., Costa, R., and Magalhães, C.. ulrb: Unsupervised Learning Based Definition of Microbial Rare Biosphere. Computational resource.. 2023. https://cran.r-project.org/web/packages/ulrb/index.html. Silva, S.G.; Keller-Costa, T.; Nunes da Rocha, R.; Costa, R.. Melange: A Snakemake workflow that streamlines structural and functional annotation of prokaryote genomes. Computational resource.. 2023. https://sandragodinhosilva.github.io/melange/. Keller-Costa, T., Toscan, R., Kozma, L., Silva, S.G., Gonçalves, J., Lago-Lestón, A., Kyprides, N., Nunes da Rocha, U.,. Metagenomics-resolved genomics provides insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome. Scientific outreach video.. 2022. https://www.youtube.com/watch?v=iQrVdXdYTTY. Costa, R. O microbioma marinho para um oceano saudável e uma bioeconomia sustentável. Keynote lecture at the Academy of Science of Lisbon. 2022. https://www.youtube.com/watch?v=4nFPU30uo3g. Keller-Costa, T., Lago-Lestón, A., Saraiva, J.P., Toscan, R., Silva, S.G., Gonçalves, J., Cox, C.J., Kyrpides, N., Nunes. New metagenomic insights into the octocoral microbiome. Scientific outreach video.. 2021. https://www.youtube.com/watch?v=jjuyYAluAg8. Raimundo, I., Silva, R., Meunier, L., Valente, S.M, Lago-Lestón, A., Keller-Costa, T., & Costa, R.. Uncovering the chitin degradation and utilization potential of marine microbiomes. Scientific outreach video.. 2021. https://www.youtube.com/watch?v=KrCFYL56NPI. Costa, R.. Distinct adaptive features in alphaproteobacterial symbionts of marine sponges. Keynote lecture. FEMS Microbiology Ecology Webinar on the Sponge Microbiome.. 2020. https://www.youtube.com/watch?v=YTDBIGvcz60.
Preprint	Michael Sweet; Helena Villela; Tina Keller-Costa; Rodrigo Costa; Stefano Romano; David Bourne; Anny Cardenas; et al. "Insights into the cultured bacterial fraction of corals". 2020. https://doi.org/10.21203/rs.3.rs-105866/v1. 10.21203/rs.3.rs-105866/v1 Karimi, Elham; Costa, Rodrigo. "Isolation and genome sequencing of 14 Spongia sp. bacterial associates expands the taxonomic and functional breadth of the cultivatable marine sponge microbiome". 2020. http://dx.doi.org/10.1101/2020.03.20.000216. 10.1101/2020.03.20.000216
Thesis / Dissertation	Hardoim, Cristiane Cassiolato Pires; Costa, Rodrigo; Cox, Cymon J.; Canario, Adelino V. M.. "Microbiome diversity and composition in the phylogenetically related marine sponges S. spinosulus and I. variabilis". PhD, 2013. http://hdl.handle.net/10400.1/6738. Costa, Rodrigo. "Microbial community structure and function in the rhizosphere of crop plants: a molecular study". PhD, 2006. Costa, Rodrigo. "Variabilidade e diversidade genética de comunidades bacterianas associadas à rizosfera de Milho (Zea mays L. Merril) em um agroecossistema do Rio de Janeiro". Master, Universidade Federal do Rio de Janeiro, 2001.

Other

Dataset

Costa, R.. Full list of communications - Rodrigo Costa https://drive.google.com/file/d/1phpycFhuNGNBslQXL50EjJfzYWayDVvf/view?usp=sharing. 2024.

Other output

Marine microbial diversity. Book Chapter. Costa, R., Kimes, N.E., Nunes da Rocha, U.,López-Pérez, M., Esteves, A.I.S., Mizuno, C.M. Marine microbial diversity. In: T.B. Rodrigues and A.E.T. Silva (eds.). Molecular Diversity of Environmental Prokaryotes. CRC Press, Boca Raton USA (2016).. 2016. Costa, Rodrigo; Kimes, N.E.; Nunes da Rocha, U.; Esteves, A.I.S.; Mizuno, C.M..
Molecular ecology of fungal and bacterial Verticillium antagonists in/on different host plants and soils. Conference Proceedings Proceedings of the meeting “Fundamental and Practical Approaches to Increase Biocontrol Efficacy”, Spa, Belgium, 2006. International Organization for Biological Control (IOBC) Bulletin 30: 249-253 (2007).. 2007. Berg, G.; Opelt, K.; Zachow, C.; Götz, M.; Costa, Rodrigo.

