French Research Institute for Exploitation of the Sea
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Phenylobacterium Ferrooxidans Sp. Nov., Isolated from a Sub-Surface Geothermal Aquifer in Iceland
No full textA novel bacterial strain, HK31-GT, was isolated from a subsurface geothermal aquifer (Hellisheidi, SW-Iceland) and was characterized using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA gene along with phylogenomic position indicated that the novel strain belongs to the genus Phenylobacterium. Cells are motile Gram-negative bacilli. Physiological characterization showed that strain HK31-GT is a mesophilic bacterium able to grow from 10 to 30 °C, at pH values between 2 and 12 and at NaCl concentrations between 0 and 0.5%. Optimal growth was observed without sodium chloride at 25 °C and pH 6. Strain HK31-GT is chemoorganoheterotroph and its major saturated fatty acids are C18:1ω7c, C16 :1ω6c and C16:0, the predominant quinone is Q-10 and the major polar lipid is phosphatidylglycerol. The new strain also possesses the capacity to use ferrous iron (Fe(II)) as the sole energy source and can also be considered as a chemolithoautotrophic microorganism. The overall genome of strain HK31-GT was estimated to be 4.46 Mbp in size with a DNA G+C content of 67.95%. Genes involved in iron metabolism were identified, but no genes typically involved in Fe(II) oxidation were found. Average nucleotide identity and digital DNA-DNA hybridization values between the genome of strain HK31-GT and the genomes of its closest relatives are below the species delineation threshold. Therefore, given the polyphasic approach used, strain HK31-GT represents a novel species of the genus Phenylobacterium, for which the name Phenylobacterium ferrooxidans sp. nov. is proposed. The type strain is HK31-GT (DSM 116432T = UBOCC-M-3429T= LMG 33376T)
Mesoscale Assemblages of Fish and Megainvertebrates as Evidence of Benthiscapes on Continental Shelves
No full textDespite the relatively small proportion of ocean surface they represent, continental shelf ecosystems are among the most productive in the world. Located at the interface between terrestrial and marine environments, these habitats are structured by strong environmental forcings, especially on the sea bottom. A clear understanding of the spatial distribution of these habitats, along with knowledge on the composition and functioning of their associated communities, is essential for fisheries management and ecosystem conservation. Here, we used data from yearly EVHOE otter trawl surveys (2008–2020) to characterize the spatial structuration of benthic communities of the entire continental shelf of the Bay of Biscay (France), and to investigate the potential environmental drivers of these patterns. Two separate biological components were studied: epibenthic megainvertebrates and bentho-demersal fish. Clustering analyses identified seven assemblages within each component. We detected a strong correlation between the spatial organization of the different assemblages identified for fish and megainvertebrates, providing evidence for broad-scale spatial structuration of benthic habitats—benthiscapes—in this shelf ecosystem. The most influential environmental variables were identified as bottom temperature, sediment type, and primary production. Patterns in certain structural parameters, such as biomass, revealed possible spatial differences in ecological functioning. For example, we observed a drop in biomass from the coast to the central part of the shelf, followed by an increase in biomass near the edge of the Armorican shelf. These patterns reflect major large-scale processes (river inputs versus shelf-break upwelling) structuring the entire Bay of Biscay ecosystem. A comparative analysis revealed that the biological features and functioning observed in this study are shared with other European continental shelves. In addition to improving our knowledge of benthic environments, studies such as this one can promote improvements in ecosystem-based management and marine spatial planning of a fast-changing ecosystem under multiple anthropogenic stresses
Comparing Two Seawater Temperatures For Human Norovirus Depuration From Oysters
No full textDespite regulations set up to monitor the microbiological quality of shellfish in producing areas, shellfish-borne gastroenteritis outbreaks still occur. Indeed, oyster depuration practices that are efficient to eliminate bacteria, fail to eliminate human norovirus from oyster flesh. In order to evaluate the impact of seawater temperature on the elimination of norovirus particles from oysters, large batches of oysters were contaminated using raw sewage containing norovirus and subjected to depuration at 8°C or 18°C. Over the experiment, quantitative RT-qPCR showed a one-log decrease of norovirus (both genogroups combined) genome copies per gram of digestive tissue after 41 days for oysters depurated at 8°C and 24 days at 18°C. The decrease of norovirus (both genogroups combined) in two batches of field-contaminated oysters depurated for two weeks at 18°C was in the same range (21 and 23 days respectively). All experiments showed a difference in genomic decay between the two norovirus genogroups, with norovirus genogroup I being more persistent in March/April compared to April/May
Inefficient transfer of diatoms through the subpolar Southern Ocean twilight zone
No full textThe Southern Ocean, a region highly vulnerable to climate change, plays a vital role in regulating global nutrient cycles and atmospheric CO2 via the biological carbon pump. Diatoms, photosynthetically active plankton with dense opal skeletons, are key to this process as their exoskeletons are thought to enhance the transfer of particulate organic carbon to depth, positioning them as major vectors of carbon storage. Yet conflicting observations obscure the mechanistic link between diatoms, opal and particulate organic carbon fluxes, especially in the twilight zone where greatest flux losses occur. Here we present direct springtime flux measurements from different sectors of the subpolar Southern Ocean, demonstrating that across large areas of the subpolar twilight zone, carbon is efficiently transferred to depth, albeit not by diatoms. Rather, opal is retained near the surface ocean, indicating that processes such as diatom buoyancy regulation and grazer repackaging can negate ballast effects of diatoms’ skeletons. Our results highlight that the presence of diatoms in surface waters of the Southern Ocean’s largest biome does not guarantee their importance as vectors for efficient carbon transfer through the subpolar twilight zone. Climate change-driven shifts in phytoplankton community composition may affect biologically sequestered carbon pools less than currently predicted
