Ramon Rosselló-Móra

Mediterranean Institute for Advanced Studies (IMEDEA), Esporles, Balearic Islands, Spain

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Publications (132)518.01 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Next generation sequencing approaches allow the retrieval of several orders of magnitude larger numbers of amplified single sequences in 16S rRNA diversity surveys than classical methods. However, the sequences are only partial and thus lack sufficient resolution for a reliable identification. The OPU approach used here, based on a tandem combination of high quality 454 sequences (mean >500nuc) applying strict OTU thresholds, and phylogenetic inference based on parsimony additions to preexisting trees, seemed to improve the identification yields at the species and genus levels. A total of thirteen biopsies of Crohn-diagnosed patients (CD) and seven healthy controls (HC) were studied. In most of the cases (73%), sequences were affiliated to known species or genera and distinct microbial patterns could be distinguished among the CD subjects, with a common depletion of Clostridia and either an increased presence of Bacteroidetes (CD1) or an anomalous overrepresentation of Proteobacteria (CD2). Faecalibacterium prausnitzii presence was undetectable in CD, whereas Bacteroides vulgatus-B. dorei characterized HC and some CD groups. Altogether, the results showed that a microbial composition with predominance of Clostridia followed by Bacteroidetes, with F. prausnitzii and B. vulgatus-B. dorei as major key bacteria, characterized what could be considered a balanced structure in HC. The depletion of Clostridia seemed to be a common trait in CD. Copyright © 2015 Elsevier GmbH. All rights reserved.
    Systematic and Applied Microbiology 07/2015; DOI:10.1016/j.syapm.2015.06.008 · 3.31 Impact Factor
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    ABSTRACT: The microbiota associated to the gastric cavity of four exemplars of the jellyfish Cotylorhiza tuberculata has been studied by means of cultured-dependent and -independent methods. The pyrosequencing approach rendered a very reduced diversity of Bacteria with four major groups shared by the four exemplars that made up to 95% of the total diversity. The culturing approach recovered low abundant organisms and some of them also detected by the pyrosequencing approach. The major key organisms were related to the genera Spiroplasma, Thalassospira, Tenacibaculum (from the pyrosequencing data), and Vibrio (from the cultivable fraction). Altogether the results indicate that C. tuberculata harbors an associated microbiota of very reduced diversity. On the other hand, some of the major key players may be potential pathogens and the host may serve as dispersal mechanism. Copyright © 2015 Elsevier GmbH. All rights reserved.
    Systematic and Applied Microbiology 07/2015; DOI:10.1016/j.syapm.2015.07.001 · 3.31 Impact Factor
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    ABSTRACT: Halophytes accumulate large amounts of salt in their tissues, and thus are susceptible to colonization by halotolerant and halophilic microorganisms that might be relevant for the growth and development of the plant. Here, the study of 814 cultured strains and 14,189 sequences obtained by 454 pyrosequencing were combined in order to evaluate the presence, abundance and diversity of halophilic, endophytic and epiphytic microorganisms in the phytosphere of leaves of members of the subfamily Salicornioideae from five locations in Spain and Chile. Cultures were screened by the tandem approach of MALDI-TOF/MS and 16S rRNA gene sequencing. In addition, differential centrifugation was used to enrich endophytes for further DNA isolation, 16S rRNA gene amplification and 454 pyrosequencing. Culturable and non-culturable data showed strong agreement with a predominance of Proteobacteria, Firmicutes and Actinobacteria. The most abundant isolates corresponded to close relatives of the species Chromohalobacter canadensis and Salinicola halophilus that comprised nearly 60% of all isolates and were present in all plants. Up to 66% of the diversity retrieved by pyrosequencing could be brought into pure cultures and the community structures were highly dependent on the compartment where the microorganisms thrived (plant surface or internal tissues). Copyright © 2015 Elsevier GmbH. All rights reserved.
