Development and validation of a video analysis software for marine benthic applications
Our aim in the EU funded JERICO project was to develop a flexible and scalable imaging platform that could be used in the widest possible set of ecological situations. Depending on research objectives, both image acquisition and analysis procedures may indeed differ. Up to now the attempts for automating image analysis procedures have consisted of the development of pieces of software specifically designed for a given objective. This led to the conception of a new software: AVIExplore. Its general architecture and its three constitutive modules: AVIExplore — Mobile, AVIExplore — Fixed and AVIExplore — ScriptEdit are presented. AVIExplore provides a unique environment for video analysis. Its main features include: (1) image selection tools allowing for the division of videos in homogeneous sections, (2) automatic extraction of targeted information, (3) solutions for long-term time-series as well as large spatial scale image acquisition, (4) real time acquisition and in some cases real time analysis, and (5) a large range of customized image-analysis possibilities through a script editor. The flexibility of use of AVIExplore is illustrated and validated by three case studies: (1) coral identification and mapping, (2) identification and quantification of different types of behaviors in a mud shrimp, and (3) quantification of filtering activity in a passive suspension-feeder. The accuracy of the software is measured comparing with visual assessment. It is: 90.2%, 82.7%, and 98.3% for the three case studies, respectively. Some of the advantages and current limitations of the software as well as some of its foreseen advancements are then briefly discussed.
(Journal of Marine Systems. vol. 162, n° 0924-7963, pp. 4-17, 01/10/2016)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Experimental Study of the Formation of Organosulfates from α-Pinene Oxidation. Part I: Product Identification, Formation Mechanisms and Effect of Relative Humidity
(Journal of Physical Chemistry A. vol. 120, n° 1089-5639, pp. 7909-7923, 30/09/2016)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
How to Assess Temporal Changes of Point and Diffuse Contamination in a Rural Karstic Watershed? Relevance of Suspended Particulate Matter (SPM) for Efficient Monitoring
(Water, Air, and Soil Pollution. vol. 227, n° 0049-6979, pp. 384, 27/09/2016)
LCE, CNRS, UFC, UBFC, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UBFC, UFC, UBFC, CNRS
Chemical Forms of Mercury in Human Hair Reveal Sources of Exposure
Humans are contaminated by mercury in different forms from different sources. In practice, contamination by methylmercury from fish consumption is assessed by measuring hair mercury concentration, whereas exposure to elemental and inorganic mercury from other sources is tested by analysis of blood or urine. Here, we show that diverse sources of hair mercury at concentrations as low as 0.5 ppm can be individually identified by specific coordination to C, N, and S ligands with high energy-resolution X-ray absorption spectroscopy. Methylmercury from seafood, ethylmercury used as a bactericide, inorganic mercury from dental amalgams, and exogenously derived atmospheric mercury bind in distinctive intermolecular configurations to hair proteins, as supported by molecular modeling. A mercury spike located by X-ray nanofluorescence on one hair strand could even be dated to removal of a single dental amalgam. Chemical forms of other known or putative toxic metals in human tissues could be identified by this approach with potential broader applications to forensic, energy, and materials science.
(Environmental Science and Technology. vol. 50, n° 0013-936X, pp. 10721-10729, 23/09/2016)
ISTerre, IFSTTAR, INSU - CNRS, USMB [Université de Savoie] [Université de Chambéry], CNRS, UGA [2016-2019], LCE, CNRS, UFC, UBFC, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, ESRF, IECB, UB, INSERM, CNRS
Why is Asari (= Manila) clam Ruditapes philippinarum fitness poor in Arcachon Bay: a meta-analysis to answer?
Asari (= Manila) clam, Ruditapes philippinarum, is the second bivalve mollusc in terms of production in the world and, in many coastal areas, can beget important socio-economic issues. In Europe, this species was introduced after 1973. In Arcachon Bay, after a decade of aquaculture attempt, Asari clam rapidly constituted neo-naturalized population which is now fished. However, recent studies emphasized the decline of population and individual performances. In the framework of a national project (REPAMEP), some elements of fitness, stressors and responses in Arcachon bay were measured and compared to international data (41 publications, 9 countries). The condition index (CI=flesh weight/shell weight) was the lowest among all compared sites. Variation in average Chla concentration explained 30% of variation of CI among different areas. Among potential diseases, perkinsosis was particularly prevalent in Arcachon Bay, with high abundance, and Asari clams underwent Brown Muscle Disease, a pathology strictly restricted to this lagoon. Overall element contamination was relatively low, although arsenic, cobalt, nickel and chromium displayed higher values than in other ecosystems where Asari clam is exploited. Finally, total hemocyte count (THC) of Asari clam in Arcachon Bay, related to the immune system activity, exhibited values that were also under what is generally observed elsewhere. In conclusion, this study, with all reserves due to heterogeneity of available data, suggest that the particularly low fitness of Asari clam in Arcachon Bay is due to poor trophic condition, high prevalence and intensity of a disease (perkinsosis), moderate inorganic contamination, and poor efficiency of the immune system.
