Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Tropical cyclone (TC) waves can severely damage coral reefs. Models that predict where to find such damage (the 'damage zone') enable reef managers to: 1) target management responses after major TCs in near-real time to promote recovery at severely damaged sites; and 2) identify spatial patterns in historic TC exposure to explain habitat condition trajectories. For damage models to meet these needs, they must be valid for TCs of varying intensity, circulation size and duration. Here, we map damage zones for 46 TCs that crossed Australia's Great Barrier Reef from 1985–2015 using three models – including one we develop which extends the capability of the others. We ground truth model performance with field data of wave damage from seven TCs of varying characteristics. The model we develop (4MW) out-performed the other models at capturing all incidences of known damage. The next best performing model (AHF) both under-predicted and over-predicted damage for TCs of various types. 4MW and AHF produce strikingly different spatial and temporal patterns of damage potential when used to reconstruct past TCs from 1985–2015. The 4MW model greatly enhances both of the main capabilities TC damage models provide to managers, and is useful wherever TCs and coral reefs co-occur.
ISSN: 2045-2322

Droits : http://creativecommons.org/licenses/by/
hal-01330362
https://hal-univ-perp.archives-ouvertes.fr/hal-01330362
https://hal-univ-perp.archives-ouvertes.fr/hal-01330362/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01330362/file/srep26009.pdf
DOI : 10.1038/srep26009

Résumé : La nécessité d'une approche intégrée des pêches est actuellement largement affirmée, notamment par la FAO, en particulier dans le contexte des pêcheries artisanales tropicales. Ces pêcheries à petites échelles, souvent multi-spécifiques sont très importantes en termes d'emploi et de production, y compris pour la sécurité alimentaire. Néanmoins ces pêcheries et la biodiversité exploitées sont souvent marquées, d'une part, par le manque de données rendant difficile leur gestion dans le cadre d'une approche écosystémique, d'autre part, par la complexité des systèmes écologiques et économiques sous-jacents incluant interactions trophiques et techniques.Cette thèse contribue à la mise au point d'outils bioéconomiques adaptés aux petites pêcheries tropicales dans la perspective d'une gestion durable des pêches fondée sur l'approche écosystémique. Dans cette perspective, la pêcherie côtière en Guyane Française constitue un cas d'étude particulièrement fécond. La thèse propose ainsi des évaluations multi-critères, des modèles bioéconomiques complexes et des scénarios de gestion viable pour cette pêcherie.Dans un premier temps l'analyse statistique multi-variée suggère un statut global satisfaisant de la pêcherie en termes de durabilité. Cependant des différences de performance sont notées au sein de la pêcherie, notamment au niveau des zones frontalières. Aussi des améliorations dans le mode de gestion sont proposées. Ensuite, à travers la modélisation bioéconomique, les projections des différents scénarios de pêche montrent qu'à long terme le niveau d'exploitation actuel peut ne pas être en adéquation avec la future augmentation de la demande locale et qu'une perte de biodiversité peut avoir lieu. Un scénario dit de « co-viabilité » conciliant des objectifs à la fois écologique, économique et social, avec une probabilité de réalisation satisfaisante, est mis en exergue. Enfin, la comparaison des comportements optimaux en situation coopératif et non coopératif, montre dans quelle mesure la viabilité est favorisée quand les acteurs coopèrent. Au-delà du diagnostic apporté pour le cas d'étude, la méthode utilisée s'avère prometteuse dans le contexte des petites pêcheries tropicales, tandis que l'approche de « co-viabilité » permet de trouver les modalités d'exploitation dans le cadre de compromis entre durabilité écologique et socio-économique, ce que les principes de gestion halieutiques traditionnels ne permettent généralement pas.
The need for an integrated approach to fisheries is now widely affirmed, including the FAO, in particular in the context of tropical artisanal fisheries. These small-scale fisheries, often multispecies are very important in terms of production, employment and food security. However these fisheries and the exploited resources are often characterized by a lack of data making difficult their management within an ecosystem approach, and by the ecological and economic system complexities including trophic and technological interactions.This thesis aims to contribute to the development of bioeconomic tools for small tropical fisheries in a sustainable management perspective based on the ecosystem approach. In this perspective, the French Guiana coastal fishery constitutes an interesting case study. The thesis proposes multi-criteria evaluations, complex bioeconomic models and viable management scenarios for this fishery. At first, multivariate statistical analysis suggests a satisfactory overall status of the fishery in terms of sustainability. However, some performance differences are noted within the fishery, particularly at border areas. Also, management improvements are proposed. Then, through bioeconomic modeling, projections of different fishing scenarios show that, in the long term, the current exploitation level may not be consistent with the future increase of local demand and a loss of biodiversity may occur. A scenario called "co-viability" reconciling ecological, economic and social objectives, with a high probability of achievement is exhibited. Finally, the comparison of optimal behavior in cooperative and non-cooperative conditions, confirms that harvest levels are greater when actors do not cooperate. Furthermore, it is shown that the state of the ecosystem depends on the fishing strategies and the type of interaction between species. Beyond the diagnosis made for the case study, the method is promising in the context of small tropical fisheries, while the co-viability approach allows finding the exploitation conditions under which ecological and socio-economic sustainability are meet, what the conventional fisheries management generally do not allow.

