Francisco Rodriguez-Valera

Summary

Affiliation: Universidad Miguel Hernandez
Location: Alicante, Spain
URL: http://egg.umh.es
Summary:
Francisco Rodriguez-Valera
Biographical sketch
I have been a pioneer in the genomic transformation of microbiology, particularly in its application to microbial ecology. Originally I focused on the biological understanding of microbial evolution using cultured isolates. However, I quickly realized the revolutionary power of genomic applications to microbial ecology and I began focusing on developing genomic and metagenomic applications to characterize microbial communities and advance microbial evolutionary theory. We have been publishing important microbial diversity papers since the mid-eighties and have been pioneers in the application of metagenomics to extreme (halophilic) and marine environments. During my career, I have gained extensive experience in Genomics, Bioinformatics and database development and maintenance, and Microbial Ecology and Evolution. Among my most relevant contributions are the following: 1-We have been the mastermind in the study of many genomes, including Haloquadratum walsbyi, Salinibacter ruber, Alteromonas macleodii, and more recently Spiribacter salinus. We described the predominance of these microbes first by molecular techniques and then we used this information to isolate them and sequence the genomes. 2-Our work produced great advances in characterization of the biodiversity and ecology of the deep and euphotic Mediterranean through genomics and metagenomics. 3-Through collaborations with Brazilian researchers, we published the first metagenomic study of the Amazon River. 4-Our studies unveiled the presence of new groups of microorganisms (e.g., low GC aquatic actinobacteria) and contributed one genome of Nanohaloarchaea using single cell genomics. 5-Our work has provided many clues as to how the life of deep dwelling microbes is influenced by CO monoxygenase, hydrogenase, ecoparalogs, and described bacteriophages very difficult to grow by fosmid cloning. 6-The most oxygen tolerant hydrogenase has been found thanks to our description of the genome of A. macleodii with important repercussions for renewable energies development. 7-The comparison of genomes with metagenomes has led us to propose a Constant-Diversity model to explain the diversity and evolution of prokaryotic populations and their phages. 8-We have multiplied by 10 the number of available marine phage genomes (2013).
I have published over 150 peer-reviewed articles, while guiding 30+ graduate students and postdoctoral fellows. I coordinated numerous interdisciplinary microbial genomics projects from the European Commission (Gene Discovery through Environmental Metagenomics (GEMINI), Microbial Diversity in Aquatic Systems (MIDAS), and Microbial marine communities diversity: from culture to function (MIRACLE)). Currently, I am the coordinating scientist for a long-term Spanish national excellence project Consolider MICROGEN directed towards establishing a strong microbial genomics community in Spain. I am also a member of the Scientific Advisory Council of the International Census of Marine Microbes (ICoMM) and an editorial board member for BMC Evolutionary Biology, BMC Saline Systems, and Archaea and Microbial Ecology journals. We also belong to a large European consortium (MACUMBA) intended to improve the cultivation techniques of marine microbes. Among my previous students there are very distinguished researchers such as P. Lopez-Garcia, D. Moreira, A. Mira, J. Anton, FJM Mojica, S. G. Acinas and A. Lopez-Lopez. Bibliography parameters: ISI H-index 44; Scopus H-index-44; Google Scholar H index 57, 9159 cites

Publications

  1. Bolhuis H, Martín Cuadrado A, Rosselli R, Pašić L, Rodriguez Valera F. Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface. BMC Genomics. 2017;18:510 pubmed publisher
    ....
  2. Lopez Perez M, Gonzaga A, Ivanova E, Rodriguez Valera F. Genomes of Alteromonas australica, a world apart. BMC Genomics. 2014;15:483 pubmed publisher
    ..Overall the hydrolytic activities of the Alteromonas genus as a whole are impressive and fit with its known capabilities to exploit sudden inputs of organic matter in their environment. ..
  3. Lopez Perez M, Ramon Marco N, Rodriguez Valera F. Networking in microbes: conjugative elements and plasmids in the genus Alteromonas. BMC Genomics. 2017;18:36 pubmed publisher
    ..These gradients of exchange frequency are probably one of the main drivers of species origin and maintenance in prokaryotes and also provide these taxa with large genetic diversity. ..
  4. Lopez Perez M, Ghai R, Leon M, Rodríguez Olmos Á, Copa Patiño J, Soliveri J, et al. Genomes of "Spiribacter", a streamlined, successful halophilic bacterium. BMC Genomics. 2013;14:787 pubmed publisher
    ..All these features are also consistent with a well-adapted fully planktonic microbe while other halophiles with more complex genomes such as Salinibacter ruber might have particle associated microniches. ..
  5. Martin Cuadrado A, Pasic L, Rodriguez Valera F. Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi. BMC Genomics. 2015;16:603 pubmed publisher
    ..This type of variation probably reflects a number of mechanisms that minimize the infection rate of predating viruses. ..
  6. Mizuno C, Ghai R, Saghaï A, López García P, Rodriguez Valera F. Genomes of Abundant and Widespread Viruses from the Deep Ocean. MBio. 2016;7: pubmed publisher
    ..They are preferentially found in deeper waters and are widely distributed all over the oceans. To our knowledge, this is the first report on complete and cosmopolitan viral genomes from the bathypelagic habitat. ..
  7. Sharma A, Walsh D, Bapteste E, Rodriguez Valera F, Ford Doolittle W, Papke R. Evolution of rhodopsin ion pumps in haloarchaea. BMC Evol Biol. 2007;7:79 pubmed
    ..In this initial study, we assess the roles of LGT and gene loss in the evolution of haloarchaeal rhodopsin ion pump genes, using phylogenetics and comparative genomics approaches...
  8. Lopez Perez M, Rodriguez Valera F. Pangenome Evolution in the Marine Bacterium Alteromonas. Genome Biol Evol. 2016;8:1556-70 pubmed publisher
    ..Models for the generation of this genomic diversity involving phage predation are discussed. ..
  9. Legault B, Lopez Lopez A, Alba Casado J, Doolittle W, Bolhuis H, Rodriguez Valera F, et al. Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics. 2006;7:171 pubmed
    ..Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present...
  10. Mizuno C, Rodriguez Valera F, Ghai R. Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics. MBio. 2015;6: pubmed publisher
    ..This work contributes to the perception of marine actinobacterial groups as important players in the marine environment with distinct and important contributions to nutrient cycling in the oceans. ..

