9 results on '"Restrepo-Ortiz, Claudia Ximena"'
Search Results
2. Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes
- Author
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Chiarello, Marlène, Auguet, Jean-Christophe, Graham, Nicholas A. J., Claverie, Thomas, Sucré, Elliott, Bouvier, Corinne, Rieuvilleneuve, Fabien, Restrepo-Ortiz, Claudia Ximena, Bettarel, Yvan, Villéger, Sébastien, and Bouvier, Thierry
- Published
- 2020
3. Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model.
- Author
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Massey, Alexander, Boennec, Corentin, Restrepo-Ortiz, Claudia Ximena, Blanchet, Christophe, Alizon, Samuel, and Sofonea, Mircea T.
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COVID-19 pandemic ,INTENSIVE care units ,STATISTICAL smoothing ,MEDICAL personnel ,FORECASTING ,STATISTICAL models ,HOSPITALS - Abstract
Projects such as the European Covid-19 Forecast Hub publish forecasts on the national level for new deaths, new cases, and hospital admissions, but not direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which is of particular interest to health professionals for planning purposes. We present a sub-national French framework for forecasting hospital strain based on a non-Markovian compartmental model, its associated online visualisation tool and a retrospective evaluation of the real-time forecasts it provided from January to December 2021 by comparing to three baselines derived from standard statistical forecasting methods (a naive model, auto-regression, and an ensemble of exponential smoothing and ARIMA). In terms of median absolute error for forecasting critical care unit occupancy at the two-week horizon, our model only outperformed the naive baseline for 4 out of 14 geographical units and underperformed compared to the ensemble baseline for 5 of them at the 90% confidence level (n = 38). However, for the same level at the 4 week horizon, our model was never statistically outperformed for any unit despite outperforming the baselines 10 times spanning 7 out of 14 geographical units. This implies modest forecasting utility for longer horizons which may justify the application of non-Markovian compartmental models in the context of hospital-strain surveillance for future pandemics. Author summary: The US and European Covid-19 Forecast Hubs focus on metrics such as deaths, new cases, and hospital admissions, but do not offer measurements of hospital strain like critical care bed occupancy, which was essential for the provisioning of healthcare resources during the COVID-19 pandemic. Furthermore, forecasting support was only guaranteed on the national level leaving many countries to look elsewhere for valuable sub-national forecasts. In France statistical modelling approaches were proposed to anticipate hospital stain at the sub-national level but these were limited by a two-week forecast horizon. We present a sub-national French modelling framework and online application for anticipating hospital strain at the four-week horizon that can account for abrupt changes in key epidemiological parameters. It was the only publicly available real-time non-Markovian mechanistic model for the French epidemic when implemented in January 2021 and, to our knowledge, it still was at the time it stopped in early 2022. Further adaptations of this surveillance system can serve as an anticipation tool for hospital strain across sub-national localities to aid in the prevention of short-noticed ward closures and patient transfers. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
4. The Mandrillus Face Database: A portrait image database for individual and sex recognition, and age prediction in a non-human primate
- Author
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Tieo, Sonia, Restrepo-Ortiz, Claudia Ximena, Roura-Torres, Berta, Sauvadet, Loic, Harté, Mélanie, Charpentier, Marie J.E., and Renoult, Julien P.