http://www.theses.fr/2013AGUY0620/document

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Functional aspects of biodiversity were investigated in a lowland tropical rainforest in French Guyana (5°2'N, annual precipitation 2200 mm). We assessed leaf '15N as a presumptive indicator of symbiotic N2 fixation, and leaf and wood cellulose '13C as an indicator of leaf intrinsic water-use efficiency (CO2 assimilation rate/leaf conductance for water vapour) in dominant trees of 21 species selected for their representativeness in the forest cover, their ecological strategy (pioneers or late successional stage species, shade tolerance) or their potential ability for N2 fixation. Similar measurements were made in trees of native species growing in a nearby plantation after severe perturbation (clear cutting, mechanical soil disturbance). Bulk soil '15N was spatially quite uniform in the forest (range 3-5‰), whereas average leaf '15N ranged from m0.3‰ to 3.5‰ in the different species. Three species only, Diplotropis purpurea, Recordoxylon speciosum (Fabaceae), and Sclerolobium melinonii (Caesalpiniaceae), had root bacterial nodules, which was also associated with leaf N concentrations higher than 20 mg gm1. Although nodulated trees displayed significantly lower leaf '15N values than non-nodulated trees, leaf '15N did not prove a straightforward indicator of symbiotic fixation, since there was a clear overlap of '15N values for nodulated and non-nodulated species at the lower end of the '15N range. Perturbation did not markedly affect the difference '15Nsoil m '15Nleaf, and thus the isotopic data provide no evidence of an alteration in the different N acquisition patterns. Extremely large interspecific differences in sunlit leaf '13C were observed in the forest (average values from m31.4 to m26.7‰), corresponding to intrinsic water-use efficiencies (ratio CO2 assimilation rate/leaf conductance for water vapour) varying over a threefold range. Wood cellulose '13C was positively related to total leaf '13C, the former values being 2-3‰ higher than the latter ones. Leaf '13C was not related to leaf '15N at either intraspecific or interspecific levels. '13C of sunlit leaves was highest in shade hemitolerant emergent species and was lower in heliophilic, but also in shade-tolerant species. For a given species, leaf '13C did not differ between the pristine forest and the disturbed plantation conditions. Our results are not in accord with the concept of existence of functional types of species characterized by common suites of traits underlying niche differentiation; rather, they support the hypothesis that each trait leads to a separate grouping of species.
ISSN: 0029-8549

hal-01032378
https://hal.archives-ouvertes.fr/hal-01032378
DOI : 10.1007/s004420050593

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : International audience
Context : Functional - structural models (FSM) of tree growth have great potential in forestry, but their development, calibration and validation are hampered by the difficulty of collecting experimental data at organ scale for adult trees. Due to their simple architecture and morphological properties, " model plants " such as Cecropia sciadophylla are of great interest to validate new models and methodologies, since exhaustive descriptions of their plant structure and mass partitioning can be gathered. * Aims : Our objective was to develop a model-based approach to analysing the influence of environmental conditions on the dynamics of trophic competition within C. sciadophylla trees. * Methods : We defined an integrated environmental factor that includes meteorological medium-frequency variations and a relative index representing the local site conditions for each plant. This index is estimated based on model inversion of the GreenLab FSM using data from 11 trees for model calibration and 7 trees for model evaluation. * Results : The resulting model explained the dynamics of biomass allocation to different organs during the plant growth, according to the environmental pressure they experienced. * Perspectives : By linking the integrated environmental factor to a competition index, an extension of the model to the population level could be considered.
ISSN: 1286-4560

hal-00780347
https://hal-ecp.archives-ouvertes.fr/hal-00780347
https://hal-ecp.archives-ouvertes.fr/hal-00780347/document
https://hal-ecp.archives-ouvertes.fr/hal-00780347/file/Letort2011AFS.pdf
DOI : 10.1007/s13595-011-0131-x