    Systematic and Applied Microbiology 06/2015; DOI:10.1016/j.syapm.2015.05.004 · 3.31 Impact Factor
  • Karl-Heinz Schleifer · Rudolf Amann · Ramon Rosselló-Móra
    Systematic and Applied Microbiology 06/2015; 38(4):207-8. DOI:10.1016/j.syapm.2015.05.002 · 3.31 Impact Factor
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    ABSTRACT: The accident of the Prestige oil tanker in 2002 contaminated approximately 900 km of the coastline along the northern Spanish shore, as well as parts of Portugal and France coast, with a mixture of heavy crude oil consisting of polycyclic aromatic hydrocarbons, alkanes, asphaltenes and resins. The capacity of the autochthonous bacterial communities to respond to the oil spill was assessed indirectly by determining the hydrocarbon profiles of weathered oil samples collected along the shore, as well as through isotope ratios of seawater-dissolved CO2, and directly by analyses of denaturing gradient gel electrophoresis fingerprints and 16S rRNA gene libraries. Overall, the results evidenced biodegradation of crude oil components mediated by natural bacterial communities, with a bias towards lighter and less substituted compounds. The changes observed in the Proteobacteria, the most abundant phylum in marine sediments, were related to the metabolic profiles of the sediment. The presence of crude oil in the supratidal and intertidal zones increased the abundance of Alpha- and Gammaproteobacteria, dominated by the groups Sphingomonadaceae, Rhodobacteraceae and Chromatiales, whilst Gamma- and Deltaproteobacteria were more relevant in subtidal zones. The phylum Actinobacteria, and particularly the genus Rhodococcus, was a key player in the microbial response to the spill, especially in the degradation of the alkane fraction. The addition of inorganic fertilizers enhanced total biodegradation rates, suggesting that, in these environments, nutrients were insufficient to support significant growth after the huge increase in carbon sources, as evidenced in other spills. The presence of bacterial communities able to respond to a massive oil input in this area was consistent with the important history of pollution of the region by crude oil.
    Environmental Science and Pollution Research 04/2015; DOI:10.1007/s11356-015-4458-y · 2.76 Impact Factor
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    ABSTRACT: The culturable fraction of aerobic, heterotrophic and extremely halophilic microbiota retrieved from sediment and brine samples of eight sampling sites in the Mediterranean, Canary Islands and Chile was studied by means of a tandem approach combining large-scale cultivation, MALDI-TOF MS targeting whole cell biomass, and phylogenetic reconstruction based on 16S rRNA gene analysis. The approach allowed the identification of more than 4200 strains and a comparison between different sampling sites. The results indicated that the method constituted an excellent tool for the discovery of taxonomic novelty. Four new genera and nine new species could be identified within the archaeal family Halobacteriaceae, as well as one new bacterial species, and a representative of Salinibacter ruber phylotype II, a group that had been refractory to isolation for the last fifteen years. Altogether, the results indicated that in order to provide better yields for the retrieval of novel taxa from the environment, performance of non-redundant environment sampling is recommended together with the screening of large sets of strains. Copyright © 2015 Elsevier GmbH. All rights reserved.
    Systematic and Applied Microbiology 02/2015; 38(4). DOI:10.1016/j.syapm.2015.02.002 · 3.31 Impact Factor
  • Ramon Rosselló-Móra · Rudolf Amann
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    ABSTRACT: Species is the basic unit of biological diversity. However, among the different microbiological disciplines there is an important degree of disagreement as to what this unit may be. In this minireview, we argue that the main point of disagreement is the definition (i.e. the way species are circumscribed by means of observable characters) rather than the concept (i.e. the idea of what a species may be as a unit of biodiversity, the meaning of the patterns of recurrence observed in nature, and the why of their existence). Taxonomists have defined species by means of genetic and expressed characters that ensure the members of the unit are monophyletic, and exhibit a large degree of genomic and phenotypic coherence. The new technologies allowing high-throughput data acquisition are expected to improve future classifications significantly and will lead to database-based taxonomy centered on portable and interactive data. Future species descriptions of Bacteria and Archaea should include a high quality genome sequence of at least the type strain as an obligatory requirement, just as today an almost full-length 16S rRNA gene sequence must be provided. Serious efforts are needed in order to re-evaluate the major guidelines for standard descriptions. Copyright © 2015 Elsevier GmbH. All rights reserved.
    Systematic and Applied Microbiology 02/2015; 38(4). DOI:10.1016/j.syapm.2015.02.001 · 3.31 Impact Factor
  • Konstantinos T. Konstantinidis · Ramon Rosselló-Móra
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    ABSTRACT: Microbial taxonomists have generally been reluctant to accept the valid publication of names of uncultured taxa given that only pure cultures allow for a thorough description of the genealogy, genetics and phenotype of the putative taxa to be classified. The classification of conspicuous uncultured organisms has been considered into the Candidatus provisional status, but this is only possible with organisms for which it is possible to retrieve basic data on phylogeny, morphology, ecology and some metabolic traits that unequivocally identify them. The current developments on modern sequencing techniques, and especially metagenomics, allow the recognition of discrete populations of DNA sequences in environmental samples, which can be considered to belong to individual closely related populations that may be identified as members of yet-to-be described species. The recognition of such populations of (meta)genomes allow the retrieval of valuable taxonomic information, i.e. genealogy, genome, phenotypic coherence with other populations, and ecological relevant traits. Such traits may be included in the Candidatus proposals of environmentally occurring, yet uncultured species not exhibiting exceptional morphologies, phenotypes or ecological relevancies.