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2024	The list below is non-exhaustive. Please find the full list of oral communications, poster presentations, and dissemination activities in this file: https://drive.google.com/file/d/1phpycFhuNGNBslQXL50EjJfzYWayDVvf/view?usp=sharing	Full List of Communications
2019	Functional signatures of the microbiomes of octocorals in health and disease.	Microbiotec19 (Coimbra, Portugal)
2019	The microbiome of keratose marine sponges: diversity, function and biotechnology.	Prokaryotic Research and Development Program Meeting, Joint Genome Institute (DOE-JGI) Laurence Berkeley National Laboratory, UC-Berkeley, USA (United States)
2019	The MicroEcoEvo bacterial culture collection	Genomic Encyclopaedia of Bacteria and Archaea (GEBA, edition VI) kick-off meeting Joint Genome Institute (DOE-JGI), Laurence Berkeley National Laboratory, UC-Berkeley, USA (United Kingdom)
2019	Functional signatures of the microbiomes of octocorals in health and disease	Science & Technology Seminar, Joint Genome Institute (DOE-JGI) Laurence Berkeley National Laboratory, UC-Berkeley, USA (United States)
2018	Versatile nutrient exchange and host detoxification and chemical defence capacities in the cultivable microbial dark matter of marine sponges	17th International Symposium on Microbial Ecology (Leipzig, Germany)
2018	On the road towards predicting microbial systems: Is modelling guiding the right way? Round table panelist	17th International Symposium on Microbial Ecology (ISME17) (Germany)
2018	Exploring the depths of microbial diversity: Metagenomics	International Microorganism Day Instituto Superior Técnico (Portugal)
2018	Metagenomic insights into the marine sponge microbiome – Illuminating the evolution and metabolism of symbiotic Alphaproteobacteria	Mini-Symposium “Networking and cooperation in Microbial Ecology” Julius Kühn Institute (Braunschweig, Germany)
2018	The Microcontrol project: strategies and protocols for microbiome manipulation of fish	1st Workshop on Beneficial Microorganisms for Marine Organisms (BMMO) UFZ-Leipzig (Germany)
2018	The microbiome of keratose marine sponges: diversity, function and biotechnology	Encontro Ciência 2018 FCT (Lisboa, Portugal)
2018	Metagenomic insights into the marine sponge microbiome – Illuminating the evolution and metabolism of symbiotic Alphaproteobacteria	iBB seminar series Instituto Superior Técnico (Portugal)
2018	The microbiome of keratose marine sponges: diversity, function and biotechnology	Elixir-Excelerate Workshop on Marine Metagenomics Instituto Calouste Gulbenkian (Portugal)
2018	The microbiome of keratose marine sponges: diversity, function and biotechnology	Seminar Series Departamento de Oceanografia e Pescas, Universidade dos Açores (Portugal)
2017	Multi-omics and laboratory-assisted evaluation of the chitin-degrading capacities of gorgonian coral-associated bacteria	Microbioec17 (Portugal)
2017	Comparative metagenomics reveals unique life strategies of the endosymbiotic consortium inhabiting the iconic bath sponge Spongia officinalis	14th Symposium on Bacterial Genetics and Ecology (United Kingdom)
2017	Diversity, function and biotechnology of marine microbial communities - a metagenomics perspective	Ciclo de Conferências redeMAR - Qual o Potencial e o Impacto da Biotecnologia Marinha nas Ciências Médicas e Farmacêuticas? University of Lisbon (Lisboa, Portugal)
2017	Meeting the aliens: morphogenesis induction of the green alga Ulva mutabilis by bacterial symbionts of marine sponges	1st AquaRio workshop on marine microbiome diversity and manipulation Rio de Janeiro Federal University (Brazil)
2017	Use of an oligrotrophic culture medium enables captivation of diverse alphaprobacterial lineages from the marine sponge Spongia officinalis	3rd Annual Conference of the interdisciplinary thematic network redeMAR - Ocean and Future(s) University of Lisbon (Portugal)

