CBMA

Currently, I am leading a research team in Bacterial Functional Genomics. Our research is strongly engaged in Systems Biology approaches using Pseudomonas selected isolates. Bacteria belonging to the Pseudomonas genus possess an intricate ability to tolerate and thrive in challenging environments such as the Human lungs, the deep sea or highly polluted soils. Such competence resides in their wide nutritional and metabolic versatility and in a complex network of adaptation mechanisms. In other words, the necessary code to efficiently cope with a wide variety of different substrates and biotic and/or abiotic stress conditions is included in their genomic catalog. Therefore, they hold great potential, as a source of novel biomolecules and cell factories, for different biotechnological applications, namely in the fields of biocatalysis, biosensors, bioremediation, and biomedicine. So far, we have sequenced the full genomes of 3 Pseudomonas isolates and set a variety of in silico and wet-lab approaches to explore the genome catalogs of the sequenced isolates, including genome assembly and annotation pipelines, RNA-Seq, expression proteomics and metabolomics approaches.

The main topics of research are:

i) Systems and synthetic biology approaches to enhance Pseudomonas biotech potential

ii) Metagenomic characterization of microbiomes from soil and cetaceans

iii) Genome-wide characterization of clinical isolates of Pseudomonas aeruginosa

Soares-Castro P, Montenegro-Silva P, Heipieper HJ, Santos PM (2017) Functional characterization of a 28-kb catabolic island from Pseudomonas sp. M1 involved in biotransformation of b-myrcene and related plant-derived volatiles. Applied Envi. Microbiol 83. doi: 10.1128/AEM.03112-16

Godoy-Vitorino F, Rodriguez-Hilario A, Alves AL, Gonçalves F, Cabrera-Colon B, Mesquita CS, Soares-Castro P, Ferreira M, Marçalo A, Vingada J, Eira C, Santos PM. (2017) The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal. Res Microbiol. 168:85-93. doi: 10.1016/j.resmic.2016.08.004.

 Soares-Castro P, Santos PM (2014) Deciphering the genome repertoire of Pseudomonas sp. M1 towards ß-myrcene biotransformation, Gen. Biology Evol. 7:1-17. doi: 10.1093/gbe/evu254.

Soares-Castro P, Marques D, Demyanchuk S, Faustino A, Santos PM (2011) The genome sequence drafts of two Pseudomonas aeruginosa clinical isolates with different antibiotic susceptibilities. J. Bacteriol. 193:5573 (issue cover)

Title: WRANA - Wastewater reuse: improving the odds by understanding natural attenuation (INDIGO-IPP1-026, ERA-NET)
Funding: Inn-INDIGO/0004/2014
Period: 2015-2018
Role: European Coordinator

Title: Cetaceans as marine ecosystem health sentinels
Funding: FCT- RECI/AAG-GLO/0470/2012
Period: 2013-2018
Role: Team member (task coordinator)

Title: Exploitation of immunogenic proteins of the Burkholderia cepacia complex to design new diagnostic and therapeutic strategies
Funding: FCT- PTDC/BBB-BIO/1958/2012
Period: 2013-2015
Role: Team member (responsible of the research activities at University of Minho)

Title: BIOMYR –Towards the metabolic engineering of beta-myrcene pathway Pseudomonas sp. M1: functional genomics and structural biochemistry approaches
Funding: FCT- PTDC/EBB-BIO/104980/2008
Period: 2010-2013
Role: Principal investigator

Title: ROOT-INT- Role of a two-component regulatory system in the early interaction between Sinorhizobium meliloti and plant root hairs
Funding: FCT-PTDC/BIA-MIC/113733/2009
Period: 2011-2014
Role: Team member (responsible of the research activities at University of Minho)

Title: NANOECOTOX-Impacts of metal nanoparticles to aquatic ecosystems: from community responses to cellular targets
Funding: PTDC/AAC-AMB/121650/2010 (2012-2015)
Period: 2012-2015
Role: Team member

Soares-Castro P, Montenegro-Silva P, Heipieper HJ, Santos PM (2017) Functional characterization of a 28-kb catabolic island from Pseudomonas sp. M1 involved in biotransformation of b-myrcene and related plant-derived volatiles. Applied Envi. Microbiol 83. doi: 10.1128/AEM.03112-16

Godoy-Vitorino F, Rodriguez-Hilario A, Alves AL, Gonçalves F, Cabrera-Colon B, Mesquita CS, Soares-Castro P, Ferreira M, Marçalo A, Vingada J, Eira C, Santos PM (2017) The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal. Res Microbiol. 168:85-93. doi: 10.1016/j.resmic.2016.08.004.

