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Auteur (up) Caro, A.; Escalas, A.; Bouvier, C.; Grousset, E.; Lautredou-Audouy, N.; Roques, C.; Charmantier, M.; Gros, O. url  doi
openurl 
  Titre Epibiotic bacterial community of Sphaeroma serratum (Crustacea, Isopoda): relationship with molt status Type Article scientifique
  Année 2012 Publication Revue Abrégée Mar. Ecol.-Prog. Ser.  
  Volume 457 Numéro Pages 11-27  
  Mots-Clés 16s ribosomal-rna; Crustacean; DGGE band pattern; Epibiotic biofilm; Molt cycle; Sphaeroma; fish; gastropod; gradient gel-electrophoresis; hydrothermal-vent; in-situ hybridization; mid-atlantic ridge; oxidizing bacteria; phylogenetic diversity; riftia-pachyptila; shrimp rimicaris-exoculata; urothoe-poseidonis  
  Résumé Sphaeroma serratum is a marine isopod species that inhabits seashores from Europe to West Africa. The individuals live under stones in direct contact with reduced sediments and harbour a diverse bacterial community on the cuticle of their pleopods. We investigated the diversity of these epibiotic bacteria on male (pubescent and senescent) and female specimens with electron microscopic observations and molecular tools. The microbial community of S. serratum was shown to be composed of at least 5 bacterial morphotypes observed on the pleopodal cuticle in all male specimens. Using fluorescence in situ hybridization, we identified 5 major phylogenetic groups (alpha-, beta-, gamma- and delta-Proteobacteria and Archaea) whereas denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments of epibiotic bacteria revealed 50 bands. The bacterial community associated with S. serratum seems more diverse than in other marine crustaceans, such as Rimicaris. The relative diversity of this bacterial community was also studied in relation to the molt cycle. The comparison of DGGE band patterns of several individuals from female, pubescent male and senescent male groups revealed that the bacterial community diversity was dependent on the sex and the age of the individuals and more generally on the molt status.  
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  Volume de collection Numéro de collection Edition  
  ISSN 0171-8630 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 564  
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Auteur (up) Carteron, A.; Jeanmougin, M.; Leprieur, F.; Spatharis, S. url  doi
openurl 
  Titre Assessing the efficiency of clustering algorithms and goodness-of-fit measures using phytoplankton field data Type Article scientifique
  Année 2012 Publication Revue Abrégée Ecol. Inform.  
  Volume 9 Numéro Pages 64-68  
  Mots-Clés 2-norm; Beta diversity; Cophenetic correlation coefficient; Dendrogram; Upgma; Ward's algorithm; beta-diversity; blooms; classification; communities; cophenetic correlation; environment; forest; functional diversity; som  
  Résumé Investigation of patterns in beta diversity has received increased attention over the last years particularly in light of new ecological theories such as the metapopulation paradigm and metacommunity theory. Traditionally, beta diversity patterns can be described by cluster analysis (i.e. dendrograms) that enables the classification of samples. Clustering algorithms define the structure of dendrograms, consequently assessing their performance is crucial. A common, although not always appropriate approach for assessing algorithm suitability is the cophenetic correlation coefficient c. Alternatively the 2-norm has been recently proposed as an increasingly informative method for evaluating the distortion engendered by clustering algorithms. In the present work, the 2-norm is applied for the first time on field data and is compared with the cophenetic correlation coefficient using a set of 105 pairwise combinations of 7 clustering methods (e.g. UPGMA) and 15 (dis)similarity/distance indices (e.g. Jaccard index). In contrast to the 2-norm, cophenetic correlation coefficient does not provide a clear indication on the efficiency of the clustering algorithms for all combinations. The two approaches were not always in agreement in the choice of the most faithful algorithm. Additionally, the 2-norm revealed that UPGMA is the most efficient clustering algorithm and Ward's the least. The present results suggest that goodness-of-fit measures such as the 2-norm should be applied prior to clustering analyses for reliable beta diversity measures. (C) 2012 Elsevier B.V. All rights reserved.  
