Rodrigo Costa

POSITION: Assistant Professor

Leader of the research theme: Marine metagenomics and microbial  ecology


Research Topics

Metagenomics and “meta-omics” in marine ecosystems

Symbiosis and host-microbe interactions

Blue Biotechnology

Functional and comparative genomics of symbiotic bacteria

Sponge, coral, fish and seaweed microbiology

Culturing the “unculturable”

Horizontal gene transfer

Research Team

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)
Bernardo Bica (MSc Student)
Francisco Pascoal (MSc Student)
Matilde Marques (MSc Student)
Patrícia Paula (MSc Student)

Full team


  • 2002 – 2006: Ph.D. in Life Sciences. Technical University of Braunschweig, Germany.
  • 1999 – 2001: Master of Science, Ecology. Rio de Janeiro Federal University (UFRJ), Brazil.
  • 1995 – 1998: Bachelor of Science, Biology. Rio de Janeiro Federal University (UFRJ), Brazil.


  • 2016 – Present: Assistant Professor, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon
  • 2008 – 2016: Research Scientist, Invited Assistant Professor and head of the “Microbial Ecology and Evolution Research Group” at the Centre of Marine Sciences, Algarve University, Portugal
  • 2006 – 2008: Post-doctoral fellow at the Microbial Ecology Department of the University of Groningen, The Netherlands.

Selected Publications

Ribeiro, L., Castanho, S., Califano, G., Soares, F., Costa, R., Mata, L., & Pousão-Ferreira, P. “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 (2017) doi:10.1007/s10695-017-0351-6.

Karimi, E., Gonçalves, J.M.S., Reis, M., Costa, R. Draft genome sequence of Microbacterium sp. strain Alg239_V18, an actinobacterium retrieved from the marine sponge Spongia sp. Genome Announcements 5:e01457-16 (2017). doi:10.1128/genomeA.01457-16.

Califano, G., Castanho, S., Soares, F., Ribeiro, L., Cox, C.J., Mata, L., Costa, R. Molecular taxonomic profiling of bacterial communities in a gilthead seabream (Sparus aurata) hatchery”. Frontiers in Microbiology 8:204 (2017). doi:10.3389/fmicb.2017.00204.

Weiss, A., Costa, R., Wichard, T. Morphogenesis of Ulva mutabilis (Chlorophyta) induced by Maribacter species (Bacteroidetes, Flavobacteriaceae). Botanica Marina, 60 (2) 197-206 (2017). doi:10.1515/bot-2016-0083.

Rotini, A., Mejia, A., Costa, R., Migliore, L., & Winters, G. Ecophysiological plasticity and bacteriome shift in the seagrass Halophila stipulacea along a depth gradient in the Northern Red Sea. Frontiers in Plant Science 7:2015 (2017). doi: 10.3389/fpls.2016.02015.

All Papers, Book Chapters and Patents

See all

Book chapters:

Costa, R., Kimes, N.E., Nunes da Rocha, U., López-Péres, 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).

van Elsas, J.D. & Costa, R. Molecular assessment of soil microbial communities with potential for plant disease suppression. In: Z.K. Punja, S.H. De Boer and H. Sanfacon (eds.). Biotechnology and Plant Disease Management. CABI Press Inc., Cambridge, MA, USA (2008).

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).

Gomes N.C.M., Costa, R. & Smalla, K. Rapid simultaneous extraction of DNA and RNA from bulk and rhizosphere soil. In: Kowalchuk, G.A., de Bruijn, F.J., Head, I.M., Akkermans, A.D.L. and van Elsas, J.D. (Editors.). Molecular Microbial Ecology Manual, 2nd Edition. Chapter 1.12: 159-170 Kluwer Academic Publishers (2004).

Papers in international journals

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).

Rotini, A., Mejia, A., Costa, R., Migliore, L., & Winters, G. The seagrass holobiont Halophila stipulacea: ecophysiological plasticity and bacteriome structure along a depth gradient (4 – 28 m) in the Northern Red Sea. Frontiers in Plant Science (2016). Accepted for publication.

Califano, G., Castanho, S., Soares, F., Ribeiro, L., Cox, C.J., Mata, L., Costa, R. Highly specific communities simultaneously shape the establishment of the gilthead seabream (Sparus aurata) bacterial consortium in fish larviculture. Frontiers in Microbiology (2016). Accepted for publication.

Weiss, A., Costa, R., Wichard, T. Morphogenesis of Ulva mutabilis (Chlorophyta) induced by Maribacter species (Bacteroidetes, Flavobacteriaceae). Botanica Marina (2016). In Press.

Keller-Costa, T., Silva, R., Lago-Lestón, A., & Costa, R. Genomic insights into Aquimarina sp. strain EL33, a bacterial symbiont of the gorgonian coral Eunicella labiataGenome Announcements (2016). doi:10.1128/genomeA.00855-16.

