Evolutionary Genomics Group, División de Microbiología - UMH

Francisco Rodriguez-Valera

Francisco Rodríguez-Valera

Departmental Affiliation: Microbiología y Producción Vegetal

Current Position: Professor of Microbiology (Catedrático), University Miguel Hernández (UMH), Elche, Spain; 1997/02/01 – present.

Address:

División de Microbiología
Universidad Miguel Hernández
Apartado 18
03550 San Juan de Alicante
Alicante, Spain

Tel: +34 965 91 9451
Fax: +34 965 91 9457 / 9576

E-mail: frvalera@umh.es


Recent Publications

2013

A. Ventosa; Rodriguez-Valera F.; C. Sánchez Porro; A.B. Fernández; Rohit Ghai; M.J. León(2013). Draft Genome of Spiribacter salinus M19-40, an Abundant Gammaproteobacterium in Aquatic Hypersaline Environments. Genome Announcements, e00179-12. 10.1128/g, pp. 179 - 212.

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Park SJ; Kim JG; Jung MY; Kim SJ; Cha IT; Ghai R; Martín-Cuadrado AB; Rodríguez-Valera F.; Rhee SK.(2013) Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle. Journal of Bacteorology. 194 - 24, pp. 6948 - 6949. 06/01/2013 Click here to view PDF

Mario López Pérez; Aitor Gonzaga; Francisco Rodríguez-Valera (2013). Genomic diversity of "deep ecotype" Alteromonas macleodii isolates: evidence for Pan-Mediterranean clonal frames. Genome Biology and Evolution, 10.1093/gbe/evt089 - 5(6), pp.1220 - 1232

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Inmaculada García Heredia; Francisco Rodríguez-Valera; Ana Belén Martín Cuadrado(2013). Novel group of podovirus infecting the marine bacterium Alteromonas macleodii. Bacteriophage, 10.4161/bact.24766 Click here to view PDF

2012

Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Mizuno CM, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F. (2012) Polyclonality of concurrent natural populations of Alteromonas macleodii. Genome Biology and Evolution , In Press Click here to view PDF
Carolina MM, Rodriguez-Valera F, Garcia-Heredia I, Martin-Cuadrado AB & Ghai R (2012) Reconstruction of novel cyanobacterial siphovirus genomes from Mediterranean metagenomic fosmids. Applied and Environmental Microbiology, In Press Click here to view PDF
Gonzaga A, López-Pérez M, Martin-Cuadrado AB, Ghai R, Rodriguez-Valera F. (2012) Complete genome of the copiotrophic marine bacterium Alteromonas macleodii type strain ATCC 27126T. Journal of Bacteriology , doi: 10.1128/JB.01565-12 Click here to view PDF
López-Pérez M, Gonzaga A, Martin-Cuadrado AB, Onyshchenko O, Ghavidel A, Ghai R & Rodriguez-Valera F (2012) Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph. Scientific Reports , doi:10.1038/srep00696 Click here to view PDF
Park SJ, Ghai R, Martin-Cuadrado AB, Rodriguez-Valera F, Jung MY, Kim JG, Rhee SK (2012) Draft genome sequence of sulfur-oxidizing bacteria Candidatus Sulfurovum sediminum AR belonging to the Epsilon-proteobacteria. Journal of Bacteriology , doi:10.1128/JB.00741-12 Click here to view PDF
Rohit Ghai, Claudia Mella Hernandez, Antonio Picazo, Carolina Megumi Mizuno, Karolina Ininbergs,Beatriz Díez, Ruben Valas, Christopher L. DuPont, Katherine D. McMahon, Antonio Camacho & Francisco Rodriguez-Valera (2012) Metagenomes of mediterranean coastal lagoons. Scientific Reports , doi:10.1038/srep00490 Click here to view PDF
Garcia-Heredia I, Martin-Cuadrado AB, Mojica FJ, Santos F, Mira A, Antón J, Rodriguez-Valera F.(2012) Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses. PLoS ONE, doi: 10.1371/journal.pone.0033802 Click here to view PDF

