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Auteur Matthews, T.J.; Triantis, K.A.; Whittaker, R.J.; Guilhaumon, F.
Titre sars: an R package for fitting, evaluating and comparing species-area relationship models Type Article scientifique
Année (down) 2019 Publication Revue Abrégée Ecography
Volume 42 Numéro 8 Pages 1446-1455
Mots-Clés accumulation; curves; diversity; diversity-area relationship; island biogeography; islands; richness; species-area relationship
Résumé The species-area relationship (SAR) constitutes one of the most general ecological patterns globally. A number of different SAR models have been proposed. Recent work has shown that no single model universally provides the best fit to empirical SAR datasets: multiple models may be of practical and theoretical interest. However, there are no software packages available that a) allow users to fit the full range of published SAR models, or b) provide functions to undertake a range of additional SAR-related analyses. To address these needs, we have developed the R package 'sars' that provides a wide variety of SAR-related functionality. The package provides functions to: a) fit 20 SAR models using non-linear and linear regression, b) calculate multi-model averaged curves using various information criteria, and c) generate confidence intervals using bootstrapping. Plotting functions allow users to depict and scrutinize the fits of individual models and multi-model averaged curves. The package also provides additional SAR functionality, including functions to fit, plot and evaluate the random placement model using a species-sites abundance matrix, and to fit the general dynamic model of oceanic island biogeography. The 'sars' R package will aid future SAR research by providing a comprehensive set of simple to use tools that enable in-depth exploration of SARs and SAR-related patterns. The package has been designed to allow other researchers to add new functions and models in the future and thus the package represents a resource for future SAR work that can be built on and expanded by workers in the field.
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Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 0906-7590 ISBN Médium
Région Expédition Conférence
Notes WOS:000477975800010 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2625
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Auteur Ranchou-Peyruse, M.; Auguet, J.-C.; Maziere, C.; Restrepo-Ortiz, C.X.; Guignard, M.; Dequidt, D.; Chiquet, P.; Cezac, P.; Ranchou-Peyruse, A.
Titre Geological gas-storage shapes deep life Type Article scientifique
Année (down) 2019 Publication Revue Abrégée Environ. Microbiol.
Volume Numéro Pages
Mots-Clés carbon; degradation; depth; desulfotomaculum; diversity; methanogenesis; microbial communities; spp.; sulfate-reducing bacteria; sulfite
Résumé 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% H-2) 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.
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Volume de collection Numéro de collection Edition
ISSN 1462-2912 ISBN Médium
Région Expédition Conférence
Notes WOS:000480010600001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2627
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Auteur Draredja, M.A.; Frihi, H.; Boualleg, C.; Gofart, A.; Abadie, E.; Laabir, M.
Titre Seasonal variations of phytoplankton community in relation to environmental factors in a protected meso-oligotrophic southern Mediterranean marine ecosystem (Mellah lagoon, Algeria) with an emphasis of HAB species Type Article scientifique
Année (down) 2019 Publication Revue Abrégée Environ. Monit. Assess.
Volume 191 Numéro 10 Pages 603
Mots-Clés coastal lagoons; Diversity; dynamics; Environmental conditions; HAB species; Mediterranean lagoon; nutrients; particulate matter; patterns; Phytoplankton monitoring; sea; temporal variations; thau lagoon; venice lagoon; water-quality
Résumé The spatial and temporal variation of phytoplankton communities including HAB species in relation to the environmental characteristics was investigated in the protected meso-oligotrophic Mellah lagoon located in the South Western Mediterranean. During 2016, a biweekly monitoring of phytoplankton assemblages and the main abiotic factors were realized at three representative stations. Taxonomic composition, abundance, and diversity index were determined. In total, 227 phytoplankton species (160 diatoms and 53 dinoflagellates) were inventoried. There was a clear dominance of diatoms (62.9%) compared with dinoflagellates (36.8%). Diatoms dominated in spring and dinoflagellates developed in summer and early autumn in Mellah showing a marked seasonal trend. Data showed that the dynamic of the phytoplankton taxa evolving in the lagoon was mainly driven by temperature and salinity. For the first time, a number of potentially toxic species have been identified, including 2 diatoms (Pseudo-nitzschia group delicatissima, Pseudo-nitzschia group seriata) and 5 dinoflagellates (Alexandrium minutum, Alexandrium tamarense/catenella, Dinophysis acuminata, Dinophysis sacculus, Prorocentrum lima). These harmful species could threat the functioning of the Mellah lagoon and human health and require the establishment of a monitoring network. Finally, our study suggests that the observed decrease of the phytoplankton diversity between 2001 and 2016 could result from the reduction in water exchanges between the lagoon and the adjacent coast following the gradual clogging of the channel.
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Volume de collection Numéro de collection Edition
ISSN 0167-6369 ISBN Médium
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Notes WOS:000484493700001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2635
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Auteur Escalas, A.; Catherine, A.; Maloufi, S.; Cellamare, M.; Hamlaoui, S.; Yepremian, C.; Louvard, C.; Troussellier, M.; Bernard, C.
