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Facilitative effects of some species on others are a major driver of biodiversity. These positive effects of a benefactor on its beneficiary can result in negative feedback effects of the beneficiary on the benefactor and reduced fitness of the benefactor. However, in contrast to the wealth of studies on facilitative effects in different environments, we know little about whether the feedback effects show predictable patterns of context dependence. We reanalyzed a global data set on alpine cushion plants, previously used to assess their positive effects on biodiversity and the nature of the beneficiary feedback effects, to specifically assess the context dependence of how small- and large-scale drivers alter the feedback effects of cushion-associated (beneficiary) species on their cushion benefactors using structural equation modelling. The effect of beneficiaries on cushions became negative when beneficiary diversity increased and facilitation was more intense. Local-scale biotic and climatic conditions mediated these community-scale processes, having indirect effects on the feedback effect. High-productivity sites demonstrated weaker negative feedback effects of beneficiaries on the benefactor. Our results indicate a limited impact of the beneficiary feedback effects on benefactor cushions, but strong context dependence. This context dependence may help to explain the ecological and evolutionary persistence of this widespread facilitative system.

National audience; La biodiversité a eu une carrière fulgurante : à peine nommée – dans les années 1980 –, elle a été l’objet d’une convention internationale à partir de 1992, à l’issue du sommet de la terre à Rio ; elle a fait l’objet de nombreux engagements régionaux, nationaux, sectoriels, etc., et maintenant d’une équipe d’expertise internationale – l’IBPES – qui vise d’être l’équivalent pour la biodiversité de ce qu’est le GIEC pour le changement climatique. Certains pronostiquent même que malgré cette ascension fulgurante, la biodiversité pourrait être proche de la retraite, supplantée ou phagocytée qu’elle pourrait être par la métaproblématique des services écosystémiques – ou services rendus par les écosystèmes à l’homme . Nous n’irons pas si loin dans ce chapitre et en resterons avec cet étrange objet de la biodiversité pour en commenter certains des aspects qui ne manquent pas d’ambiguïté. Nous insisterons en premier lieu sur la variabilité de la définition de la biodiversité. Puis nous passerons à une composante de la biodiversité – la diversité des espèces – et insisterons sur deux ambiguïtés sous-jacentes à cette notion : d’abord, sur sa décomposition en deux composantes indépendantes – richesse spécifique et équitabilité –, qui en fait n’est pas si simple que cela ; ensuite, sur son lien ténu avec la viabilité des espèces. Ainsi, alors que la biodiversité fait l’objet d’une attention publique grandissante, il reste à identifier et éventuellement lever des zones de flou dans ce concept qui n’est peut-être pas aussi stabilisé que son emploi fréquent ne le laisse suggérer.

Les characées sont des macro-algues bio-indicatrices des eaux oligo-mésotrophes dont la plupart des espèces sont gravement menacées d'extinction. Leur conservation nécessite l'acquisition de connaissances sur leur écologie et sur l'évolution potentielle de leur distribution dans un contexte de changement climatique. Deux analyses de la distribution des espèces menées à l'échelle régionale (Suisse) démontrent qu'elles n'occupent pas toutes le même macro-habitat. A l'horizon 2050, un climat plus chaud et plus sec pourrait défavoriser les espèces lacustres mais favoriser les espèces inféodées aux petits plans d'eau pouvant s'assécher. Les résultats du suivi temporel d'un milieu semi-permanent montrent que la variabilité des conditions d'inondations gouverne effectivement les dynamiques de la communauté de characées. D'après leur réponse aux variations locales de température et de niveau d'eau et leur distribution dans d'autres régions géographiques, plusieurs espèces de characées disposeraient finalement de potentialités d'adaptation à une plus grande variété d'habitats que ceux observés en Suisse.

Contribution to the Theme Section ‘Trophodynamics in marine ecology’.-- 12 pages, 7 figures, 3 tables, supplementary material https://doi.org/10.3354/meps10946, We performed a global assessment of how fish biomass has changed over the last 100 yr, applying a previously developed methodology using ecological modeling. Our assessment built on more than 200 food web models representing marine ecosystems throughout the world covering the period from 1880 to 2007. All models were constructed based on the same approach, and have been previously documented. We spatially and temporally distributed fish biomasses delivered by these models based on fish habitat preferences, ecology, and feeding conditions. From these distributions, we extracted over 68000 estimates of biomass (for predatory and prey fishes separately, including trophic level of 3.5 or higher, and trophic level between 2.0 and 3.0, respectively), and predicted spatial-temporal trends in fish biomass using multiple regression. Our results predicted that the biomass of predatory fish in the world oceans has declined by twothirds over the last 100 yr. This decline is accelerating, with 54% occurring in the last 40 yr. Results also showed that the biomass of prey fish has increased over the last 100 yr, likely as a consequence of predation release. These findings allowed us to predict that there will be fish in the future ocean, but the composition of fish assemblages will be very different from current ones, with small prey fish dominating. Our results show that the trophic structure of marine ecosystems has changed at a global scale, in a manner consistent with fishing down marine food webs. © Inter-Research 2014, This is a contribution from Sea Around Us, a scientific cooperation between the University of British Columbia (UBC) and the Pew Charitable trust. V.C. acknowledges support from the Natural Sciences and Engineering Research Council of Canada. M.C. was partially funded by the EC Marie Curie Career Integration Grant Fellowships to the BIOWEB project and the Spanish National Program Ramon y Cajal.

