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Auteur Mostajir, B.; Amblard, C.; Buffan-Dubau, E.; De Wit, R.; Lensi, R.; Sime-Ngando, T.
Titre Microbial Food Webs in Aquatic and Terrestrial Ecosystems Type Chapitre de livre
Année 2015 Publication Revue Abrégée
Volume Numéro Pages 485-509
Mots-Clés Biodiversity; Biogeochemical cycles; Ecological interactions; Microbial Ecology; Microbial food webs; Microbial loop
Résumé In microbial food webs, different types of interactions occur between microorganisms themselves and with meio- and macroorganisms. After an historical and general introduction, the biological components of the microbial food webs in the pelagic and benthic marine and lake ecosystems, as well as in the terrestrial ecosystems, are presented. The functioning of the microbial food webs in different ecosystems is illustrated and explained, including the trophic pathways and transfer of matter from microbial food webs toward meio- and macroorganisms of the superior trophic levels, the nutrient recycling in the aquatic environments, and the decomposition of organic matter in soils. Finally, the factors regulating microbial food webs, primarily “top-down” and “bottom-up” controls, are described with a special focus on the role of viruses in the aquatic microbial food webs.
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Auteur institutionnel Thèse
Editeur (down) Springer Netherlands Lieu de Publication Éditeur Bertrand, J.-C.; Caumette, P.; Lebaron, P.; Matheron, R.; Normand, P.; Sime-Ngando, T.
Langue en Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé Environmental Microbiology: Fundamentals and Applications
Volume de collection Numéro de collection Edition
ISSN ISBN 978-94-017-9117-5 978-94-017-9118-2 Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ alain.herve @ collection 1394
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Auteur Granger, V.; Fromentin, J.-M.; Bez, N.; Relini, G.; Meynard, C.; GAERTNER, J.-C.; Maiorano, P.; Garcia Ruiz, C.; Follesa, C.; Gristina, M.; Peristeraki, P.; BRIND'AMOUR, A.; Carbonara, P.; Charilaou, C.; Esteban, A.; Jadaud, A.; Joksimovic, A.; Kallianiotis, A.; Kolitari, J.; Manfredi, C.; Massuti, E.; Mifsud, R.; Quetglas, T.; Refes, W.; Sbrana, M.; Vrgoc, N.; SPEDICATO, M.T.; Mérigot, B.
Titre Large-scale spatio-temporal monitoring highlights hotspots of demersal fish diversity in the Mediterranean Sea Type Article scientifique
Année 2015 Publication Progress in Oceanography Revue Abrégée
Volume 130 Numéro Pages 65-74
Mots-Clés Functional diversity; Phylogenetic diversity; Rao’s quadratic entropy; Regression tree; Large scale
Résumé Increasing human pressures and global environmental change may severely affect the diversity of species assemblages and associated ecosystem services. Despite the recent interest in phylogenetic and functional diversity, our knowledge on large spatio-temporal patterns of demersal fish diversity sampled by trawling remains still incomplete, notably in the Mediterranean Sea, one of the most threatened marine regions of the world. We investigated large spatio-temporal diversity patterns by analysing a dataset of 19,886 hauls from 10 to 800 m depth performed annually during the last two decades by standardized scientific bottom trawl field surveys across the Mediterranean Sea, within the MEDITS program. A multi-component (eight diversity indices) and multi-scale (local assemblages, biogeographic regions to basins) approach indicates that only the two most traditional components (species richness and evenness) were sufficient to reflect patterns in taxonomic, phylogenetic or functional richness and divergence. We also put into question the use of widely computed indices that allow comparing directly taxonomic, phylogenetic and functional diversity within a unique mathematical framework. In addition, demersal fish assemblages sampled by trawl do not follow a continuous decreasing longitudinal/latitudinal diversity gradients (spatial effects explained up to 70.6% of deviance in regression tree and generalized linear models), for any of the indices and spatial scales analysed. Indeed, at both local and regional scales species richness was relatively high in the Iberian region, Malta, the Eastern Ionian and Aegean seas, meanwhile the Adriatic Sea and Cyprus showed a relatively low level. In contrast, evenness as well as taxonomic, phylogenetic and functional divergences did not show regional hotspots. All studied diversity components remained stable over the last two decades. Overall, our results highlight the need to use complementary diversity indices through different spatial scales when developing conservation strategies and defining delimitations for protected areas.
Adresse Institute of Oceanography and Fisheries, Split, Croatia
Auteur institutionnel Thèse
Editeur (down) Elsevier BV Lieu de Publication Éditeur
Langue Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 0079-6611 ISBN Médium
Région Expédition Conférence
Notes Co-auteur au Sud Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ 32743 collection 980
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Auteur Mouton, T.L.; Matheson, F.E.; Stephenson, F.; Champion, P.D.; Wadhwa, S.; Hamer, M.P.; Catlin, A.; Riis, T.
Titre Environmental filtering of native and non-native stream macrophyte assemblages by habitat disturbances in an agricultural landscape Type Article scientifique
Année 2019 Publication Revue Abrégée Sci. Total Environ.
