Ramon Rosselló-Móra

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

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Publications (148)517.19 Total impact

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    ABSTRACT: Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes from type. A workshop was organized with broad representation from the bacterial taxonomic community to review the proposal, the GenBank Microbial Genomic Taxonomy Workshop, Bethesda MD, May 12–13, 2015.
    No preview · Article · Dec 2016 · Standards in Genomic Sciences
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    ABSTRACT: Two halophilic archaea, designated strains WSM-64(T) and WSM-66, were isolated from a sample taken from a borehole in the currently unexploited Barycz mining area belonging to the "Wieliczka" Salt Mine Company, in Poland. Strains are red pigmented and form non-motile cocci that stain Gram-negative. Strains WSM-64(T) and WSM-66 showed optimum growth at 40°C, in 20% NaCl and at pH 6.5-7.5. The strains were facultative anaerobes. The major polar lipids of the two strains were phosphatidylglycerol (PG2), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulfated diglycosyl diether (S-DGD). Menaquinone MK-8 was the major respiratory quinone. The DNA G+C content of strain WSM-64(T) was 61.2mol% by HPLC method; 61.0mol% by genome sequencing. Analysis of the almost complete 16S rRNA gene sequence indicated that the strains WSM-64(T) and WSM-66 (99.7% identity) represented a member of the genus Halorhabdus in the family Halobacteriaceae. Both strains formed a distinct cluster and were most closely related to Halorhabdus tiamatea SARL4B(T) and Halorhabdus utahensis AX-2(T) (DSM 12940(T)) (95.4% and 95.6%, respectively). ANI values of WSM-64(T) with the closest relative type strains were <78.5%. Based on 16S rRNA gene sequence and whole genome analyses, physiological and biochemical characteristics we describe a new species represented by strain WSM-64(T) (=DSM 29498(T) =CECT 8673(T)) for which we propose the name Halorhabdus rudnickae sp. nov.
    Full-text · Article · Dec 2015 · Systematic and Applied Microbiology
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    Michael Richter · Ramon Rosselló-Móra · F. O. Glo ckner · Jörg Peplies
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    ABSTRACT: JSpecies Web Server (JSpeciesWS) is a user-friendly online service for in silico calculating the extent of identity between two genomes, a parameter routinely used in the process of polyphasic microbial species circumscription. The service measures the average nucleotide identity (ANI) based on BLAST+ (ANIb) and MUMmer (ANIm), as well as correlation indexes of tetra-nucleotide signatures (Tetra). In addition, it provides a Tetra Correlation Search function, which allows to rapidly compare selected genomes against a continuously updated reference database with currently about 32 000 published whole and draft genome sequences. For comparison, own genomes can be uploaded and references can be selected from the JSpeciesWS reference database. The service indicates whether two genomes share genomic identities above or below the species embracing thresholds, and serves as a fast way to allocate unknown genomes in the frame of the hitherto sequenced species. Availability and implementation: JSpeciesWS is available at http://jspecies.ribohost.com/jspeciesws. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: mrichter{at}ribocon.com
    Full-text · Article · Nov 2015 · Bioinformatics
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    ABSTRACT: Hypersaline environments are considered one of the most extreme habitats on earth and microorganisms have developed diverse molecular mechanisms of adaptation to withstand these conditions. The present study was aimed at identifying novel genes from the microbial communities of a moderate-salinity rhizosphere and brine from the Es Trenc saltern (Mallorca, Spain), which could confer increased salt resistance to Escherichia coli. The microbial diversity assessed by pyrosequencing of 16S rRNA gene libraries revealed the presence of communities that are typical in such environments and the remarkable presence of three bacterial groups never revealed as major components of salt brines. Metagenomic libraries from brine and rhizosphere samples, were transferred to the osmosensitive strain E. coli MKH13, and screened for salt resistance. Eleven genes that conferred salt resistance were identified, some encoding for well-known proteins previously related to osmoadaptation such as a glycerol transporter and a proton pump, whereas others encoded proteins not previously related to this function in microorganisms such as DNA/RNA helicases, an endonuclease III (Nth) and hypothetical proteins of unknown function. Furthermore, four of the retrieved genes were cloned and expressed in Bacillus subtilis and they also conferred salt resistance to this bacterium, broadening the spectrum of bacterial species in which these genes can function. This is the first report of salt resistance genes recovered from metagenomes of a hypersaline environment.
    Full-text · Article · Nov 2015 · Frontiers in Microbiology
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    ABSTRACT: The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature.
    Full-text · Article · Nov 2015 · International Journal of Systematic and Evolutionary Microbiology
  • Josefa Antón · Rudolf Amann · Ramon Rosselló-Mora