These experiments are part of the actual problematic of understanding the poorknown effects of pesticides mixtures in soil ecosystem. The herbicidal commercial formulations of S-metolachlor (Dual Gold Safeneur®), mesotrione (Callisto®) and nicosulfuron (Milagro®) were applied in mixtures at the recommended field rate. Formulated compounds are more toxic than active ingredients alone (Microtox®) and no synergistic or antagonistic effects were recorded. However, these mixtures impaired rapidly and transitory the Limagne soil microbial communities, without modifying the global parameters of structure and abundance. Effects were also recorded on sensitive communities, such as phototrophic, nitrifying and denitrifying communities. A comparison of mixtures effects on phototrophic communities from two soils underlined the high toxicity of Dual Gold Safeneur® and challenged its use from an ecotoxicological point of view.., Ces travaux s’inscrivent dans une problématique actuelle de compréhension des effets, encore peu connus, des mélanges de pesticides dans le sol. Les formulations d’herbicides S-métolachlore (Dual Gold Safeneur®), mésotrione (Callisto®) et nicosulfuron (Milagro®) ont été appliquées en mélanges et à la dose agronomique recommandée. Les molécules formulées sont plus toxiques que les molécules actives seules (Microtox®) et aucun effet synergique ou antagoniste des mélanges n’a été observé. Cependant, ces mélanges impactent transitoirement et à court terme les communautés microbiennes du sol de Limagne, sans modifier les paramètres généraux de structure et d’abondance. Toutefois, des effets ont été mis en évidence sur des communautés sensibles telles que les phototrophes ou celles impliquées dans les processus de nitrification et de dénitrification. De plus, une comparaison des effets des mélanges sur les communautés phototrophes de deux sols souligne l’importante toxicité du Dual Gold Safeneur® et remet en cause son utilisation d’un point de vue écotoxicologique.

International audience; The shallow submarine hydrothermal field of the Prony Bay (New Caledonia) discharges hydrogen- and methane-rich fluids with low salinity, temperature (

The whale shark (Rhincodon typus, Smith, 1828) is a migratory species (classed as Vulnerable by the IUCN) with genetic and circumstantial evidence for inter-ocean connectivity. Given this migratory behaviour, populationwide occurrence trends can only be contextualized by examining the synchrony in occurrence patterns among locations where they occur. We present a two-step modelling approach of whale shark spatial and temporal probability of occurrence in the Atlantic and Pacific Oceans using generalized linear mixed-effects models. To test the hypothesis that the probability of whale shark occurrence is asynchronous across oceans, as expected if inter-ocean migration occurs, we used long-term datasets of whale shark sightings derived from tuna purseseine logbooks covering most of the central-east Atlantic (19802010) and western Pacific (20002010). We predicted seasonal habitat suitability to produce maps in each area, and then evaluated the relative effect of time (year) on the probability of occurrence to test whether it changed over the study period. We also applied fast Fourier transforms to determine if any periodicity was apparent in whale shark occurrences in each ocean. After partialling out the effects of seasonal patterns in spatial distribution and sampling effort, we found no evidence for a temporal trend inwhale shark occurrence in the Atlantic, but therewas aweak trend of increasing probability of occurrence in the Pacific. The highest-ranked model for the latter included a spatial predictor of occurrence along with fishing effort, a linear term for time, and a random temporal effect (year), explaining 15% of deviance in whale shark probability of occurrence. Fast Fourier transforms revealed a prominent 15.5-year cycle in the Atlantic. The increase in the probability of occurrence in the Pacific is concurrent with a decrease previously detected in the Indian Ocean. Cyclic patterns driven by migratory behaviour would better explain temporal trends in whale shark occurrence at the oceanic scale. However, despite cycles partially explaining observations of fewer sharks in some years, overall reported sighting rate has been decreasing. As a result, we suggest that the current IUCN status of the species should be re-assessed, but more data are needed to examine the flow of individuals across oceans and to identify possible reasons for asynchronous occurrences.

15 pages, 11 figures, 4 tables, 2 annex, 3 tables supporting information http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0085670, Background: The expansion of fishing activities has intensively transformed marine ecosystems worldwide. However, available time series do not frequently cover historical periods. Methodology: Fishers’ perceptions were used to complement data and characterise changes in fishing activity and exploited ecosystems in the Spanish Mediterranean Sea and Gulf of Cadiz. Fishers’ interviews were conducted in 27 fishing harbours of the area, and included 64 fishers from ages between 20 to > 70 years old to capture the experiences and memories of various generations. Results are discussed in comparison with available independent information using stock assessments and international convention lists. Principal Findings: According to fishers, fishing activity substantially evolved in the area with time, expanding towards deeper grounds and towards areas more distant from the coast. The maximum amount of catch ever caught and the weight of the largest species ever captured inversely declined with time. Fishers (70%) cited specific fishing grounds where depletion occurred. They documented ecological changes of marine biodiversity during the last half of the century: 94% reported the decline of commercially important fish and invertebrates and 61% listed species that could have been extirpated, with frequent mentions to cartilaginous fish. Declines and extirpations were in line with available quantitative evaluations from stock assessments and international conventions, and were likely linked to fishing impacts. Conversely, half of interviewed fishers claimed that several species had proliferated, such as cephalopods, jellyfish, and small-sized fish. These changes were likely related to trophic cascades due to fishing and due to climate change effects. The species composition of depletions, local extinctions and proliferations showed differences by region suggesting that regional dynamics are important when analysing biodiversity changes. Conclusions/Significance: Using fishers’ perceptions, fishing and ecological changes in the study area were documented. The recovery of local ecological knowledge provides valuable information complementing quantitative monitoring and evaluation surveys, MC was supported by the Marie Curie EC CIG grant to BIOWEB and the Spanish Research Program Ramon y Cajal. GG was funded through the EC program Science in Society EC. FP7 (ref # 266544-GAP2)

Introduction L'un des axes de recherche du programme Petits Barrages dans sa composante limnologique est, en relation avec les différents facteurs agissant sur les écosystèmes, l'identification des éléments structuraux et fonctionnels qui en expliquent la productivité (Cecchi, 1998). Tout écosystème, d'une façon générale, est en équilibre entre l'homogénéité et l'hétérogénéité (Legendre et Troussellier, 1993) et cela sous la pression de trois forces : exogènes, comme les énergies auxiliaires,...