Thomas, T.,  Moitinho-Silva, L., Lurgi, M., Björk, J.R., Easson, C., Astudillo-Garcia, C., Olson, J., Erwin, P., Lopez-Legentil, S., Luter, H., Chaves-Fonnegra, A., Costa, R., Schupp, P., Steindler, L., Erpenbeck, D., Gilbert, J., Knight, R., Ackerman, G., Lopez, J., Taylor, M., Thacker, R.W., Montoya, J., Hentschel, U., & Webster, N. Global Sponge Microbiome: Diversity, structure and convergent evolution of symbiont communities across the phylum Porifera. Nature Communications (2016). In Press.

Coelho, F.J.R.C., Cleary, D.F.R., Costa, R., Ferreira, M., Polónia, A.R.M., Silva, A.M.S., Simões, M.M.Q., Oliveira, V., & Gomes, N.C.M. Multi-taxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution. Molecular Ecology (2016). In Press.

Franco, T., Califano, G., Gonçalves, A.C.S., & Costa, R. Draft genome sequence of Vibrio sp. strain Evh12, a bacterium retrieved from the gorgonian coral Eunicella verrucosaGenome Announcements 4(1):e01729-15 (2016). doi:10.1128/genomeA.01729-15.

Cúcio, A.C.B.; Engelen, A.H., Costa, R. & Muyzer, G. Rhizosphere microbiomes of European seagrasses are not species-specific, but shaped by their environment. Frontiers in Microbiology 7:440 (2016). doi: 10.3389/fmicb.2016.00440.

Grueneberg, J., Engelen, A.H., Costa, R., & Wichard, T. Macroalgal morphogenesis induced by waterborne compounds and bacteria in coastal seawater. PLoS ONE 11(1): e0146307 (2016). doi:10.1371/journal.pone.0146307.

Kopf, A., Bicak, M., Kottmann, R., Schnetzer, J., et al. The Ocean Sampling Day consortium. GigaScience 4:27 (2015). doi: 10.1186/s13742-015-0066-5.

Califano, G., Franco, T., Gonçalves, A.C.S., Castanho, S., Soares, F., Ribeiro, L., Mata, L., & Costa, R. Draft genome sequence of Aliivibrio fischeri strain 5LC, a bacterium retrieved from gilthead seabream (Sparus aurata) larvae reared in aquaculture. Genome Announcements 3(3):e00593-15 (2015). doi:10.1128/genomeA.00593-15.

Gonçalves, A.C.S., Franco, T., Califano, G., Dowd, S.E., Pohnert, G., & Costa, R. Draft genome sequence of Vibrio sp. strain Vb278, an antagonistic bacterium isolated from the marine sponge Sarcotragus spinosulus. Genome Announcements 3(3):e00521-15 (2015). doi:10.1128/genomeA.00521-15.

Coelho, F.J.R.C., Cleary, D.F.R., Rocha, R.J.M., Calado, R., Castanheira, J.M., Rocha, S.M., Silva, A.M.S., Simões, M.M.Q., Oliveira, V., Lillebø, A.I., Almeida, A., Cunha, A., Lopes, I., Ribeiro, R., Moreira-Santos, M., Marques, C.R., Costa, R., Pereira, R. & Gomes, N.C.M.. Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities. Global Change Biology (2015). doi:10.1111/gcb.12801.

Silva, Y.J., Manco, S., Costa, R., Rodrigues, V., Dias, J., Ferreira, H., Pousão-Ferreira, P., Almeida, A., Cunha, A., Calado, R., & Gomes, N.C.M. Effect of different culture conditions on the structural diversity of prokaryote communities in the sediment of earth ponds stocked with gilthead seabream Sparus aurataAquaculture Research 46: 1760-1769 (2015). doi:10.1111/are.12336.

Hardoim, C.C.P., Cardinale, M., Cúcio, A.C.B., Esteves, A.I.S., Berg, G., Xavier, J.R., Cox, C.J., & Costa, R. Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges. Frontiers in Microbiology 5: 611 (2014). doi: 10.3389/fmicb.2014.00611.

Hardoim, C.C.P. & Costa, R. Microbial communities and bioactive compounds in marine sponges of the family Irciniidae – a review. Marine Drugs 12: 5089-5122 (2014). doi:10.3390/md12105089.

Alexandrino, M., Costa, R., Canário, A.V.M., & Costa, M.C. Clostridia initiate heavy metal bioremoval in mixed sulfidogenic cultures. Environmental Science & Technology 48(6): 3378-3385 (2014).

Hardoim, C.C.P. & Costa, R. Temporal dynamics of prokaryotic communities in the marine sponge Sarcotragus spinosulusMolecular Ecology 23(12): 3097–3112 (2014).

Keller-Costa, T., Jousset, A., van Overbeek, L., van Elsas, J.D., & Costa, R. The freshwater sponge Ephydatia fluviatilis harbours diverse Pseudomonas spp. with broad spectrum antimicrobial activity. PLoS ONE  9(2): e88429 (2014).

Esteves, A.I.S., Hardoim, C.C.P., Xavier, J.B.T., Gonçalves, J.M.S., & Costa, R. Molecular richness and biotechnological potential of bacteria cultured from Irciniidae sponges in the Northeast Atlantic. FEMS Microbiology Ecology 85: 519-536 (2013).