    No preview · Chapter · Sep 2015
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    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.
    No preview · Article · Jul 2015 · Systematic and Applied Microbiology
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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.
    No preview · Article · Jul 2015 · Systematic and Applied Microbiology
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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.
    Full-text · Article · Jun 2015 · Systematic and Applied Microbiology
  • Karl-Heinz Schleifer · Rudolf Amann · Ramon Rosselló-Móra

    No preview · Article · Jun 2015 · Systematic and Applied Microbiology
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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.
    Full-text · Article · Apr 2015 · Environmental Science and Pollution Research
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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.
    No preview · Article · Feb 2015 · Systematic and Applied Microbiology
  • 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.
    No preview · Article · Feb 2015 · Systematic and Applied Microbiology
  • 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.
    No preview · Article · Jan 2015 · Systematic and Applied Microbiology
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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.
    Full-text · Article · Jan 2015 · Systematic and Applied Microbiology
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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.
    Full-text · Article · Aug 2014 · Nature Reviews Microbiology
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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.
    Full-text · Article · Aug 2014 · PLoS Biology
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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.
    Full-text · Article · Aug 2014 · PLoS Biology
  • Ruben Moraga · Alexander Galán · Ramón Rossello-Mora · Rubén Araya · Jorge Valdés
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    ABSTRACT: Conventional denitrification and anaerobic ammonium oxidation (anammox) contributes to nitrogen loss in oxygen-deficient systems, thereby influencing many aspects of ecosystem function and global biogeochemistry. Mejillones Bay, northern Chile, presents ideal conditions to study nitrogen removal processes, because it is inserted in a coastal upwelling system, its sediments have anoxia and hypoxia conditions and under the influence of the Oxygen Minimum Zone (OMZ), unknown processes that occur there and what are the microbial communities responsible for their removal. Microbial communities associated with coastal sediments of Mejillones Bay were studied by denaturing gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH), by incubation experiments with 15N isotope tracers were studied nitrogen loss processes operating in these sediments. DGGE analysis showed high bacterial diversity, certain redundant phylotypes and differences in community structure given by the depth; this reflects the microbial community adaptations to environmental conditions. A large fraction (up to 70%) of DAPI-stained cells hybridized with the bacterial probes. Nearly 52-90% of the cell could be further identified to know phyla. Members of the Cytophaga-Flavobacterium cluster were most abundant in the sediments (13-26%), followed by Proteobacteria. Isotopic tracer experiments for the sediments studied indicated that nitrogen loss processes that predominated were performed by denitrifying communities (43.31-111.20 M d-1) was not possible to detect anammox in the area and not anammox bacteria were detected.
    No preview · Article · Aug 2014 · Revista de Biologia Marina Y Oceanografia
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    Rubén Moraga · Alexander Galan · Ramón Rossello-Mora · Rubén Araya · Jorge Valdés

    Full-text · Article · Aug 2014 · Revista de Biologia Marina Y Oceanografia

Publication Stats

8k Citations
517.19 Total Impact Points

Institutions

  • 2011-2015
    • Mediterranean Institute for Advanced Studies (IMEDEA)
      • Department of Ecology and Marine Resources
      Esporles, Balearic Islands, Spain
  • 1994-2014
    • University of the Balearic Islands
      • Departamento de Biología
      Palma, 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
  • 1995-2006
    • Technische Universität München
      • Chair of Technical Microbiology
      München, Bavaria, Germany
  • 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 Alicante
      • Phisiology, Genetics and Microbiology
      Alicante, Valencia, Spain
  • 1999
    • Max Planck Institute for Marine Microbiology
      Bremen, Bremen, Germany
  • 1995-1996
    • Deutsches Herzzentrum München
      München, Bavaria, Germany