Éditeur(s) : Ecole Nationale Supérieure Agronomique de Rennes
Résumé : Long-line fishing has been growing on the island of La Réunion since the beginning of the 1990s. The target species is the swordfish (Xiphias gladius), fished mainly in the tropical waters surrounding the island between longitudes 45 degree E and 60 degree E, and latitudes 17 degree S and 27 degree S. From 1998 to 2000, a finalised research programme enabled the collection of precise data concerning the lines' positions and the parameters of the fishing efforts: 3,602 nettings were thus informed by the catches (in numbers of individuals caught) and 12 descriptive variables of the effort. In parallel with this collection effort, satellite maps that described the ocean's landscape of this region of the Indian Ocean exploited by La Réunion's fisheries were made available to sailors and scientists. Extractions from these environmental variables were made at the fishing lines' positions, which allowed us to propose 20 variables describing the environmental conditions of swordfish catches applied to the nettings. In an early part of this study, after a descriptive analysis and a first selection of the variables, we used several GAM (Generalised Additive Models) to model the respective effects of effort and environmental variables on the variability of swordfish catches. We thus highlighted the predominance of factors linked to fishermen (fishing effort) on oceanographic factors in the explanation of this variability. Following these results, a summary on the biology and ecology of the swordfish was proposed in order to draw up hypotheses on the characteristics of this species' population in the Indian Ocean. The aspects linked to the individual behaviour and movements of the population were particularly highlighted. In a latter part of this study and in order to complete the empirical approach by an exploratory constructivist approach, we proposed a modelling tool in order to simulate the possible movements of individuals within the oceanic landscape described by the available satellite maps. After reading in the literature about the various forms of modelling the movements of the large pelagics, we developed an original computer modelling architecture of the multi-agent type that made it possible to manipulate in a dynamic way the satellite maps (and derived products), the individual movements of "animats" whose behaviours were based on this environmental information, and agents that clarify the process of long-line fishing in a geographical way. The computer model that was implemented (MUFINS, for MUlti-Fish INdian ocean Simulator) was next used by calibrating the behaviour of the animats on the real data originally from the analysis of commercial catches proposed in the first part, using robust techniques based on fuzzy logic. The results of the simulations were compared, on the one hand, with the large-scale hypotheses of movement proposed in the first part, and, on the other hand, to swordfish catches both real and corrected for the effect of the fishing effort modelled by the GAM models. Even if the results of these simulations in this study do not allow for proposing convincing interpretations of the underlying processes, the MUFINS tool showed its ability to address questions associated with the swordfish's behaviour in the tropical oceanic landscape and to the effects of scale transfers between the individual level and the collective level. We now envisage its use in a more operational framework, as an interface for dialogue between fishermen and scientists with a goal of sustainable management of the resource.
La peche palangriere s'est developpee a l'ile de La Reunion depuis le debut des annees 1990. L'espece cible est l'espadon (Xiphias gladius), principalement exploite dans les eaux tropicales autour de l'ile entre les longitudes 45 degree E et 60 degree E, et les latitudes 17 degree S et 27 degree S. De 1998 a 2000, un programme de recherche finalisee a permis de collecter des informations precises concernant les positions des lignes et les parametres de l'effort de peche : 3602 filages sont ainsi renseignes par les captures (en nombre d'individus captures) et 12 variables descriptives de l'effort. En parallele de cet effort de collecte, des cartes satellitales ont pu etre mises a la disposition des marins et des scientifiques, decrivant le paysage oceanique de cette region de l'ocean Indien exploitee par la pecherie reunionnaise. Des extractions de ces variables environnementales ont ete effectuees aux positions des lignes de peche, nous permettant de proposer 20 variables descriptives des conditions environnementales de captures d'espadon appliquees aux filages. Dans une premiere partie de ce travail, apres une analyse descriptive et une premiere selection des variables, on a modelise par plusieurs modeles GAM (Generalized Additive Models) les effets respectifs des variables d'effort et des variables environnementales sur la variabilite des captures d'espadon. On a ainsi mis en evidence la predominance des facteurs lies aux pecheurs (effort de peche) sur les facteurs oceanographiques dans le caractere explicatif de cette variabilite. A la suite de ces resultats, une synthese sur la biologie et l'ecologie de l'espadon a ete proposee afin de degager des hypotheses sur les caracteristiques de la population de cette espece dans l'ocean Indien. Les aspects lies au comportement individuel et aux deplacements de la population ont ete particulierement mis en evidence. Dans une deuxieme partie de ce travail et afin de completer l'approche empirique par une approche constructiviste exploratoire, nous avons propose un outil de modelisation afin de simuler les deplacements possibles d'individus au sein du paysage oceanique decrit par les cartes satellitales disponibles. Apres avoir passe en revue dans la litterature les differentes formes de modelisation des deplacements des grands, pelagiques, nous avons developpe une architecture originale de modelisation informatique de type multi-agents permettant de manipuler de maniere dynamique les cartes satellitales (et les produits derives), les mouvements individuels < d'animats >, dont les comportements sont bases sur cette information environnementale, et des agents qui explicitent le processus de capture palangriere de maniere geographique. Le modele informatique ainsi implemente (MUFINS, pour MUlti-Fish INdian ocean Simulator) a ensuite ete utilise en calibrant les comportements des animats sur les donnees reelles issues de l'analyse des captures commerciales proposee en premiere partie, a partir de techniques robustes basee sur la logique floue. Les resultats des simulations ont ete confrontes d'une part aux hypotheses de deplacement a grande echelle proposees en premiere partie, et d'autre part aux captures d'espadon reelles et corrigees de l'effet de l'effort de peche modelise par les modeles GAM. Meme si les resultats de simulations presentes dans ce travail ne permettent pas de proposer d'interpretations convaincantes des processus sous-jacents, l'outil MUFINS a demontre son aptitude a aborder les questions liees au comportement de l'espadon dans le paysage oceanique tropical et aux effets des transferts d'echelle entre le niveau individuel et le niveau collectif. On envisage desormais son utilisation dans un cadre plus operationnel, comme interface de dialogue entre les pecheurs et les scientifiques a des fins de gestion durable de la ressource.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2005/these-2592.pdf
http://archimer.ifremer.fr/doc/00000/2592/

Éditeur(s) : Elsevier Science Bv
Résumé : Small-scale fisheries have traditionally received less research effort than large-scale fisheries and are generally under-studied in Europe. In spite of their comparatively low volume of catches and economic importance, small-scale fisheries are socially important and an integral part of the European coastal zone. Considering the high heterogeneity of situations and the paucity of quantitative data, we used an analytical methodology based on the comparative method. We carried out an analysis of small-scale fisheries (SSFs) in Europe based on a selection of nine case studies. Our objective was to obtain a comprehensive description of small-scale fleets covering different areas/fisheries/species, encompassing the diversity and specific conditions under which SSFs operate, in order to demonstrate the ecological and social sustainability of this often overlooked fisheries segment. A common approach formulated so that the case studies could be compared with the case histories of other competing users, required that for each set of criteria – technical, biological, socio-economic, and institutional – a set of relevant items and indicators was established. An analysis of characteristics common to the selected case studies is conducted and an attempt made to extend our comparisons to the whole of the European Union. Our results show that (as compared with large-scale fleets, their main competitor) small-scale fleets: (i) are composed of smaller vessels and, consequently, travel lower distances to fishing grounds, and are more reliant on coastal areas; (ii) have smaller crews (although the global employment figure is similar to that of large-scale fleets in Europe); (iii) use mostly, but not exclusively, passive gears; (iv) use multi-purpose fishing approaches, and can change the fish species they target during the year; (v) have lower extraction rates; (vi) have lower total capital investments (including fishing rights), turnover and costs; and (vii) have lower fuel consumption, making them less sensitive to changing oil prices. Dependence on subsidies is lower (viii). Involvement in fisheries management is variable, conservation and access regulation measures are largely local in origin. For the selected case studies, the most significant competitors are large-scale fleets, and recreational fisheries, but other sources of interaction (water quality, invasive species, etc.) cannot be ignored.
Fisheries Research (0165-7836) (Elsevier Science Bv), 2013-02 , Vol. 140 , P. 1-13