- Published
- 2023
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5. Deep ocean prokaryotic communities are remarkably malleable when facing long-term starvation
- Author
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Sebastian, Marta, Auguet, J.-C., Restrepo-Ortiz, Claudia Ximena, Montserrat Sala, Maria, Marrase, Celia, Gasol, Josep M., Universidad de Granada (UGR), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), and Universidad de Granada = University of Granada (UGR)
- Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems ,[SDE.MCG]Environmental Sciences/Global Changes ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,[SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography - Abstract
International audience; The bathypelagic ocean is one of the largest ecosystems on Earth and sustains half of the ocean's microbial activity. This microbial activity strongly relies on surface-derived particles, but there is growing evidence that the carbon released through solubilization of these particles may not be sufficient to meet the energy demands of deep ocean prokaryotes. To explore how bathypelagic prokaryotes respond to the absence of external inputs of carbon, we followed the long-term (1 year) dynamics of an enclosed community. Despite the lack of external energy supply, we observed a continuous succession of active prokaryotic phylotypes, which was driven by recruitment of taxa from the seed bank (i.e., initially rare operational taxonomic units [OTUs]). A single OTU belonging to Marine Group I of Thaumarchaeota, which was originally rare, dominated the microbial community for similar to 4 months and played a fundamental role in this succession likely by introducing new organic carbon through chemolithoautotrophy. This carbon presumably produced a priming effect, because after the decline of Thaumarchaeota, the diversity and metabolic potential of the community increased back to the levels present at the start of the experiment. Our study demonstrates the profound versatility of deep microbial communities when facing organic carbon deprivation.
- Published
- 2018
6. Biology and population ecology of uncultured Archaea in natural environments analyzed by taxon-specific molecular markers = Biología y ecología poblacional de Archaeas no cultivadas en ambientes naturales analizadas mediante marcadores moleculares específicos
- Author
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Restrepo Ortiz, Claudia Ximena, Ortega Casamayor, Emilio, Muñoz Garcia, Isabel, Universitat de Barcelona. Departament d'Ecologia, and Muñoz Gràcia, Isabel
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Biología de poblaciones ,Procariotas ,Marcadores genéticos ,Marcadors genètics ,Genetic markers ,Biologia de poblacions ,Prokaryotes ,Population biology ,Ciències Experimentals i Matemàtiques ,Procariotes - Abstract
The annual dynamics of three different ammonia-oxidizing archaea (AOA) ecotypes (amoA gene) and of the SAGMCG-1 (Nitrosotalea-like aquatic Thaumarchaeota) group (16S rRNA gene) were studied by newly designed specific primers and quantitative PCR analysis in a deep oligotrophic high mountain lake (Lake Redon, Limnological Observatory of the Pyrenees, Spain). We observed segregated distributions of the main AOA populations, peaking separately in time and space, and under different ammonia concentrations and irradiance conditions. Strong positive correlation in gene abundances was found along the annual survey between 16S rRNA SAGMCG-1 and one of the amoA ecotypes, suggesting the potential for ammonia oxidation in the freshwater SAGMCG-1 clade. We also observed dominance of Nitrosotalea-like ecotypes over Nitrosopumilus-like (MG 1.1a), and not the same annual dynamics for the two thaumarchaeotal clades. The fine scale segregation in space and time of the different AOA ecotypes indicated the presence of phylogenetically close but ecologically segregated AOA species specifically adapted to specific environmental conditions. It remains to be elucidated what would be such environmental drivers. Subsequently quantitative environmental distribution of two widely distributed uncultured freshwater Euryarchaeota with unknown functional role, was explored by newly designed qPCR primers targeting the 16S rRNA gene of clades MEG (Miscellaneous Euryarchaeota Group containing the groups pMC2A384 and VALII/Eury4) and DSEG (Deep-Sea Euryarchaeotal Groups, targeting the cluster named VALIII containing the DHVE-3/DSEG, BC07-2A-27/DSEG-3, and DSEG-2 groups), respectively. The summer surface plankton of 28 lakes was analyzed and one additional dimictic deep lake, Lake Redon, was temporally and vertically surveyed covering seasonal limnological variability. A trophic range between 0.2 and 5.2 μg/L Chl a, and pH span from 