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. doi request reprint Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface
    Henk Bolhuis
    Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research NOIZ and Utrecht University, Den Hoorn, The Netherlands
    BMC Genomics 18:510. 2017
  2. pmc Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi
    Ana Belén Martín-Cuadrado
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, Apartado 18, San Juan de Alicante, Alicante, Spain
    BMC Genomics 16:603. 2015
  3. pmc RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages
    Nikole E Kimes
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Apartado 18, San Juan, Alicante, 03550, Spain
    BMC Genomics 15:938. 2014
  4. pmc The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity
    Henk Bolhuis
    Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, The Netherlands
    BMC Genomics 7:169. 2006
  5. pmc Evolution of rhodopsin ion pumps in haloarchaea
    Adrian K Sharma
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    BMC Evol Biol 7:79. 2007
  6. pmc Micro-Mar: a database for dynamic representation of marine microbial biodiversity
    Ravindra Pushker
    Evolutionary Genomics Group, Universidad Miguel Hernandez, Apartado 18, 03550 San Juan de Alicante, Alicante, Spain
    BMC Bioinformatics 6:222. 2005
  7. ncbi request reprint Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern
    Susana Benlloch
    Division de Microbiologia, Universidad Miguel Hernandez, Alicante, Spain
    Environ Microbiol 4:349-60. 2002
  8. ncbi request reprint Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea
    Arantxa Lopez-Lopez
    Division de Microbiologia, Universidad Miguel Hernandez, Campus de San Juan, 03550 San Juan de Alicante, Spain
    Environ Microbiol 7:649-59. 2005
  9. doi request reprint Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter
    Elena Ivars-Martínez
    Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Alicante, Spain
    ISME J 2:1194-212. 2008
  10. pmc Comparative genomics of gene-family size in closely related bacteria
    Ravindra Pushker
    Evolutionary Genomics Group, Universidad Miguel Hernandez, Campus de San Juan, Apartado 18, 03550 San Juan de Alicante, Alicante, Spain
    Genome Biol 5:R27. 2004

Collaborators

Detail Information

Publications53

  1. doi request reprint Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface
    Henk Bolhuis
    Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research NOIZ and Utrecht University, Den Hoorn, The Netherlands
    BMC Genomics 18:510. 2017
    ..We have performed a transcriptomic analysis of one of these isolates, the Spanish strain HBSQ001 in order to investigate gene transcription under light and dark conditions...
  2. pmc Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi
    Ana Belén Martín-Cuadrado
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, Apartado 18, San Juan de Alicante, Alicante, Spain
    BMC Genomics 16:603. 2015
    ..walsbyi enriched metagenomic fosmid library and recovered seven novel version of its cell-wall associated genomic island. The fosmid inserts were sequenced and analysed...
  3. pmc RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages
    Nikole E Kimes
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Apartado 18, San Juan, Alicante, 03550, Spain
    BMC Genomics 15:938. 2014
    ..In this study, we investigate the transcriptional response of these two strains to varying growth conditions in order to investigate differences in their ability to adapt to varying environmental parameters...
  4. pmc The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity
    Henk Bolhuis
    Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, The Netherlands
    BMC Genomics 7:169. 2006
    ..walsbyi has specialized into its narrow and hostile ecological niche and found ways to cope with the desiccation stress...
  5. pmc Evolution of rhodopsin ion pumps in haloarchaea
    Adrian K Sharma
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    BMC Evol Biol 7:79. 2007
    ..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...
  6. pmc Micro-Mar: a database for dynamic representation of marine microbial biodiversity
    Ravindra Pushker
    Evolutionary Genomics Group, Universidad Miguel Hernandez, Apartado 18, 03550 San Juan de Alicante, Alicante, Spain
    BMC Bioinformatics 6:222. 2005
    ..However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes...
  7. ncbi request reprint Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern
    Susana Benlloch
    Division de Microbiologia, Universidad Miguel Hernandez, Alicante, Spain
    Environ Microbiol 4:349-60. 2002
    ..Both clusters, however, showed a considerable degree of microdiversity. The meaning of such microdiversity remains to be determined...