Droits : 2012 Elsevier B.V. All rights reserved
http://archimer.ifremer.fr/doc/00118/22934/20757.pdf
DOI:10.1016/j.fishres.2012.11.008
http://archimer.ifremer.fr/doc/00118/22934/

Éditeur(s) : HAL CCSD Springer Verlag (Germany)
Résumé : International audience
Mass bleaching events resulting in coral mortality are among the greatest threats to coral reefs, and are projected to increase in frequency and intensity with global warming. Achieving a better understanding of the consistency of the response of coral assemblages to thermal stress, both spatially and temporally, is essential to determine which reefs are more able to tolerate climate change. We compared variations in spatial and taxonomic patterns between two bleaching events at the scale of an island (Moorea Island, French Polynesia). Despite similar thermal stress and light conditions, bleaching intensity was significantly lower in 2007 (approximately 37 % of colonies showed signs of bleaching) than in 2002, when 55 % of the colonies bleached. Variations in the spatial patterns of bleaching intensity were consistent between the two events. Among nine sampling stations at three locations and three depths, the stations at which the bleaching response was lowest in 2002 were those that showed the lowest levels of bleaching in 2007. The taxonomic patterns of susceptibility to bleaching were also consistent between the two events. These findings have important implications for conservation because they indicate that corals are capable of acclimatization and/or adaptation and that, even at small spatial scales, some areas are consistently more susceptible to bleaching than others.
ISSN: 0167-6369

hal-00905944
https://hal.archives-ouvertes.fr/hal-00905944
DOI : 10.1007/s10661-012-2923-3

Éditeur(s) : HAL CCSD PubMed
Résumé : International audience
To investigate thermal response, hydration behaviour and performance over flatwater kayaking races in tropical conditions (36.8°C and 68 % rh). Five internationally-ranked subjects participated in the 2012 Surfski Ocean Racing World Cup in Guadeloupe to the “Ze Caribbean Race 2012” [i.e., a 35-km downwind race]. Core temperature (T°C) and heart rate (HR) were measured using portable telemetry units whereas water intake was deduced from backpacks absorption. The kayakers were asked to rate both their comfort sensation and thermal sensation on a scale before and after the race. The performance was related to an increase in T°C, high HR and low water intake (WI); and (2) high values of final T°C were related to high pre T°C and greater increases in T°C being obtained with low pre T°C and (3) WI being related to high pre T°C. The present study demonstrated that the fastest kayakers were those able to paddle at the highest intensities, increasing their T°C and drinking little water without any interference from thermal sensations. Water intake was positively related to pre-race T°C, which reinforces the importance of beginning surfski races with a low T°C. This study demonstrated that well-trained kayakers drinking ad libitum were able to anticipate their intensity/heat storage ratio to prevent heat illness and severe dehydration and maintain high performance.
ISSN: 0860-021X

hal-01137286
https://hal.univ-antilles.fr/hal-01137286

Éditeur(s) : HAL CCSD Royal Society, The
Résumé : International audience
Infectious marine diseases can decimate populations and are increasing among some taxa due to global change and our increasing reliance on marine environments. Marine diseases become emergencies when significant ecological, economic or social impacts occur. We can prepare for and manage these emergencies through improved surveillance, and the development and iterative refinement of approaches to mitigate disease and its impacts. Improving surveillance requires fast, accurate diagnoses, forecasting disease risk and real-time monitoring of disease-promoting environmental conditions. Diversifying impact mitigation involves increasing host resilience to disease, reducing pathogen abundance and managing environmental factors that facilitate disease. Disease surveillance and mitigation can be adaptive if informed by research advances and catalysed by communication among observers, researchers and decision-makers using information-sharing platforms. Recent increases in the awareness of the threats posed by marine diseases may lead to policy frameworks that facilitate the responses and management that marine disease emergencies require.
ISSN: 0962-8436

hal-01282464
https://hal-univ-perp.archives-ouvertes.fr/hal-01282464
DOI : 10.1098/rstb.2015.0364

Éditeur(s) : HAL CCSD Springer Verlag
Résumé :  
Quantitative genetic diversity is a fundamental component of the interaction between natural populations and their environment. In breeding programmes, quantitative genetic studies on tropical trees have so far focused on fast-growing, light-demanding species, but no information exists on shade-tolerant, slow-growing species. For this study, 27 3-year-old open-pollinated families of the Neotropical shade-tolerant rainforest tree Sextonia rubra were measured in semicontrolled conditions for 20 morphological, growth, and photosynthesis traits; the effect of genetic relatedness, habitat of provenance, and mother tree status on seedling traits was analysed. Nine traits displayed significant genetic effects, while mother tree status and habitat effects were not significant (P>0.05) for an y trait. Estimated heritability varied between 0.14 and 0.28, with growth-related traits having the highest values. Additive genetic variation correlated positively with nonheritable variation, suggesting that ecological-evolutionary factors increasing or decreasing additive genetic variance may also affect nonheritable variation in the same direction. Our results suggest that quantitative genetic variability should be taken into account in ecological studies on, and in the management of, natural tropical rainforests; further research is needed to investigate genetic × environment interactions, in particular from the point of view of the genetic response of shade-tolerant plant species to variations in light availability.
ISSN: 1614-2942

hal-01032145
https://hal.archives-ouvertes.fr/hal-01032145
DOI : 10.1007/s11295-009-0251-8