Micronekton is a major component of oceanic tuna diet. Within micronekton species, Vinciguerria nimbaria, was found to constitute the main forage fish for tuna in the [10–20° W, 0–5° N] area where a large seasonal tuna fishery occurs. The relationships linking the Vinciguerria abundance, its spatial distribution and behaviour to its dynamical or biological environment, were investigated as part of the Picolo program, devoted to the study of the mechanisms leading to the high seasonal tuna concentration in that area. During the Picolo 1 cruise, in January–February 1997, the 1° S–4° N transect was sailed nine times back and forth along 15° W. Micronekton and Vinciguerria were acoustically surveyed, hydrological conditions sampled, phytoplankton and zooplankton biomasses measured. South of 0° 30’ N, a marked divergence (upwelling) was found, with high abundance of zooplankton and micronekton. From there to 4° N a stable situation occurred with a well mixed surface layer, a strong Deep Chlorophyll Maximum (DCM) but less zooplankton and micronekton. While most micronekton performed large diel vertical migrations, schools of Vinciguerria remained at the surface by day in the stable zone, therefore becoming vulnerable to tuna in contrast to the upwelling area. It is concluded that Vinciguerria fits its behaviour according to zooplankton abundance, having to spend more time in the surface layer for feeding in poor areas. More precisely, they remain during the day near the strong DCM where they find aggregated zooplankton, and they become available for tuna. This could explain why a rather poor area may hold and sustain a high biomass of tuna. © 2000 Ifremer/CNRS/IRD/Editions scientifiques et medicales Elsevier SAS micronekton / tuna / food / Atlantic ocean / acoustics

We investigate the patterns of abundance-spatial occupancy relationships of adult parasite nematodes in mammal host populations (828 populations of nematodes from 66 different species of terrestrial mammals). A positive relationship between mean parasite abundance and host occupancy, i.e. prevalence, is found which suggests that local abundance is linked to spatial distribution across species. Moreover, the frequency distribution of the parasite prevalence is bimodal, which is consistent with a core-satellite species distribution. In addition, a strong positive relationship between the abundance (log-transformed) and its variance (log-transformed) is observed, the distribution of worm abundance being lognormally distributed when abundance values have been corrected for host body size. Hanski et al. proposed three distinct hypotheses, which might account for the positive relationship between abundance and prevalence in free and associated organisms: 1) ecological specialisation, 2) sampling artefact, and 3) metapopulation dynamics. In addition, Gaston and co-workers listed five additional hypotheses. Four solutions were not applicable to our parasitological data due to the lack of relevant information in most host-parasite studies. The fifth hypothesis, i.e. the confounded effects exerted by common history on observed patterns of parasite distributions, was considered using a phylogeny-based comparison method. Testing the four possible hypotheses, we obtained the following results: 1) the variation of parasite distribution across host species is not due to phylogenetic confounding effects; 2) the positive relationship between mean abundance and prevalence of nematodes may not result from an ecological specialisation, i.e. host specificity, of these parasites; 3) both a positive abundance-prevalence relationship and a negative coefficient of variation of abundance-prevalence relationship are likely to occur which corroborates the sampling model developed by Hanski et al. We argue that demographic explanations may be of particular importance to explain the patterns of bimodality of prevalence when testing Monte-Carlo simulations using epidemiological modelling frameworks, and when considering empirical findings. We conclude that both the bimodal distribution of parasite prevalence and the mean-variance power function simply result from demographic and stochastic patterns (highlighted by the sampling model), which present compelling evidence that nematode parasite species might adjust their spatial distribution and burden in mammal hosts for simple epidemiological reasons.

The populations of the potential intermediate hosts of #Schistosoma mansoni$ and #S. haematobium$ were studied for a year at transmission sites near three villages in the lower delta of the Senegal River. #Biomphalaria pfeifferi$, found to be widely distributed and increasingly abundant, appears to be well adapted to the new areas of irrigation (created by the dams at Diama and Manantali) thanks to its ability to withstand changes in temperature and to aestivate. This species is responsible for intense transmission of #S. mansoni$ during the rainy season. In contrast, #Bulinus globosus$, the species responsible for the transmission of #S. haematobium$ (which occurs during the dry season), had a more limited distribution. The changing distributions of these two snail species appear to be linked to changes in local ecology, themselves the result of the recent programme of water-development in the delta. (Résumé d'auteur)

Tuna distribution may be directly linked to food availability, the density of which can be assessed by echo-sounding. A study was performed in the French Polynesian EEZ (Economic Exclusive Zone) between 1995 and 1997 with a 38 kHz echo sounder working down to 500 m depth. With the settings used, acoustic back-scattered energy may be considered as representative of micronektonic fish biomass and provided information on horizontal and vertical micronekton variabilities and the structure of the echograms. Three different zones were defined by multivariate analysis. The classical biomass decreasing gradient from the equator to higher latitudes did not appear. Instead, the maximum micronekton abundance was found between Marquesas Archipelagos and a west-northwest/east-southeast oriented line stretching between 11 and 14°S, i.e. in a weak convergence, favourable to micronekton development due to the concentration of lower trophic levels with no oxygen limitation in the deep layers. Two zones with very different hydrological features, but with comparable micronektonic abundances, surround the richest micronekton zone. To the north, waters are enriched by the equatorial upwelling, but intense organic matter remineralisation limits oxygen availability under the thermocline. To the south, waters are influenced by the great southern gyre and present oligotrophic characteristics less favourable to micronekton development. The present results suggest that prediction of tuna forage distribution should take not only trophic parameters into account, but also environmental ones. They also suggest that echo-sounding data should be used more extensively in the validation of models predicting tuna forage.

In West Africa different insecticides had been applied in selected river areas for the reduction of the blackfly populations vectors of Onchocerca volvulus, a parasite causing blindness. To evaluate the possible long term effects of the larvicides on the non target fauna an aquatic monitoring programme has been up from the initial phase of the project. Addressing the attention to the invertebrates data collected in four countries during a maximum period ranging from 1977 to 1996, this paper shows and discusses the data analysis strategy for the measure and interpretation of the biological variation. In particular the application of quantitative ecological analysis methods: Principal Component Analysis, rank abundance models and the community diversity indexes, is critically discussed and comments are given to the ecological interpretation of the results. ©1998 Elsevier Science Ltd. All rights reserved

International audience; The influence of human activities on soil arthropods of vertisols was assessed in several plots characterized by different land uses in the south-eastern part of Martinique (French West Indies). Abundance acid diversity of soil invertebrate groups and collembolan species were measured in a 40-year-old secondary forest, a 15-year-old fallow, a 4-year-old fellow, a 4-year-old pasture, a 15-year-old pasture and a 20-year-old market-garden. Agricultural practices modified abundance and species distribution of soil arthropods, compared to forest. Arthropod richness (number of taxa present) decreased from forest to market-garden, according to a gradient of intensification of agricultural use (pesticides, tillage, weed control). In the old pasture, the arthropod diversity was lower in spite of a high carbon content. Species richness of Collembola decreased together with plant diversity and water availability.

