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José Paulo Sampaio


José Paulo Sampaio

BSc 1986 Universidade de Lisboa
PhD 1996 Universidade Nova de Lisboa

Faculdade de Ciências e Tecnologia
Universidade Nova de Lisboa
Quinta da Torre
2829-516 Caparica

Email: jss@fct.unl.pt

Telephone:  00 351 21 294 8500 ext  11107


1986: Graduation in Biology, Universidade de Lisboa, Portugal
1988–1996: Teaching Assistant, Universidade Nova de Lisboa, Portugal
1996: PhD in Microbiology, Universidade Nova de Lisboa, Portugal
1996–Present: Assistant Professor, Universidade Nova de Lisboa, Portugal


Research Topic

Our lab is currently involved in two research themes. One concerns yeast ecology, particularly of species of the genus Saccharomyces, within an evolutionary framework. We are interested in understanding the global phylogeography of wild lineages of species that are used in man-made fermentations, like S. cerevisiae, S. uvarum or S. eubayanus, and in comparing these patterns with those of purely wild species such as S. paradoxus. The identification of the natural habitats of the different species and the ecological interactions of sympatric Saccharomyces species are also being investigated. Our central hypothesis is that adaptation to different temperature regimes played a critical role in the (ecological) evolution of the different Saccharomyces species. Another research theme is the study of the domestication processes with relevance for the domestication of beer and wine yeasts. Domestication of Saccharomyces probably started with the onset of agriculture and involved complex phenomena like inter-species hybridizations. We are interested in learning where, when and how the domestication occurred and in understanding the genetic basis of the man-driven evolution of useful fermentation traits.

The second research theme consists in investigating sexual mechanisms in red yeasts, a basal lineage of Basidiomycetes, and the co-existance of sexual and asexual species in this lineage. We are interested in comparing the mating systems of these yeasts with those of the remaining Basidiomycetes, in understanding the evolution of sexual mechanisms in deep-branching lineages of Basidiomycetes, and in finding associations between the type of sexual mechanism and lifestyle (e.g. saprobes vs plant parasites).

Another ongoing research concerns the basidiomycete yeast Phaffia rhodozyma, an astaxanthin-producing yeast. We recently showed that this yeast has a remarkable association with different tree hosts and that a single (and distinct) phylogenetic lineage is found in each host. We want to explore the consequences of such a pattern in terms of biogeography, genetic flow and species / population structure.

Since we hypothesize that speciation in fungi might also be related with the loss or modification of the typical sexual cycle, Pseudozyma and Rhodosporidium yeasts are presently being used as models to study the evolutionary consequences of loss of sexual competence.

Link to Lab web page

Research Team

Paula Gonçalves (PI Functional and Comparative Genomics of Yeasts) Marco Coelho (Post-Doc) Márcia Palma (PhD student) Pedro Almeida (PhD student)

Current Funding

  • Out of Gondwana – a phylogeographic hypothesis for the radiation of Saccharomyces. PTDC/BIA-EVF/118618/2010.

  • Tracing domestication in microbes - the case of Saccharomyces cerevisiae. PTDC/AGR-ALI/118590/2010

Recent publications

Papers in international journals

Libkind D, Hittinger CT, Valerio E, Gonçalves C, Dover J, Johnston M, Gonçalves P, Sampaio JP. 2011. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proceedings of the National Academy of Sciences of the United States of America. 108: 14539-14544.

Coelho MA, Gonçalves P, Sampaio JP. 2011. Evidence for maintenance of sex determinants but not of sexual stages in red yeasts, a group of early diverged basidiomycetes. BMC Evolutionary Biology 11: 249.

Gonçalves P, Valério E, Correia C, Almeida JMGCF, Sampaio JP 2011 Evidence for divergent evolution of growth temperature preference in sympatric Saccharomyces species. PLoS ONE 6 (6): e20739.

Libkind D, Moliné M, Sommaruga R, Sampaio JP, van Broock, M. 2011. Phylogenetic distribution of fungal mycosporines within the Pucciniomycotina (Basidiomycota). Yeast 28: 619-627.

Libkind D, Tognetti C; Ruffini A, Sampaio JP, van Broock M. 2011. Xanthophyllomyces dendrorhous (Phaffia rhodozyma) on stromata of Cyttaria hariotii in northwestern Patagonian Nothofagus forests. Revista Argentina de Microbiologia 43: 226-232.

Burgaud G, Arzur D, Sampaio JP, Barbier, G. 2011. Candida oceani sp. nov., a novel yeast isolated from a Mid-Atlantic Ridge hydrothermal vent (-2300 meters). Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 100: 75-82.

Hittinger, C.T., Gonçalves, P., Sampaio, J.P., Dover, J., Johnston, M. and Rokas. A. 2010. Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 464: 54-58.

Coelho, M. A, Almeida, J.M.F, Martins, I. M., Jorge da Silva A. and Sampaio, JP. 2010. The dynamics of the yeast community of the Tagus river estuary – testing the hypothesis of the multiple origins of estuarine yeasts. Antonie van Leeuwenhoek 98: 331-342.