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
Under physiological conditions, the liver sinusoidal endothelial cells (LSECs) mediate hepatic immune tolerance toward self or foreign antigens through constitutive expression of anti-inflammatory mediators. However, upon viral infection or Toll-like receptor 2 (TLR2) activation, LSECs can achieve proinflammatory functions, but their role in hepatic inflammation during acute viral hepatitis is unknown. Using the highly virulent mouse hepatitis virus type 3 (MHV3) and the attenuated variants 51.6-MHV3 and YAC-MHV3, exhibiting lower tropism for LSECs, we investigated in vivo and in vitro the consequence of LSEC infection on their proinflammatory profiles and the aggravation of acute hepatitis process. In vivo infection with virulent MHV3, in comparison to attenuated strains, resulted in fulminant hepatitis associated with higher hepatic viral load, tissue necrosis, and levels of inflammatory mediators and earlier recruitment of inflammatory cells. Such hepatic inflammatory disorders correlated with disturbed production of interleukin-10 (IL-10) and vascular factors by LSECs. We next showed in vitro that infection of LSECs by the virulent MHV3 strain altered their production of anti-inflammatory cytokines and promoted higher release of proinflammatory and procoagulant factors and earlier cell damage than infection by attenuated strains. This higher replication and proinflammatory activation in LSECs by the virulent MHV3 strain was associated with a specific activation of TLR2 signaling by the virus. We provide evidence that TLR2 activation of LSCEs by MHV3 is an aggravating factor of hepatic inflammation and correlates with the severity of hepatitis. Taken together, these results indicate that preservation of the immunotolerant properties of LSECs during acute viral hepatitis is imperative in order to limit hepatic inflammation and damage. IMPORTANCE Viral hepatitis B and C infections are serious health problems affecting over 350 million and 170 million people worldwide, respectively. It has been suggested that a balance between protection and liver damage mediated by the host's immune response during the acute phase of infection would be determinant in hepatitis outcome. Thus, it appears crucial to identify the factors that predispose in exacerbating liver inflammation to limit hepatocyte injury. Liver sinusoidal endothelial cells (LSECs) can express both anti- and proinflammatory functions, but their role in acute viral hepatitis has never been investigated. Using mouse hepatitis virus (MHV) infections as animal models of viral hepatitis, we report for the first time that in vitro and in vivo infection of LSECs by the pathogenic MHV3 serotype leads to a reversion of their intrinsic anti-inflammatory phenotype toward a proinflammatory profile as well to as disorders in vascular factors, correlating with the severity of hepatitis. These results highlight a new virus-promoted mechanism of exacerbation of liver inflammatory response during acute hepatitis.
ISSN: 0022-538X

hal-01390974
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390974
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390974/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390974/file/Mouse%20Hepatitis%20Virus%20Infection_accepted.pdf
DOI : 10.1128/JVI.01069-16

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In order to perform a human and ecological risk assessment of pharmaceutical products (PPs) in natural waters, it is necessary to accurately quantify a broad variety of PPs at low concentrations. Although numerous currently implemented analytical methodologies, less is known about the preservation of PPs in natural water samples within the period before analysis (holding time, storage conditions). This paper is the first literature review about the stability of PPs in natural waters (surface and groundwaters) during sample storage. The current work focuses on a comparison of the performances of the available preservation techniques (filtration, container materials, storage temperature, preservative agents, etc.) for PPs in samples. All 58 reviewed PPs may be successfully stabilized during 7 days in surface waters by at least one appropriate methodology regarding temperature, acidic and non-acidic preservatives. When temperature is not a sufficient preservation parameter f! or some PPs (hormones and fluoxetine) its combination with the addition of chemical agents into the samples may prolong the integrity of the PPs during storage in surface water. There is a strong need to use standard protocols to assess and compare the stability of PPs in environmental water matrices during storage as well as during analytical preparation or analysis (European criteria 2002/657/EC). Since the stability of PPs during sample storage is a critical parameter that could call into question the quality of the data provided for the concentrations, the design of stability studies should rigorously take into account all critical parameters that could impact the concentrations of the PPs with time.
Talanta

insu-00839186
https://hal-insu.archives-ouvertes.fr/insu-00839186
DOI : 10.1016/j.talanta.2013.01.042