Biomass and production of bacterial and phytoplanktonic communities were measured during diurnal cycles at different stations in 3 shallow tropical reservoirs (Ivory Coast). Investigations were conducted in 1995 during 2 typical hydrological seasons (dry season in March and following rainy season in December). Bacterial production in the plankton ranged from 1.2 to 26.2 microg C/l/h and bacterial biomass ranged from 11 to 163 microg C/l. A slope of 0.625 (n = 93) for the regression of log-transformed bacterial biomass versus log-transformed production suggests that the bacteria were strongly controlled by bottom-up processes. Ratios between net primary production and bacterial production averaged 67% (range 38 to 140%), indicating that the reservoirs studied can be considered as meso-eutrophic ecosystems. Average bacterial carbon demand corresponded to 97% of the net primary production, suggesting that the biological systems studied are based on autotrophic metabolism. These relationships are the result of a close metabolic coupling between bacterioplankton and phytoplankton, with a large fraction of primary production routed through heterotrophic bacteria and the microbial loop. (Résumé d'auteur)

Arsenic is a widespread toxic metalloid which is a major issue of public health. Its presence in the environment is naturally due to the geochemical background, i.e. the weathering of parent material and volcanic eruptions, but the main contamination sources are anthropogenic activities such as mining and metalworking industry. We describe a real-time PCR assay for the quantitative detection of arsB and ACR3(1) arsenite transporter gene families, two ubiquitous and key determinants of arsenic resistance in prokaryotes. The aioA gene encoding the large subunit of arsenite-oxidase was monitored in parallel. This study aimed to determine whether diversity, abundance and expression of these arsenite efflux pumps could serve as suitable biomarkers of metalloid stress and provide means to assess the impact of contamination on soil bacterial communities. The assay was applied in batch growth experiments using a wasteland soil bacterial community as an inoculum to investigate the effect of increasing arsenic concentrations on genes and transcripts abundances. To confirm previous results, further studies on the abundance and expression of arsB and ACR3(1) in indigenous soil bacterial communities exposed to different levels of arsenic over various time periods have helped to gain a better understanding of how these genes contribute to the adaptation of the communities to arsenic stress and their role in shaping the community structure and diversity. On the other hand, metal transporting PIB-type ATPases are critical components of bacterial resistance to cadmium, zinc and lead. We therefore designed degenerate PCR primers targeting PIB-type ATPases and tested their specificity on reference strains, metal-resistant soil isolates and soil metagenomic DNA; La mesure des effets des éléments en traces métalliques (ETM) sur les microorganismes, acteurs majeurs du fonctionnement des sols, constitue une approche complémentaire des analyses physico-chimiques dans l'évaluation de leur impact éco-toxicologique. La démarche scientifique présentée ici visait à déterminer dans quelle mesure la diversité, l'abondance et l'expression de gènes bactériens de résistance aux métaux et métalloïdes pourraient constituer des biomarqueurs pertinents des concentrations biodisponibles en ETM dans les sols contaminés et de leur impact sur les communautés bactériennes. Dans cette étude, nous nous sommes focalisés sur les gènes de résistance arsB/ACR3(1) codant les pompes d'efflux de l'arsénite, largement répandues chez les procaryotes, et aioA codant une arsénite-oxydase. Une technique de PCR en temps réel, utilisant des amorces dégénérées conçues au cours de travaux de thèse précédents (Achour et al., 2007 ; Quéméneur et al., 2008), a été développée pour quantifier ces gènes cibles et leurs transcrits dans des systèmes d'étude de plus en plus complexes, de la culture liquide aux microcosmes de sols. Cette recherche d'interprétations physiologiques et écologiques des réponses bactériennes à une exposition à l'arsenic a été intégrée dans le projet ANR Multipolsite (ANR CES 2008). Il a dès lors été possible d'étudier, dans un contexte d'atténuation naturelle et de phytoremédiation, l'abondance des gènes arsB, ACR3(1) et aioA in situ et sur le long terme en fonction de différents traitements telles que la présence de végétation et la désorption-thermique de ce sol multi-contaminé aux HAP et aux ETM. Ces travaux ont également abouti à la conception d'amorces dégénérées ciblant les gènes de résistance aux cadmium, zinc et plomb, gènes codant les ATPases de type PIB étant des pompes d'efflux spécifiques de ces ETM

Large-scale studies focused on the diversity of continental slope ecosystems are still rare, usually restricted to a limited number of diversity indices and mainly based on the empirical comparison of heterogeneous local data sets. In contrast, we investigate large-scale fish diversity on the basis of multiple diversity indices and using 1454 standardized trawl hauls collected throughout the upper and middle slope of the whole northern Mediterranean Sea (36 degrees 3' - 45 degrees 7' N; 5 degrees 3'W - 28 degrees E). We have analyzed (1) the empirical relationships between a set of 11 diversity indices in order to assess their degree of complementarity/redundancy and (2) the consistency of spatial patterns exhibited by each of the complementary groups of indices. Regarding species richness, our results contrasted both the traditional view based on the hump-shaped theory for bathymetric pattern and the commonly-admitted hypothesis of a large-scale decreasing trend correlated with a similar gradient of primary production in the Mediterranean Sea. More generally, we found that the components of slope fish diversity we analyzed did not always show a consistent pattern of distribution according either to depth or to spatial areas, suggesting that they are not driven by the same factors. These results, which stress the need to extend the number of indices traditionally considered in diversity monitoring networks, could provide a basis for rethinking not only the methodological approach used in monitoring systems, but also the definition of priority zones for protection. Finally, our results call into question the feasibility of properly investigating large-scale diversity patterns using a widespread approach in ecology, which is based on the compilation of pre-existing heterogeneous and disparate data sets, in particular when focusing on indices that are very sensitive to sampling design standardization, such as species richness.