  8. ncbi request reprint Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea
    Arantxa Lopez-Lopez
    Division de Microbiologia, Universidad Miguel Hernandez, Campus de San Juan, 03550 San Juan de Alicante, Spain
    Environ Microbiol 7:649-59. 2005
    ..The results indicate the existence of both lineages of global distribution and ecotypes adapted to specific conditions such as deep or more diluted (the Black Sea) waters...
  9. doi request reprint Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter
    Elena Ivars-Martínez
    Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Alicante, Spain
    ISME J 2:1194-212. 2008
    ..The genomic data are also consistent with a picture of incipient speciation driven by niche specialization...
  10. pmc Comparative genomics of gene-family size in closely related bacteria
    Ravindra Pushker
    Evolutionary Genomics Group, Universidad Miguel Hernandez, Campus de San Juan, Apartado 18, 03550 San Juan de Alicante, Alicante, Spain
    Genome Biol 5:R27. 2004
    ..Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear...
  11. doi request reprint Intra- and intergenomic variation of ribosomal RNA operons in concurrent Alteromonas macleodii strains
    Mario Lopez-Perez
    Division de Microbiologia, Universidad Miguel Hernandez, San Juan, Alicante, Spain
    Microb Ecol 65:720-30. 2013
    ..These findings highlight the potential of rRNA fingerprinting methods to misrepresent species diversity while simultaneously failing to recognize the ecological significance of individual strains...
  12. ncbi request reprint Diversity of bacteria and Archaea in sulphate-reducing enrichment cultures inoculated from serial dilution of Zostera noltii rhizosphere samples
    Ana Cifuentes
    Division de Microbiologia, Depart de Producción Vegetal y Microbiología, Campus de San Juan, Universidad Miguel Hernandez, San Juan de Alicante, Spain
    Environ Microbiol 5:754-64. 2003
    ..Surprisingly, a 16S rDNA sequence corresponding to an archaeon, i.e. a non-extremophile Crenoarchaeota, was retrieved from several of the SRB enrichment cultures even after subsequent transfers...
  13. pmc Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics
    Alex Mira
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Apartado 18, San Juan 03550, Alicante, Spain
    BMC Evol Biol 4:50. 2004
    ..Taking advantage of the recent completion of the Fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of Fusobacterium genes by phylogenetic analysis and comparative genomics tools...
  14. ncbi request reprint Thalassospira lucentensis gen. nov., sp. nov., a new marine member of the alpha-Proteobacteria
    Arantxa Lopez-Lopez
    Division de Microbiologia, Universidad Miguel Hernandez, San Juan de Alicante, Spain
    Int J Syst Evol Microbiol 52:1277-83. 2002
    ..This report describes the classification of strain QMT2T (= DSM 14000T = CECT 5390T) as a new genus and species, Thalassospira lucentensis gen. nov, sp. nov., in the family Rhodospirillaceae...
  15. pmc Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber
    Lejla Pasic
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Apartado 18, San Juan 03550, Alicante, Spain
    BMC Genomics 10:570. 2009
    ..This kind of analysis reveals the presence of metagenomic islands, i.e. highly variable regions among the different lineages in the population...
  16. ncbi request reprint Prevalence and microdiversity of Alteromonas macleodii-like microorganisms in different oceanic regions
    Jesús García-Martínez
    Division de Microbiologia, Universidad Miguel Hernandez, Campus de San Juan, 03550 Alicante, Spain
    Environ Microbiol 4:42-50. 2002
    ....
  17. ncbi request reprint Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea
    Milagros Zaballos
    Division de Microbiologia and Evolutionary Genomics Group, Universidad Miguel Hernandez, San Juan de Alicante, Spain
    FEMS Microbiol Ecol 56:389-405. 2006
    ..Depth was also an important factor and, although both deep-water samples had overall similarities, there were important differences that could be due to the warmer waters at depth of the Mediterranean Sea...
  18. ncbi request reprint Molecular characterization of a Spanish isolate of Mycobacterium malmoense
    Montserrat Ruiz
    Servicio de Microbiologia, Hospital General Universitario de Elche, Alicante, Spain
    Res Microbiol 153:33-6. 2002
    ..Molecular techniques facilitate a rapid diagnosis and enable a better understanding of the epidemiology of this microorganism...
  19. doi request reprint Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing
    Rohit Ghai
    Departmento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernandez, Apartado 18 San Juan de Alicante, Alicante, Spain
    ISME J 4:1154-66. 2010
    ..marinus subsp. pastoris, thus unexpectedly providing a feasible method to obtain large genomic fragments from other less prevalent members of this community...
  20. doi request reprint Explaining microbial population genomics through phage predation
    Francisco Rodriguez-Valera
    Departmento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Spain
    Nat Rev Microbiol 7:828-36. 2009
    ..Periodic selection and phage predation dynamics are not mutually exclusive; we compare their predictions to shed light on the ecological circumstances under which each type of dynamics could predominate...
  21. pmc Complete genome sequence of the copiotrophic marine bacterium Alteromonas macleodii strain ATCC 27126T
    Aitor Gonzaga
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Apartado 18, San Juan, Alicante, Spain
    J Bacteriol 194:6998. 2012
    ..The genome of Alteromonas macleodii strain ATCC 27126(T) has been resequenced and closed into a single contig. We describe here the genome of this important and globally distributed marine bacterium...
  22. pmc Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species
    Boris A Legault
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Apartado 18, San Juan 03550, Alicante, Spain
    BMC Genomics 7:171. 2006
    ..Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present...
  23. pmc CO dehydrogenase genes found in metagenomic fosmid clones from the deep mediterranean sea
    Ana Belén Martín-Cuadrado
    Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Spain
    Appl Environ Microbiol 75:7436-44. 2009
    ..The identities of the microbes that carry out these processes were not established, but they seem to be representatives of either Bacteroidetes or Chloroflexi...
  24. pmc Reconstruction of novel cyanobacterial siphovirus genomes from Mediterranean metagenomic fosmids
    Carolina Megumi Mizuno
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Alicante, Spain
    Appl Environ Microbiol 79:688-95. 2013
    ..This suggests that, as more siphoviral genomes become available, we will be better able to assess the abundance and influence of this diverse and polyphyletic group in the marine habitat...
  25. pmc A hybrid NRPS-PKS gene cluster related to the bleomycin family of antitumor antibiotics in Alteromonas macleodii strains
    Carolina Megumi Mizuno
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Alicante, Spain
    PLoS ONE 8:e76021. 2013
    ..Such sequence-based approaches will be crucial to fully explore and analyze the diversity and potential of secondary metabolite production, especially from increasingly important sources like marine microbes. ..
  26. ncbi request reprint IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships
    Giuseppe D'Auria
    Evolutionary Genomics Group and Division de Microbiologia, Universidad Miguel Hernandez Campus de San Juan, 03550 San Juan de Alicante, Spain
    Bioinformatics 22:527-31. 2006
    ..On the other hand this mosaic of variability makes the ITS a sequence difficult to analyze and compare...
  27. doi request reprint Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions
    Ana Belén Martín-Cuadrado
    Division of Microbiology, Universidad Miguel Hernandez, Alicante, Spain
    ISME J 2:865-86. 2008
    ..These observations, along with variations in GC content, led us to hypothesize that the two groups of organisms have fundamentally different lifestyles...
  28. ncbi request reprint Detection and identification of bacterial DNA in patients with cirrhosis and culture-negative, nonneutrocytic ascites
    Jose Such
    Unidad Hepática, Hospital General Universitario, Universidad Miguel Hernandez, Campus de San Juan, San Juan de Alicante, c Pintor Baeza s n, 03010 Alicante, Spain
    Hepatology 36:135-41. 2002
    ..In conclusion, we have detected bactDNA in serum and AF in 32% of all patients studied, and this likely represents single clone episodes of translocation and systemic seeding. E. coli is the most frequently identified bacteria...
  29. ncbi request reprint Sequence diversity of the internal transcribed spacer (ITS) region of the rRNA operons among different serogroups of Legionella pneumophila isolates
    Sara Perez-Luz
    Labaqua S A, and División de Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Spain
    Syst Appl Microbiol 25:212-9. 2002
    ..Two of the 16S-23S rRNA ITS presented a tRNA Ala and the third one a tRNA Ile. Nevertheless, the variability expected in this region of the operon was not found and the rest of the ITS contained only punctual mutations...
  30. doi request reprint Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC
    Rohit Ghai
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, Apartado 18, San Juan de Alicante, Alicante, Spain Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin Madison, Madison, WI 53706, USA
    Environ Microbiol Rep 4:29-35. 2012
    ....
  31. ncbi request reprint Environmental genomics, the big picture?
    Francisco Rodriguez-Valera
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Campus de San Juan, 03550 San Juan de Alicante, Spain
    FEMS Microbiol Lett 231:153-8. 2004
    ..Such a tool could be just the right way to complement "organismal genomics". Its potential to advance our understanding of microbial ecology and prokaryotic diversity and evolution is discussed...
  32. ncbi request reprint The Neolithic revolution of bacterial genomes
    Alex Mira
    Evolutionary Genomics Group, Division of Microbiology, Universidad Miguel Hernandez, San Juan 03550, Alicante, Spain
    Trends Microbiol 14:200-6. 2006
    ..These genomic changes are absent in related species that are not specialized in humans...
  33. pmc Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii
    Sergio G Bartual
    Division de Microbiologia and Evolutionary Genomics Group, Campus de San Juan, Universidad Miguel Hernandez, San Juan de Alicante, Spain
    J Clin Microbiol 43:4382-90. 2005
    ..The MLST scheme provides a high level of resolution and an excellent tool for studying the population structure and long-term epidemiology of A. baumannii...
  34. ncbi request reprint Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis
    Elena Ivars-Martínez
    Division de Microbiologia, Universidad Miguel Hernandez, Campus de San Juan, 03550 Alicante, Spain
    Mol Ecol 17:4092-106. 2008
    ..It can thus achieve intraspecific identification to the level of genotypes and, by comparison with relevant environmental data, ecotypes...
  35. pmc Networking in microbes: conjugative elements and plasmids in the genus Alteromonas
    Mario Lopez-Perez
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Apartado 18, San Juan, 03550, Alicante, Spain
    BMC Genomics 18:36. 2017
    ..In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time...
  36. doi request reprint Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics.
    Carolina Megumi Mizuno
    Evolutionary Genomics Group, Departamento de Producci n Vegetal y Microbiolog a, Universidad Miguel Hern ndez, San Juan de Alicante, Alicante, Spain
    MBio 6:. 2015
    ..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...
  37. doi request reprint Flexible genomic islands as drivers of genome evolution
    Francisco Rodriguez-Valera
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, 03550 Alicante, Spain Electronic address
    Curr Opin Microbiol 31:154-60. 2016
    ..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. ..
  38. pmc Genomes of Alteromonas australica, a world apart
    Mario Lopez-Perez
    Division de Microbiologia, Evolutionary Genomics Group, Universidad Miguel Hernandez, Apartado 18, San Juan, 03550 Alicante, Spain
    BMC Genomics 15:483. 2014
    ..australica DE170 was isolated in the South Adriatic (Mediterranean) at 1000 m depth while A. australica H17T was isolated from a sea water sample collected in St Kilda Beach, Tasman Sea...
  39. pmc Genomes of "Spiribacter", a streamlined, successful halophilic bacterium
    Mario Lopez-Perez
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Apartado 18, San Juan 03550, Alicante, Spain
    BMC Genomics 14:787. 2013
    ..Two strains belonging to this group have been isolated from saltern ponds of intermediate salinity in two Spanish salterns and were named "Spiribacter"...