Volume 659 Numéro Pages 1370-1381
Mots-Clés Agricultural impacts; classification; ecological impacts; eutrophication; Functional diversity; functional diversity measures; Functional traits; land-use; management; metaanalysis; Non-native flora; restoration; RLQ and fourth-corner analyses; species traits; trait responses
Résumé Understanding how inter-specific variation in functional traits affects native and non-native species responses to stream disturbances, is necessary to inform management strategies, providing tools for biomonitoring, conservation and restoration. This study used a functional trait approach to characterise the responses of macrophyte assemblages to reach-scale disturbances (measured by lack of riparian shading, altered hydromorphology and eutrophication), from 97 wadeable stream sites in an agriculturally impacted region of New Zealand. To determine whether macrophyte assemblages differed due to disturbances, we examined multidimensional assemblage functional structure in relation to eleven functional traits and further related two functional diversity indices (entropy and originality) to disturbances. Macrophyte assemblages showed distinct patterns in response to disturbances, with riparian shading and hydromorphological conditions being the strongest variables shaping macrophyte functional structure. In the multidimensional space, most of the non-native species were associatedwith disturbed conditions. These species had traits allowing faster colonisation rates (higher number of reproductive organs and larger root-rhizome system) and superior competitive abilities for resources (tall and dense canopy, heterophylly and greater preferences for light and nitrogen). In addition, lack of riparian shading increased the abundance of functionally distinct species (i.e. entropy), and eutrophication resulted in the growth of functionally unique species (i.e. originality). We demonstrated that stream reach-scale habitat disturbances were associated to a dominance of more productive species, equating to a greater abundance of non-native species. This, can result in a displacement of native species, habitat alterations, and changes to higher trophic level assemblages. Our results suggests that reachscale management efforts such as the conservation and restoration of riparian vegetation that provides substantial shading and hydromorphologically diverse in-stream habitat, would have beneficial direct and indirect effects on ecosystem functioning, and contribute to the mitigation of land-use impacts. (C) 2018 Published by Elsevier B.V.
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Auteur institutionnel Thèse
Editeur (down) Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 0048-9697 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2571
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Auteur Mante, C.; Kide, S.O.; Yao-Lafourcade, A.-F.; Mérigot, B.
Titre Fitting the truncated negative binomial distribution to count data A comparison of estimators, with an application to groundfishes from the Mauritanian Exclusive Economic Zone Type Article scientifique
Année 2016 Publication Revue Abrégée Environ. Ecol. Stat.
Volume 23 Numéro 3 Pages 359-385
Mots-Clés Birth-and-dead models; classification; curves; diversity; habitat; Log-series; Minimum Hellinger distance; Negative binomial; parametric models; population; series; Species abundance; species abundance distributions; zeros
Résumé Modeling empirical distributions of repeated counts with parametric probability distributions is a frequent problem when studying species abundance. One must choose a family of distributions which is flexible enough to take into account very diverse patterns and possess parameters with clear biological/ecological interpretations. The negative binomial distribution fulfills these criteria and was selected for modeling counts of marine fish and invertebrates. This distribution depends on a vector of parameters, and ranges from the Poisson distribution (when ) to Fisher's log-series, when . Moreover, these parameters have biological/ecological interpretations which are detailed in the literature and in this study. We compared three estimators of K, and the parameter of Fisher's log-series, following the work of Rao CR (Statistical ecology. Pennsylvania State University Press, University Park, 1971) on a three-parameter unstandardized variant of the negative binomial distribution. We further investigated the coherence underlying parameter values resulting from the different estimators, using both real count data collected in the Mauritanian Exclusive Economic Zone (MEEZ) during the period 1987-2010 and realistic simulations of these data. In the case of the MEEZ, we first built homogeneous lists of counts (replicates), by gathering observations of each species with respect to “typical environments” obtained by clustering the sampled stations. The best estimation of was generally obtained by penalized minimum Hellinger distance estimation. Interestingly, the parameters of most of the correctly sampled species seem compatible with the classical birth-and-dead model of population growth with immigration by Kendall (Biometrika 35:6-15, 1948).
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Auteur institutionnel Thèse
Editeur (down) Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 1352-8505 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ alain.herve @ collection 2067
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Auteur Auguet, J.C.; Casamayor, E.O.
Titre A hotspot for cold crenarchaeota in the neuston of high mountain lakes Type Article scientifique
Année 2008 Publication Revue Abrégée Environ Microbiol
Volume 10 Numéro 4 Pages 1080-1086
Mots-Clés 16S/genetics Spain *Water Microbiology; Archaeal/genetics RNA; Biodiversity Crenarchaeota/*classification/genetics/*isolation & purification Fresh Water/*microbiology In Situ Hybridization; Fluorescence Indoles Phylogeny RNA; Ribosomal
Résumé We have surveyed the first 1 m of 10 oligotrophic high mountain lakes in the Central Pyrenees (Spain) for both abundance and predominant phylotypes richness of the archaeaplankton assemblage, using CARD-FISH and 16S rRNA gene sequencing respectively. Archaea inhabiting the air-water surface microlayer (neuston) ranged between 3% and 37% of total 4,6-diamidino-2-phenylindole (DAPI) counts and were mainly Crenarchaeota of a new freshwater cluster distantly related to the Marine Group 1.1a. Conversely, most of the Archaea from the underlying waters (the remaining first 1 m integrated) were mainly Euryarchaeota of three distantly related branches ranging between 0.4% and 27% of total DAPI counts. Therefore, a consistent qualitative and quantitative spatial segregation was observed for the two main archaeal phyla between neuston and underlying waters at a regional scale. We also observed a consistent pattern along the lakes surveyed between lake area, lake depth and water residence time, and the archaeal enrichment in the neuston: the larger the lake the higher the proportion of archaea in the neuston as compared with abundances from the underlying waters (n = 10 lakes; R(2) > 0.80; P < 0.001, in all three cases). This is the first report identifying a widespread non-thermophilic habitat where freshwater planktonic Crenarchaeota can be found naturally enriched. High mountain lakes offer great research opportunities to explore the ecology of one of the most enigmatic and far from being understood group of prokaryotes.
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Auteur institutionnel Thèse
Editeur (down) Lieu de Publication Éditeur
Langue Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1300
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