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2024 - Current	This list of supervisions contains completed PhD (n=6) and Master's theses (n=28) as well as ongoing PhD (n=5) and Master's (n = 6) theses. For a full list containing undergraduate monographs/projects, please consult the full CV at: https://drive.google.com/file/d/1TEj7hpMElFkqLhJSL9OEMzBqmafYvVGC/view?usp=sharing Supervisor
2023 - Current	From chitin degradation to antibiotics production: leveraging the marine bacterial genus Aquimarina for the blue circular economy Co-supervisor	Biotechnology and Biosciences (PhD) Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - Current	Assessment of symbiosis related traits in octocoral-associated Endozoicomonas spp. using a comparative genomics-, bioassay-, and taxonomy-guided approach Supervisor	Microbiology (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - Current	Culturing the unculturable: Captivating hard-to-cultivate bacterial symbionts from octocorals using host chemical cues and microaerophilic conditions. Co-supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - Current	Uncovering the macroalgae microbiome: a quest for bacterial symbionts to promote the sustainable production of algal biomass in aquaculture facilities. Supervisor	Biotechnology (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - Current	Genomic analysis of Antarctic permafrost samples: assessing the impact of defrosting on the ecosystem’s toxicity Supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - Current	Comparative and functional genomics of octocoral symbionts Supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - Current	Assessing the rhizosphere e¿ect on Hg-resistant bacteria in salt marsh sediments Supervisor	Bioengineering (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/06/22 - Current	Sustainable production of bioactive metabolites from octocoral symbionts. MIT-Portugal PhD programme. Co-supervisor of Joana F. Couceiro	Programa Doutoral em Biotecnologia e Biociências (PhD) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/05/01 - Current	Microbiome therapy for improved coral health and reef resilience. MIT Portugal Programme. Supervisor	Biotechnology and Biosciences (PhD) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/01/01 - Current	Deciphering the roles of the prokaryotic rare biosphere in the Arctic Ocean under climate change. PhD Programme in Biology, Faculty of Sciences, Porto University, Portugal. Co-supervisor	PhD Program in Biology (PhD) Universidade do Porto Faculdade de Ciências, Portugal
2020 - Current	Chitin degradation capacities of synthetic microbial communities Supervisor	Bioengineering (PhD) Université Libre de Bruxelles, Belgium
2020/03 - 2023/06/07	Cracking the code: exploring the virome of the marine sponge S. officinalis. Supervisor	Molecular and Microbioal Biology (Master) Universidade do Algarve, Portugal
2018/09 - 2023/06	Secondary metabolite biosynthesis by Aquimarina species: emerging properties and bioactivities from the rare marine biosphere Supervisor	Biotechnology and Biosciences (PhD) Universidade de Lisboa Instituto Superior Técnico, Portugal
2017/09 - 2023/06	Uncovering the chitin degradation potential in the microbiomes of marine sponges and octocorals Supervisor	Biotechnology and Biosciences (PhD) Universidade de Lisboa Instituto Superior Técnico, Portugal
2022 - 2023	GFP-tagging of Vibrio fish pathogens for studying interactions with beneficial microbiomes. Co-supervisor	Biological Engineering (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2022/06	Astrobiology analyses of icy biomes as a proxy for extra-terrestrial life in icy moons Supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022	Marine bacteria associated with Phaeodactylum tricornutum and Nannochloropsis oceanica: identification, characterization and biotechnological potential Co-supervisor	Master's Programme in Microbiology (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022	Exploring planktonic microbiome diversity in the coastal ecosystems of the North of Portugal Co-supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - 2022	Use of environmentally-sustainable procedures to prevent disease incidence in fish larviculture Supervisor	Biotechnology and Biosciences (PhD) Universidade de Lisboa Instituto Superior Técnico, Portugal
2020/02 - 2021/01	Discovering the polar microbiome: structure and diversity of prokaryotic communities in ice and seawater along a salinity gradient in the Subarctic. Supervisor of Joana F. Couceiro	Masters Programme in Biological Engineering (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2020/09 - 2021	Identification, phenotypic characterization and selection of Gilthead seabream (Sparus aurata) associated bacteria for Application as putative probiotics in fish larviculture Supervisor of André Magalhães	Microbiology (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - 2021	Captivating the uncultivated: a quest for so-far uncultured bacterial symbionts from the healthy octocoral holobiont Co-supervisor	École Polytechnique Fédérale de Lausanne, Switzerland
2020 - 2021	Getting to know a barley population's stomata: on how AI algorithms can improve stomatal density analysis Co-supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2019	Assessment of antimicrobial activities of marine bacteria against human pathogens Supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2019	Assessment of anticancer activities in marine sponge- and coral- associated bacteria Supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2019	Tackling the diversity of the marine microbial rare biosphere: methodological challenges and ecological insights Supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2019	Antimicrobial efficacy of Chlorhexidine Gluconate against Salmonella isolates from pet reptiles Co-supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - 2018	Addressing the relationship between Staphylococcus aureus abundance in the human skin microbiome and atopic dermatitis: a metagenomics approach Supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - 2018	Chitinolytic activity of bacterial symbionts from the gorgonian coral Eunicella labiata Supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - 2018	Chitin breakdown by bacterial symbionts of marine sponges: integrating experimental and genomics approaches Co-supervisor	Université Libre de Bruxelles, Belgium
2017 - 2018	Bacterial diversity of the gorgonian coral Eunicella labiata: how much can we cultivate? Supervisor	Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2017 - 2018	Deep-sea bacteria: a quest for sulfur and manganese oxidizers Co-supervisor	Universidade de Lisboa Instituto Superior Técnico, Portugal
2013 - 2018	Metagenomics and functional genomics of bacterial symbionts of Spongia (Porifera, Dictyoceratida) specimens from the Algarvian shore (South Portugal) Supervisor	Universidade do Algarve, Portugal
2016 - 2017	A bioinformatic approach to the pathogenic potential of Vibrio crassostreae in marine sponges and corals Supervisor	Master's programme in Biological Engineering (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2017	Approaching the mutualistic versus pathogenic duality in symbiotic Vibrio species: a comparative genomics endeavor Supervisor
2016 - 2017	Nitrification: hunting for soil prokaryotes. Co-supervisor	M.Sc. Programme in Microbiology (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2016	Diversity and specificity of the marine sponge microbiome inspected by next generation sequencing Supervisor	Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2014 - 2015	Worldwide diversity of sponge-associated Acidobacteria Supervisor
2013 - 2014	The potential of Asparagopsis armata to control the bacterial load associated to live feed to improve Seabream (Sparus aurata) larvae performance Co-supervisor	Universidade do Algarve, Portugal
2010 - 2014	Microbiome diversity and composition in the phylogenetically related marine sponges Sarcotragus spinosulus and Ircinia variabilis Supervisor	Universidade do Algarve, Portugal
2012 - 2013	Molecular characterization of microbial communities in marine sponges and green algae: structural and functional aspects Supervisor
2011 - 2012	Molecular exploration of bacterial communities associated with azooxanthellate gorgonians in the coast of Algarve, South Portugal Supervisor	Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2011 - 2012	Temperature tolerance in temperate gorgonians and their associated bacterial communities: a short-term experimental study Supervisor	Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2011 - 2012	The response of sediment microeukaryotic communities to petroleum contamination and global change: a microcosm experiment Supervisor	Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2010 - 2011	Fito- e bacterioplâncton em albufeiras dominadas por cianobactérias no Algarve Co-supervisor	Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal

Event organisation

	Event name Type of event (Role)	Institution / Organization
2023 - 2023	Costa, R. Chair and organizer of the session Microbiomes in the Environment. 2nd Microbiome PT Summit Lisbon, Portugal (26-27.10.2023). https://biodata.pt/microbiome (2023 - 2023) Conference (Member of the Organising Committee)
2023 - 2023	Chair and organizer of the thematic session “Biotechnology and Blue Bioeconomy – strategies for ocean conservation and health promotion. Ciência 2023, Aveiro, Portugal (July 05-07, 2023). https://www.encontrociencia.pt/2023/program/en/?dia=07#1430 (2023 - 2023) Round table (President of the Organising Committee)
2023 - 2023	Promoter of the 1st Meta_Microbial Workshop¿ (in the quality of Ambassador of the International Society for Microbial Ecology - ISME in Portugal). Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Porto, Portugal (September 12, 2023). https://isme17.isme-microbes.org/sites/default/files/meta_microbial_report_rc_MS_signed.pdf (2023 - 2023) Workshop (Member of the Organising Committee)
2023 - 2023	Costa, R., Couceiro, J., Almeida, J. Exposition “The wonderful world of marine bacteria”. International Microorganism Day. September 16, 2023, IST, Portugal. (2023 - 2023) Exhibition (President of the Organising Committee)
2023 - 2023	Dia do Técnico 2023 exhibitor: engagement with school children and the public, showcasing ‘The wonderful world of marine bacteria and coral reef microbiomes’ Instituto Superior Técnico, Lisbon, Portugal (19-20.05.2023) (2023 - 2023) Exhibition (President of the Organising Committee)
2022 - 2023	Costa, R. Chair and organizer of the session Host-microbe symbioses 16th Symposium on Bacterial Genetics and Ecology, BAGECO, Copenhagen, Denmark (26-30.06.2023). https://bageco2023.org/ (2023 - 2023)
2022 - 2022	International Microorganism Day - IMD 2022, exhibitor and part of organizing committee Instituto Superior Técnico, Lisbon, Portugal http://diainternacionaldomicrorganismo.tecnico.ulisboa.pt/ (2022 - 2022) Exhibition (Co-organisor)
2020 - 2020	Promoter, in the quality of ambassador of the International Society for Microbial Ecology (ISME) in Portugal, of the Blue Think Conference – Share Science, Spread Knowledge. Porto, September 17, 2020 (2020 - 2020) Conference (Other)
2020 - 2020	Chair of the session Marine Biotechnology. Blue Think Conference – Share Science, Spread Knowledge. Porto, September 17, 2020. (2020 - 2020) Conference (Member of the Organising Committee)
2019/05/26 - 2019/05/30	Chair of the 15th Symposium on Bacterial Genetics and Ecology (BAGECO15, https://www.bageco.org/). Lisbon, May 26-30, 2019. (2019/05/26 - 2019/05/30) Conference (President of the Organising Committee)
2019 - 2019	Dia National do Mar - National Day of the Sea - 2019, exhibitor at the "Museu Nacional de História Natural e da Ciência" (National Museum of Natural History and Science) in Lisbon (16.11.2019) (2019 - 2019) Exhibition (Co-organisor)
2019 - 2019	International Microorganism Day - IMD 2019, exhibitor and speaker, Instituto Superior Técnico, Lisbon, Portugal (17.09.2019) (2019 - 2019) Exhibition (Co-organisor)
2019 - 2019	Keep in Touch Event (KIT) - Dia do Técnico 2019 exhibitor; engagement with the public, showcasing „The wonderful world of marine bacteria“ Instituto Superior Técnico, Lisbon, Portugal (23.05.2019) (2019 - 2019) Exhibition (Co-organisor)
2019 - 2019	Contributor to the 17th European Union Science Olympiad (EUSO) in the formulation of tasks and experiments to be performed with marine microorganisms during EUSO2019, held in Lisbon (invitation by Prof. Arsénio Fialho, DBE-IST). http://euso.eu/ (2019 - 2019) Exhibition (Co-organisor)
2016 - 2016	Organizer of the 1st Advanced Workshop in Microbial Ecology, an event sponsored by the International Society for Microbial Ecology (ISME) under the ISME Ambassadors Programme. IST, December 2016. (2016 - 2016) Workshop (President of the Organising Committee)
2016 - 2016	Creator of the theoretical-practical module marine microbial metagenomics in the framework of the 1st Advanced Technologies and Training Workshop in Marine Genomics, Centre of Marine Sciences, Faro, Portugal, 14-16 September 2016. http://att.ccmar.ualg.pt/marine_genomics_2016/ (2016 - 2016) Workshop (Co-organisor)
2010 - 2012	Organizer of the internal Centre of Marine Sciences -CCMAR- seminar series. Planning and scheduling of seminars in all areas within the marine sciences. Given by local researchers as well as guest and invited speakers. Once a week during four semesters (winter 2010 – summer 2012). (2010 - 2012) Seminar (President of the Organising Committee)