Viruses thrive in all types of ecosystems where life is found. They represent the most abundant biological entity of our biosphere. Though several studies have been conducted on viral abundance and dynamics in mesophilic aquatic ecosystems, these aspects remain largely unexplored in extremophilic environments, such as hot springs. In this study, prokaryotic and associated viral communities of the French Southern and Antarctic Lands hot springs were explored. First, prokaryotic cells and Virus-like particles (VLP) were enumerated in several terrestrial and inshore hot springs. The results reveal an abundance of 105 - 106 particles/ml in both types of hot springs studied. The virus-to-prokaryote ratios (VPR) were generally low, confirming thus actual knowledge in these types of ecosystems. The morphological diversity of VLP was then studied in raw samples as well as in enrichment cultures containing Thermococcales and Thermotogales. Several isolates obtained from these samples were then screened for viral particles which led to the discovery and description of a temperate phage (GTV1) of a thermophilic bacterium belonging to the genus Geobacillus. The effect of NaCl and anoxic stress on the viral production was studied. The genomic characterization of the GTV1 was started and revealed a 38441 bp genome with 71predicted ORF. Finally, microbial diversity studies led also to the discovery of a new extremely thermophilic bacterium, Calditerricola clavaformis sp.nov., Les virus peuvent être retrouvés dans tout les écosystèmes où de la vie est présente. Ils constituent l’entité biologique la plus abondante de la biosphère. Si de nombreuses données sont disponibles sur l’abondance et la dynamique virale dans les écosystèmes aquatiques tempérées, peu d’études ont été menées sur ces aspects dans les milieux extrêmes, dont les sources hydrothermales. Dans l’étude présentée dans ce manuscrit, les communautés procaryotiques et virales des sources hydrothermales des Terres australes et antarctiques françaises (TAAF) ont été explorées. Dans un premier temps, les cellules procaryotiques et les particules de type viral (VLP) ont été dénombrées dans plusieurs sources chaudes terrestres et marines côtières. L’abondance microbienne et virale est de l’ordre de 105 - 106 particules/ml dans les deux types de source avec des rapports VLP/procaryotes (VPR) qui sont généralement faibles, concordant ainsi avec les données rares actuellement disponibles dans la littérature. Dans un second temps, la diversité morphologique des VLP a été analysée par observation au microscope électronique à transmission. La présence de VLP de morphologies différentes a pu être constatée dans quelques échantillons bruts, mais également dans des cultures d’enrichissement, où elles étaient associées à des Thermococcales et des Thermotogales. Finalement, quelques souches isolées de ces échantillons ont été criblées pour la présence de virus aboutissant à la description d’un nouveau bactériovirus tempéré associé à une bactérie thermophile Geobacillus. L’effet d’un choc osmotique en présence de NaCl et l’effet d’un stress anoxique sur la production virale ont également été étudiés. La caractérisation du virus GTV1 a ensuite été entamée. Il appartient à la famille des Myoviridae et a un génome composé d’ADN double brin de 38841 pb, composé de 71 ORF prédits. Enfin, l’étude de la diversité microbienne a permis de décrire une nouvelle espèce bactérienne hautement thermophile, Calditerricola clavaformis sp.nov.

International audience; Mangroves are threatened ecosystems that provide numerous ecosystem services, especially through their wide biodiversity, and their bioremediation capacity is a challenging question in tropical areas. In a mangrove in Mayotte, we studied the potential role of microbial biofilm communities in removing nutrient loads from pre-treated wastewater. Microbial community samples were collected from tree roots, sediments, water, and from a colonization device, and their structure and dynamics were compared in two areas: one exposed to sewage and the other not. The samples from the colonization devices accurately reflected the natural communities in terms of diversity. Communities in the zone exposed to sewage were characterized by more green algae and diatoms, higher bacteria densities, as well as different compositions. In the area exposed to sewage, the higher cell densities associated with specific diversity patterns highlighted adapted communities that may play a significant role in the fate of nutrients.

International audience; A French programme, "Réseau de mesure de la qualité des sols: biodiversité des organismes" (RMQS BioDiv) was de-veloped in Brittany (27,000 km² in the western part of France) as an initial assessment of soil biodiversity on a regional scale in relation to land use and pedoclimatic parameters. The nematode community assemblages were compared among the land use categories. Crops were characterised by a high abundance of bacterial-feeders, particularly oppor-tunistic bacterial-feeders belonging to Rhabditidae. Meadows presented a higher total abundance of nematodes than did crops (20.6 ind·g −1 dry soil vs. 13.1 ind·g −1 dry soil), and they were mainly linked to the great abundance of plant-parasitic nematodes, particularly Meloidogyne, but with a very high heterogeneity between sampled plots. The nematodes were most abundant in forests (23.7 ind·g −1 dry soil) and presented the most structured community (SI = 82.2 in forests vs. 58.6 and 55.5 in crops and meadows, respectively). Forests had also the higher fungal component (fungal-feeders and facultative plant-feeders belonging to the Tylenchidae) leading to a significant higher part of the fungal decomposition pathway in forests than in crops. The ability of different taxonomic levels of nematode identifica-tion to discriminate among different cropping systems (i.e., continuous cropping system, crop with meadow in the rota-tion, meadow with crop in the rotation and permanent meadow) was also tested. The family level (48 families identified in these samples) was more efficient than the other taxonomic levels (86 taxa, 17 functional guilds and 6 trophic groups): best statistical significant discrimination for time spent in identification. The relation between the nematode ecological indices, the abundance of nematode trophic groups and the crop management practices were studied. The effects of fertilization, ploughing frequency, use of pesticides and management systems on ecological indices, particu-larly on the Maturity Indices, were observed.

10 pages; National audience; Les départements et régions d’Outre-Mer présentent une biodiversité remarquable et un fort taux d’endémisme,mais cet endémisme a pour conséquence une plus grande fragilité et un plus grand risque d’extinction. Les enjeuxde conservation de la biodiversité sont alors importants et l’élaboration de mesures de gestion se heurte biensouvent à une profonde méconnaissance de la biologie des espèces. Dans ce contexte, la Grive à Pieds Jaunes,oiseau endémique de quatre îles des Petites Antilles (statut vulnérable, UICN) est un modèle de choix dans la miseen place de mesures de gestion et de conservation. Les premiers résultats d’un programme d’étude dédié à cetteespèce ont permis d’améliorer les connaissances sur cet oiseau : abondance, répartition, domaines vitaux et fluxde populations.