Silva IN, Santos PM, Santos MR, Zlosnik JE, Speert DP, Buskirk SW, Bruger EL, Waters CM, Cooper VS, Moreira LM (2016) Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection. mSystems. 2016 May 24;1(3). pii: e00029-16.

Baptista P, Reis F, Pereira E, Tavares RM, Santos PM, Richard F, Selosse M, Lino-Neto T (2015) Soil DNA pyrosequencing and fruitbody surveys reveal contrasting diversity for various fungal ecological guilds in chestnut orchards. Environ Microbiol Rep doi: 10.1111/1758-2229.12336

Freschi L, Jeukens J, Kukavica-Ibrulj I, Boyle B, Dupont M-J, Laroche J, Larose S, Maaroufi H, Fothergill JL, Moore M, Winsor GL, Aaron SD, Barbeau J, Bell SC, Burns JL, Camara M, Cantin A, Charette SJ, Dewar K, Déziel É, Grimwood K, Hancock REW, Harrison JJ, Heeb S, Jelsbak L, Jia B, Kenna DT, Kidd TJ, Klockgether J, Lam JS, Lamont IL, Lewenza S, Loman N, Malouin F, Manos J, McArthur AG, McKeown J, Milot J, Naghra H, Nguyen D, Pereira SK, Perron GG, Pirnay J-P, Rainey PB, Rousseau S, Santos PM, Stephenson A, Taylor V, Turton JF, Waglechner N, Williams P, Thrane SW, Wright GD, Brinkman FSL, Tucker NP, Tümmler B, Winstanley C and Levesque RC (2015) Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Front. Microbiol. 6:1036. doi: 10.3389/fmicb.2015.01036

Silva I, Santos PM, Moreira L (2015) Draft Genome Sequence of Two Burkholderia multivorans Sequential Isolates from a Chronic Lung Infection of a Cystic Fibrosis Patient, Genome Annouc ;3(1). pii: e01531-14. doi: 10.1128/genomeA.01531-14

Soares-Castro P, Santos PM (2014) Deciphering the genome repertoire of Pseudomonas sp. M1 towards ß-myrcene biotransformation, Gen. Biology Evol. 7:1-17. doi: 10.1093/gbe/evu254.

Madeira A, dos Santos, AC, Santos PM, Coutinho CP, Tyrrell J, McClean S, Callaghan M, Sá-Correia I (2013), Proteomic profiling of Burkholderia cenocepacia clonal isolates with different virulence potential retrieved from a cystic fibrosis patient during chronic lung infection, PLOS ONE 8: e83065.

Soares-Castro P, Santos PM (2013) Towards the description of the genome catalog of Pseudomonas sp. M1. Genome Announcements (doi: 10.1128/genomeA.00146-12)

Soares-Castro P, Marques D, Demyanchuk S, Faustino A, Santos PM (2011) The genome sequence drafts of two Pseudomonas aeruginosa clinical isolates with different antibiotic susceptibilities. J. Bacteriol. 193:5573 (issue cover)

Madeira A, Santos PM, Coutinho CP, Pinto-de-Oliveira A, Sá-Correia I (2011) Quantitative proteomics (2-D-DIGE) reveals molecular strategies employed by Burkholderia cenocepacia to adapt to the airways of cystic fibrosis patients under antimicrobial therapy. PROTEOMICS, 11:1313-1328.

Roma-Rodrigues C, Santos PM, Benndorf D, Rapp E, Sá-Correia I (2010) Response of Pseudomonas putida KT2440 to phenol at the level of membrane proteome. Journal of Proteomics, 73:1461-1478

Santos PM, Sá-Correia  (2009) Adaptation to beta-myrcene catabolism in Pseudomonas sp. M1: an expression proteomics analysis. Proteomics 9:5101-11.

Teixeira MC, Santos PM, Rodrigues C, Sá-Correia I(2009) Teaching Expression Proteomics: From the Wet-Lab to the Laptop. Biochem. Mol. Biol. Education 37:279–286.

Santos PM, Simões T, Sá-Correia I (2009) Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach. Proteomics 9:657-670.

Cosme AM, Becker A, Santos MR, Sharypova LA, Santos PM, Moreira LM (2008) The outer membrane protein TolC from Sinorhizobium meliloti affects protein secretion, polysaccharide biosynthesis, antimicrobial resistance and symbiosis. Molecular Plant-Microbe Interactions 21:947-957.