Event participation

	Activity description Type of event	Event name Institution / Organization
2019 - Current	Interactive presentation The wonderful world of marine/coral reef bacteria exhibited at the Instituto Superior Técnico Opens Days, once a year since 2019. Exhibition	Open Days Instituto Superior Técnico
2018 - Current	Dissemination lecture for secondary scholars: Microbiomes: what are they? And why we cannot live without them? Once a year, since 2018. Department of Bioengineering Open Days (IST-ULisbon) Exhibition
2017 - Current	Interactive presentation “The wonderful world of marine/coral reef bacteria” exhibited at the International Microorganism Day. Once a year since 2017. Exhibition	International Microorganism Day
2023 - 2023	Chair of the Session Soluções para o futuro - Jornada de Engenharia do Ambiente do Instituto Superior Técnico (JEAmbi). March 8-10, 2023. Instituto Superior Técnico, Portugal. Meeting
2016 - 2020	Member of the Editorial Team of the internal communication letter “Newsletter DBE”, a monthly on-line publication that notifies the research community within DBE (and beyond) of the latest developments and news regarding research, teaching, and outreach performed by members of the Department of Bioengineering at IST. Other	Newsletter DBE Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2019	Interactive presentation The wonderful world of marine/coral reef bacteria exhibited at The National Day of the Sea, 2019. Exhibition	The National Day of the Sea
2018 - 2018	Interactive presentation The wonderful world of marine/coral reef bacteria exhibited at O Mar de Alto a Baixo exposition celebrating the 20 years of the EXPO Europe event (Pavilhão do Conhecimento, Lisbon, May 2018) Exhibition	EXPO 20 Years