2011

Rohit Ghai, Lejla Pašic, Ana Beatriz Fernández, Ana-Belen Martin-Cuadrado, Carolina Megumi Mizuno, Katherine D. McMahon, R. Thane Papke, Ramunas Stepanauskas, Beltran Rodriguez-Brito, Forest Rohwer, Cristina Sánchez-Porro, Antonio Ventosa & Francisco Rodríguez-Valera (2011) New Abundant Microbial Groups in Aquatic Hypersaline Environments. Scientific Reports , doi:10.1038/srep00135 Click here to view PDF
Céline Brochier-Armanet, Philippe Deschamps, Purificación López-García, Yvan Zivanovic, Francisco Rodríguez-Valera and David Moreira (2011) Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea. The ISME Journal , Vol 5, 1291–1302; doi:10.1038/ismej.2011.16 Click here to view PDF
Rohit Ghai, Francisco Rodriguez-Valera, Katherine D. McMahon, Danyelle Toyama, Raquel Rinke, Tereza Cristina Souza de Oliveira, José Wagner Garcia, Fernando Pellon de Miranda, Flavio Henrique-Silva (2011) Metagenomics of the Water Column in the Pristine Upper Course of the Amazon River. PLoS ONE, Vol 6; 8; e23785; doi:10.1371/journal.pone.0023785 Click here to view PDF
Rohit Ghai, Katherine D. McMahon, Francisco Rodriguez-Valera (2011) Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC Environmental Microbiology Reports; Society for Applied Microbiology and Blackwell Publishing Ltd , DOI: 10.1111/j.1758-2229.2011.00274.x Click here to view PDF

2010

Alex Mira, Ana B. Martín-Cuadrado, Giuseppe D’Auria,Francisco Rodríguez-Valera.; The bacterial pan-genome:a new paradigm in microbiology. International microbiology, 2010; 13:45-57; doi: 10.2436/20.1501.01.110 Click here to view PDF
Beltran Rodriguez-Brito, LinLin Li, Linda Wegley, Mike Furlan, Florent Angly, Mya Breitbart, John Buchanan, Christelle Desnues, Elizabeth Dinsdale, Robert Edwards, Ben Felts, Matthew Haynes, Hong Liu, David Lipson, Joseph Mahaffy, Ana Belen Martin-Cuadrado, Alex Mira, Jim Nulton, Lejla Pašic, Steve Rayhawk, Jennifer Rodriguez-Mueller, Francisco Rodriguez-Valera, Peter Salamon, Shailaja Srinagesh, Tron Frede Thingstad, Tuong Tran, Rebecca Vega Thurber, Dana Willner, Merry Youle and Forest Rohwer ; Viral and microbial community dynamics in four aquatic environments. ISME Journal, 2010 Jun;4(6):739-51. Epub 2010 Feb 11. Click here to view PDF
Ghai R, Martin-Cuadrado AB, Gonzaga A, Garcia-Heredia I, Cabrera R, Martin J, Verdú M, Deschamps P, Moreira D, López-Garcia P, Mira A and Rodriguez-Valera F.; Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. ISME Journal, Sep;4(9):1154-66. Epub 2010 Apr 15. Click here to view PDF

2009

Martin-Cuadrado AB, Ghai R, Gonzaga A, Rodriguez-Valera F.CO dehydrogenase genes found in metagenomic fosmid clones from the deep mediterranean sea. Applied and Environmental Microbiology, doi: 10.1128/AEM.01283-09. Click here to view PDF
Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pasic L, Thingstad TF, Rohwer F, Mira A. Explaining microbial population genomics through phagepredation. Nature Reviews Microbiology, doi:10.1038/nrmicro2235.
Pasic L, Rodriguez-Mueller B, Martin-Cuadrado AB, Mira A, Rohwer F, Rodriguez-Valera F. Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber. BMC Genomics , doi:10.1186/1471-2164-10-570. Click here to view PDF

2008

Sanchez-Perez G, Mira A, Nyiro G, Pasic L, Rodriguez-Valera F. Adapting to environmental changes using specialized paralogs. Trends in Genetics, doi:10.1016/j.tig.2008.01.002. Click here to view PDF
Martin-Cuadrado AB, Rodriguez-Valera F, Moreira D, Alba JC, Ivars-Martínez E, Henn MR, Talla E, López-García P. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparativemetagenomic analyses of bathypelagic plankton of different oceanic regions. ISME Journal, doi:10.1038/ismej.2008.40. Click here to view PDF
Quaiser A, López-García P, Zivanovic Y, Henn MR, Rodriguez-Valera F, Moreira D. Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton. Environmental Microbiology, doi:10.1111/j.1462-2920.2008.01691.x. Click here to view PDF
Ivars-Martinez E, Martin-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodriguez-Valera F. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME Journal, doi:10.1038/ismej.2008.74. Click here to view PDF
Ivars-Martínez E, D'Auria G, Rodríguez-Valera F, Sánchez-Porro C, Ventosa A, Joint I, Mühling M. Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis. Molecular Ecology, doi: 10.1111/j.1365-294X.2008.03883.x. Click here to view PDF
Ivars-Martínez E, D'Auria G, Rodríguez-Valera F, Sânchez-Porro C, Ventosa A, Joint I, Mühling M. Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis. Molecular Ecology, doi: 10.1111/j.1365-294X.2008.03883.x. Click here to view PDF

