Rodrigo Costa

(Assistant Professor) *

Alternative Pages: Google Scholar; Research ID; iBB webpage; IST webpage; Microbial Ecology and Evolution Research at BSRG  

Status at iBB - Institute for Bioengineering and Biosciences:  

·         Researcher of the Biological Sciences Research Group


·         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.

Research Activities:

·        Molecular Microbial Ecology and Evolution

·         Environmental Microbiology

·         Symbiosis and host-microbe interactions

·         Metagenomics

·         Microbial biogeography

·         Functional and comparative genomics of microorganisms


Projects as PI:

1. Research Grants  

  • Harnessing the power of the microbial metamobilome: using marine sponges as models to uncover novel biotechnological appliances from symbiont communities. Financial support: FCT. Project id: PTDC/MAR-BIO/1547/2014. Period: July 2016 – June 2019. Funding: 191.436,00 €  
  • Deciphering the codes of communication between marine sponges and their symbionts: an integrative metabolomics-transcriptomics approach. Financial support: VW Stiftung, Germany Context: bilateral collaboration Germany-Portugal. Ancillary research project in the framework of the Lichtenberg Professorship granted to Prof. Georg Pöhnert (Institute of Inorganic and Analytical Chemistry, Jena University, Germany). Period: September 2014 – August 2016. Funding: 49.560,00 €  
  • Single-cell genomics and metagenomics-aided cultivation of the unculturable: uncovering the function and metabolic features of Acidobacteria symbionts of marine sponges. Financial support: FCT. Project id: PTDC/BIA-MIC/3865/2012 Period: June 2013 – November 2015. Funding: 110.740,00 €  
  • Unlocking the bacterial diversity encrypted in the metagenomes of marine sponges. Financial Support: Portuguese Foundation for Science and Technology (FCT). Project id: PTDC/MAR/101431/2008. Period: January 2010 - June 2013. Funding: 179.732,00 €  

2. Mobility Grants / Minor Research Grants  

  • Rules of attraction: unveiling bacterial behavior in a host-driven chemical sphere. Financial support: FCT and Deutscher Akademischer Austauschdienst (DAAD), Germany. Partner Laboratory: Dr. Thomas Wichard,  Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena Period: January 2012 – December 2013. Context: bilateral cooperation programme to promote the mobility of early-career graduate students. Funding: 6.000, 00 €  
  • Will an increase in extreme temperature anomalies limit the ability of marine organisms to adapt to long-term climate change? Financial support: Association of European Marine Biological Laboratories (ASSEMBLE) Period: July 2013 – July 2014. Funding: Travel costs, accommodation and access to the laboratories and infrastructure offered by the Observatoire Océanologique de Banyuls-sur-mer, France.  
  • Functional and taxonomic profiling of microbial communities in caves of the Algarve, Southern Portugal. Financial support: National Speleological Foundation, USA. Period: January 2015 – December 2015. Funding: 1.500,00 U$ (financing of sequencing costs).


·         Nominated ambassador of the International Society for Microbial Ecology (ISME) in Portugal (2015).

·         Independent Research Grant under the “FCT Investigator” Programme, Portugal (2015).

·         Independent Research Grant under the FCT “Ciência 2007” Programme, Portugal (2008-2013).

·         Research Article Highlight 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).

Selected Publications:

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

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 labiata. Genome 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 verrucosa. Genome 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 aurata. Aquaculture 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 spinosulus. Molecular 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 fluviatilis. Microbial 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 fulva. Brazilian 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).