Theme Leader: Rodrigo Costa

It is conceivable that no known living entity in the major multicellular, eukaryotic lineages is completely devoid of microorganisms. Ranging from simple associations dominated by a single or few mutualist(s), such as the squid-Vibrio and gutless worm symbioses, to the complex “microbiomes” associated with e.g. the human gut, plant roots or marine corals and sponges, it seems indisputable that microorganisms in the three domains of life are capable of populating any micro-niche offered by their animal and plant hosts. Indeed, life, as we know, is strongly underpinned by inter-domain symbiotic relationships (Bacteria-Archaea-Eukarya).

In this context, the Marine Metagenomics and Microbial Ecology Team at BSRG seek to understand the causes and consequences of microbial diversity and function in nature, with emphasis on prokaryote-eukaryote symbiotic relationships in the marine realm. It applies molecular and bioinformatics tools in conjunction with creative experimental designs to unravel the composition and function of symbiotic consortia in natural settings and microcosms, with the ultimate aim to harness and exploit the metabolic versatility of complex microbiomes for the development of renewable sources of biotechnological appliances.

Find out more

Our current projects within this subject include

  • Evolutionary and ecological relationships between hosts and symbionts;
  • In-faunal and ad-plantae biogeochemical cycling;
  • Symbiotic microorganisms and host developmental biology;
  • Antibiotic biosynthesis and resistance;
  • Horizontal gene transfer;
  • Cultivation of as-yet uncultured symbiotic bacteria;
  • Microbe-microbe and host-microbe chemical signalling;
  • Potential biotechnological appliances and services deriving from symbiont-host biological activities;
  • Responses of microbial communities to climate change and pollution;
  • Model study systems include the microbiomes of marine sponges, corals, algae, seagrasses and fish, as well as rhizosphere- and human-associated microbial communities;


Rodrigo Costa (Professor and team leader)

Tina Keller-Costa (Pos-Doc researcher)

Rúben Silva (PhD Student)

Lígia Fonseca Coelho (PhD Student)

Sandra Silva (PhD Student)

Gracinda Sanches Fernandes (PhD Student)

Inês Gonçalves Raimundo (MSc Student)

Francisco Pascoal (MSc Student)

Matilde Marques (MSc Student)

Patrícia Paula (MSc Student)



Some of our latest Publications

Diez, C., Esteves, A.I.S., Costa, R., Nielsen, C., & Thomas, T. Detecting signatures of a sponge-associated lifestyle in bacterial genomes.
Environmental Microbiology Reports (2018).

Karimi, E., Beate, S., Soares, A., Jochen B., Henstchel-Humeida, U., Costa, R.* Metagenomic binning reveals versatile nutrient cycling and distinct
adaptive features in alphaproteobacterial symbionts of marine sponges. FEMS Microbiology Ecology (2018).

Karimi, E., Ramos, M., Gonçalves, J.M.S., Xavier, J.R., Reis, M.P., & Costa, R.* Comparative metagenomics reveals the distinctive features of the Spongia officinalis endosymbiotic
consortium. Frontiers in Microbiology 8:2499 (2017).

Keller-Costa, T., Eriksson, D., Gonçalves, J.M.S., Gomes, N.C.M., Lago-Lestón, A., & Costa,R.  The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation. FEMSMicrobiology Ecology (2017).

Moitinho-Silva, L., Nielsen L., et al. (40 authors). The sponge microbiome project. GigaScience, 6(10): 1-7 (2017).


External Collaborators

Dr. Newton Carlos C.M. Gomes, Aveiro University, Portugal

Dr. Cymon J. Cox, Centre of Marine Sciences, Algarve University, Portugal

Dr. Jorge Gonçalves, Centre of Marine Sciences, Algarve University, Portugal

Dr. Joana R. Xavier, University of Bergen, Norway

Prof. Jan Dirk van Elsas, University of Groningen, The Netherlands

Prof. Ute Hentschel-Humeida, University of Kiel, Germany

Prof. Thomas Wichard, Jena University, Germany

Prof. Georg Pohnert, Jena University, Germany

Prof. Soren Sorensen, University of Copenhagen, Denmark

Prof. Raquel Peixoto, Rio de Janeiro University, Brazil

Recent Projects


“MicroControl: exploiting the healing capacity of nature’s microbiomes for improved fish larviculture”

Role: Coordinator / Principal Investigator.

Financial support: FCT/FEDER. Project id: PTDC/BIA-MIC/31996/2017.

Period: October 2018 – September 2021.

Funding: 229.967,43 €.

Brief description:

The goal of MicroControl is to develop multi-species cocktails of beneficial fish symbionts to prevent bacterial disease incidence during fish larval rearing, a stage at which fish individuals are highly susceptible to acute outbreaks that pronouncedly impact land-based rearing of hundreds of economically important species. The team will conduct larval rearing trials under “microbiome therapy” to address the effectiveness of the approach in gilthead seabream (Sparus aurata), one of the most cultivated fish species worldwide.

The project is headed by Rodrigo Costa from BSRG-iBB in close collaboration with the Aquaculture Research Station of Instituto Português do Mar e da Atmosfera (IPMA), with Dr. Laura Ribeiro as Co-PI.

“Harnessing the power of the microbial metamobilome: using marine sponges as models to uncover novel biotechnological appliances from symbiont communities”

Role: Coordinator / Principal Investigator.

Financial support: FCT. Project id: PTDC/MAR-BIO/1547/2014.

Period: January 2016 – December 2018.

Funding: 191.436,00 €.