    Systematic and Applied Microbiology 01/2015; 38(4). DOI:10.1016/j.syapm.2015.01.001 · 3.31 Impact Factor
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    ABSTRACT: The family Chlamydiaceae (order Chlamydiales, phylum Chlamydiae) comprises important, obligate intracellular bacterial pathogens of humans and animals. Subdivision of the family into the two genera Chlamydia and Chlamydophila has been discussed controversially during the past decade. Here, we have revisited the current classification in the light of recent genomic data and in the context of the unique biological properties of these microorganisms. We conclude that neither generally used 16S rRNA sequence identity cut-off values nor parameters based on genomic similarity consistently separate the two genera. Notably, no easily recognizable phenotype such as host preference or tissue tropism is available that would support a subdivision. In addition, the genus Chlamydophila is currently not well accepted and not used by a majority of research groups in the field. Therefore, we propose the classification of all 11 currently recognized Chlamydiaceae species in a single genus, the genus Chlamydia. Finally, we provide emended descriptions of the family Chlamydiaceae, the genus Chlamydia, as well as the species Chlamydia abortus, Chlamydia caviae and Chlamydia felis.
    Systematic and Applied Microbiology 01/2015; 38(2). DOI:10.1016/j.syapm.2014.12.004 · 3.31 Impact Factor
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    ABSTRACT: Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.
    Nature Reviews Microbiology 08/2014; 12(9):635-45. DOI:10.1038/nrmicro3330 · 23.32 Impact Factor
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    ABSTRACT: Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet’s most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently,11,000). This effort will provide an unprecedented level of coverage of our planet’s genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
    PLoS Biology 08/2014; 12(8):e1001920. DOI:10.1371/journal.pbio.1001920.t001 · 12.69 Impact Factor
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    [Show abstract] [Hide abstract]
    ABSTRACT: Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently ∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
    PLoS Biology 08/2014; 12(8):e1001920. DOI:10.1371/journal.pbio.1001920 · 11.77 Impact Factor
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    Edited by Nationale Akademie der Wissenschaften Leopoldina, 06/2014; Deutsche Akademie der Naturforscher Leopoldina e.V. Nationale Akademie der Wissenschaften., ISBN: 978-3-8047-3281-0
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    ABSTRACT: The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.
    The ISME Journal 06/2014; 9(1). DOI:10.1038/ismej.2014.95 · 9.27 Impact Factor
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    Extremophile Bacteria, 06/2014: chapter Salinibacter ruber: the never ending microdiversity?;
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    ABSTRACT: The novel ciliate Platynematum salinarum (Scuticociliatia) was isolated only recently from a thalassohaline solar saltern pond (12%) in Portugal. Scanning electron microscopy showed numerous bacterial-shaped cells covering the complete surface of the ciliate. The rod-shaped epibionts were identified and characterized following the “Full-Cycle rRNA Approach”. The almost full-length 16S rRNA gene sequence was obtained using archaeal-specific primers and two species-specific probes were designed for fluorescence in situ hybridization. The 16S rRNA gene sequence of the epibiotic cells showed 87% sequence identity with the type strain sequence of the closest characterized species Halolamina pelagica. Phylogenetic reconstructions affiliated the novel organism to the genus Halolamina (Halobacteria, Archaea). Attempts to isolate the epibionts failed and, therefore, growth experiments incorporating the antibiotic anisomycin were conducted in order to investigate the potential symbiotic relationship between P. salinarum and the epibionts. The results suggested an obligate symbiosis between the two organisms and revealed the first symbiotic representative of the Halobacteria. Based on the phylogenetic analyses and growth experiments we propose the classification of this novel organism in a new genus, with the taxon name “Candidatus Haloectosymbiotes riaformosensis”.
    Systematic and Applied Microbiology 06/2014; 37(4). DOI:10.1016/j.syapm.2014.01.001 · 3.31 Impact Factor
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    Edited by Nationale Akademie der Wissenschaften Leopoldina, 06/2014; Deutsche Akademie der Naturforscher Leopoldina e.V. Nationale Akademie der Wissenschaften (German National Academy of Sciences)., ISBN: 978-3-8047-3291-9
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    ABSTRACT: Salinibacter ruber is an extremely halophilic bacterium of the Bacteroidetes phylum that thrives in hypersaline environments. This bacterium shares the environment, as well as many phenotypic traits, with extremely halphilic Archaea. The study of the wide collection of strains of S. ruber isolated from around the world has shown that the species is very homogeneous from a phylogenetic point of view although it shows a very wide genomic microdiversity. In this chapter, we provide stat-of-the art data on abundance, distribution, metabolomic and genomic microdiversity of S. ruber and discuss the contribution of recombination and lateral gene transfer to the shaping of this species.