Éditeur(s) : HAL CCSD
Résumé : The bacterial microbiota of ants (Hymenoptera: Formicidae) is known to have a defensive role in social insects, particularly for leaf-cutting ants (Formicidae: Attini) due to the use of antimicrobial molecules produced by cuticular actinobacteria. In this thesis, we studied the bacterial microbiota of ants in French Guyana using different approaches based on natural products chemistry and molecular ecology. The first chapter describes the isolation, identification, culture and biological evaluations of 43 cuticular actinobacteria. Antagonism bioassays of isolated strains and antibiotic activities of the culture extracts against human pathogens are presented as well as the identification of an antimicrobial cyclic dipeptide (Cyclo (LPro-LPhe)) isolated from a strain close to Streptomyces thioluteus. Moreover, the implementation of molecular networks applied to UPLC/MS/MS analysis of actinobacterial cocultures allowed us to explore the diversity of metabolites produced under these conditions. The second chapter presents a methodological study to evaluate the capacity of four DNA extraction methods, in terms of richness and composition of the cuticular bacterial microbiota, in high-throughput sequencing from Atta cephalotes and Pseudomyrmex penetrator. The results of metabarcoding highlight two methods of extraction and reveal inter- and intraspecific differences in the composition of cuticular bacterial communities. Finally, chapter three describes the composition of the cuticular bacterial microbiota of Camponotus femoratus and Crematogaster levior in ant garden and the results reveal the acquisition in the environment of a part of the microbiota. In parallel, metabolomic analyses of ant’s cuticle show, on the contrary, a greater specificity related to the ant species. Future researches focusing on statistical analysis strategies combining metabarcoding and metabolomics data are discussed.
Le microbiote bactérien cuticulaire des fourmis (Hymenoptera : Formicidae) est connu pour avoir un rôle défensif chez ces insectes sociaux, notamment chez les fourmis attines (Formicidae : Attini) grâce l’utilisation de molécules antimicrobiennes produites par des actinobactéries cuticulaires. Dans le cadre de cette thèse, nous avons étudié le microbiote bactérien des fourmis de Guyane en utilisant différentes approches en chimie des produits naturels et en écologie moléculaire. Le premier chapitre décrit l’isolement, l’identification, la culture et l’évaluation biologique de 43 actinobactéries cuticulaires de fourmis de Guyane. Les tests d’antagonismes des souches isolées et l’activité antibiotique des extraits de culture contre des micro-organismes pathogènes humains sont présentés ainsi que l’identification d’un dipeptide cyclique (Cyclo(LPro-LPhe)) antimicrobien qui a été isolé à partir d’une souche proche de Streptomyces thioluteus. Par ailleurs, la mise en œuvre de réseaux moléculaires appliqués à une analyse par UPLC/MS/MS de cocultures d’actinobactéries a permis d’explorer la diversité des métabolites produits dans ces conditions. Le deuxième chapitre présente une étude méthodologique pour comparer quatre méthodes d’extraction d’ADN, en termes de richesse et de composition du microbiote bactérien cuticulaire, par séquençage haut débit à partir des espèces Atta cephalotes et Pseudomyrmex penetrator. Les résultats du métabarcoding ADN mettent en lumière deux méthodes d’extraction et révèlent des différences inter- et intraspécifiques dans la composition des communautés bactériennes cuticulaires. Enfin, le chapitre trois décrit la composition du microbiote bactérien cuticulaire des espèces Camponotus femoratus et Crematogaster levior dans les jardins de fourmis. Les résultats soulignent l’acquisition d’une partie du microbiote dans l’environnement. En parallèle l’analyse métabolomique des cuticules montre à contrario une plus grande spécificité liée à l’espèce de fourmi. Les recherches futures axées sur les stratégies d’analyses statistiques combinant le métabarcoding et la métabolomique sont discutées.
https://tel.archives-ouvertes.fr/tel-01537793

NNT : 2017YANE0003
tel-01537793
https://tel.archives-ouvertes.fr/tel-01537793
https://tel.archives-ouvertes.fr/tel-01537793/document
https://tel.archives-ouvertes.fr/tel-01537793/file/thesecarolinebirer.pdf

Éditeur(s) : Academic Press Ltd- Elsevier Science Ltd
Résumé : Ensuring the sustainability of fish resources necessitates understanding their interaction with coastal habitats, which is becoming ever more challenging in the context of ever increasing anthropogenic pressures. The ability of coastal lagoons, exposed to major sources of disturbance, to provide resources and suitable habitats for growth and survival of juvenile fish is especially important. We analysed three lagoons with different ecological statuses and habitat quality on the basis of their eutrophication and ecotoxicity (Trix test) levels. Fish abundances were sampled using fishing and horizontal beaming acoustic surveys with the same protocols in the same year. The relative abundance of Anguilla anguilla, Dicentrarchus labrax or the Mugilidae group was not an indicator of habitat quality, whereas Atherina boyeri and Sparus aurata appeared to be more sensitive to habitat quality. Fish abundance was higher in the two lagoons with high eutrophication and ecotoxicity levels than in the less impacted lagoon, while fish sizes were significantly higher in the two most severely impacted lagoons. This leads us to suggest low habitat quality may increase fish growth rate (by the mean of a cascading effect), but may reduce lagoon juvenile abundance by increasing larval mortality. Such a hypothesis needs to be further validated using greater investigations which take into account more influences on fish growth and recruitment in such variable environments under complex multi-stressor conditions.
Estuarine Coastal And Shelf Science (0272-7714) (Academic Press Ltd- Elsevier Science Ltd), 2013-07 , Vol. 126 , P. 1-6

Droits : 2013 Elsevier Ltd. All rights reserved
http://archimer.ifremer.fr/doc/00148/25963/24083.pdf
DOI:10.1016/j.ecss.2013.03.011
http://archimer.ifremer.fr/doc/00148/25963/