3.8 to 9.5 was explored at altitudes between 632 and 2590 m above sea level. The primers showed to be highly selective with c. 85% coverage and 100% specificity. Only pH significantly explained the changes observed in gene abundances and environment. In Lake Redon, DSEG bloomed in deep stratified waters both in summer and early spring, and MEG at intermediate depths during the ice-cover period. Overall, MEG and DSEG showed a differential ecological distribution although correlational analyses indicated lack of coupling of both euryarchaeota with phytoplankton (chlorophyll a). However, an intriguing positive and significant relationship was found between DSEG and putative ammonia oxidizing Thaumarchaeota. The ribosomal-RNA (rRNA) approach to microbial evolution and ecology has become an integral part of environmental microbiology. Based on the conservation of rRNA, oligonucleotide probes can be designed with specificities that range from the species level to the level of phyla or even domains. When these probes are labelled with the enzyme horseradish peroxidase (HRP), they can be used to identify single microbial cells directly by fluorescence in situ hybridization. Based on comparative analyses of 16S rRNA sequences we have located sites specific for the SAGMCG-1 group of Thaumarchaeota, including the species Nitrosotalea devanaterra. Oligonucleotides complementary to these signature regions were evaluated as potential nucleic acid probes for the differentiation of SAGMCG-1 lineage. Hybridization conditions were optimized by the addition of increasing formamide concentrations to the hybridization buffer. The fluorescence intensity was enhanced and the effects on the cell visualization were improved by design of two adjacent helpers for the probe. CARD-FISH hybridization using N. devanaterra demonstrated high probe specificity in vitro, and whole cell hybridization with fluorescent probe derivatives allowed the identification and quantification in selected soil samples of individual microbial cells in situ. The probes will be useful for determinative studies and for the in situ monitoring of population distribution and dynamics in microbial communities closely related to the N biogeochemical cycling., Los microorganismos del Dominio Archaea son un componente común del plancton que ha pasado, mayoritariamente desapercibido para la Limnología durante mucho tiempo. Sólo tras la aplicación de técnicas moleculares en ecología microbiana se ha descubierto su enorme riqueza biológica y abundancia tanto en ambientes acuáticos como terrestres, más allá del grupo de las archaea metanógenas. Estudios recientes han demostrado que los hábitats de agua dulce tienen la mayor diversidad filogenética y representan entornos prometedores para el descubrimiento de nuevos linajes de Archaea. Uno de los ambientes que constituyen una fuente inexplorada de riqueza de nuevos filotipos de Archaea son los lagos alpinos, donde diferencias llamativas en la composición filogenética y abundancia de las arqueas se han reportado recientemente. Esto hace que los sistemas lacustres sean un modelo útil para comprender los factores ecológicos y la influencia de la heterogeneidad del hábitat sobre la composición de microorganismos Archaea, y para vincular los rasgos ecológicos y metabólicos de las arqueas con el funcionamiento del ecosistema. Esta tesis tiene como objetivo combinar microbiología ambiental, técnicas moleculares y aproximaciones bioinformáticas para progresar en el conocimiento de la distribución ecológica y ecofisiología de filotipos representativos de las arqueas de agua dulce superando la limitación de su baja cultivabilidad. Para este propósito, se diseñaron y optimizaron cebadores específicos para el gen SAGMGC-1 16S rRNA y los diferentes ecotipos de archaea oxidadoras de amonio, AOA (gen amoA), y se cuantifico mediante qPCR las distribuciones espacio-temporales a lo largo de una exploración anual en un lago profundo de alta montaña, donde las deposiciones atmosféricas son la principal fuente de nitrógeno reactivo. Adicionalmente se exploraron las diferencias espacio-temporales en el plancton superficial de un gran conjunto de lagos con gradientes ambientales marcados, mediante el diseño y optimización de cebadores específicos para el gen 16S rRNA de los grupos de euryarchaeota MEG y DSEG. Por último, se construyo una base de datos genética detallada del gen ribosómico 16S rRNA de Archaea utilizando SILVA y nuestros propios datos genéticos generados a partir de trabajos anteriores, a partir de esto se diseño y optimizo la sonda específica de CARDFISH para el grupo taumarchaeota SAGMGC-1, combinando aproximaciones in silico, in vitro e in situ. Posteriormente se cuantificó selectivamente dicha población a lo largo de un gradiente ambiental.