no abstract

Arsenic is a widespread toxic metalloid which is a major issue of public health. Its presence in the environment is naturally due to the geochemical background, i.e. the weathering of parent material and volcanic eruptions, but the main contamination sources are anthropogenic activities such as mining and metalworking industry. We describe a real-time PCR assay for the quantitative detection of arsB and ACR3(1) arsenite transporter gene families, two ubiquitous and key determinants of arsenic resistance in prokaryotes. The aioA gene encoding the large subunit of arsenite-oxidase was monitored in parallel. This study aimed to determine whether diversity, abundance and expression of these arsenite efflux pumps could serve as suitable biomarkers of metalloid stress and provide means to assess the impact of contamination on soil bacterial communities. The assay was applied in batch growth experiments using a wasteland soil bacterial community as an inoculum to investigate the effect of increasing arsenic concentrations on genes and transcripts abundances. To confirm previous results, further studies on the abundance and expression of arsB and ACR3(1) in indigenous soil bacterial communities exposed to different levels of arsenic over various time periods have helped to gain a better understanding of how these genes contribute to the adaptation of the communities to arsenic stress and their role in shaping the community structure and diversity. On the other hand, metal transporting PIB-type ATPases are critical components of bacterial resistance to cadmium, zinc and lead. We therefore designed degenerate PCR primers targeting PIB-type ATPases and tested their specificity on reference strains, metal-resistant soil isolates and soil metagenomic DNA, La mesure des effets des éléments en traces métalliques (ETM) sur les microorganismes, acteurs majeurs du fonctionnement des sols, constitue une approche complémentaire des analyses physico-chimiques dans l'évaluation de leur impact éco-toxicologique. La démarche scientifique présentée ici visait à déterminer dans quelle mesure la diversité, l'abondance et l'expression de gènes bactériens de résistance aux métaux et métalloïdes pourraient constituer des biomarqueurs pertinents des concentrations biodisponibles en ETM dans les sols contaminés et de leur impact sur les communautés bactériennes. Dans cette étude, nous nous sommes focalisés sur les gènes de résistance arsB/ACR3(1) codant les pompes d'efflux de l'arsénite, largement répandues chez les procaryotes, et aioA codant une arsénite-oxydase. Une technique de PCR en temps réel, utilisant des amorces dégénérées conçues au cours de travaux de thèse précédents (Achour et al., 2007 ; Quéméneur et al., 2008), a été développée pour quantifier ces gènes cibles et leurs transcrits dans des systèmes d'étude de plus en plus complexes, de la culture liquide aux microcosmes de sols. Cette recherche d'interprétations physiologiques et écologiques des réponses bactériennes à une exposition à l'arsenic a été intégrée dans le projet ANR Multipolsite (ANR CES 2008). Il a dès lors été possible d'étudier, dans un contexte d'atténuation naturelle et de phytoremédiation, l'abondance des gènes arsB, ACR3(1) et aioA in situ et sur le long terme en fonction de différents traitements telles que la présence de végétation et la désorption-thermique de ce sol multi-contaminé aux HAP et aux ETM. Ces travaux ont également abouti à la conception d'amorces dégénérées ciblant les gènes de résistance aux cadmium, zinc et plomb, gènes codant les ATPases de type PIB étant des pompes d'efflux spécifiques de ces ETM

Avec les remerciements pour Jodie Thénard; International audience; Agricultural intensification has led to reduced soil biodiversity in arable lands. The potential benefits from organic farming and from low-input cropping systems have not yet been precisely assessed. Earthworm, having important agro-ecological functions, may be affected by pesticide applications, especially those species living mainly in the surface soil layer. We used a five-year experimental database including conventional and organic cropping systems to establish simple relationships between the Treatment Frequency Index - a phytosanitary indicator of pesticide pressure - and the abundance of three important earthworm species. We found that insecticides have more negative influence on earthworm species than herbicides and fungicides, and that species living in the soil's surface layer were the most affected by pesticides. Density of these earthworm species could be multiplied by a factor 1.5-4 if the Treatment Frequency Index was halved, as is currently required by some European regulations. Our results thus demonstrate that a reduction in pesticide application would increase earthworm population density in agricultural fields.

Este estudo investigou os bancos de sementes em pastagens implantadas na região de Manaus (Amazonas, Amazônia Central). Em quatro pastagens, foram coletadas 20 amostras de solo de 15 x 15 cm na profundidade de 0 cm a 5 cm e 6 amostras nas profundidades de 5 cm a 10 cm e 10 a 30 cm. Para a contagem e identificação das sementes utilizou-se o método de emergência de plântulas em casa de vegetação. As plântulas foram identificadas por morfotipo e, quando possível, até o nível de espécie. O acompanhamento foi feito durante nove meses. Verificou-se a existência de diferença significativa entre as densidades de sementes das quatro pastagens, variando de 304 a 6153 sementes por metro quadrado, na profundidade de 0 a 5 cm, o que mostra uma alta variação entre as áreas. O número de espécies variou de 17 a 27 na camada superficial. Os bancos de sementes apresentaram-se constituídos predominantemente por herbáceas e espécies lenhosas pioneiras, características de ambientes perturbados. A sucessão vegetal que se desenvolverá necessitará de um intervalo de tempo maior para apresentar estratos arbustivos-arbóreos com maior importância e a floresta será, provavelmente, bem menos heterogênea que a original.

International audience; Europa is one of the Eparses Islands, French islands scattered in the Mozambique Channel. They are isolated islands of coral origin, without permanent human population. This situation makes them good candidates to evaluate the evolution of biodiversity without direct anthropogenic influences. Knowledge is still scarce because their accessibility is limited. With the idea of classifying them as Marine Protected Areas, a management plan is required based on the coral reef communities. Among several aims, the program BioReCIE (Biodiversity, Resources and Conservation of Eparses Islands) was to complete the inventories of several marine groups, including the echinoderms, which had never been assessed before. In November 2011, a multidisciplinary team explored the reef slopes of the island by scuba diving down to 20 meters (10 sites), and the reef flats at low tide (14 sites, including the lagoon surrounded by mangrove), collecting and taking photos of the organisms which have been preserved in 95% ethanol and identified. The total species richness for echinoderms was 39 including 4 Crinoidea, 8 Echinoidea, 5 Asteroidea, with Aquilonastra chantalae a new species, 13 Ophiuroidea and 9 Holothuroidea. Twenty three species were collected on the slopes and 21 on the reef flats. Given the limited number of sites studied, the occurrence of the different species in each class is presented as frequent, infrequent or rare. The semi quantitative measure of abundance identified populations with high densities, as Stichopus chloronotus, Ophiocoma scolopendrina and Echinometra mathaei on the reef flats. Several species were only collected as juveniles. On the slopes Echinostrephus molaris, Ophiothela danae and diadematids were frequent, but with lower densities. On the whole the echinoderm fauna is not very diverse, nor abundant, except on the reef flats; the presence of holothurians near the lagoon entrance, in a mangrove habitat is notable.

