French Research Institute for Exploitation of the Sea
ArchiMer - Institutional Archive of IfremerNot a member yet
24806 research outputs found
Sort by
Otolith stable isotopes highlight the importance of local nursery areas as the origin of recruits to yellowfin tuna (Thunnus albacares) fisheries in the western Indian Ocean
Yellowfin tuna (Thunnus albacares) supports the second largest tuna fishery worldwide, and in the Indian Ocean, it is overfished and subject to overfishing. This situation presents a significant challenge to fisheries management, requiring effective measures to rebuild and then maintain the stock at sustainable levels. A single stock of yellowfin is currently assumed by the Indian Ocean Tuna Commission (IOTC) for stock assessments in the Indian Ocean. However, the relative contribution of different spawning components to the total catches, and the degree of mixing rates of yellowfin tuna in the Indian Ocean by individuals from different production zones, are still unknown. This study uses otolith core oxygen and carbon stable isotope composition (δ18O and δ13C) of young-of-the-year yellowfin tuna from nursery areas located in the western (FAO Area 51) and eastern (FAO area 57) Indian Ocean, either side of 80 ºE, to establish a reference baseline of isotopic signatures. Then, a mixed population program (HISEA) and Random Forest (RF) assignment approaches were used to predict the most likely origin (west or east) of sub-adult and adult yellowfin tuna captured from four fishery areas of the western Indian Ocean (offshore Pakistan, Seychelles, Reunion, and South Africa) by comparing their otolith core values to that of the baseline. Both approaches show that the western Indian Ocean fisheries are mainly composed of west origin fish (> 95 %). We also found some individuals with an otolith isotopic signature that was not characteristic of either of the samples available in the baseline. We simulated an alternative baseline group formed by individuals with mean and standard deviation δ13C and δ18O values above the maximum ranges of the original baseline. We then used RF to infer again the most likely origin of fish in the mixed sample considering 3 possible sources (west, east, alternative). About one third of the samples were assigned to the alternative group, possibly indicating that they differ in geographical or temporal terms with the origins represented in the original baseline. Findings of otolith stable isotope composition of yellowfin tuna in the western Indian Ocean can provide a more comprehensive understanding of the species’ spatial structure and connectivity beyond the current assumption of an ocean basin single stock
Vibrio harveyi uses both type III secretion system and quorum sensing for the colonization of the European abalone
The vibriosis of the European abalone, Haliotis tuberculata, is characterized by the rapidity of the infection by the pathogen Vibrio harveyi ORM4, leading to death of animals only after two days. The lethality of the pathogen is linked to the production of the type III secretion system (T3SS) and to genes regulated by quorum sensing (QS). The aim of this study was to investigate the colonization of the European abalone by both virulent and avirulent V. harveyi strains, as well as the involvement of T3SS and QS during infection. Our results emphasize the importance of gills for the bacterial establishment as the bacterial concentration of the avirulent V. harveyi strain significantly decreased from 189.3 ± 98.6 CFU/mg to 0.8 ± 0.5 CFU/mg between 24 and 48 h post-infection (hpi). In opposition, the pathogen V. harveyi ORM4 was able to maintain itself on the gills, with a concentration of 461.9 ± CFU/mg at 48 hpi, which was allowed by the production of T3SS and a functional QS. Following the infection cycle of V. harveyi ORM4 inside H. tuberculata, we also demonstrated that QS is essential for the ability of V. harveyi ORM4 to colonize the abalone hemolymph and to maintain in it. In response to the presence of V. harveyi, an increase in reactive oxygen species production was recorded, while the phagocytosis activity remained unchanged. We also highlighted the involvement of both QS and T3SS to escape the immune system activity, and that an overproduction of T3SS induced hemocyte mortality. This study provides the evidence that both T3SS and QS are essential for the establishment of V. harveyi ORM4 inside the European abalone
Genomic selection for individual feed efficiency in the European seabass: Response to selection on efficiency, commercial traits and sex
Feed efficiency is a key factor in the sustainability of fish farming. Improving feed efficiency not only results in cost savings, but also helps to reduce the environmental footprint associated with feed production and to mitigate competition for feed resources. However, improving feed efficiency through genetic selection poses challenges, mainly due to the difficulty of accurately estimating it in a large population, especially under conventional rearing conditions. In a previous study, a methodology was developed to estimate the individual feed efficiency of sea bass in separate tanks under controlled feeding regimes during the juvenile phase. This approach allowed precise measurement of growth, feed intake and individual feed conversion ratio (iFCR) of each fish. Daily growth rate (iDGC) was found to be highly heritable (h2 = 0.75), and a reliable predictor of iFCR under restricted feeding conditions. In the present study, we aim to demonstrate the response to selection on feed efficiency, commercial traits and sex.