Jury of academic degree

	Topic Role	Candidate name (Type of degree) Institution / Organization
2024	The "Jury of academic degree" activities contain only my participation as external examiner in Ph.D. and M.Sc. jurys. For an overview of my participation in jurys as supervisor, please see the list of supervisions or the full CV at https://drive.google.com/file/d/1TEj7hpMElFkqLhJSL9OEMzBqmafYvVGC/view?usp=sharing	Note (Other)
2023	Distribution and diversity of bacterial biosynthetic genes across multiple ecosystems (Thesis) Main arguer	Adriana Isabel Correia Rego (PhD) Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2023	Cross-feeding as a mechanism for pathogen biocontrol (Thesis) Main arguer	Smilla Adler (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2023	Drought stress in grapevine: exploring the potential of the soil microbiome (Thesis) Main arguer	Júlio L. Maciel (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2022	Antibiotic activity of bacteria associated to the marine sponges Hymeniacidon perlevis and Halichondria panicea: focus on Vagococcus fluvialis isolates (Thesis) Main arguer	Ana Rodriguez Jimenez (PhD) Université Libre de Bruxelles, Belgium
2022	Taxonomic and functional characterization of novel microbial diversity in sponges (Thesis) Main arguer	Viet Hung Nguyen (PhD) University of New South Wales, Australia
2021	Modelling the role of spatial structure in bacterial warfare (Thesis) Main arguer	Daniel Figueiredo de Oliveira (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021	Machine learning assisted identification of bioindicators in metagenomics – A study over transcription factor genes in a nitrate reducing microcosms (Thesis) Main arguer	Afonso O.S. Goulart (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021	Exploring the potential of microbes for modulating aquaculture bacterioplankton (Thesis) Main arguer	Joaquim M.G. de Sousa (Master) Universidade de Aveiro, Portugal
2018	Modelling Biofilm Microbial Community to Optimize Water Quality and Fish Health in a Marine Recirculating Aquaculture System (Thesis) Main arguer	Diana Bastos Serrano de Almeida (PhD) Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2018	Production and screening of Nannochloropsis oceanica knockout libraries for desirable traits of industrial applications (Thesis) Main arguer	Daniel R. Figueiredo (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2017	SEAVENTzymes II: an integrated step-forward approach using whole-genome sequencing for the identification of industrial relevant enzymes from deep-sea vent prokaryotes (Thesis) Main arguer	Ana Sofia Eria Oliveira (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2017	Isolamento Endógeno de Plasmídeos e Avaliação do Potencial Biotecnológico em Bactérias Associadas a Esponjas Marinhas (Thesis) Main arguer	DANIEL BOER BONIFACIO (Master) Universidade de Aveiro, Portugal
2016	Salinity as a key selector on the activity and diversity of ammonia oxidizers in estuarine systems	João Filipe Rodrigues Pereira Santos (Master) Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2015	Microbioma de Quercus: decifrando as comunidades microbianas da rizosfera de sobreiro e carvalho (Thesis) Main arguer	DIOGO FIGUEIREDO PINHO (PhD) Universidade de Aveiro, Portugal
2015	Characterization of the epiphytic microbial communities associated with seagrasses in a changing environment (Thesis) Main arguer	Astrid Mejia (PhD) Università degli Studi di Roma Tor Vergata, Italy
2015	Bacteriobenthos diversity in the surface of different sediment environments in the Ria Formosa lagoon (Thesis) Main arguer	ANA FLOR TORRES VIDAL (Master) Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2014	The impact of urbanisation on coral reef ecosystems (Thesis) Main arguer	Ana Rita Nunes Moura Polónia Correia (PhD) Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2014	Microbiologia Molecular na Aquicultura: Abusca de uma comunidade microbiana saudável (Thesis) Main arguer	LETICIA NOVAES DUARTE (PhD) Universidade de Aveiro, Portugal
2014	O papel das bactérias na doença da murchidão do pinheiro (Thesis) Main arguer	MARTA SALGUEIRO ALVES (PhD) Universidade de Aveiro, Portugal
2014	Cultivation of bacteria from marine sponges (Thesis) Main arguer	Nimra Amer (Master) University of New South Wales, Australia
2012	Organic amendments in avocado crop: influence on soil microbiota and implications for the suppression of Rosellinia necatrix (Thesis) Main arguer	Nuria Bonilla Ruiz (PhD)
2012	Descontaminação de petróleo por comunidades microbianas bênticas (Thesis) Main arguer	António Miguel de Oliveira Louvado (PhD) Universidade de Aveiro, Portugal
2012	Microbial ecology in Azores deep-seafloor hydrothermal environments (Thesis) Main arguer	Maria Teresa de Sousa Barros Cerqueira (PhD) Universidade dos Açores Faculdade de Ciências e Tecnologia, Portugal
2010	Interacções entre bactérias e hidrocarbonetos de petróleo em ambientes costeiros (Thesis) Main arguer	Francisco José Riso Da Costa Coelho (PhD) Universidade de Aveiro, Portugal
2010	Mediação microbiana na recuperação de sapais contaminados com hidrocarbonetos (Thesis) Main arguer	Vanessa Jesus de Oliveira (PhD) Universidade de Aveiro, Portugal
2009	Genetic Diversity of Structural Species, and Stability of Population and Ecossystems (Thesis) Main arguer	Sónia Isabel Rodrigues Aldeia Sanches Massa (PhD) Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2009	Characterization of extreme halophilic prokaryotic consortia of a traditional solar saltern in Olhão, Algarve (Portugal) (Thesis) Main arguer	Cristina Ruzene Nespoli (Master) Universidade do Algarve, Portugal
2008	Biotic Interactions and the Sucess of Invasive Species: the Case of the Bacterial Flora of Caulerpa Taxifolia (Thesis) Main arguer	Tânia Raquel dos Santos Aires (PhD) Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal

Association member

	Society Organization name	Role
2015 - Current	Ambassador of the International Society for Microbial Ecology (ISME) in Portugal (since 2015 - https://www.isme-microbes.org/ambassadors).	Senior Ambassador
2015 - Current	American Society for Microbiology (ASM)	Associated Member
2011 - Current	Portuguese Society for Microbiology, Federation of European Microbiological Societies (FEMS)	Associated Member
2009 - Current	International Society for Microbial Ecology (ISME)	Ambassador of the society in Portugal since 2015

Committee member

	Activity description Role	Institution / Organization
2019 - Current	Invited Member of the Editorial Board of Scientific Reports (since 2019).