Reconciling the environmental implications of late Quaternary faunal and pollen records in southern Africa
No full textAcross southern Africa, the Pleistocene-Holocene transition was associated with changes in community composition of large mammalian herbivores, which included the extinction and extirpation of numerous grazers. Past research has often linked these changes to the contraction and disappearance of grasslands; however, the relationship between faunal and pollen records spanning this transition has not been systematically analyzed. Here, we investigate changes in fossil ungulate community composition and grass pollen abundance from late Quaternary sites across southern Africa to evaluate the extent to which these communities track paleovegetation change across this interval. Our dataset draws from faunal and pollen records across southern Africa. Results from the comparison of compositional changes in both records suggest a sub-continental-scale decoupling of grass cover and ungulate community composition during the Pleistocene-Holocene transition. Although there is strong evidence for a regional-scale decline in grazers from the Last Glacial-Interglacial Transition to the early Holocene, there is no evidence for regional-scale declines in grassy vegetation. Several potential mechanisms may account for this decoupling of grazers and grass abundance. The possible strengthening of winter rainfall systems during glacial Pleistocene may have played a role by enhancing year-round availability of grasses in the interior and by elevating moisture availability and productivity in the Cape Floristic Region. Alternatively, current paleoecological data allow for the possibility that Pleistocene ‘grazers’ consumed more dicots, such that their decline at the onset of the Holocene reflects dietary niche contraction rather than vegetation change. These findings contribute to a growing body of evidence challenging the link between grass abundance and grazer diversity and complicate our understanding of the drivers of late Quaternary extinctions in southern Africa
Widespread presence of metallic compounds and organic contaminants across Pacific coral reef fish
No full textCoral reef fishes represent an invaluable source of macro- and micro-nutrients for tropical coastal populations. However, several potentially toxic compounds may jeopardize their contribution to food security. Concentrations of metallic compounds and trace elements (MTEs), and persistent organic pollutants (POPs, including pesticides and polychlorobiphenyls PCBs), totalizing 36 contaminants, were measured in coral reef fish from several Pacific islands. The objective of this study was to describe the spatial distribution of these compounds and contaminants in order to identify potential variables explaining their distribution at a Pacific-wide scale. To achieve this, we applied Boosted Regression Trees to model species-specific and community-level contaminant and inorganic compound concentrations at the scale of the tropical Pacific Ocean. Overall, using 15 easily accessible explanatory variables, we successfully explained between 60 and 87 % of the global variation, with fish body size being the most important correlate of MTEs and POPs concentrations in reef fish. Our modeling approach allowed us to estimate and map the distribution of the community-level concentration of 19 contaminants and inorganic compounds at the scale of the equatorial and south Pacific Ocean. Spatial patterns varied significantly depending on the compound, with modeled quantities per 100 g of fish flesh generally being higher in the central and southwest Pacific than in the eastern part of the basin. These patterns were influenced by a combination of biological, environmental, anthropogenic and biogeographical variables. Overall, this approach represents an important step toward the estimation of concentrations of the main compounds on the basis of species identity and fishing location. Our results enhance our understanding of the extent of contamination in the Pacific while underscoring the urgent need for long-term and large-scale spatial monitoring of diverse compounds in this region
Biogeographical Regions and Climate Change: Lanternfishes Shed Light on the Role of Climatic Barriers in the Southern Ocean
No full textTo predict the spatial responses of biodiversity to climate change, studies typically rely on species‐specific approaches, such as species distribution models. In this study, we propose an alternative methodology that investigates the collective response of species groups by modelling biogeographical regions. Biogeographical regions are areas defined by homogeneous species compositions and separated by barriers to dispersal. When climate acts as such a barrier, species within the same region are expected to respond similar to changing climatic conditions, enabling the prediction of entire region shifts in response to future climate scenarios. We applied this approach to the Southern Ocean, which exhibits sharp climatic transitions known as oceanic fronts, focusing on the mesopelagic lanternfishes (family Myctophidae). We compiled occurrence data for 115 lanternfish species from 1950 onwards and employed a network‐based analysis to identify two major biogeographical regions: a southern and a subtropical region. These regions were found to be distinct, with minimal overlap in species distributions along the temperature gradient and a separation around 8°C, indicating that temperature likely acts as a climatic barrier. Using an ensemble modelling approach, we projected the response of these regions to future temperature changes under various climate scenarios. Our results suggest a circumpolar expansion of the subtropical region and a contraction of the southern region, with the Southern Ocean becoming a cul‐de‐sac for southern species. Ultimately, our results suggest that when support is found for the climatic barrier hypothesis, community‐level models from a ‘group first, then predict’ strategy may effectively predict future shifts in species assemblages