From a cohort of 399 sea bass with known iDGC and genotyped for 1110 SNP markers, we selected 27 future efficient parents (Eff+), 35 intermediate parents (Eff0) and 29 inefficient parents (Eff-) by genomic selection (GBLUP). Three years later, 3 groups of offspring were produced from 9 Eff + parents, 13 Eff0 parents and 19 Eff- parents. Performances in individual aquaria (iDGC, iFCR) were assessed for 259 of them, as well as group feed efficiency (gFCR) from 142 g. At 240 g, the fish were slaughtered to assess processing traits.
The results showed that the Eff + group had superior efficiency (iFCR and iDGC) and better adaptability to tank conditions compared to the other groups. In the group evaluation phase, significant differences in feed efficiency were observed between Eff- (gFCR = 1.83) and Eff + (gFCR = 1.61) (p < 0.001), with Eff0 being intermediate. In addition, Eff + fish were larger (266 g, 27.4 cm) and leaner with lower Fulton K values compared to Eff0 (234 g, 26.1 cm) and Eff- (223 g, 25.5 cm). Although there were no differences in fillet yield, Eff + had a slightly higher viscerosomatic index. There was also a higher proportion of females in the Eff- (57.1 %) and Eff0 (51.6 %) groups compared to Eff + (43.9 %).
In conclusion, selection for feed efficiency in individual tanks is an effective strategy for improving the performance of sea bass, resulting in significant improvements with a marked effect on growth rates. Despite a slight increase in the viscerosomatic index, fillet yield was not significantly affected
Bottom Depth Carving the Pelagic Spatial Organisation in Large Marine Ecosystem: The Case of North West Africa
This study aimed to examine the spatial organization of pelagic communities within the water column along a horizontal gradient extending from the coast to the offshore area, categorized into three zones: inshore, offshore, and transition. A total of 29,000 nautical miles of acoustic transects collected during 14 annual standardized surveys were analyzed using two complementary acoustic methods: (i) extraction of sound scattering layers (SSL) and (ii) echointegration (EI) across the entire water column, both horizontally and vertically averaged. The results revealed significant differences between the three bathymetric areas based on SSL and EI descriptors, with nektonic communities in the transition area exhibiting intermediate characteristics between those in the inshore and offshore areas. The relative abundance of nektonic communities decreased from shallow coastal areas to deep offshore areas. The inshore area is different from transition and offshore area, which is confirmed by diel vertical migration (DVM) analyse through vertical profiles. All areas exhibited classic DVM type I; however, offshore and transition areas also presented unexpected DVMs of type II, i.e., organisms descend deeper during the night, displaying distinct vertical profiles compared to the inshore area. This suggests that the functional and specific composition of pelagic nektonic communities differed between inshore and offshore areas, indicating that organisms adjust their responses to their environment. Over two decades, the three bathymetric areas showed a significant increase in pelagic relative biomass and variation in SSL spatial structure. Nevertheless, nektonic communities reacted differently to interannual changes depending on the bathymetric areas, such as the minimal depth of the shallowest SSL. Fluctuations in SSL descriptors were highlighted over the study period, which may be related to multi-decadal oscillations in the Atlantic Ocean
A multi-tagged SAR ocean image dataset identifying atmospheric boundary layer structure in winter tradewind conditions