  40. pmc Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses
    Inmaculada Garcia-Heredia
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Alicante, Spain
    PLoS ONE 7:e33802. 2012
    ..Many environmental viruses belong to unknown groups or prey on uncultured and little known cellular lineages, and hence might not be present in databases...
  41. pmc Expanding the marine virosphere using metagenomics
    Carolina Megumi Mizuno
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Alicante, Spain
    PLoS Genet 9:e1003987. 2013
    ..The availability of many genomes from the same sample allows a direct approach to viral population genomics confirming the remarkable mosaicism of phage genomes. ..
  42. pmc Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria
    Rohit Ghai
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, 03550, Alicante, Spain
    Sci Rep 3:2471. 2013
    ..Their geographic distribution mirrors that of picocyanobacteria and there appears to be an association between these microbial groups. A new sub-class, 'Candidatus Actinomarinidae' is proposed to designate these microbes...
  43. pmc Genomic diversity of "deep ecotype" Alteromonas macleodii isolates: evidence for Pan-Mediterranean clonal frames
    Mario Lopez-Perez
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Alicante, Spain
    Genome Biol Evol 5:1220-32. 2013
    ..Although this type was more conserved within each CF, we found examples of recombination among distantly related CFs including English Channel and Mediterranean isolates...
  44. pmc Polyclonality of concurrent natural populations of Alteromonas macleodii
    Aitor Gonzaga
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Alicante, Spain
    Genome Biol Evol 4:1360-74. 2012
    ..The results indicate that this natural A. macleodii population has multiple clones with a potential for different phage susceptibility and exploitation of resources, within a seemingly unstructured habitat...
  45. pmc Metagenomics of the deep Mediterranean, a warm bathypelagic habitat
    Ana Belen Martin Cuadrado
    Division de Microbiologia, Universidad Miguel Hernandez, San Juan de Alicante, Spain
    PLoS ONE 2:e914. 2007
    ..Most marine metagenomic analyses have been nearly exclusively devoted to photic waters...
  46. pmc Metagenomics of the water column in the pristine upper course of the Amazon river
    Rohit Ghai
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Alicante, Spain
    PLoS ONE 6:e23785. 2011
    ..In particular, these river microbes appear to be specialized in taking up and mineralizing allochthonous carbon derived from plant material...
  47. pmc Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph
    Mario Lopez-Perez
    Division de Microbiologia, Universidad Miguel Hernandez, San Juan 03550, Alicante, Spain
    Sci Rep 2:696. 2012
    ..The finding of CRISPR protospacers of AltDE in a lysogenic phage in the Atlantic (English Channel) isolate illustrates a flow of genetic material among these clades and a remarkably wide distribution of this phage...
  48. pmc Metagenomes of Mediterranean coastal lagoons
    Rohit Ghai
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Alicante, Spain
    Sci Rep 2:490. 2012
    ....
  49. pmc New abundant microbial groups in aquatic hypersaline environments
    Rohit Ghai
    Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernádez, San Juan de Alicante, Alicante, Spain
    Sci Rep 1:135. 2011
    ..These discoveries reveal the combined power of an unbiased metagenomic and single cell genomic approach...
  50. ncbi request reprint Approaches to prokaryotic biodiversity: a population genetics perspective
    Francisco Rodriguez-Valera
    Division de Microbiologia, Universidad Miguel Hernandez, Campus de San Juan, 03550 Alicante, Spain
    Environ Microbiol 4:628-33. 2002
    ....
  51. ncbi request reprint Genomic plasticity in prokaryotes: the case of the square haloarchaeon
    Sara Cuadros-Orellana
    Evolutionary Genomics Group, Division of Microbiology, Universidad Miguel Hernandez, Alicante, Spain
    ISME J 1:235-45. 2007
    ..Rather than containing different genes it consisted of homologs with low similarity. This variation might reflect a phage evasion strategy...