Conference scientific committee

	Conference name	Conference host
2023 - Current	16th Symposium on Bacterial Genetics and Ecology	Soren Sorensen
2023 - 2023	2nd Microbiome PT Summit	Ana T. Freitas
2020 - 2020	BTC - Blue Think Conference	CIIMAR, Porto

Consulting

	Activity description	Institution / Organization
2018 - Current	Since 2018: Consultant in several R&D Projects within the national research landscape. Consultancy usually provided in guiding and analysis of experiments using next-generation metagenomic sequencing approaches
2023/04 - 2023/09	One of fifteen specialists invited by the Portuguese government to propose a package of legislative, financial, and scientific competitive measures for the development of the Blue Biotechnology Sector in Portugal. file:///E:/New%20Research/Projects/Blue%20Biotech%20Hub%20Matosinhos/Despacho%20N%C2%BA%204539_2023%20-%20Nomea%C3%A7%C3%A3o%20do%20Comite%20Tecnico.pdf	Universidade de Lisboa Instituto Superior Técnico, Portugal
2014 - 2016	Responsible for microbial identification services. Services and Technology Centre, Centre of Marine Sciences (CCMar)	Centro de Ciências do Mar, Portugal
2014 - 2016	Responsible for antimicrobial activity services. Services and Technology Centre, Centre of Marine Sciences (CCMar).	Centro de Ciências do Mar, Portugal

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2022 - Current	Founder, coordinator, and main teacher of the Curricular Unit Microbiomes (6 ECTS, Bachelor's programmes in Biological Engineering and Biomedical Engineering. Once a year since 2022).	Bioengineering, Biomedical engineering (Licenciatura)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - Current	Teaches theoretical lectures in the Curricular Unit Introduction to Biological Sciences (Bachelor's in Biological Engineering and in Biomedical Engineering, teaching load of approx. 1.5 ECTS, once a year since 2021)	(Licenciatura)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - Current	Teaches theoretical lectures in the Curricular Unit Introduction to Biological Sciences (Bachelor's programmes in Environmental Engineering and Physics, teaching load of approx. 2 ECTS, once a year since 2021).	(Licenciatura)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - Current	Member of the Committee for the creation of the novel, multidisciplinary course “Engineering Sciences” at Instituto Superior Técnico, to be taught entirely in English for both national and international students. Starting date: 2025/26	(Mestrado integrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - Current	Founder, coordinator, and main teacher of the Curricular Unit Microbiomes (6 ECTS, Master's programmes in Microbiology, Biotechnology, Bioengineering, and Erasmus. Once a year since 2020).	Microbiology, Biotechnology, Bioengineering, Medical Engineering (Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - Current	Founder, coordinator, and main teacher of the new Curricular Unit Microbiomes and Metagenomics (6 ECTS, Ph.D. programme in Biotechnology and Biosciences, since 2020)	Biotecnologia e Biociências (Doutoramento)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - Current	Coordinator and main teacher of the Curricular Unit Fundamentals of Ecology (6 ECTS, once a year since 2016).	Engenharia do Ambiente (Licenciatura)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - Current	Teaches lab practicals in the Curricular Unit Microbiology.	Bioengenharia (Doutoramento)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2022	Taught theory and practicals in the Curricular Unit Functional and Comparative Genomics.	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2022	Taught theory in the Curricular Unit Comparative Genomics and Bioinformatics.	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2018	Taught lab practicals in the Curricular Units Molecular Biotechnology and Genetic Engineering.	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2018	Taught lab practicals in the Curricular Unit Molecular Biology and Biochemistry.	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal

Journal scientific committee

	Journal title (ISSN)	Publisher
2019 - Current	Scientific Reports
2014 - Current	Frontiers in Marine Science
2023 - 2023	Marine Drugs
2022 - 2023	Scientific Reports
2012 - 2013	Brazilian Journal of Microbiology

Mentoring / Tutoring

	Topic	Student name
2018 - Current	Tutor of 15 undergrad students enrolled in the integrated master’s programme in Bioengineering (Once in every two years).	15 students every two years

Other jury / evaluation

	Activity description	Institution / Organization
2023 - Current	Since 2023: Evaluator of scientific research proposals submitted to DFG (Deutsche Forschungsgemeinschaft) and to FCT (Portuguese Foundation for Science and Technology)
2017 - Current	Since 2017: Evaluator of individual PhD and post-doctoral research grant proposals submitted to “Agência Regional para o Desenvolvimento da Investigação, Tecnologia e Inovação” (ARDITI, Madeira, Portugal).
2015 - Current	Since 2015 (yearly): Evaluator of R&D Proposals submitted to the programme “Pro-Polar” fostered by Fundação para a Ciência e a Tecnologia (FCT), Portugal.
2014 - 2018	From 2014 to 2018 (yearly): Evaluator of proposals submitted to the marine research network programmes ASSEMBLE (www.assemblemarine.org) and EUROMARINE (http://www.euromarinenetwork.eu/call2015/).