A dataset of multi-tagged sea surface roughness synthetic aperture radar (SAR) satellite images was established near Barbados from January to June 2016 to 2019. It is an advancement of the Sentinel-1 Wave Mode TenGeoP-SARwv (a labelled SAR imagery dataset of 10 geophysical phenomena from Sentinel-1 wave mode) dataset that targets SAR marine atmospheric boundary layer (MABL) coherent structures. Twelve tags define roll vortices, convective cells, mixed rolls and convective cells, fronts, rain cells, cold pools and low winds. Examples are provided for each signature. The final dataset is comprised of 2100 Sentinel-1 wave mode SAR images acquired at 36 incidence angle over an 8° × 8°region centered at 51° W, 15° N. Each image is tagged with one or multiple phenomena by five experts. This strategy extends the TenGeoP-SARwv by identifying coexisting phenomena within a single SAR image and by the addition of mixed roll/cell states and cold pools. The dataset includes PNG-formatted SAR image files along with two text files containing the file name, the central latitude/longitude, expert tags for each image, and all dataset metadata. There is a high degree of consensus among expert tags. The dataset complements existing hand-labelled ocean SAR image datasets and offers the potential for new deep-learning SAR image classification model developments. Future use is also expected to yield new insights into the tradewind MABL processes such as structure transitions and their relation to the stratification
Diversity and biogeography of the bacterial microbiome in glacier-fed streams
The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change1,2. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms2,3. However, current knowledge on the GFS microbiome is scarce4,5, precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth’s major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem
A predictive krill distribution model for Euphausia pacifica and Thysanoessa spinifera using scaled acoustic backscatter in the Northern California Current
Euphausiids (krill) are globally significant zooplankton prey for many commercially important or endangered predator species. In the productive upwelling system of the Northern California Current (NCC), two krill species, Euphausia pacifica and Thysanoessa spinifera, dominate the preyscape and constitute an important food resource for many seabirds, cetaceans, and fish. In this study, we use five years of hydroacoustic and net tow data collected in the NCC to develop integrative models predicting acoustic backscatter scaled for E. pacifica or T. spinifera separately. Boosted Regression Trees and Generalized Additive Models are applied in an original ensemble hurdle framework to predict krill presence and abundance from a diverse set of topographic and oceanographic predictors. Krill metrics had significant relationships with seabed depth, distance to submarine canyons, and variables indicative of dynamic ocean conditions (e.g., total deviance explained in acoustic data: 25 % in the presence-absence model & 49 % in the abundance model). Predictions of krill abundance at 5 km resolution averaged by month indicate differential habitat preferences between the two species: T. spinifera was constrained to the continental shelf, around and inshore of the 200 m isobath, whereas E. pacifica was found in greater abundances just offshore of the 200 m isobath and into offshore water in lower abundances. E. pacifica was generally more abundant than T. spinifera (10:1.3 ratio). Both species increased in abundance in the spring and summer, followed by a rapid decline in the fall, and lowest abundances in the winter. These models can produce fine-scale spatial and year-round weekly predictions of E. pacifica and T. spinifera abundance in the NCC, which will provide essential knowledge and new spatial layers about critical ecosystem components to support research and management
Strong genotype-by-environment interaction across contrasted sites for summer mortality syndrome in the Pacific oyster Crassostrea gigas
Genotype-by-environment (GxE) interaction in aquaculture is usually estimated for continuous traits and based on data from a limited number of 2–3 rearing sites. Here we report the results of a GxE study for resistance to Pacific oyster mortality syndrome (POMS), a multi-factorial disease that severely impacts Pacific oyster production worldwide. The syndrome is largely associated with Ostreid Herpes Virus 1 (OsHV-1). Resistance to OsHV-1 in Crassostrea gigas has been shown to be heritable, meaning that selective breeding is a suitable strategy for reducing mortalities. However, limited information was available about GxE interaction or the possible need to consider it in selective