    Halophiles: Genetics and Genomes, Edited by R. Thane Papke and Aharon Oren, 05/2014: chapter Salinibacter ruber: The Never Ending Microdiversity?; Caister Academic Press., ISBN: 978-1-908230-65-2
  • Luís França · Arantxa Lopéz-Lopéz · Ramon Rosselló-Móra · Milton S da Costa
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    ABSTRACT: The microbial abundance and diversity at source, after bottling, and through six months of storage of a commercial still natural mineral water were assessed by culture-dependent and -independent methods. The results revealed clear shifts of the dominant communities present in the three different stages. The borehole waters displayed low cell densities that increased 1.5 fold upon bottling and storage, reaching a maximum (6.2x10(8) cells.l(-1) ) within 15 days after bottling, but experienced a significant decrease in diversity. In all cases communities were largely dominated by Bacteria. The culturable heterotrophic community was characterized by recovering 3,626 isolates, which were primarily affiliated with the Alpha-, Beta- and Gammaproteobacteria. This study indicates that bottling and storage induce quantitative and qualitative changes in the microbial assemblages that seem to be similar as revealed by the two sample batches collected on two consecutive years. To our knowledge, this is the first study combining culture-independent with culture-dependent methods, and repeated tests, to reveal the microbial dynamics occurring from source to stored bottled water.
    Environmental Microbiology 02/2014; 17(3). DOI:10.1111/1462-2920.12430 · 6.24 Impact Factor
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    C Saro · M J Ranilla · A Cifuentes · R Rosselló-Mora · M D Carro
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    ABSTRACT: The aim of this study was to compare automated ribosomal intergenic spacer analysis (ARISA) and denaturing gradient gel electrophoresis (DGGE) techniques to assess bacterial diversity in the rumen of sheep. Sheep were fed two diets with 70% of either alfalfa hay or grass hay, and the solid (SOL) and liquid (LIQ) phases of the rumen were sampled immediately before feeding (0 h) and at 4 and 8 h post-feeding. Both techniques detected similar differences between forages, with alfalfa hay promoting greater (P < 0.05) bacterial diversity than grass hay. In contrast, whereas ARISA analysis showed a decrease (P < 0.05) of bacterial diversity in SOL at 4 h post-feeding compared with 0 and 8 h samplings, no variations (P > 0.05) over the post-feeding period were detected by DGGE. The ARISA technique showed lower (P < 0.05) bacterial diversity in SOL than in LIQ samples at 4 h post-feeding, but no differences (P > 0.05) in bacterial diversity between both rumen phases were detected by DGGE. Under the conditions of this study, the DGGE was not sensitive enough to detect some changes in ruminal bacterial communities, and therefore ARISA was considered more accurate for assessing bacterial diversity of ruminal samples. The results highlight the influence of the fingerprinting technique used to draw conclusions on factors affecting ruminal bacterial diversity.
    Journal of Animal Science 02/2014; 92(3). DOI:10.2527/jas.2013-7175 · 1.92 Impact Factor

Publication Stats

7k Citations
518.01 Total Impact Points

Institutions

  • 2011–2015
    • Mediterranean Institute for Advanced Studies (IMEDEA)
      • Department of Ecology and Marine Resources
      Esporles, Balearic Islands, Spain
  • 2006–2011
    • Justus-Liebig-Universität Gießen
      • Institute of Applied Microbiology
      Gieben, Hesse, Germany
  • 2008–2009
    • Catalan Institution for Research and Advanced Studies
      Barcino, Catalonia, Spain
  • 2004
    • Universidad de Salamanca
      • Department of Microbiology and Genetics
      Helmantica, Castille and León, Spain
  • 2003
    • University of Veterinary Medicine in Vienna
      • Institute of Bacteriology, Mycology and Hygiene
      Wien, Vienna, Austria
  • 2002
    • University of Vienna
      Wien, Vienna, Austria
    • University of Alicante
      • Phisiology, Genetics and Microbiology
      Alicante, Valencia, Spain
  • 1994–2001
    • University of the Balearic Islands
      • Departamento de Biología
      Palma, Balearic Islands, Spain
  • 1999
    • Max Planck Institute for Marine Microbiology
      Bremen, Bremen, Germany
  • 1995–1996
    • Deutsches Herzzentrum München
      München, Bavaria, Germany
    • University of Technology Munich
      • Chair of Technical Microbiology
      München, Bavaria, Germany