The amendment of vermicompost is a management practice that may contribute to sustainable agroecosystems by making them less dependent on inorganic fertilizers. However, little is known about the impact of this practice on soil biota and the flow of microbes to the water system. Using a 30-days laboratory experiment, we investigated the development of the peregrine earthworm species, Dichogaster bolaui , in presence of compost or vermicompost, and assessed its impact on the flow of bacteria and viruses to the water system. The dynamics of soil bacterial diversity (assessed by DGGE) and concentration in water together with their viral parasites were also assessed through an incubation of solution during 5 days (comparison between T 0 and T 5 ). This study highlights the rapid development of D. bolaui after compost amendment. However, the low quality of vermicompost and the absence of organic amendment in the control treatment allowed the survival but not the development of D. bolaui . Higher bacterial and viral abundances in compost and vermicompost substrates led to more important transfer of these communities from the soil to the water system in comparison with the untreated soil, but no difference was observed between compost and vermicompost treatments. In terms of abundance, the bacterial to virus ratio was rather stable in the soil solution but no such a relation was observed in the soil. A reduction of bacterial diversity (OTU) was measured at the end of the incubation period for all the treatments. However, higher number of OTU at T 5 for the compost treatment suggested a better adaptation and/or resistance of soil bacteria to the aquatic system, in comparison with the control treatment. Vermicompost treatment led to intermediate conclusions. The presence of D. bolaui significantly reduced bacterial abundance in the soil organic layer (both compost and vermicompost treatments) but it did not influence bacterial and viral abundance in water, suggesting independent processes. Earthworms buffered bacterial DGGE patterns after five days of incubation, probably through a facilitation of soil bacterial groups more able to resist in solution.

No-take marine reserves are one of the oldest and most versatile tools used across the Pacific for the conservation of reef resources, in particular for invertebrates traditionally targeted by local fishers. Assessing their actual efficiency is still a challenge in complex ecosystems such as coral reefs, where reserve effects are likely to be obscured by high levels of environmental variability. The goal of this study was to investigate the potential interference of small-scale habitat structure on the efficiency of reserves. The spatial distribution of widely harvested macroinvertebrates was surveyed in a large set of protected vs. unprotected stations from eleven reefs located in New Caledonia. Abundance, density and individual size data were collected along random, small-scale (20×1 m) transects. Fine habitat typology was derived with a quantitative photographic method using 17 local habitat variables. Marine reserves substantially augmented the local density, size structure and biomass of the target species. Density of Trochus niloticus and Tridacna maxima doubled globally inside the reserve network; average size was greater by 10 to 20% for T. niloticus. We demonstrated that the apparent success of protection could be obscured by marked variations in population structure occurring over short distances, resulting from small-scale heterogeneity in the reef habitat. The efficiency of reserves appeared to be modulated by the availability of suitable habitats at the decimetric scale ("microhabitats") for the considered sessile/low-mobile macroinvertebrate species. Incorporating microhabitat distribution could significantly enhance the efficiency of habitat surrogacy, a valuable approach in the case of conservation targets focusing on endangered or emblematic macroinvertebrate or relatively sedentary fish species.

no abstract

EA SPE EcolDur; National audience

International audience; Comment les sociétés du Sahara, connues pour leurs capacités à « gérer » les périodes de famine et de pénurie de ressources, font-elles face aux situations d’abondance alimentaire ? C’est la question à laquelle ce texte tente d’apporter quelques éléments de réponse, à travers l’exemple d’une institution originale de l’Ouest saharien, la geyṭna, qui a lieu chaque année sur le littoral mauritanien et qui consiste tout à la fois en la capture, le traitement et la consommation du mulet jaune, animal marin auquel on prête des qualités singulières. La description de cette institution dévoile tout un système alimentaire et son rôle de régulation, que le passage récent à une économie de marché a largement disloqué et folklorisé.

The analysis of 8 selected cores through fringing reefs in New Caledonia reveals that accretion in the Holocene has been less than 6 m. The cores exhibit three main facies: branching coral (Acropora, dominantly), massive coral heads (Porites, mainly) and coral sand/ rubble, principally made up of acroporid fragments. Subordinate facies are composed of coralline algae and alcyonarian spiculite. The initiation of growth varies according to location. The southern reefs (i.e. early settled reefs) generally began to grow first, prior to 5000 y BP. The northern structures (i.e. more recently settled reefs) are younger, occurring after 4200 y BP. This retardation could be ascribed to differences in local physical conditions (nature of substrate, wave energy). Vertical accretion rates were generally higher in areas of lower energy (3.25–6.4 mm·y-1) versus those exposed to higher energy conditions (1.4–3.1 mm·y-1). Vertical development through time was accompanied by changes in composition of biological assemblages which reflect changes in hydrodynamics. The basal Acropora-dominated facies was replaced upwards by a Porites-dominated framework. The New Caledonian fringing reefs reached the sea surface generally between 5000 and 2500 y BP after the stabilization of sea level. Hence all of these reefs can be classified as catch-up reefs.