Automated denoising techniques for sea surface temperature and salinity data from opportunity vessels: application to the Ocean Globe Race 2023-2024
No full textEver more often, opportunity vessels are used to provide in-situ sea surface temperature and salinity data. In particular, sailing vessels participating in oceanic races are often utilized, as they usually cover remote areas not reached by commercial vessels, such as the southern oceans. The received signal from temperature and salinity sensors -especially the latter- is often disturbed either by bubbles, due to strong turbulent flows, or by non-renewal of the water in contact with the sensor. Until now, only manual methods have been successfully used to filter this data, since no automated procedure has been developed. In this paper, we present (i) a sensor housing to be placed on the keel, designed to reduce the aforementioned physical issues, and (ii) an automatic filtering method to override the manual procedure. The physical system was mounted on the historic sailboat Pen Duick VI and has served to collect data along the Ocean Globe Race route (2023-2024). This initiative was a collaboration between the crew of the boat, the Institute of Marine Sciences (ICM-CSIC) in Barcelona, and the Laboratoire d’Océanographie Physique et Spatiale (Ifremer). The housing for sensors consisted of a 3D-printed hydrodynamic support, designed to reduce drag. The automated filtering approach was based on wavelet denoising techniques and simple moving averages. The results are presented in an open dataset and show that procedure yielded good performance in identifying and rejecting outliers, while operating with far greater speed than manual filtering. The method is intended to become a standard procedure for similar in-situ datasets, and an open-source software is provided for this purpose. This work is a step forward in oceanographic data processing and aims to provide a tool with a wide range of applications
Évaluation de la qualité des zones de production conchylicole. Département du Finistère. Période 2022-2024
No full textAprès un rappel des objectifs, du fonctionnement et de la méthode d’interprétation des résultats des réseaux de contrôle microbiologique REMI et d’observation des contaminants chimiques ROCCH, ce rapport inclut un bilan national et décrit le programme annuel du département du Finistère. Il présente l’ensemble des résultats obtenus, en particulier l’estimation de la qualité des zones de production de coquillages classées et l’évolution de leur qualité. Sur la période 2022-2024, pour les coquillages du groupe II, sept zones montrent une estimation de leur qualité dégradée (zones 2229.00.02, 29.01.900, 29.02.041, 29.07.040, 29.08.042, 29.08.061, 2956.08.100) et une zone avec une qualité qui s’est améliorée (zone 29.04.070). Pour les coquillages du groupe III, quatre zones présentent une estimation de la qualité plus défavorable (zones 29.01.070, 29.07.010, 29.08.061, 2956.08.100). Trois zones n’ont pu obtenir une estimation de leur qualité en raison d’un nombre insuffisant de données. L’estimation de la qualité sanitaire des autres zones conchylicoles reste inchangée
Conservation and restoration in the context of deep-seabed mining
No full textDEEP REST is a BiodivRestore European project that gathered natural and social scientists from 8 countries to investigate polymetallic nodule fields in the Clarion-Clipperton Zone (CCZ) and hydrothermal vents on the northern Mid-Atlantic Ridge (nMAR) as ecosystems threatened by seabed mining. DEEP REST research enhanced our knowledge on 1) the faunal and functional diversity of these ecosystems and their interconnections, which is fundamental to inform protection and preservation, including conservation decisions, 2) potential restoration actions, including passive (e.g., protection after impact) or active restoration (e.g., substratum deployment, transplants) actions that can be placed within the framework of the mitigation hierarchy and 3) stakeholder perspectives and governance issues related to deep-sea mining. The recommendations and insights presented in this document are based on the results of DEEP REST research and the integration of many years of exploration and experimentation initiated before the start of this project.DEEP REST est un projet européen BiodivRestore qui a rassemblé des chercheurs en sciences naturelles et sociales de 8 pays pour étudier les champs de nodules polymétalliques dans la zone de Clarion-Clipperton (CCZ) et les cheminées hydrothermales sur la dorsale médio-atlantique nord (nMAR) en tant qu'écosystèmes menacés par l'exploitation minière des fonds marins. La recherche DEEP REST a permis d'améliorer nos connaissances sur 1) la diversité faunistique et fonctionnelle de ces écosystèmes et leurs interconnexions, ce qui est fondamental pour informer la protection et la préservation, y compris les décisions de conservation, 2) les actions de restauration potentielles, y compris les actions de restauration passive (par exemple, la protection après l'impact) ou active (par exemple, le déploiement du substrat) qui peuvent être placées dans le cadre de la hiérarchie d'atténuation et 3) les perspectives des parties prenantes et les questions de gouvernance liées à l'exploitation minière des grands fonds marins. Les recommandations et les idées présentées dans ce document sont basées sur les résultats de la recherche DEEP REST et sur l'intégration de nombreuses années d'exploration et d'expérimentation commencées avant le début de ce projet