(Estuarine, Coastal and Shelf Science. vol. 179, n° 0272-7714, pp. 226-235, 20/09/2016)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, LEMAR, IRD, IFREMER, UBO EPE, CNRS, PHYC, DYNECO, IFREMER, LERAR, COAST, IFREMER, LRHA, HGS, IFREMER
Assessing and managing the risks of hypoxia in transitional waters: a case study in the tidal Garonne River (South-West France)
The Gironde estuary (S-W France) is one of the largest European macrotidal estuaries. In the tidal Garonne River, its main tributary, episodes of low (<5 mg L−1) to hypoxic (<2 mg L−1) dissolved oxygen (DO) concentrations have been occasionally recorded close to Bordeaux, about 100 km from the mouth. Projected long-term environmental changes (increase in temperature and population, decrease in river discharge) suggest the establishment of summer chronic oxygen deficiency in the tidal Garonne River in the next decades. Assessing and managing the risk of hypoxia on such a large, hyper-turbid fluvio-estuarine system is complex, due to the different forcing factors (temperature, river discharge, turbidity, urban wastes) acting over a wide range of temporal and spatial scales. In this context, we show the interest of a real-time, high-frequency monitoring of the water quality, the MAGEST network, which continuously records since 2005 temperature, salinity, turbidity, and dissolved oxygen in surface waters in Bordeaux. Through the analysis of the 10-year DO records, we demonstrate the interest of a high-frequency, long-term database to better document DO variability and to define the controlling factors of DO concentrations. This real-time monitoring is also of great interest for the development of manager’s oriented tools and the follow-up of DO objectives in the tidal Garonne River.
(Environmental Science and Pollution Research. vol. 24, n° 0944-1344, pp. 3251-3259, 14/09/2016)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Assessing the toxicity of sediments using the medaka embryo-larval assay and 2 other bioassays
Sediments are sinks for aquatic pollutants, and analyzing toxicity in such complex matrices is still challenging. To evaluate the toxicity of bioavailable pollutants accumulated in sediments from the Bizerte lagoon (Tunisia), a novel assay, the medaka embryo–larval assay by sediment contact, was applied. Japanese medaka (Oryzias latipes) embryos were incubated in direct contact with sediment samples up to hatching. Lethal and sublethal adverse effects were recorded in embryos and larvae up to 20 d postfertilization. Results from medaka embryo–larval assay were compared with cytotoxicity (Microtox®), genotoxicity (SOS chromotest), and pollutant content of sediments. The results highlight differences in the contamination profile and toxicity pattern between the different studied sediments. A significant correlation was shown between medaka embryo–larval assay by sediment contact and SOS chromotest responses and concentrations of most organic pollutants studied. No correlation was shown between pollutant levels and Microtox. According to the number of sediment samples detected as toxic, medaka embryo–larval assay by sediment contact was more sensitive than Microtox, which in turn was more sensitive than the SOS chromotest; and medaka embryo–larval assay by sediment contact allowed sediment toxicity assessment of moderately polluted sediments without pollutant extraction and using an ecologically realistic exposure scenario. Although medaka embryo–larval assay by sediment contact should be tested on a larger sample set, the results show that it is sensitive and convenient enough to monitor the toxicity of natural sediments.