Titre Drivers and ecological consequences of dominance in periurban phytoplankton communities using networks approaches Type Article scientifique
Année (down) 2019 Publication Revue Abrégée Water Res.
Volume 163 Numéro Pages Unsp-114893
Mots-Clés blooms; climate-change; Co-occurrence network; Community cohesion; Community functioning; cooccurrence patterns; cyanobacteria dominance; diversity; Dominance; fresh-waters; lakes; light; Periurban waterbodies; Phytoplankton; resource use efficiency; species richness
Résumé Evaluating the causes and consequences of dominance by a limited number of taxa in phytoplankton communities is of huge importance in the current context of increasing anthropogenic pressures on natural ecosystems. This is of particular concern in densely populated urban areas where usages and impacts of human populations on water ecosystems are strongly interconnected. Microbial biodiversity is commonly used as a bioindicator of environmental quality and ecosystem functioning, but there are few studies at the regional scale that integrate the drivers of dominance in phytoplankton communities and their consequences on the structure and functioning of these communities. Here, we studied the causes and consequences of phytoplankton dominance in 50 environmentally contrasted waterbodies, sampled over four summer campaigns in the highly-populated Ile-de-France region (IDF). Phytoplankton dominance was observed in 32-52% of the communities and most cases were attributed to Chlorophyta (35.5-40.6% of cases) and Cyanobacteria (30.3-36.5%). The best predictors of dominance were identified using multinomial logistic regression and included waterbody features (surface, depth and connection to the hydrological network) and water column characteristics (total N, TN:TP ratio, water temperature and stratification). The consequences of dominance were dependent on the identity of the dominant organisms and included modifications of biological attributes (richness, cohesion) and functioning (biomass, RUE) of phytoplankton communities. We constructed co-occurrence networks using high resolution phytoplankton biomass and demonstrated that networks under dominance by Chlorophyta and Cyanobacteria exhibited significantly different structure compared with networks without dominance. Furthermore, dominance by Cyanobacteria was associated with more profound network modifications (e.g. cohesion, size, density, efficiency and proportion of negative links), suggesting a stronger disruption of the structure and functioning of phytoplankton communities in the conditions in which this group dominates. Finally, we provide a synthesis on the relationships between environmental drivers, dominance status, community attributes and network structure. (C) 2019 Elsevier Ltd. All rights reserved.
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Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 0043-1354 ISBN Médium
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Notes WOS:000483006400038 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2636
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Auteur Leroy, B.; Dias, M.S.; Giraud, E.; Hugueny, B.; Jezequel, C.; Leprieur, F.; Oberdorff, T.; Tedesco, P.A.
Titre Global biogeographical regions of freshwater fish species Type Article scientifique
Année (down) 2019 Publication Revue Abrégée J. Biogeogr.
Volume Numéro Pages
Mots-Clés actinopterygians; biogeographical regions; biogeography; bioregionalization; bioregions; connectivity; dispersal; diversity; evolution; freshwater fish; history; homogenization; network; patterns; richness; transition zones; vicariance; world; zoogeographical regions
Résumé Aim To define the major biogeographical regions and transition zones for freshwater fish species. Taxon Strictly freshwater species of actinopterygian fish (i.e. excluding marine and amphidromous fish families). Methods We based our bioregionalization on a global database of freshwater fish species occurrences in drainage basins, which, after filtering, includes 11,295 species in 2,581 basins. On the basis of this dataset, we generated a bipartite (basin-species) network upon which we applied a hierarchical clustering algorithm (the Map Equation) to detect regions. We tested the robustness of regions with a sensitivity analysis. We identified transition zones between major regions with the participation coefficient, indicating the degree to which a basin has species from multiple regions. Results Our bioregionalization scheme showed two major supercontinental regions (Old World and New World, 50% species of the world and 99.96% endemics each). Nested within these two supercontinental regions lie six major regions (Nearctic, Neotropical, Palearctic, Ethiopian, Sino-Oriental and Australian) with extremely high degrees of endemism (above 96% except for the Palearctic). Transition zones between regions were of limited extent compared to other groups of organisms. We identified numerous subregions with high diversity and endemism in tropical areas (e.g. Neotropical), and a few large subregions with low diversity and endemism at high latitudes (e.g. Palearctic). Main conclusions Our results suggest that regions of freshwater fish species were shaped by events of vicariance and geodispersal which were similar to other groups, but with freshwater-specific processes of isolation that led to extremely high degrees of endemism (far exceeding endemism rates of other continental vertebrates), specific boundary locations and limited extents of transition zones. The identified bioregions and transition zones of freshwater fish species reflect the strong isolation of freshwater fish faunas for the past 10-20 million years. The extremely high endemism and diversity of freshwater fish fauna raises many questions about the biogeographical consequences of current introductions and extinctions.
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Volume de collection Numéro de collection Edition
ISSN 0305-0270 ISBN Médium
Région Expédition Conférence
Notes WOS:000484392300001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2637
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