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Auteur Auguet, J.C.; Nomokonova, N.; Camarero, L.; Casamayor, E.O.
Titre Seasonal changes of freshwater ammonia-oxidizing archaeal assemblages and nitrogen species in oligotrophic alpine lakes Type Article scientifique
Année 2011 Publication Revue Abrégée (up) Appl Environ Microbiol
Volume 77 Numéro 6 Pages 1937-1945
Mots-Clés 16S/genetics Seasons Spain; Ammonia/*metabolism Archaea/classification/genetics/*metabolism Biodiversity Fresh Water Molecular Sequence Data Nitrogen/*metabolism Oxidoreductases/genetics Phylogeny Polymerase Chain Reaction RNA; Ribosomal
Résumé The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% +/- 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1304
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Auteur Hillen, J.E.J.; Coscia, I.; Vandeputte, M.; Herten, K.; Hellemans, B.; Maroso, F.; Vergnet, A.; Allal, F.; Maes, G.E.; Volckaert, F.A.M.
Titre Estimates of genetic variability and inbreeding in experimentally selected populations of European sea bass Type Article scientifique
Année 2017 Publication Revue Abrégée (up) Aquaculture
Volume 479 Numéro Pages 742-749
Mots-Clés Artificial selection; ddRAD; fish; genetic diversity; Genomics; Inbreeding
Résumé The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was selected for growth over three generations and the second line for both high and low weight loss under a starvation regime over two generations. We used a genomic approach (2549 single nucleotide polymorphism markers derived from double digest restriction site associated DNA sequencing) in combination with eight microsatellites to estimate genetic variation, relatedness, effective population size and genetic differentiation across generations. Individual heterozygosity estimates indicated that the selected lines showed no significant reduction in diversity compared with wild populations. There was, however, a decreasing trend in allelic richness, suggesting the loss of low frequency alleles. We compared the estimates of effective population size from genetic markers with pedigree information and found good correspondence between methods. This study provides important insights in the genetic consequences of selective breeding and demonstrates the operational use of the latest genomic tools to estimate variability, inbreeding and at a later stage domestication and artificial selection.
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ISSN 0044-8486 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2183
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Auteur Zubia, M.; De Clerck, O.; Leliaert, F.; Payri, C.; Mattio, L.; Vieira, C.; Cambert, H.; Quod, J.P.; Loiseau, N.; Golubic, S.; Lin, S.-M.; Liu, S.-L.; Pinault, M.
Titre Diversity and assemblage structure of tropical marine flora on lava flows of different ages Type Article scientifique
Année 2018 Publication Revue Abrégée (up) Aquat. Bot.
Volume 144 Numéro Pages 20-30
Mots-Clés climate-change; coral-reefs; Reunion island; Cyanobacteria; phase-shifts; cyanobacterial diversity; Ecological succession; eparses scattered islands; genus lobophora dictyotales; Macroalgae; mozambique channel; Piton de la fournaise; reunion island; volcanic habitats; western indian-ocean
Résumé Recent volcanic lava flows extending into the ocean represent an ideal opportunity to study the long-term successional development of marine floral assemblages on the bare new substratum. We describe the floral assemblages of nine lava flows of different ages (prehistoric to 2007) at Piton de la Fournaise (Reunion Island, Indian Ocean) based on a survey of 37 stations. We identified 159 species including 148 macroalgae, 1 seagrass, and 10 cyanobacteria. Fifty-one of those represent new records for Reunion Island, and at least 9 taxa were identified as new to science. Recent lava flows were characterized by the dominance of ephemeral, opportunistic species, such as Pseudobryopsis hainanensis and Acrocladus dotyanus, while prehistoric lava flows were mainly characterized by perennial species, particularly Sargassum portiericuzum and Turbinaria ornata. A canonical correspondence analysis revealed that the environmental factor that most significantly correlated to the variation in floral assemblages was the distance to the most recent lava flow (2007). This factor was also highly correlated to coral cover. The composition of the different floral assemblages is discussed in relation to abiotic and biotic factors to explain ecological succession in a tropical environment.
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ISSN 0304-3770 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 2259
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Auteur Villeger, S.; Brosse, S.; Mouchet, M.; Mouillot, D.; Vanni, M.J.
Titre Functional ecology of fish: current approaches and future challenges Type Article scientifique
Année 2017 Publication Revue Abrégée (up) Aquat. Sci.
Volume 79 Numéro 4 Pages 783-801
Mots-Clés biodiversity; centrarchid fishes; coral-reef fishes; dietary-morphological relationships; ecosystem processes; Ecosystem services; fish; food-web; fresh-water fish; functional trait; global change; labrid fishes; life-history strategies; ocean; phosphorus-limitation; population regulation; river
Résumé Fish communities face increasing anthropogenic pressures in freshwater and marine ecosystems that modify their biodiversity and threaten the services they supply to human populations. To address these issues, studies have been increasingly focusing on functions of fish that are linked to their main ecological roles in aquatic ecosystems. Fish are indeed known to control other organisms through predation, mediate nutrient fluxes, and can act as ecosystem engineers. Here for each of the key functions played by fish, we present the functional traits that have already been used to assess them. We include traits measurable from observations on living individuals, morphological features measured on preserved organisms or traits categorized using information from the literature, and we discuss their respective advantages and limitations. We then list future research directions to foster a more complete functional approach for fish ecology that needs to incorporate functional traits describing, food provisioning and cultural services while accounting more frequently for intraspecific variability. Finally, we highlight ecological and evolutionary questions that could be addressed using meta-analyses of large trait databases, and how a trait-based framework could provide valuable insights on the mechanistic links between global changes, functional diversity of fish assemblages, and ecosystem services.
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Volume de collection Numéro de collection Edition
ISSN 1015-1621 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 2211
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Auteur Cheng, L.; Blanchet, S.; Loot, G.; Villeger, S.; Zhang, T.; Lek, S.; Lek-Ang, S.; Li, Z.
Titre Temporal changes in the taxonomic and functional diversity of fish communities in shallow Chinese lakes: the effects of river–lake connections and aquaculture Type Article scientifique
Année 2014 Publication Revue Abrégée (up) Aquatic Conservation: Marine and Freshwater Ecosystems
Volume 24 Numéro 1 Pages 23-34
Mots-Clés biodiversity loss; biotic homogenization; Functional richness; lakes; Yangtze River basin
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ISSN 1099-0755 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1160
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