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Auteur (up) 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 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 (up) Authier, M.; Saraux, C.; Péron, C.
Titre Variable selection and accurate predictions in habitat modelling: a shrinkage approach Type Article scientifique
Année 2017 Publication Revue Abrégée Ecography
Volume 40 Numéro 4 Pages 549-560
Mots-Clés account; distributional data; Ecology; indian-ocean; inference; Mediterranean Sea; regression methods; small pelagic fish; spatial autocorrelation; species distribution models
Résumé Habitat modelling is increasingly relevant in biodiversity and conservation studies. A typical application is to predict potential zones of specific conservation interest. With many environmental covariates, a large number of models can he investigated but multi-model inference may become impractical. Shrinkage regression overcomes this issue by dealing with the identification and accurate estimation of effect size for prediction. In a Bayesian framework we investigated the use of a shrinkage prior, the Horseshoe, for variable selection in spatial generalized linear models (GLM). As study cases, we considered 5 datasets on small pelagic fish abundance in the Gulf of Lion (Mediterranean Sea, France) and 9 environmental inputs. We compared the predictive performances of a simple kriging model, a full spatial GLM model with independent normal priors for regression coefficients, a full spatial GLM model with a Horseshoe prior for regression coefficients and 2 zero-inflated models (spatial and non-spatial) with a Horseshoe prior. Predictive performances were evaluated by cross validation on a hold-out subset of the data: models with a Horseshoe prior performed best, and the full model with independent normal priors worst. With an increasing number of inputs, extrapolation quickly became pervasive as we tried to predict from novel combinations of covariate values. By shrinking regression coefficients with a Horseshoe prior, only one model needed to be fitted to the data in order to obtain reasonable and accurate predictions, including extrapolations.
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Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
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ISSN 0906-7590 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 2130
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Auteur (up) Avadi, A.; Freon, P.
Titre A set of sustainability performance indicators for seafood : direct human consumption products from Peruvian anchoveta fisheries and freshwater aquaculture Type Article scientifique
Année 2015 Publication Revue Abrégée Ecological Indicators
Volume 48 Numéro Pages 518-532
Mots-Clés Employment; Gross profit; Life cycle assessment; Nutrition; Seafood industry; Sustainability assessment
Résumé Different seafood products based on Peruvian anchoveta (Engraulis ringens) fisheries and freshwater aquaculture of trout (Oncorhynchus mykiss), tilapia (Oreochromis spp.) and black pacu (Colossoma macropomum), contribute at different scales to the socio-economic development, environmental degradation and nutrition of the Peruvian population. Various indicators have been used in the literature to assess the performance of these industries regarding different aspects of sustainability, notably their socio-economic performance. In this study, a novel set of indicators is proposed to evaluate the sustainability performance of these industries in Peru, based on life cycle assessment (LCA) and nutritional profiling, as well as on energy and socio-economic assessment approaches. The emphasis is put on the potential of different products to contribute to improving the nutrition of the Peruvian population in an energy-efficient, environmentally friendly and socio-economically sound way. The set of indicators includes biotic resource use (BRU), cumulative energy demand (CED), energy return on investment (EROI), production costs, gross profit generation, added value, and nutritional profile in terms of vitamins, minerals and essential fatty acids; as well as a number of life cycle impact assessment indicators commonly used in seafood studies, and some recently proposed indicators of resource status (measuring the impacts of fish biomass removal at the species and ecosystem levels). Results suggest that more energy-intensive/highly processed products (cured and canned anchoveta products) represent a higher burden, in terms of environmental impact, than less energy-intensive products (salted and frozen anchoveta products, semi-intensive aquaculture products). This result is confirmed when comparing all products regarding their industrial-to-nutritional energy ratio. Regarding the other attributes analysed, the scoring shows that salted and frozen anchoveta products generate fewer jobs and lower gross profit than canned and cured, while aquaculture products maximise them. Overall, it was concluded that less energy-intensive industries (anchoveta freezing and salting) are the least environmentally impacting but also the least economically interesting products, yet delivering higher nutritional value. Aquaculture products maximise gross profit and job creation, with lower energy efficiency and nutritional values. The proposed set of sustainability indicators fulfilled its goal in providing a multi-criteria assessment of anchoveta direct human consumption and freshwater aquaculture products. As often the case, there is no ideal product and the best trade-off must be sought when making decision regarding fisheries and seafood policy. No threshold for performance of the different indicators is offered, because the goal of the comparison is to contrast the relative performance among products, not of products against reference values.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1143
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Auteur (up) Ayata, S.-D.; Irisson, J.-O.; Aubert, A.; Berline, L.; Dutay, J.-C.; Mayot, N.; Nieblas, A.-E.; D'Ortenzio, F.; Palmiéri, J.; Reygondeau, G.; Rossi, V.; Guieu, C.