Scientific expedition

	Activity description	Institution / Organization
2015 - 2015	Coordinator of the “MyOSD citizen” initiative (MyOSD, https://www.microb3.eu/myosd). In collaboration with the “Centro de Ciência Viva” of the Algarve, this activity enabled the public to collect seawater samples for microbial metagenome analysis during OSD 2015.
2014 - 2014	Sampling site coordinator for the “Faro Island” and “Ria Formosa lagoon” sites in the framework of the global network initiative Ocean Sapling Day (OSD, https://www.microb3.eu/osd) within the EU 7FP-funded project MicroB3 (https://www.microb3.eu/home).

Distinctions

Award

2023	Excellent Teacher, Curricular Unit Microbiomes, Class of 2022/23 Universidade de Lisboa Instituto Superior Técnico, Portugal
2022	Excellent Faculty member at IST-ULisbon (2022). Universidade de Lisboa Instituto Superior Técnico, Portugal
2022	Excellent Teacher, Curricular Unit Fundamentals of Ecology, Class of 2021/2022
2021	Excellent Teacher, Fundamentals of Ecology Class of 2020/21
2021	Excellent Teacher, Curricular Unit Microbiology, Class of 2020/21
2021	Excellent Teacher, Curricular Unit Molecular Biology and Biochemistry, Class of 2020/21_1Sem Universidade de Lisboa Instituto Superior Técnico, Portugal
2021	Excellent Teacher, Curricular Unit Molecular Biology and Biochemistry, Class of 2020/21_2sem Universidade de Lisboa Instituto Superior Técnico, Portugal
2020	Excellent Teacher, Curricular Unit Microbiomes, Class of 2019/20 Universidade de Lisboa Instituto Superior Técnico, Portugal
2019	Excellent Teacher, Fundamentals of Ecology Class of 2018/19 Universidade de Lisboa Instituto Superior Técnico, Portugal
2019	Excellent Faculty member at IST-ULisbon (2019). Universidade de Lisboa Instituto Superior Técnico, Portugal
2015	Ambassador of the International Society for Microbial Ecology (ISME) in Portugal (since 2015 - https://www.isme-microbes.org/ambassadors).
2015	Independent Research Scientist Contract under the FCT Investigator Programme, Portugal (2015) Fundação para a Ciência e a Tecnologia, Portugal
2008	Independent Research Scientist Contract under the FCT Ciência 2007 Programme, Portugal (2008-2013) Fundação para a Ciência e a Tecnologia, Portugal
2006	Magna cum laude mentioning on Ph.D. Diploma. Technical University of Braunschweig, Germany (2006) Technische Universität Braunschweig, Germany
2001	Excellent grade on M.Sc. studies. Federal University of Rio de Janeiro, Brazil (2001) Universidade Federal do Rio de Janeiro, Brazil
1998	Cum laude mentioning on B.Sc. Diploma (grade: 8.4 in 10). Federal University of Rio de Janeiro, Brazil (1998) Universidade Federal do Rio de Janeiro, Brazil

Other distinction

2023	Invited by the Portuguese Government to join a panel of fifteen specialists to propose a package of legislative, financial and scientific competitive measures for the development of the Blue Biotechnology Sector in Portugal
2023	Coordinator of the large-scale Recovery and Resilience Plan Agenda Blue Bioeconomy Pact at IST-UL (Global funding: 133 MEu, 83 partners. Promoter: INOVAMAR, S.A. Funding at IST-UL: 1.5 MEu). Member of the Executive Direction of the Agenda (2023-2025).
2023	Guest Editor. Special Issue Reef Ecology and Marine Drug Discovery. Journal: Marine Drugs. https://www.mdpi.com/journal/marinedrugs/special_issues/coral_reef_ecology
2023	Guest Editor. Collection Aquaculture. Journal: Scientific Reports. https://www.nature.com/collections/hjfiidffbe
2023	Article "Harnessing the microbiome to prevent global biodiversity loss" selected by Nature Portfolio for a collection of top-articles addressing UN Sustainable Development Goals. https://www.nature.com/collections/bhfffjiadc
2019	Chair of the 15th Symposium on Bacterial Genetics and Ecology (BAGECO15, https://www.bageco.org/). Lisbon, May 26-30, 2019.
2019	Invited affiliate (Research Scientist) of the Lawrence Berkeley National Laboratory (LBNL), Department of Energy of the USA, Joint Genome Institute (DOE-JGI), Berkeley, USA (2019-2012).
2019	Invited Member of the Editorial Board of Scientific Reports (since 2019).
2013	Research Article Highlight (Editor Choice) in FEMS Microbiology Ecology, September 2013 Issue, for Molecular richness and biotechnological potential of bacteria cultured from Irciniidae sponges in the Northeast Atlantic (corresponding author).
2009	Supervisor of the PhD Grant proposal by Cristiane C.P. Hardoim, ranked #1 nationwide by the Biological Sciences evaluation panel of FCT