breeding. Survival of two cohorts (C1 and C2), consisting of a total of 104 full-sib families, was evaluated during the summer of 2013 in 7 sites along the French Atlantic, Channel and Mediterranean coasts. Mean survivals in autumn 2013 were 12.6% ± 10.9 and 4.6% ± 6.4 for C1 and C2, respectively. Genetic parameters were computed by MCMC, which is suitable for binary data like survival. Heritability estimates ranged from 0.16 to 0.42 depending on site and cohort, with a mean of 0.24 [0.20; 0.27] when including all data. GxE interactions were estimated by the genetic correlations between pairs of sites. Genetic correlations were high ( > 0.80) for C1 between most tidal Atlantic and Channel sites, and intermediate between tidal sites and a Mediterranean lagoon site, while they were lower and more variable for C2 (0.21–0.77). Expected genetic gains were maximal when production site was the same as selection site. They were closed to this expected maximum when the selection site was different from the production site along the Atlantic or Channel coast. Limited GxE interaction along the French Atlantic coast is favorable to wide dissemination of genetically improved oysters along this coast. Limited potential improvement was shown in the Mediterranean site if selection was carried out elsewhere, confirming the specificity of this environment. Consequently, a specific strategy such as dedicated breeding should be used to achieve genetic progress for this site
Phases of Magmatism and Tectonics Along the Madagascar‐Comoros Volcanic Chain, and Synchronous Changes in the Kinematics of the Lwandle and Somalia Plates
This paper aims to solve the longstanding debate on the origin of the Comoros volcanic archipelago (Mozambique Channel, Indian Ocean) concerning whether it represents a hotspot trail or a boundary between the Lwandle and Somalia plates in possible connection with the East African Rift System (EARS). To achieve this goal, we analyzed rock samples from recently discovered and previously uninvestigated volcanoes and edifices by means of geochemistry and geochronology. Major‐trace element analyses and radiometric dating (40Ar/39Ar, K‐Ar, and (U‐Th)/He) allow us to identify a widespread phase of Comorian volcanism initiated at 9–8 Ma, involving the Zélée, Geyser, and Leven banks, three atolls east of the Comoros. Another tectono‐magmatic phase initiated at 2.5 Ma led to a N‐S widening of seamount volcanism, and to the progressive development of en‐échelon NW‐SE structures. With this new addition of atolls and seamounts, the Comoros Archipelago becomes a ∼700 km‐long, ∼200 km‐wide E‐W chain extending from the Cenozoic volcanoes of Madagascar to the EARS. The reactivation of this chain at 9–8 and 2.5 Ma coincides with abrupt changes in the motion of the Somalia plate relative to the Lwandle plate, and with plate boundary modifications. The en‐échelon reorganization of structures also matches the kinematic evolution of Somalia relative to Lwandle, from transtension (>3 Ma) to pure dextral slip (≤3 Ma) in the northern Mozambique Channel. We conclude that the Madagascar‐Comoros volcanic chain is a branch of the EARS and a plate boundary, further strengthening the link between magmatism and the Rovuma‐Lwandle‐Somalia plate kinematics
Breaking onset and breaking strength of focused wave packets: Linear prediction model and nonlinear numerical simulations
The possibility of predicting the occurrence of wave breaking and the intensity of the breaking events using linear wave models is investigated. For this purpose, a new linear breaking onset criterion is proposed, based on the definition of a linear-equivalent wave, which has the same energy and impulse as the associated nonlinear wave. The strength of breaking is characterized by the parameter introduced by Derakhtiet al. (2018) and we derive an empirical law to estimate the breaking strength from the linear-equivalent wave model. The predictive ability of this criterion is assessed through comparisons with results of fully nonlinear potential flow simulations, for focused wave packets of various characteristics. For the considered configurations, the proposed approach is able to predict the onset and strength of breaking with good accuracy