Éditeur(s) : HAL CCSD
Résumé :   Diffusion du document : INRA Antilles-Guyane, UMR ECOFOG, F97387 Kourou, Guyane (France) Diplôme : DEA
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
This work on tropic al humid forest of Paracou includes 16 permanent sample plots covering a total surface of 119 hectares. Ten hectares of them are taken up by floodplains which characteristic is a continuous no-deep underground water level with phases of strong surface water logging. Three items have been studied : (i) Checking that during dry season the maps of the underground water level including its limits are reliable, (ii) Characterising the most suitable ecological niches for certain species, (iii) Additional updating the floodplains characterisation by precisely analysing the chemical soil content as well as the physiological reaction of the Symphonia Globulifera . Checking the underground water level in dry season enabled to put down to a quite good measurement reliability by GIS. The classification ecological of species proposed in this work is based on the relative density in floodplain and drain soil very similar to that which concerns a surface located ten or more kilometres further. This lets us assess that this classification is of a good reliability as long as the climate conditions are quite similar to ours in Paracou. Furthermore the presence of pneumatophores in the Symphonia Globulifera is a good biological criterion as long as it shows a long time ground moisture saturation. By analysing the life litter and the soil we mentioned that the leaf content and the soil content indicate a better nutritional value (phosphorus, calcium and potassium) in the floodplains. For phosphorus the relation between the life litter and the soil results put forward that the Olsen method gives a better explanation of the real phosphorus availability for the trees.
Le dispositif de recherche sur la forêt tropicale humide de Paracou est composé de 16 parcelles permanentes couvrant au total 119 ha, dont 10 ha sont occupés par des bas-fonds, caractérisés par l'existence permanente d'une nappe peu profonde et par des périodes de fort engorgement en surface. Notre étude avait trois objectifs : (i) vérifier la fiabilité des cartes de la profondeur de nappe en saison sèche, qui délimitent ces bas-fonds, (ii) caractériser les préférences écologiques de quelques espèces et (iii) compléter la caractérisation des bas-fonds par l'analyse de la richesse chimique du sol et l'étude de la réaction physiologique du Symphonia globulifera. La vérification sur la profondeur de nappe en saison sèche a montré que les imprécisions des cartes étaient d'ampleur limitée, sans incidence forte par rapport à l'ensemble des données. Le classement écologique des espèces proposé dans cette étude, basé sur leurs densités relatives dans les bas-fonds et hors des bas-fonds, est très similaire à celui présenté par une autre étude, dans un dispositif situé à plusieurs dizaines de kilomètres. Cela suggère que ce classement a une bonne validité, tant que les conditions climatiques ne diffèrent pas trop de celles rencontrées à Paracou. Par ailleurs, la présence des pneumatophores du Symphonia globulifera est un bon critère biologique signalant un engorgement hydrique prolongé du sol. Au niveau des analyses de la litière et du sol, les teneurs foliaires et les teneurs dans le sol semblent indiquer que la nutrition en phosphore, calcium et potassium est meilleure en bas-fonds. Au niveau de la méthode de mesure du phosphore assimilable, les relations entre les résultats de la litière et celles du sol suggèrent que la méthode d'Olsen rend mieux compte de la disponibilité effective du phosphore pour les arbres de la forêt tropicale humide que la méthode de Duchaufour.
https://hal.archives-ouvertes.fr/hal-01189229

hal-01189229
https://hal.archives-ouvertes.fr/hal-01189229
PRODINRA : 17050

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between alpha- and beta-diversity of soil fungi and trees. Both fungal and plant community beta-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant-fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.
ISSN: 1751-7362

hal-01032405
https://hal.archives-ouvertes.fr/hal-01032405
DOI : 10.1038/ismej.2013.66

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : L’incendie de forêt reste incontestablement un des facteurs de dégradation les plus dévastateurs dans le bassin méditerranéen, lequel est caractérisé par une végétation très inflammable et des conditions climatiques chaudes et sèches. Le Maroc, pays du pourtour méditerranéen, n’est pas épargné par ce fléau, avec 3000 ha de forêts qui partent annuellement en fumée ; cette situation est aggravée par les difficultés de régénération et de restauration des espaces, marqués par une vulnérabilité naturelle telle que celle de la Mâamora. Pour répondre à cela, la conception d’un plan d’aménagement anti-feux visant à conférer à la forêt de la Mâamora une immunité élevée contre les incendies, nécessite non seulement une connaissance approfondie du milieu, mais aussi une analyse appropriée du phénomène « incendie ». La présente étude qui se penche sur le diagnostic et l’analyse des incendies survenus en Mâamora, a permis de constater que les zones d’interface homme-forêt (routes, douars, etc.) n’ont pas d’influence sur l’occurrence des incendies. Il ressort également que l’activité pastorale, pratiquée d’une certaine façon, pourrait jouer un rôle important dans la diminution des risques d’incendie. En outre l’étude révèle que la charge du combustible représente le facteur prépondérant qui régit à la fois l’éclosion des incendies et leur propagation, cette charge étant étroitement liée à la qualité de la station (sol et pluviométrie).
Forest fires are the main disturbance and the degradation factor most devastating that can affect forested areas, especially in the Mediterranean basin when species are highly flammable and climate conditions are marginal. Morocco as a Mediterranean country is not spared from this phenomenon, thus 3000 ha of forest are burned every year, and this situation is aggravated by the low rate of regeneration and restoration of the unbalanced ecosystems such as the Mâamora. To mitigate this situation, the establishment of an effective management plan for forest fire prevention requires not only an intimate knowledge of environment but also a perfect analysis of fire phenomenon. Therefore in this study, we focused our diagnosis on the analysis of old fires occurred in the past in Mâamora forest. The study highlighted that human-forest interface areas (roads, villages) have no influence on fires occurrence. Besides it was shown that grazing practiced in a well-balanced way, could play a key role in reducing fire hazards. In addition the study reveals that fuel load of is the major factor that governs both fire ignition and fire spread of, this load is closely related to site quality (soil and rainfall)
Maroc

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.10978
http://journals.openedition.org/etudescaribeennes/10978