Research Interests

We explore bacterial diversity in natural environments, specifically aquatic marine environments including the sea itself, coastal lagoons and hypersaline environments derived from evaporation of seawater. For this, we use molecular identity markers such as the ribosomal RNA gene amplified by PCR techniques from natural samples. We combine this approach with new techniques to retrieve in culture novel organisms with potential in biotechnology. It has been estimated that the potential harvest of useful products and processes from this unknown prokaryotic diversity dwarfs that of the rainforest. Now we use mostly metagenomics as the strategy to study of marine and coastal hypersaline environments. This strategy will most certainly have a profound impact in the study of prokaryotic diversity from both, environmental and population, perspectives. We are also interested in how diversity is maintained and generated in bacterial populations and how they change with time. This dimension of evolutionary or population Microbiology is extremely important and largely unexplored. The structure of diversity is an extraordinarily complex problem but one that is essential to understand and predict issues of paramount importance such as the spread of antibiotic resistance or the emergence of new and deathly bacterial infections. The Evolutionary Genomics Group formed after the incorporation to the group of Dr. Alex Mira (a genomicist) addresses these issues.

Education and Positions after Ph.D.

Bachelor's Degree in Biology (Master), University of Barcelona (Spain), 1974.
Doctor Degree in Biology (Ph.D.), University of Granada (Spain), 1978.
Professor, Departamento de Producción vegetal y Microbiología, Miguel Hernandez University (Spain), 1997-Present.
Professor of Microbiology, University College of Alicante (Spain), 1991-1997.
Head of the Department of Genetics and Microbiology, University of Alicante (Spain), 1989-1997.
Professor, Department of Genetics and Microbiology, University of Alicante (Spain), 1984-1997.
Senior Lecturer (Prof. Titular), Faculty of Medicine, University of Alicante (Spain), 1982-1991.
Lecturer (Prof. Adjunto), Microbiology, University of Alicante (Spain), 1982-1983.
Senior Lecturer (Prof. Agregado), Faculty of Pharmacy, University of Sevilla (Spain), 1981-1982.
Lecturer (Prof. Adjunto), Microbiology, University College of Alicante (Spain), 1978-1981.

Pre- and postdoctoral Research at foreign institutions.

1979 (3 months): Postdoctoral student, Marine Biological Laboratory, Woods Hole , USA
1980 (9 months) Postdoctoral student, Department of Biology, University of Ottawa, Canada
1983 (3 months), Postdoctoral student, Institut für Mikrobiologie, Universität Bonn, Germany
1985 (12 months), Postdoctoral student, Biochemistry and Biophysics Department, University of California San Francisco, USA
1992 (3 months), Visiting Professor, Department of Biochemistry, Dalhousie University, Nova Scotia, Canada
1996 (3 months), Visiting Professor, Department of Microbiology (G08), University of Sydney, Sydney, New South Wales, Australia
2002 (3 months), Visiting Professor, Department of Biochemistry, Dalhousie University, Nova Scotia, Canada

National and International Research Grants (since 2000):