- Published
- 2016
7. Geological gas‐storage shapes deep life.
- Author
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Ranchou‐Peyruse, Magali, Auguet, Jean‐Christophe, Mazière, Camille, Restrepo‐Ortiz, Claudia Ximena, Guignard, Marion, Dequidt, David, Chiquet, Pierre, Cézac, Pierre, and Ranchou‐Peyruse, Anthony
- Subjects
COAL gas ,MICROBIAL ecology ,NATURAL gas storage ,GAS storage ,MICROBIAL diversity ,NATURAL gas - Abstract
Summary: Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high‐throughput sequencing and show the importance of sulfate‐reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate‐reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate‐reducers. This aquifer was used to store town gas (containing at least 50% H2) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate‐reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas‐impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
8. Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes.
- Author
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Compte‐Port, Sergi, Borrego, Carles M., Moussard, Hélène, Jeanbille, Mathilde, Restrepo‐Ortiz, Claudia Ximena, de Diego, Alberto, Rodriguez‐Iruretagoiena, Azibar, Gredilla, Ainara, Fdez‐Ortiz de Vallejuelo, Silvia, Galand, Pierre E., Kalenitchenko, Dimitri, Rols, Jean‐Luc, Pokrovsky, Oleg S., Gonzalez, Aridane G., Camarero, Lluis, Muñiz, Selene, Navarro‐Navarro, Enrique, and Auguet, Jean‐Christophe
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ARCHAEBACTERIA ,CARBON cycle ,LAKE sediments ,METAL toxicology ,METHANOGENS - Abstract
Summary: Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high‐mountain lakes under contrasted metal levels from different origins (bedrock erosion, past‐mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta‐community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance. Methanogenesis appeared as a process of central importance in the carbon cycle within sediments of alpine lakes as indicated by the absolute abundance of methanogen 16S rRNA and mcrA gene transcripts (10
5 to 109 copies g−1 ). We showed that methanogen abundance and activity were significantly reduced with increasing concentrations of Pb and Cd, two indicators of airborne metal contaminations. Considering the ecological importance of methanogenesis in sediment habitats, these metal contaminations may have system wide implications even in remote area such as alpine lakes. Overall, this work was pioneer in integrating the effect of long‐range atmospheric depositions on archaeal communities and indicated that metal contamination might significantly compromise the contribution of Archaea to the carbon cycling of the mountain lake sediments. [ABSTRACT FROM AUTHOR]- Published
- 2018
- Full Text
- View/download PDF
9. Deep ocean prokaryotic communities are remarkably malleable when facing long-term starvation.
- Author
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Sebastián M, Auguet JC, Restrepo-Ortiz CX, Sala MM, Marrasé C, and Gasol JM
- Subjects
- Ecosystem, Microbiota, Oceans and Seas, Archaea classification, Archaea metabolism, Carbon metabolism, Organic Chemicals metabolism, Seawater microbiology
- Abstract
The bathypelagic ocean is one of the largest ecosystems on Earth and sustains half of the ocean's microbial activity. This microbial activity strongly relies on surface-derived particles, but there is growing evidence that the carbon released through solubilization of these particles may not be sufficient to meet the energy demands of deep ocean prokaryotes. To explore how bathypelagic prokaryotes respond to the absence of external inputs of carbon, we followed the long-term (1 year) dynamics of an enclosed community. Despite the lack of external energy supply, we observed a continuous succession of active prokaryotic phylotypes, which was driven by recruitment of taxa from the seed bank (i.e., initially rare operational taxonomic units [OTUs]). A single OTU belonging to Marine Group I of Thaumarchaeota, which was originally rare, dominated the microbial community for ∼ 4 months and played a fundamental role in this succession likely by introducing new organic carbon through chemolithoautotrophy. This carbon presumably produced a priming effect, because after the decline of Thaumarchaeota, the diversity and metabolic potential of the community increased back to the levels present at the start of the experiment. Our study demonstrates the profound versatility of deep microbial communities when facing organic carbon deprivation., (© 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2018
- Full Text
- View/download PDF
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