Titre Regionalisation of the Mediterranean basin, a MERMEX synthesis Type Article scientifique
Année 2018 Publication Progress in Oceanography Revue Abrégée
Volume 163 Numéro Pages 7-20
Mots-Clés Mediterranean Sea; regionalisation; biogeochemistry; circulation; mesoscale features; epipelagic ocean; management; spatial planning
Résumé Regionalisation aims at delimiting provinces within which physical conditions, chemical properties, and biological communities are reasonably homogeneous. This article proposes a synthesis of the many recent regionalisations of the open-sea regions of the Mediterranean Sea. The nine studies considered here defined regions based on different, and sometimes complementary, criteria: dynamics of surface chlorophyll concentration, ocean currents, three-dimensional hydrological and biogeochemical properties, or the distribution of organisms. Although they identified different numbers and patterns of homogeneous regions, their compilation in the epipelagic zone identifies nine consensus frontiers, eleven consensus regions with relatively homogeneous conditions, and four heterogeneous regions with highly dynamical conditions. The consensus frontiers and regions are in agreement with well-known hydrodynamical features of the Mediterranean Sea, which constrain the distribution of hydrological and ecological variables. The heterogeneous regions are rather defined by intense mesoscale activity. The synthesis proposed here could constitute a reference step for management actions and spatial planning, such as the application of the European Marine Strategy Framework Directive, and for future biogeochemical and ecological studies in the Mediterranean Sea.
Adresse Center for Prototype Climate Modeling, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
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Editeur Elsevier BV Lieu de Publication Éditeur
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ISSN 0079-6611 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ 51673 collection 2349
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Auteur (up) Ban, N.C.; Maxwell, S.M.; Dunn, D.C.; Hobday, A.J.; Bax, N.J.; Ardron, J.; Gjerde, K.M.; Game, E.T.; Devillers, R.; Kaplan, D.M.; Dunstan, P.K.; Halpin, P.N.; Pressey, R.L.
Titre Better integration of sectoral planning and management approaches for the interlinked ecology of the open oceans Type Article scientifique
Année 2014 Publication Revue Abrégée Marine Policy
Volume Numéro Pages
Mots-Clés Areas beyond national jurisdiction; Benthic-pelagic interlinkages; High seas; marine conservation; Marine Protected Areas; sustainable fisheries
Résumé Open oceans are one of the least protected, least studied and most inadequately managed ecosystems on Earth. Three themes were investigated that differentiate the open ocean (areas beyond national jurisdiction and deep area within exclusive economic zones) from other realms and must be considered when developing planning and management options: ecosystem interactions, especially between benthic and pelagic systems; potential effects of human activities in open oceans on ecological linkages; and policy context and options. A number of key ecological factors differentiate open oceans from coastal systems for planners and managers: (1) many species are widely distributed and, especially for those at higher trophic levels, wide ranging; (2) the sizes and boundaries of biogeographical domains (patterns of co-occurrence of species, habitats and ecosystem processes) vary significantly by depth; (3) habitat types exhibit a wide range of stabilities, from ephemeral (e.g., surface frontal systems) to hyper-stable (e.g., deep sea); and (4) vertical and horizontal linkages are prevalent. Together, these ecological attributes point to interconnectedness between open ocean habitats across large spatial scales. Indeed, human activities – especially fishing, shipping, and potentially deep-sea mining and oil and gas extraction – have effects far beyond the parts of the ocean in which they operate. While managing open oceans in an integrated fashion will be challenging, the ecological characteristics of the system demand it. A promising avenue forward is to integrate aspects of marine spatial planning (MSP), systematic conservation planning (SCP), and adaptive management. These three approaches to planning and management need to be integrated to meet the unique needs of open ocean systems, with MSP providing the means to meet a diversity of stakeholder needs, SCP providing the structured process to determine and prioritise those needs and appropriate responses, and adaptive management providing rigorous monitoring and evaluation to determine whether actions or their modifications meet both ecological and defined stakeholder needs. The flexibility of MSP will be enhanced by the systematic approach of SCP, while the rigorous monitoring of adaptive management will enable continued improvement as new information becomes available and further experience is gained.
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Numéro d'Appel LL @ pixluser @ collection 317
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