Evolución del Genoma de Escherichia coli, naturaleza del DNA de distribución  opcional en diferentes cepas de la colección ECOR y del DNA diferencial en diferentes cepas uropatógenas (G.B2). ; Ref. PM00-0078; Favored Entity: MEC (Ministerio de Educación); Principal investigator: Francisco Rodríguez Valera; Funding: 60.133€; 2000-2003
Caracterización de la microbiota asociada a invertebrados marinos productores de sustancias con potencial interés farmacológico; Ref. AR\BIO2000-085-P4-04; Favored Entity: MEC (Ministerio de Educación); Principal investigator: Francisco Rodríguez Valera; Funding: 100.970,04€; 2001-2004
Microbial Marine Communities Diversity: From Culture to Function (MIRACLE) ; Acciones Especiales del Pan Nacional de I+D+i; Ref. BIO2002-10816-E.; Ministerio de Ciencia y Tecnología; Principal Investigator: Francisco Rodríguez Valera; Funding: 48.000€; 2002-2005
Genne Discovery through Environmental Metagenomics (GEMINI), Ref. QLK3-CT-2002-02056.  Favored Entity: European Commission, ; Principal Investigator: Francisco Rodríguez Valera; Funding: 255.3500 €; 2002-2006.
Genne Discovery through Environmental Metagenomics (GEMINI), Acciones Especiales del Pan Nacional de I+D+i; Ref. BIO2002-10815-E. Favored Entity: Ministerio de Ciencia y Tecnología; Principal investigator: Prof. Dr. Francisco Rodríguez Valera; Funding: 36.000€; 2003-2006.
Estudio Metagenómico del bacteriplancton en el Mar Mediterráneo profundo, Ref.CTM2005-04564; Favored Entity: MEC (Ministerio de Educación) ; Principal investigator: Prof. Dr. Francisco Rodríguez Valera; Funding: 50.000€; 2005-2008.
Microbial Diversity in Aquatic Systems (MIDAS), Ref. MAS3-CT97-0154. Favored Entity: European Commission, Principal Investigator (Coordinator): Francisco Rodríguez Valera. Funding: 200.000€; 1998-2001.
Microbial marine communities diversity : from culture to function (MIRACLE); Favored Entity: European Commission, Ref. EVK3-CT-2002-00087. Principal Investigator (Coordinator): Francisco Rodríguez Valera. Funding: 295.779€; 2003-2005.
Acción complementaria: Secuenciación y análisis de 65 fósmidos de librerías metagenómicas del Mediterráneo (GEN2007-30014-E); Favored Entity: MEC (Ministerio de Educación) ; Principal investigator: Prof. Dr. Francisco Rodríguez Valera; Funding: 25.000€; 2006-2008.
Genomique Evolutive et des Populations de Microorganismes Non-cultivables de L´Ocean Profond. Agence  National de la Recherche – ANR (France). Principal investigator: Purificación López García. Other investigators: Francisco Rodríguez Valera, David Moreira, Celine Brochier-Armanet, Yvan Zivanovic, Ana Belén Martín Cuadrado. Funding: 25.000€; 2008-2012.
Identificacion de bioindicadores microbianos en la rizosfera de quercineas (Quercus ilex ballota and Q. pyrenaica) asociados a cambio climatico y evolucion post-incendio. Financial entity: Junta de Andalucía. Programa de Incentivos a los Agentes del Sistema Andaluz del Conocimiento. 2008. Principal investigator: Manuel Fernández López (Investigador del CSIC, Estación Experimental del Zaidin, CSIC). Other Investigators: Francisco Rodríguez Valera, Ana Belén Martín Cuadrado.
Identificación de nuevos compuestos naturales de origen marino con potencial aplicación terapeútica e industrial. Financial entity: Ministerio de Educación y Ciencia, Plan Nacional de I+D+I,  Programa de fomento de la Investigación Técnica (PROFIT). Participating entities: UMH  (Francisco Rodríguez Valeraand  MEDITERRÁNEO SERVICIOS MARINOS. Nº CONVENIO 170/07 (20-DIC-2007). 2007- 2009. Funding: 2007:10.000€, 2008: 30.000€, 2009: 30.000 €.
Metagenomics and dynamics of prokaryots genomes (MAGYK); Financial entity: MICINN, CONVOCATORIA 2008 , Financial amount:  330.000€ ; Favored Entity: Universidad Miguel Hernández; Principal investigator (Coordinator): Prof. Dr. Francisco Rodríguez Valera; Funding: 330.000€; 2008/9-2012/3.
Ayuda complementaria: Metagenomics and dynamics of prokaryots genomes; Ref: ACOMP/2009/359; Financial entity: Consellería de educación (Generalitat Valenciana),CONVOCATORIA 2009 , Financial amount:  10.000€ ; Favored Entity: Universidad Miguel Hernández; Principal investigator: Prof. Dr. Francisco Rodríguez Valera; 2009.
Microbial comparative genomics (MICROGEN); Financial entity: MICINN, CONSOLIDER INGENIO 2009, Convocatoria 2009; Participating entities: Universidad Miguel Hernández (UMH), Instituto de Recursos Naturales y Agrobiología CSIC (IRNAS-CSIC),Centro de Investigación y Tecnología Animal (CITA-IVIA), Universidad de Granada (UGR), Universidad de Valencia (UV), Universidad Politécnica de Madrid (UPM), Universidad del País Vasco (UPV), Universitat de les Illes Balears (UIB), Estación Experimental del Zaidín CSIC (EEZ-CSIC), Centro Superior de Investigación en Salud Pública (CSISP); Principal investigator (Coordinator): Prof. Dr. Francisco Rodríguez Valera; Funding: 3.800.000€ (467.000€); 2009-2013.
Genetic diversity of the Mediterranean Sea by Metagenomics (DIMEGEN); Financial entity: Generalitat Valenciana, Programa Prometeo para Grupos de Investigación de Excelencia , Convocatoria 2010, Financial amount:  46.500€; Favored Entity: Universidad Miguel Hernández ; Principal investigator: Prof. Dr. Francisco Rodríguez Valera; 2010.

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Complete list of publications

Publications PDF

Material de apoyo a la docencia

Manual de Practicas

Slide Shows