Santos PM, Sá-Correia I. (2007) Characterization of the unique organization and co-regulation of a gene cluster required for phenol and benzene catabolism in Pseudomonas sp. M1. Journal of Biotechnology 131:371-378.

Santos PM, Roma V, Benndorf D, von Bergen M, Harms H, Sá-Correia I (2007) Mechanistic insights into the global response to phenol in the phenol-biodegrading strain Pseudomonas sp. M1, revealed by quantitative proteomics. OMICS: A Journal of Integrative Biology 11:233-251.

Mendes ND, Casimiro A., Santos PM, Sá-Correia I, Oliveira A.L. Freitas AT (2006) MUSA: A parameter free algorithm for the identification of biologically significant motifs. Bioinformatics 22:2996-3002.

Teixeira MC, Santos PM, Fernandes AR, Sá-Correia I (2005) A proteome analysis of the yeast response to the herbicide 2,4-dichlorophenoxyacetic acid. Proteomics 5:1889-1901.

Santos PM, Benndorf D, Sá-Correia I (2004) Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 4:2640-2652.

Fernandes AR, Durão PJ, Santos PM, Sá-Correia I (2003) Activation and significance of vacuolar H+-ATPase in Saccharomyces cerevisiae adaptation and resistance to the herbicide 2,4-dichlorophenoxyacetic acid. Biochemical and Biophysical Research Communications 312:1317-1324.

Kabelitz N, Santos PM, Heipieper HJ (2003) Effect of aliphatic alcohols on growth and degree of saturation of membrane lipids in Acinetobacter calcoaceticus. FEMS Microbiology Letters 220:223-227.

Santos PM, Mignogna G, Heipieper HJ, Zennaro E (2002) Occurrence and properties of glutathione S- transferases in phenol-degrading Pseudomonas strains. Research in Microbiology 153:89-98.

Santos PM, Leoni L, Di Bartolo I, Zennaro E (2002) Integration host factor is essential for the optimal expression of styABCD operon in Pseudomonas fluorescens ST. Research in Microbiology 153: 527-536.

Santos PM, Di Bartolo I, Blatny JM, Valla S, Zennaro E (2001) New broad-host-range promoter probe vectors based on the plasmid RK2 replicon. FEMS Microbiology Letters 195:91-96.

Santos PM, Blatny JM, Di Bartolo I, Valla S, Zennaro E (2000) Physiological analysis of the expression of the styrene degradation gene cluster in Pseudomonas fluorescens ST. Applied and Environmental Microbiology 66:1305-1310.

Isken S, Santos PM, de Bont JAM (1997) Effect of solvent adaptation on antibiotic resistance in Pseudomonas putida S12. Applied Microbiology and Biotechnology 48:642-647.

---------

ResearcherID: B-5908-2009
Url: http://www.researcherid.com/rid/B-5908-2009

Mesquita CS, Soares-Castro P and Santos PM (2013) Pseudomonas aeruginosa: phenotypic flexibility and antimicrobial resistance. In “Microbial pathogens and strategies for combating them: science, technology and education” (eds Mendez-Vilas A) Formatex Research Center, Vol I, 650-655. 

 Santos PM, Teixeira MC, Sá-Correia I (2004) A análise proteómica quantitativa na revelação de mecanismos de resposta a stresse químico em microrganismos. Boletim de Biotecnologia 77:7-17.

On going Supervisions and co-supervisions
Post-doc researchers

Pedro Soares-Castro (Wrana project)

Ph.D. thesis

Ana Cristina Mesquita (SFRH/BD/98558/2013) Genomic contextualization of heterogeneity in Pseudomonas aeruginosa isolates (supervision)

Diana Cláudia Martins da Costa Barros (SFRH/BD/80407/2011) Proteomic and physiological responses to metal nanoparticles in aquatic microbes (co-supervision)

Bruno Alexandre da Silva Panta Ferreira (SFRH/BD/113216/2015) Effects of sewage outfalls on marine protected species (co-supervision)

Msc

Sara Martins (2016-17) A metagenomic approach to identify and characterize wastewater populations, Master in Bioinformatics

Pedro Montenegro (2016-17) Regulatory mechanisms controlling myrcene catabolism in Pseudomonas, Master in Applied Biochemistry

Helena Rodrigues (2016-17) The Microbiome of cetaceans as an health status marker, Master in Applied Biochemistry

Eduardo Silva (2016-17) Effects of radiation on the molecular dynamics of Pseudomonas aeruginosa, Master in Applied Biochemistry