Coelho, F. Rocha, R., Pires, A., Ladeira, B., Castanheira, J., Costa, R., Almeida, A. et al. Development and validation of an experimental life support system for assessing the effects of global climate change on coastal and estuarine marine benthic communities. Global Change Biology 19:2584-95 (2013).

Costa, R., Keller-Costa, T., Gomes, N.C.M., Nunes da Rocha, U., van Overbeek, L., & van Elsas, J.D. Evidence for selective bacterial community structuring in the freshwater sponge Ephydatia fluviatilisMicrobial Ecology 65:232-244 (2013).

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 fulvaBrazilian Journal of Microbiology 44: 329-334 (2013).

Hardoim, C.C.P., Esteves, A.I.S., Pires, F.R., Gonçalves, J.M.S., Cox, C., Xavier, J.B.T. & Costa, R. Phylogenetically and spatially close marine sponges harbour divergent bacterial communities. PLoS ONE 7(12): e53029 (2012).

Gomes, N.C.M., Cleary, D.F.R., Calado, R., & Costa, R. Mangrove bacterial richness. Communicative & Integrative Biology 4 (4): 419-423 (2011).

Alexandrino, M., Macías, F., Costa, R., 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: 362-370 (2011).

Van Elsas, J.D. Semenov, A.V., Costa, R., & Trevors, J.T. Survival of Escherichia coli in the environment – fundamental and public health aspects. The ISME Journal 5: 173–183 (2011).

Gomes, N.C.M., Flocco C., Costa, R., Junca H., Vilchez R., Pieper D.H., Krögerrecklenfort, E., Paranhos R., Mendonça-Hagler L.C.S. & Smalla, K. Mangrove micro-niches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia. FEMS Microbiology Ecology 74:276-290 (2010).

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: 337-349 (2010).

Costa, R., van Aarle, I., 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: 159-175 (2009).

Hardoim, C.C.P., Costa, R., Araújo, F.V., Hajdu, E., Peixoto, R., Lins, U., Rosado, A.S., & van Elsas, J.D. Diversity of bacteria in the marine sponge Aplysina fulva in Brazilian coastal waters. Applied and Environmental Microbiology 75: 3331-3343 (2009).

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: 591-601 (2008).

Costa, R., Gomes, N.C.M., Opelt, K., Berg, G., & Smalla, K. Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analysis. Environmental Microbiology 9: 2260–2273 (2007).

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: 2818–2828 (2007).

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: 2136–2149 (2006).

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: 236-249 (2006).

Costa, R., Gomes, N.C.M., Peixoto, R.S., Rumjanek, N.G., 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: 2434-2447 (2006).

Berg, G., Opelt, K., Schmidt, S., 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: 250-261 (2006).

Götz, M., Gomes, N.C.M., Dratwinski, A., Costa, R., Berg, G., Peixoto, R.S., Mendonça-Hagler, L.C.S. & 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: 207-218 (2006).

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: 4203-4213 (2005).

Meier, J., Costa, R., Smalla, K., Boeher, 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: 261-274 (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): 230-234 (2004).

Gomes, N.C.M., Fagbola, O., Costa, R., Rumjanek, N.G., Buchner, A., Mendonça-Hagler, L.C.S. & Smalla, K. Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics. Applied and Environmental Microbiology 69(7): 3758-3766 (2003).

Gomes, N.C.M., Heuer, H.,  Schönfeld, J., Costa, R., Mendonça-Hagler, L.C. & 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: 167-180 (2001).

Papers in national journals with referees:

Esteves, A.I.S. & Costa, R. Esponjas marinhas: do mar à farmácia. Boletim de Biotecnologia, Série 2, Número 5. Sociedade Portuguesa de Biotecnologia (2014).

Papers in conference proceedings:

Lago-Léston, M.A., Hardoim, C.C.P., Pires, F.R., Gonçalves, J.M.S., Cox, C.J., Xavier, J.R., & Costa, R. Tackling the specificity of the marine sponge microbiome: a biogeographical approach. Proceedings of the 2nd International Conference on Microbial Diversity: Microbial Interactions in Complex Ecosystems. Turin, Italy (2013).

Wichard, T., Grueneberg, J., Engelen, A., & Costa R. Chemosphere of the marine green alga Ulva: induction of algal morphogenesis by bacterial compounds. European Journal of Phycology 46: 86-86 (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. 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).

Peixoto, R, Götz, M., Milling, A., Berg, G., Costa, R., Rosado, A., Mendonça-Hagler, L.C. & Smalla, K. Monitoring gfp-tagged bacterial antagonists in the rhizosphere of tomato plants. Proceedings of the meeting “Multitrophic Interactions in Soil and Integrated Control”, Bad Honnef, Germany, 2003. International Organisation for Biological Control (IOBC) Bulletin 37: 219-225 (2004).


Costa, R. Microbial community structure and function in the rhizosphere of crop plants: a molecular study. PhD Thesis. Technical University of Braunschweig. 150p. (2006).

Costa, R. Variabilidade e diversidade genética de comunidades bacterianas associadas à rizosfera de Milho (Zea mays L. Merril) em um agroecossistema do Rio de Janeiro. Master Thesis. Rio de Janeiro Federal University. 125p. (2001).

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