(Environmental Toxicology and Chemistry. vol. 35, n° 0730-7268, pp. 2270-2280, 01/09/2016)
UCAR, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Living (stained) benthic foraminifera from the Mozambique Channel (eastern Africa): Exploring ecology of deep-sea unicellular meiofauna
Live (Rose-Bengal stained) deep-sea foraminiferal faunas have been studied at four stations between 530–3200-m depth in the Mozambique Channel (eastern Africa) to understand how complex environmental conditions (e.g., organic matter, oxygenation) control their ecological structure (i.e., diversity, density, and microhabitats). Two upper-slope stations, located at 530- and 780-m depth off Madagascar, are bathed by well-oxygenated bottom waters. They are characterized by fine sediments enriched in highly degraded organic matter (low amino-acid bio-availability and reduced chlorophyllic freshness). Mineralization of organic compounds results in relatively moderate oxygen penetration depth (i.e., 15 and 30 mm) in sediment. Interestingly, foraminiferal species richness (S) is exceptionally high at both sites. The highest densities are observed in the 780-m deep station, where peculiar sedimentary facies of organic matter are recorded (OC >2.0% DW). Redox conditions and sedimentary organic matter control the composition and the vertical distribution (i.e. microhabitat) of benthic faunas at both upper-slope sites. Bolivina alata, Bulimina marginata, Haplophragmoides bradyi and Nouria compressa are relevant bio-indicators of enhanced burial of organic matter prevailing at the 780-m deep station (i.e., eutrophic conditions), whereas Uvigerina hispida and Uvigerina semiornata are dominant at the 530-m deep station (i.e., relatively mesotrophic conditions). Two other stations are located on well-ventilated terraces from the deep-sea canyons of Tsiribihina and Zambezi (>3000-m depth). They are characterized by carbonate ooze, which is depleted in degraded organic matter and, where oxygen penetration depth is relatively deep (i.e., > 80 mm). Because of food scarcity, S and densities are relatively low, and agglutinated and organic-walled taxa dominate foraminiferal faunas. Hospitella fulva, a foraminiferal species belonging to Allogromiida, occupies very deep infaunal microhabitat, what disrupts the classical scheme of microhabitat patterns in oligotrophic settings.
(Deep Sea Research Part I: Oceanographic Research Papers. vol. 115, n° 0967-0637, pp. 159-174, 01/09/2016)
GM, IFREMER, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, LEP, EEP, IFREMER
Loss of connectivity among island-dwelling Peary caribou following sea ice decline
Global warming threatens to reduce population connectivity for terrestrial wildlife through significant and rapid changes to sea ice. Using genetic fingerprinting, we contrasted extant connectivity in island-dwelling Peary caribou in northern Canada with continental-migratory caribou. We next examined if sea-ice contractions in the last decades modulated population connectivity and explored the possible impact of future climate change on long-term connectivity among island caribou. We found a strong correlation between genetic and geodesic distances for both continental and Peary caribou, even after accounting for the possible effect of sea surface. Sea ice has thus been an effective corridor for Peary caribou, promoting inter-island connectivity and population mixing. Using a time series of remote sensing sea-ice data, we show that landscape resistance in the Canadian Arctic Archipelago has increased by approximately 15% since 1979 and may further increase by 20–77% by 2086 under a high-emission scenario (RCP8.5). Under the persistent increase in greenhouse gas concentrations, reduced connectivity may isolate island-dwelling caribou with potentially significant consequences for population viability.
(Biology Letters. vol. 12, n° 1744-9561, pp. 20160235, 01/09/2016)
DMI, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, CEN, ULaval, UNIFR, LECA, USMB [Université de Savoie] [Université de Chambéry], CNRS, UGA [2016-2019]
Dynamics of the Upogebia pusilla–Gyge branchialis marine host–parasite system
The influence of burrowing invertebrates on the functioning of soft-bottom ecosystems is tightly dependent on their physiological state, which may itself be strongly affected by parasite infestation. However, the dynamics, prevalence and physiological consequences of parasitism remain poorly known in many species, such as sediment-dwelling crustaceans. During the present study, we investigated the effects of the ectoparasite (bopyrid) isopod Gyge branchialis on the fitness of the gebiidean mud shrimp Upogebia pusilla. A spatial survey conducted in June 2013 at 10 stations scattered across intertidal seagrass meadows of Arcachon Bay (44°40′N, 1°10′W) showed that on average 16 % of mud shrimp were infested by G. branchialis. Moreover, a temporal survey carried out at one of these stations over the year 2014 revealed that prevalence remained relatively high throughout the year, ranging from 10 to 33 %. This interaction has various physiological consequences for U. pusilla. In particular, infested mud shrimp consistently exhibited a significant deficit in total length and individual dry weight as compared with non-infested specimens. Moreover, 89 % of infested males were feminized (i.e., developed female secondary sexual characters), whereas infested females were never ovigerous. Our results demonstrate that G. branchialis strongly impair U. pusilla fitness including its ability to reproduce. Accordingly, through their (1) potential impact on mud shrimp abundances and (2) alteration of their physiological state, high bopyrid infestation could profoundly alter the bioturbation activity of mud shrimp populations and overall their influence on the functioning of soft-bottom ecosystems in Arcachon Bay.
(Marine Biology. vol. 163, n° 0025-3162, 30/08/2016)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS