Javier Diéguez-Uribeondo

PhD Uppsala University
Vicedirector of Research
Spanish National Research Coun... · Real Jardín Botanico

Publications

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    Francisco Javier Galindo, Fernando Alonso, Javier Diéguez-Uribeondo
    Quercus. 08/2014; 74(342).
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    ABSTRACT: Aphanomyces astaci, the causal agent of the crayfish plague, has recently been confirmed to infect also freshwater-inhabiting crabs. We experimentally tested the resistance of freshwater shrimps, another important decapod group inhabiting freshwaters, to this pathogen. We exposed individuals of two Asian shrimp species, Macrobrachium dayanum and Neocaridina davidi, to zoospores of the pathogen strain isolated from Procambarus clarkii, a known A. astaci carrier likely to get into contact with shrimps. The shrimps were kept in separate vessels up to seven weeks; exuviae and randomly chosen individuals were sampled throughout the experiment. Shrimp bodies and exuviae were tested for A. astaci presence by a species-specific quantitative PCR. The results were compared with amounts of A. astaci DNA in an inert substrate to distinguish potential pathogen growth in live specimens from persisting spores or environmental DNA attached to their surface. In contrast to susceptible crayfish Astacus astacus, we did not observe mortality of shrimps. The amount of detected pathogen DNA was decreasing steadily in the inert substrate, but it was still detectable several weeks after zoospore addition, which should be considered in studies relying on molecular detection of A. astaci. Probably due to moulting, the amount of A. astaci DNA was decreasing in N. davidi even faster than in the inert substrate. In contrast, high pathogen DNA levels were detected in some non-moulting individuals of M. dayanum, suggesting that A. astaci growth may be possible in tissues of this species. Further experiments are needed to test for the potential of long-term A. astaci persistence in freshwater shrimp populations.
    Journal of Invertebrate Pathology 07/2014; 121:97-104. · 2.67 Impact Factor
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    Dataset: Figure S2
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    Dataset: Figure S1
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    J. Vladimir Sandoval-Sierra, María P. Martín, Javier Diéguez-Uribeondo
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    ABSTRACT: The lack of a robust taxonomy in the genus Saprolegnia (Oomycetes) is leading to the presence of incorrectly named isolates in culture collections and of an increasing number of misassigned named sequences in DNA databases. Accurate species delimitation is critical for most biological disciplines. A recently proposed approach to solve species delimitation (taxon diagnosis system) of difficult organisms is the definition of molecular operational taxonomic units (MOTUs) using molecular data. In this study, we have analyzed 961 sequences of internal transcribed spacer from main culture collection of Saprolegniales (461 sequences) and GenBank (500 sequences). For this purpose, we have used two phylogenetic analyses, i.e, Maximum Parsimony and Bayesian inference, and also a clustering optimization analysis using arbitrary options regarding the distance threshold values and the clustering algorithm. Thus, we have identified 29 DNA-based MOTUs in agreement with phylogenetic analyses of species. The molecular clusters support the validity of 18 species of Saprolegnia and identify 11 potential new species. Based on this system, we have listed a number of incorrectly named isolates from culture collections, misassigned species names to GenBank sequences, and type sequences for species. We conclude that GenBank represents the main source of errors for identifying species since it possesses a high number of misassigned sequences, and the presence of sequences with sequencing errors. The presented taxonomic diagnosis system might help setting the basis for a suitable identification of species in this economically important genus.
    Fungal Biology 07/2014; 118(7):559-578. · 2.08 Impact Factor
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    S. Rezinciuc, J.V. Sandoval-Sierra, J. Diéguez-Uribeondo
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    ABSTRACT: Some species of the genus Saprolegnia, such as Saprolegnia diclina and Saprolegnia ferax are responsible for devastating infections on salmonid eggs. Members of this group cause saprolegniasis, a disease resulting in considerable economic losses in aquaculture. Although both S. diclina and S. ferax have received much attention, the role of other Saprolegnia species in infecting fish eggs is less known. For this purpose, we have investigated the aetiology of chronic egg mortality events occurring in farmed brown trout, Salmo trutta. A total of 48 isolates were obtained from eggs with signs of infection as well as from water samples. A molecular analysis based on rnDNA internal transcribed spacer (ITS) operational taxonomic units indicated that the majority of the isolates correspond to Saprolegnia australis. All isolates of S. australis exhibited the same random amplified polymorphic DNA (RAPD) band patterns suggesting that a single strain is implicated in egg infections. The isolates followed Koch postulates using trout eggs and fry. Under standard concentrations of bronopol commonly used in farms, these isolates could grow, but not sporulate. However, both growth and sporulation were recovered when treatment was removed. This study shows that S. australis can infect and kill salmon eggs, and helps in defining oomycetes core pathogens.
    Fungal Biology 07/2014; 118(7):591-600. · 2.08 Impact Factor
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    ABSTRACT: DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    Database The Journal of Biological Databases and Curation 05/2014; · 4.20 Impact Factor
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    [Show abstract] [Hide abstract]
    ABSTRACT: DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    Database The Journal of Biological Databases and Curation 05/2014; · 4.20 Impact Factor
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    [Show abstract] [Hide abstract]
    ABSTRACT: DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    Database The Journal of Biological Databases and Curation 05/2014; · 4.20 Impact Factor
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    ABSTRACT: Animals and plants are increasingly suffering from diseases caused by fungi and oomycetes. These emerging pathogens are now recognized as a global threat to biodiversity and food security. Among oomycetes, Saprolegnia species cause significant declines in fish and amphibian populations. Fish eggs have an immature adaptive immune system and depend on nonspecific innate defences to ward off pathogens. Here, meta-taxonomic analyses revealed that Atlantic salmon eggs are home to diverse fungal, oomycete and bacterial communities. Although virulent Saprolegnia isolates were found in all salmon egg samples, a low incidence of Saprolegniosis was strongly correlated with a high richness and abundance of specific commensal Actinobacteria, with the genus Frondihabitans (Microbacteriaceae) effectively inhibiting attachment of Saprolegniato salmon eggs. These results highlight that fundamental insights into microbial landscapes of fish eggs may provide new sustainable means to mitigate emerging diseases.The ISME Journal advance online publication, 27 March 2014; doi:10.1038/ismej.2014.44.
    The ISME Journal 03/2014; · 8.95 Impact Factor
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    ABSTRACT: Aphanomyces astaci is an invasive pathogenic oomycete responsible for the crayfish plague, a disease that has devastated European freshwater crayfish. So far, five genotype groups of this pathogen have been identified by applying random amplified polymorphic DNA analysis on axenic cultures. To allow genotyping of A. astaci in host tissue samples, we have developed co-dominant microsatellite markers for this pathogen, tested them on pure cultures of all genotype groups, and subsequently evaluated their use on tissues of (1) natural A. astaci carriers, i.e, North American crayfish species, and (2) A. astaci-infected indigenous European species from crayfish plague outbreaks. Out of over 200 potential loci containing simple sequence repeat (SSR) motifs identified by 454 pyrosequencing of SSRenriched library, we tested 25 loci with highest number of repeats, and finally selected nine that allow unambiguous separation of all known genotype groups of A. astaci from axenic cultures. Using these markers, we were able to identify A. astaci strains from DNA isolates from infected crayfish tissues when crayfish had a moderate to high level of infection according to quantitative PCR analyses. The results support the hypothesis that different North American crayfish hosts carry different genotype groups, and confirm that various genotypes of the pathogen, including the one originally introduced to Europe in the 19th century, cause crayfish plague outbreaks in Central Europe. So far undocumented A. astaci genotype seems to have caused one of the analysed outbreaks from the Czech Republic. The newly developed culture-independent approach allowing direct genotyping of this pathogen in both axenic cultures and mixed genome samples opens new possibilities in studies of crayfish plague pathogen distribution, diversity and epidemiology.
    Veterinary Microbiology 02/2014; 170:317-324. · 3.13 Impact Factor
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    Javier Dieguez-Uribeondo, Lage Cerenius
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    ABSTRACT: Nascent fungal infections are currently considered as one of the main threats for biodiversity and ecosystem health, and have driven several animal species into critical risk of extinction. Sea turtles are one of the most endangered groups of animals and only seven species have survived to date. Here, we described two pathogenic species, i.e., Fusarium falciforme and Fusarium keratoplasticum, that are globally distributed in major turtle nesting areas for six sea turtle species and that are implicated in low hatch success. These two fungi possess key biological features that are similar to emerging pathogens leading to host extinction, e.g., high virulence, and a broad host range style of life. Their optimal growth temperature overlap with the optimal incubation temperature for eggs, and they are able to kill up to 90% of the embryos. Environmental forcing, e.g., tidal inundation and clay/silt content of nests, were correlated to disease development. Thus, these Fusarium species constitute a major threat to sea turtle nests, especially to those experiencing environmental stressors. These findings have serious implications for the survival of endangered sea turtle populations and the success of conservation programs worldwide.
    PLoS ONE 01/2014; 9(1):e85853. · 3.73 Impact Factor
  • Jose Vladimir Sandoval-Sierra, Fadua Latif, María P. Martín, Luis Zaror, Javier Diéguez-Uribeondo
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    ABSTRACT: The rapid increase in the aquaculture production of salmonids has been followed by a rise in several diseases. In particular, saprolegniasis can account for at least 10% of the annual economic loss in salmonids. In this study, we investigated the main Saprolegnia species involved in saprolegniosis of salmonids in Chile, and their association with specific developmental stages of the host fish. For this purpose, we studied 244 isolates of Saprolegnia-affected Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), and king salmon (Oncorhynchus tshawytscha) from the main salmon farming regions, using a recently developed identification strategy based on molecular taxonomical operational units. We found that the Saprolegnia species associated with diseased salmon were S. australis, S. delica, S. diclina, S. ferax, S. parasitica and two new Saprolegnia species observed during this study. In order to determine whether there were any specific species associations with different stages in the fish life cycle, we applied mosaic plots and correspondence analyses for categorical data. These analyses showed a strong association of S. parasitica with samples from the adult stage of the fish (χ2 = 196.29, p < 0.0001), while the species S. australis, S. diclina and Saprolegnia sp.2 were strongly associated with embryonic stages (eggs or alevins), (χ2 = 196.29, p < 0.0001). This work represents the first detailed molecular characterization of Saprolegnia species involved in saprolegniasis in Chile, and the first study showing specific association of different Saprolegnia species with different stages in the salmonid life cycle.
    Aquaculture 01/2014; · 2.01 Impact Factor
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    ABSTRACT: Habitat bioaugmentation and introduction of protective microbiota have been proposed as potential conservation strategies to rescue endangered mammals and amphibians from emerging diseases. For both strategies, insight into the microbiomes of the endangered species and their habitats is essential. Here, we sampled nests of the endangered sea turtle species Eretmochelys imbricata that were infected with the fungal pathogen Fusarium falciforme. Metagenomic analysis of the bacterial communities associated with the shells of the sea turtle eggs revealed approximately 16,664 operational taxonomic units, with Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes as the most dominant phyla. Subsequent isolation of Actinobacteria from the eggshells led to the identification of several genera (Streptomyces, Amycolaptosis, Micromomospora Plantactinospora and Solwaraspora) that inhibit hyphal growth of the pathogen F. falciforme. These bacterial genera constitute a first set of microbial indicators to evaluate the potential role of microbiota in conservation of endangered sea turtle species.
    PLoS ONE 01/2014; 9(4):e95206. · 3.73 Impact Factor
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    Javier Diéguez-Uribeondo
    Aquaculture 01/2014; 274(2-4):208-217. · 2.01 Impact Factor
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    svetlana rezinciuc, javier galindo, joan montserrat, javier diéguez-uribeondo
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    ABSTRACT: Aphanomyces astaci (Oomycetes) is responsible for the crayfish plague disease. This species is endemic of North America and five genotypes have been described using RAPD-PCR. The red swamp crayfish, Procambarus clarkii, is one of the most widely spread North American species and invasive in the world. However, no outbreaks on its specific genotype, i.e., genotype D, have ever been described in nature. We investigated three major series of crayfish plague outbreaks in indigenous crayfish populations of Austropotamobius pallipes, located in the areas of influence of P. clarkii. All samples collected tested positive for A. astaci using a rnDNA ITS-PCR test. We also performed an AFLP-PCR analysis on 19 isolates, and found that all isolates belong to genotype D. These isolates exhibited similar properties, i.e., adaptation to warm temperatures. We demonstrate, for the first time, the transmission of A. astaci genotype D to indigenous European populations of crayfish, and confirm that the properties of adaptation to warm water temperatures seem to be a specific character of genotype D. The results of this work emphasize once more the need of controlling invasive species and its trade, since they can carry harmful pathogens with specific adaptations or increased virulence in new environments.
    Fungal Biology 01/2014; · 2.08 Impact Factor
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    Phillip S. Wharton, Javier Diéguez-Uribeondo

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