La variabilité à long terme de 18 peuplements de poissons a été étudiée dans des rivières françaises et ouest africaines. Les principaux résultats sont les suivants : 1) le coefficient de variation (CV) de la richesse spécifique, le CV de l'abondance totale et le CV moyen des espèces constitutives du peuplement augmentent avec la durée de l'étude; 2) selon la classification proposée par GROSSMAN et al. (1990) basée sur le CV moyen de l'abondance des espèces, tous les peuplements étudiés rentrent dans la catégorie des peuplements à fortes fluctuations interannuelles. Cependant certaines populations (les salmonidés en Bretagne par exemple) présentent une faible variabilité de leur densité; 3) dans le Rhône, les peuplements dont les populations manifestent une grande variabilité interannuelle sont ceux présentant le plus grand taux de renouvellement en espèces. Ce résultat est en accord avec l'hypothèse de HORWITZ (1978, "extermination hypothesis"). (Résumé d'auteur)

Cet article propose une démarche de suivi des dynamiques spatiales de la biodiversité survenues durant ces 40 dernières années en Amazonie brésilienne, dans la communauté agricole de Benfica (État du Pará). Elle est conçue pour estimer « où » se produisent les changements, « quand » interviennent-ils, « combien » de surfaces sont concernées et « pourquoi » surviennent-ils ? L’objectif visé est de contribuer à l’évaluation de l’impact de politiques de colonisation sur ces dynamiques. Les données produites à la fois sur les disparités spatiales et sur les rythmes de ces transformations sont un apport qui devrait enrichir les connaissances sur l’évolution de la biodiversité en région pionnière. En l’état actuel des recherches, la démarche propose d’évaluer la biodiversité en ayant recours à une échelle de valeurs combinant plusieurs indicateurs. Chacun d’eux contribue à estimer des changements qui se produisent lors de la mise en culture des terres forestières. La biodiversité est ensuite évaluée à deux niveaux : celui des différentes formes d’exploitation des ressources en rapportant la mesure de biodiversité au niveau du composant paysager (forêt, jachère et culture/pâturage) et celui de la catégorie d’acteur (du colon au petit fermier), en rapportant la mesure de biodiversité à l’unité de territoire qu’ils exploitent préférentiellement. Le procédé de suivi de ce territoire est aisément reconductible dans le temps. En effet, il ne dépend que de la disponibilité des images satellites. Bien que cette démarche soit en cours de validation, elle devrait pouvoir être réutilisée dans d’autres régions forestières anthropisées. This article proposes a method for monitoring spatial dynamics of biodiversity which have occurred along the past 40 years ago in a farming community, Benfica, State of Pará, Brazilian Amazon. It is designed to assess "where", “when”, “why” changes have occurred, and "how much" surface is impacted. ? The goal is to help assess the impact of settlement policies on these dynamics. Data collected on both spatial disparities and rhythms of transformation should enrich knowledge on biodiversity evolution. In the current approach biodiversity is assessed by a scale of values resulting from several indicators combined. Each one contributes to estimate changes which occur during the land use change from forest to cropping. Biodiversity is then evaluated at two levels : one encountering the various forms of resources exploitation and attributing the measure of biodiversity to a landscape component (forest, fallow and crop / pasture) ; and the other, the category of actors (smallholders vs farmers), and reporting the extent of biodiversity to territory units which is preferentially operated. This monitoring process of this territory is easily replicable in time. In fact, it only depends on the availability of satellite images. This approach is on the process of validation to be used in further works dealing with similar anthropic forest regions. Este artigo propõe uma abordagem de acompanhamento das dinâmicas espaciais da biodiversidade que ocorreram durante os 40 últimos anos na Amazônia brasileira, na comunidade agrícola de Benfica (Estado do Pará). Ela é projetada para estimar « aonde » acontecem as mudanças, « quando » acontecem, de « quanta » superfície se trata e « porque » elas acontecem ? O objectivo apontado é de contribuir para a avaliação do impacto de políticas de colonização sobre estas dinâmicas. Os dados produzidos sobre as disparidades espaciais e sobre os ritmos destas transformações, são uma contribuição que deve enriquecer os conhecimentos sobre a evolução da biodiversidade em frentes pioneiras. No estado atual das pesquisas, a abordagem propõe avaliar a biodiversidade usando uma escala de valores combinando diversos indicadores. Cada um deles contribui para avaliar mudanças que acontecem durante o cultivo das terras florestais. A biodiversidade é depois avaliada em dois níveis : o nível das diferentes formas de exploração dos recursos calculando a medida da biodiversidade ao nível do componente da paisagem (floresta, capoeira, cultivo/pastagem), e ao nível da categoria de ator (do colono, ao pequeno fazendeiro), calculando a medida da biodiversidade da unidade de território que cada um explora preferencialmente. O processo de acompanhamento deste território no tempo é facilmente realizável. De fato ele somente depende da disponibilidade de imagens de satélites. Ainda que esta abordagem seja em validação, ela poderia ser reutilizada em outras regiões florestais antropizadas.

Marine N2 fixing microorganisms, termed diazotrophs, are a key functional group in marine pelagic ecosystems. The biological fixation of dinitrogen (N2) to bioavailable nitrogen provides an important new source of nitrogen for pelagic marine ecosystems and influences primary productivity and organic matter export to the deep ocean. As one of a series of efforts to collect biomass and rates specific to different phytoplankton functional groups, we have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling about 12 000 direct field measurements of cyanobacterial diazotroph abundances (based on microscopic cell counts or qPCR assays targeting the nifH genes) and N2 fixation rates. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. The database is limited spatially, lacking large regions of the ocean especially in the Indian Ocean. The data are approximately log-normal distributed, and large variances exist in most sub-databases with non-zero values differing 5 to 8 orders of magnitude. Reporting the geometric mean and the range of one geometric standard error below and above the geometric mean, the pelagic N2 fixation rate in the global ocean is estimated to be 62 (52–73) Tg N yr−1 and the pelagic diazotrophic biomass in the global ocean is estimated to be 2.1 (1.4–3.1) Tg C from cell counts and to 89 (43–150) Tg C from nifH-based abundances. Reporting the arithmetic mean and one standard error instead, these three global estimates are 140 ± 9.2 Tg N yr−1, 18 ± 1.8 Tg C and 590 ± 70 Tg C, respectively. Uncertainties related to biomass conversion factors can change the estimate of geometric mean pelagic diazotrophic biomass in the global ocean by about ±70%. It was recently established that the most commonly applied method used to measure N2 fixation has underestimated the true rates. As a result, one can expect that future rate measurements will shift the mean N2 fixation rate upward and may result in significantly higher estimates for the global N2 fixation. The evolving database can nevertheless be used to study spatial and temporal distributions and variations of marine N2 fixation, to validate geochemical estimates and to parameterize and validate biogeochemical models, keeping in mind that future rate measurements may rise in the future. The database is stored in PANGAEA (doi:10.1594/PANGAEA.774851).