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  Volume de collection Numéro de collection Edition  
  ISSN 1574-9541 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 457  
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Auteur (up) Catherine, A.; Selma, M.; Mouillot, D.; Troussellier, M.; Bernard, C. url  doi
openurl 
  Titre Patterns and multi-scale drivers of phytoplankton species richness in temperate peri-urban lakes Type Article scientifique
  Année 2016 Publication Revue Abrégée Science of The Total Environment  
  Volume 559 Numéro Pages 74-83  
  Mots-Clés Lake- and catchment-scale; Phytoplankton; Productivity–diversity relationship; Random forest; Residuals analysis; species richness  
  Résumé Local species richness (SR) is a key characteristic affecting ecosystem functioning. Yet, the mechanisms regulating phytoplankton diversity in freshwater ecosystems are not fully understood, especially in peri-urban environments where anthropogenic pressures strongly impact the quality of aquatic ecosystems. To address this issue, we sampled the phytoplankton communities of 50 lakes in the Paris area (France) characterized by a large gradient of physico-chemical and catchment-scale characteristics. We used large phytoplankton datasets to describe phytoplankton diversity patterns and applied a machine-learning algorithm to test the degree to which species richness patterns are potentially controlled by environmental factors. Selected environmental factors were studied at two scales: the lake-scale (e.g. nutrients concentrations, water temperature, lake depth) and the catchment-scale (e.g. catchment, landscape and climate variables). Then, we used a variance partitioning approach to evaluate the interaction between lake-scale and catchment-scale variables in explaining local species richness. Finally, we analysed the residuals of predictive models to identify potential vectors of improvement of phytoplankton species richness predictive models. Lake-scale and catchment-scale drivers provided similar predictive accuracy of local species richness (R2 = 0.458 and 0.424, respectively). Both models suggested that seasonal temperature variations and nutrient supply strongly modulate local species richness. Integrating lake- and catchment-scale predictors in a single predictive model did not provide increased predictive accuracy; therefore suggesting that the catchment-scale model probably explains observed species richness variations through the impact of catchment-scale variables on in-lake water quality characteristics. Models based on catchment characteristics, which include simple and easy to obtain variables, provide a meaningful way of predicting phytoplankton species richness in temperate lakes. This approach may prove useful and cost-effective for the management and conservation of aquatic ecosystems.  
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  ISSN 0048-9697 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1566  
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Auteur (up) Cazelles, K.; Mouquet, N.; Mouillot, D.; Gravel, D. doi  openurl
  Titre On the integration of biotic interaction and environmental constraints at the biogeographical scale Type Article scientifique
  Année 2016 Publication Revue Abrégée Ecography  
  Volume 39 Numéro 10 Pages 921-931  
  Mots-Clés biodiversity; climate-change; cooccurrence; distributions; ecological communities; evolutionary; food webs; networks; niche; species distribution models  
  Résumé Biogeography is primarily concerned with the spatial distribution of biodiversity, including performing scenarios in a changing environment. The efforts deployed to develop species distribution models have resulted in predictive tools, but have mostly remained correlative and have largely ignored biotic interactions. Here we build upon the theory of island biogeography as a first approximation to the assembly dynamics of local communities embedded within a metacommunity context. We include all types of interactions and introduce environmental constraints on colonization and extinction dynamics. We develop a probabilistic framework based on Markov chains and derive probabilities for the realization of species assemblages, rather than single species occurrences. We consider the expected distribution of species richness under different types of ecological interactions. We also illustrate the potential of our framework by studying the interplay between different ecological requirements, interactions and the distribution of biodiversity along an environmental gradient. Our framework supports the idea that the future research in biogeography requires a coherent integration of several ecological concepts into a single theory in order to perform conceptual and methodological innovations, such as the switch from single-species distribution to community distribution.  
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  Volume de collection Numéro de collection Edition  
  ISSN 0906-7590 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 1683  
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Auteur (up) Celeste Lopez-Abbate, M.; Molinero, J.-C.; Perillo, G.M.E.; Barria de Cao, M.S.; Pettigrosso, R.E.; Guinder, V.A.; Uibrig, R.; Berasategui, A.A.; Vitale, A.; Marcovecchio, J.E.; Hoffmeyer, M.S. doi  openurl
  Titre Long-term changes on estuarine ciliates linked with modifications on wind patterns and water turbidity Type Article scientifique
  Année 2019 Publication Revue Abrégée Mar. Environ. Res.  
  Volume 144 Numéro Pages 46-55  
  Mots-Clés Acartia tonsa; bahia-blanca estuary; biogenic carbon; community structure; diversity; driven; Estuaries; ocean acidification; Oligotrichs; sea-level; shallow; suspended clay; Tintinnids; Turbidity; variability; Wind  
  Résumé Planktonic ciliates constitute a fundamental component among microzooplankton and play a prominent role in carbon transport at the base of marine food webs. How these organisms respond to shifting environmental regimes is unclear and constitutes a current challenge under global ocean changes. Here we examine a multi-annual field survey covering 25 years in the Bahfa Blanca Estuary (Argentina), a shallow, flood-plain system dominated by wind and tidal energy. We found that the estuary experienced marked changes in wind dominant regimes and an increase in water turbidity driven from the joint effect of persistent long-fetch winds and the indirect effect of the Southern Annular Mode. Along with these changes, we found that zooplankton components, i.e. ciliates and the dominant estuarine copepod Acartia tonsa, showed a negative trend during the period 1986-2011. We showed that the combined effects of wind and turbidity with other environmental variables (chlorophyll, salinity and nutrients) consistently explained the variability of observed shifts. Tintinnids were more vulnerable to wind patterns and turbidity while showed a loss of synchrony with primary productivity. Water turbidity produced a dome-like pattern on tintinnids, oligotrichs and A. tonsa, implying that the highest abundance of organisms occurred under moderate values (similar to 50 NTU) of turbidity. In contrast, the response to wind patterns was not generalizable probably owing to species-specific traits. Observed trends denote that wind induced processes in shallow ecosystems with internal sources of suspended sediments, are essential on ciliate dynamics and that such effects can propagate trough the interannual variability of copepods.  
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  Volume de collection Numéro de collection Edition  
  ISSN 0141-1136 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2546  
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