Coelho, M.A., Sampaio, J.P. and Gonçalves, P. 2010. A deviation from the bipolar-tetrapolar mating paradigm in an early diverged basidiomycete. PLoS Genetics 6(8): e1001052. doi:10.1371/journal.pgen.1001052.

Libkind, D., Sampaio, J.P. and van Broock, M. 2010. Cystobasidiomycetes yeasts from Patagonia (Argentina): description of Rhodotorula meli sp. nov. from glacial meltwater. International Journal of Systematic and Evolutionary Microbiology (in press). DOI 10.1099/ijs.0.018499-0

Russo, G., Libkind, D. Ulloa, R.J., de García, V. Sampaio, J.P. and van Broock, M.R. 2010. Cryptococcus agrionensis sp. nov., a basidiomycetous yeast of the acidic rock drainage ecoclade, isolated from acidic aquatic environment of volcanic origin (River Agrio, Argentina). International Journal of Systematic and Evolutionary Microbiology (in press). DOI 10.1099/ijs.0.012534-0

Libkind, D., Gadanho, M., van Broock, M. and Sampaio, J.P. 2009. Cystofilobasidium lacus-mascardii sp. nov., a basidiomycetous yeast species isolated from aquatic environments of the Patagonian Andes, and Cystofilobasidium macerans sp. nov., the sexual stage of Cryptococcus macerans. International Journal of Systematic and Evolutionary Microbiology 59: 622 - 630. DOI 10.1099/ijs.0.004390-0

Lourenço, M.J.L. and Sampaio, J.P. 2009. Microbial deterioration of gelatin emulsion photographs: Differences of susceptibility between black and white and colour materials. International Biodeterioration & Biodegradation 63: 496-502. doi:10.1016/j.ibiod.2008.10.011

Gadanho, M. and Sampaio, J.P. 2009. Cryptococcus ibericus sp. nov., Cryptococcus aciditolerans sp. nov. and Cryptococcus metallitolerans sp. nov., a new ecoclade of anamorphic basidiomycetous yeast species from an extreme environment associated with acid rock drainage in São Domingos pyrite mine, Portugal. International Journal of Systematic and Evolutionary Microbiology 59 :2375-2379. DOI 10.1099/ijs.0.008920-0

Libkind, D., Moliné, M., Sampaio, J.P and van Broock, M. 2009. Yeasts from high-altitude lakes: influence of UV radiation. FEMS Microbiology Ecology 69: 353-362. DOI: 10.1111/j.1574-6941.2009.00728.x

Sampaio, J.P. and Gonçalves, P. 2008. Natural populations of Saccharomyces kudriavzevii in Portugal are associated with oak bark and sympatric with S. cerevisiae and S. paradoxus. Applied and Environmental Microbiology 74: 2144-2152. DOI:10.1128/AEM.02396-07

Valério, E., Gadanho, M. and Sampaio, J.P. 2008 Sporidiobolus johnsonii and Sporidiobolus salmonicolor revisited. Mycological Progress 7: 125-131.

Valério, E., Gadanho, M. and Sampaio, J.P. 2008. A reappraisal of the Sporobolomyces roseus species complex and description of Sporidiobolus metaroseussp. nov. International Journal of Systematic and Evolutionary Microbiology 58: 736-741.

Margesin, R., Fonteyne, P.-A., Schinner, F. and Sampaio, J.P. 2007. Novel psychrophilic basidiomycetous yeast species from alpine environments: Rhodotorula psychrophila sp. nov., Rhodotorula psychrophenolica sp. nov., and Rhodotorula glacialissp. nov. International Journal of Systematic and Evolutionary Microbiology 57: 2179-2184.

Libkind, D., Ruffini, A., van Broock, M. Alves, L and Sampaio, J.P. 2007. Biogeography, host-specificity and molecular phylogeny of the basidiomycetous yeast Phaffia rhodozyma and its sexual state Xanthophyllomyces dendrorhous. Applied and Environmental Microbiology 73: 1120-1125.

Hibbett, D. et al. (47 other authors) 2007. A higher-level phylogenetic classification of the Fungi. Mycological Research 111: 509-547.

Sampaio, A., Sampaio, J.P. and Leão, C. 2007. Dynamics of yeast populations recovered from decaying leaves in a nonpolluted stream: a 2-year study on the effects of leaf litter type and decomposition time. FEMS Yeast Research 7: 595-603.

Chapters in books

Sampaio, J.P. 2004. Diversity, phylogeny and classification of basidiomycetous yeasts. In Frontiers in Basidiomycote Mycology, Agerer, Blanz, Piepenbring (eds.). IHW Verlag, Germany, pp 4980.

 Fell, J.W., Boekhout, T., Fonseca, A. and Sampaio, J.P. 2001. Basidiomycetous yeasts In The Mycota - vol VII, Systematics and Evolution, D.J. McLaughlin, E.G. McLaughlin and P.A. Lemke (eds.), Springer-Verlag, Berlin.


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