Detail Information

Publications12

  1. Bolhuis H, Martín Cuadrado A, Rosselli R, Pašić L, Rodriguez Valera F. Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface. BMC Genomics. 2017;18:510 pubmed publisher
    ....
  2. Lopez Perez M, Gonzaga A, Ivanova E, Rodriguez Valera F. Genomes of Alteromonas australica, a world apart. BMC Genomics. 2014;15:483 pubmed publisher
    ..Overall the hydrolytic activities of the Alteromonas genus as a whole are impressive and fit with its known capabilities to exploit sudden inputs of organic matter in their environment. ..
  3. Lopez Perez M, Ramon Marco N, Rodriguez Valera F. Networking in microbes: conjugative elements and plasmids in the genus Alteromonas. BMC Genomics. 2017;18:36 pubmed publisher
    ..These gradients of exchange frequency are probably one of the main drivers of species origin and maintenance in prokaryotes and also provide these taxa with large genetic diversity. ..
  4. Lopez Perez M, Ghai R, Leon M, Rodríguez Olmos Á, Copa Patiño J, Soliveri J, et al. Genomes of "Spiribacter", a streamlined, successful halophilic bacterium. BMC Genomics. 2013;14:787 pubmed publisher
    ..All these features are also consistent with a well-adapted fully planktonic microbe while other halophiles with more complex genomes such as Salinibacter ruber might have particle associated microniches. ..
  5. Martin Cuadrado A, Pasic L, Rodriguez Valera F. Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi. BMC Genomics. 2015;16:603 pubmed publisher
    ..This type of variation probably reflects a number of mechanisms that minimize the infection rate of predating viruses. ..
  6. Mizuno C, Ghai R, Saghaï A, López García P, Rodriguez Valera F. Genomes of Abundant and Widespread Viruses from the Deep Ocean. MBio. 2016;7: pubmed publisher
    ..They are preferentially found in deeper waters and are widely distributed all over the oceans. To our knowledge, this is the first report on complete and cosmopolitan viral genomes from the bathypelagic habitat. ..
  7. Sharma A, Walsh D, Bapteste E, Rodriguez Valera F, Ford Doolittle W, Papke R. Evolution of rhodopsin ion pumps in haloarchaea. BMC Evol Biol. 2007;7:79 pubmed
    ..In this initial study, we assess the roles of LGT and gene loss in the evolution of haloarchaeal rhodopsin ion pump genes, using phylogenetics and comparative genomics approaches...
  8. Lopez Perez M, Rodriguez Valera F. Pangenome Evolution in the Marine Bacterium Alteromonas. Genome Biol Evol. 2016;8:1556-70 pubmed publisher
    ..Models for the generation of this genomic diversity involving phage predation are discussed. ..
  9. Legault B, Lopez Lopez A, Alba Casado J, Doolittle W, Bolhuis H, Rodriguez Valera F, et al. Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics. 2006;7:171 pubmed
    ..Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present...
  10. Mizuno C, Rodriguez Valera F, Ghai R. Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics. MBio. 2015;6: pubmed publisher
    ..This work contributes to the perception of marine actinobacterial groups as important players in the marine environment with distinct and important contributions to nutrient cycling in the oceans. ..
  11. Rodriguez Valera F, Martin Cuadrado A, Lopez Perez M. Flexible genomic islands as drivers of genome evolution. Curr Opin Microbiol. 2016;31:154-160 pubmed publisher
    ..They are better understood as parts rather than the whole. Multiple genomes are required to understand how the population interacts with its biotic and abiotic environment. ..
  12. Cabello Yeves P, Zemskaya T, Rosselli R, Coutinho F, Zakharenko A, Blinov V, et al. Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal. Appl Environ Microbiol. 2018;84: pubmed publisher
    ..Among them, there was a broad set of streamlined microbes with small genomes/intergenic spacers, including a new nonmarine Pelagibacter-like (subtype I/II) genome. ..