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : La mer des Caraïbes abrite une diversité de biotopes littoraux qui favorisent l’installation de trois écosystèmes - les récifs coralliens, les mangroves et les herbiers – riches et complexes. On y trouve également d’autres formations uniques tels les stromatolithes ou les trous bleus. Des conditions climatiques et océanographiques homogènes permettent à l’ensemble du bassin Caraïbe de constituer une unité sur les plans floristique et faunistique. Cette unité n’exclut pas une diversité biologique exceptionnelle avec notamment des espèces endémiques à la zone ; ce qui confère aux côtes des pays caribéens un intérêt écologique, paysager et scientifique certain. La reconnaissance sur le plan international et régional de l’importance de la Mer des Caraïbes mais aussi de sa fragilité a permis au milieu marin caribéen d’acquérir son statut de patrimoine naturel.En plus des services écosystémiques qu’elle rend (ressources halieutiques, protection des littoraux…), la Mer des Caraïbes constitue un atout indéniable dans le cadre du développement touristique de la zone aussi bien par le balnéaire que, plus récemment, par l’écotourisme. Ce dernier s’appuie généralement sur des aires marines protégées et doit permettre un développement durable des îles.A partir d’une étude de cas, le parc marin de Saba, l’objectif de cette étude est d’analyser les rapports entre patrimoine naturel marin et l’écotourisme, ainsi que les impacts économiques, sociaux et environnementaux de la mise en valeur de ces ressources.
The Caribbean Sea is home to a diversity of coastal habitats that support the installation of three rich and complex ecosystems - coral reefs, mangroves and seagrasses -. There are also other unique formations such as stromatolites or blue holes. Oceanographic and climatic conditions allow homogeneous throughout the Caribbean basin to form a unit in terms of flora and fauna. This unit does not exclude an exceptional biological diversity, including species endemic to the area, which give the coasts of the Caribbean countries an ecological, landscape and some science. Recognition on the international and regional importance of the Caribbean Sea but also its fragile marine environment has allowed the Caribbean to gain its status as a natural heritage.In addition to the ecosystem services it render (fisheries, coastal protection ...), the Caribbean Sea is a definite asset in the development of tourism in the area by the seaside as well as, more recently, ecotourism. The latter is generally based on marine protected areas and should facilitate the sustainable development of islands.From a case study, the Saba Marine Park, the objective of this study is to analyze the relationship between natural heritage and marine ecotourism, as well as economic, social and environmental development of these resources.
Saba

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.5487
http://journals.openedition.org/etudescaribeennes/5487

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Demographic processes and spatial dispersal of Triatoma dimidiata, a triatomine species vector of Chagas disease, are modeled by integrodifference equations to estimate invasion capacity of this species under different ecological conditions. The application of the theory of orthogonal polynomials and the steepest descent method applied to these equations, allow a good approximation of the abundance of the adult female population and the invasion speed. We show that: (1) under the same mean conditions of demography and dispersal, periodic spatial dispersal results in an invasion speed 2.5 times larger than the invasion speed when spatial dispersal is continuous; (2) when the invasion speed of periodic spatial dispersal is correlated to adverse demographic conditions, it is 34.7% higher as compared to a periodic dispersal that is correlated to good demographic conditions. From our results we conclude, in terms of triatomine population control, that the invasive success of T. dimidiata may be most sensitive to the probability of transition from juvenile to adult stage. We discuss our main theoretical predictions in the light of observed data in different triatomines species found in the literature.
ISSN: 0022-5193

hal-01298098
https://hal-univ-perp.archives-ouvertes.fr/hal-01298098
DOI : 10.1016/j.jtbi.2016.01.017

Éditeur(s) : HAL CCSD
Résumé : One critical challenge for plants is to maintain an adequate nutrient supply under fluctuating environmental conditions. This is particularly true for epiphytic species that have limited or no access to the pedosphere and often live in harsh climates. Bromeliads have evolved key innovations such as epiphytism, water-absorbing leaf trichomes, tank habit and Crassulacean acid metabolism (CAM) photosynthesis that enable them to survive under various environmental conditions. Bromeliads encompass diverse ecological types that live on different substrates (they can be terrestrial, epilithic or epiphytic) and vary in their ability to retain water (they can be tank-forming or tankless) and photosynthetic pathway (i.e. C3 or CAM). In this review, we outline the nutritional modes and specializations that enable bromeliads to thrive in a wide range of nutrient-poor (mostly nitrogen-depleted) environments.Important FindingsBromeliads have evolved a great diversity of morphologies and functional adaptations leading to the existence of numerous nutritional modes. Focusing on species that have absorptive foliar trichomes, we review evidence that bromeliads have evolved multi-faceted nutritional strategies to respond to fluctuations in the supply of natural nitrogen (N). These plants have developed mutualistic associations with many different and functionally diverse terrestrial and aquatic microorganisms and metazoans that contribute substantially to their mineral nutrition and, thus, their fitness and survival. Bacterial and fungal microbiota-assisted N provisioning, protocarnivory, digestive mutualisms and myrmecotrophic pathways are the main strategies used by bromeliads to acquire nitrogen. The combination of different nutritional pathways in bromeliads represents an important adaptation enabling them to exploit nutrient-poor habitats. Nonetheless, as has been shown for several other vascular plants, multiple partners are involved in nutrient acquisition indicating that there have been convergent adaptations to nutrient scarcity. Finally, we point out some gaps in the current knowledge of bromeliad nutrition that offer fascinating research opportunities.
ISSN: 1752-9921

hal-01532637
https://hal.archives-ouvertes.fr/hal-01532637
DOI : 10.1093/jpe/rtv052
PRODINRA : 384521