Accurately predicting total sea-level including tides and storm surges is key to protecting and managing our coastal environment. However, dynamically forecasting sea level extremes is ...computationally expensive. Here a novel alternative based on ensembles of artificial neural networks independently trained at over 600 tide gauges around the world, is used to predict the total sea-level based on tidal harmonics and atmospheric conditions at each site. The results show globally-consistent high skill of the neural networks (NNs) to capture the sea variability at gauges around the globe. While the main atmosphere-driven dynamics can be captured with multivariate linear regressions, atmospheric-driven intensification, tide-surge and tide-tide non-linearities in complex coastal environments are only predicted with the NNs. In addition, the non-linear NN approach provides a simple and consistent framework to assess the uncertainty through a probabilistic forecast. These new and cheap methods are relatively easy to setup and could be a valuable tool combined with more expensive dynamical model in order to improve local resilience.
Unlike the rapid sea ice losses reported in the Arctic, satellite observations show an overall increase in Antarctic sea ice concentration over recent decades. However, observations of decadal trends ...in Antarctic ice thickness, and hence ice volume, do not currently exist. In this study a model of the Southern Ocean and its sea ice, forced by atmospheric reanalyses, is used to assess 1992–2010 trends in ice thickness and volume. The model successfully reproduces observations of mean ice concentration, thickness, and drift, and decadal trends in ice concentration and drift, imparting some confidence in the hindcasted trends in ice thickness. The model suggests that overall Antarctic sea ice volume has increased by approximately 30 km³ yr−1(0.4% yr−1) as an equal result of areal expansion (20 × 10³ km² yr−1or 0.2% yr−1) and thickening (1.5 mm yr−1or 0.2% yr−1). This ice volume increase is an order of magnitude smaller than the Arctic decrease, and about half the size of the increased freshwater supply from the Antarctic Ice Sheet. Similarly to the observed ice concentration trends, the small overall increase in modeled ice volume is actually the residual of much larger opposing regional trends. Thickness changes near the ice edge follow observed concentration changes, with increasing concentration corresponding to increased thickness. Ice thickness increases are also found in the inner pack in the Amundsen and Weddell Seas, where the model suggests that observed ice-drift trends directed toward the coast have caused dynamical thickening in autumn and winter. Modeled changes are predominantly dynamic in origin in the Pacific sector and thermodynamic elsewhere.
► The storm surge associated to Xynthia is hindcasted accurately in the Bay of Biscay. ► The importance of young and steep waves in enhancing storm surge is demonstrated. ► Periodic oscillations in ...storm surge is explained by resonance on the shelf.
This study aims to hindcast and analyze the storm surge associated with Xynthia, a mid-latitude depression that severely hit the French central part of the Bay of Biscay on the 27–28th of February 2010. The main losses in human lives and damages were caused by the associated storm surge, which locally exceeded 1.5m and peaked at the same time as a high spring tide, causing the flooding of low-lying coasts. A new storm surge modeling system was developed, based on the unstructured-grid circulation model SELFE and the spectral wave model WaveWatchIII. The modeling system was implemented over the North-East Atlantic Ocean and resulted in tidal and wave predictions with errors of the order of 3% and 15%, respectively. The storm surge associated with Xynthia was also well predicted along the Bay of Biscay, with only a slight underestimation of the surge peak by 3–8%. Numerical experiments were then performed to analyze the physical processes controlling the development of the storm surge and revealed firstly that the wind caused most of the water level anomaly through an Ekman setup process. The comparison between a wave-dependant and a quadratic parameterization to compute wind stress showed that the storm surge was strongly amplified by the presence of steep and young wind-waves, related to their rapid development in the restricted fetch of the Bay of Biscay. In the central part of the Bay of Biscay, both observed and predicted water level anomalies at landfall displayed ∼6h oscillations, with amplitudes of up to 0.2m (10–20% of the surge peak). An analytical shelf resonance model and numerical experiments demonstrated that the period of the observed oscillations corresponds to the resonant mode of the continental shelf in the central part of the Bay of Biscay. It is concluded that these oscillations originate from the interactions between the water level perturbation and the continental shelf and this phenomenon is expected to be relevant at other places along the world’s coastlines.
Vaccination is one of the most effective strategies for preventing infectious diseases but individual vaccine responses are highly heterogeneous. Host genetics and gut microbiota composition are 2 ...likely drivers of this heterogeneity. We studied 94 animals belonging to 4 lines of laying hens: a White Leghorn experimental line genetically selected for a high antibody response against the Newcastle Disease Virus (NDV) vaccine (ND3) and its unselected control line (CTR), and 2 commercial lines (White Leghorn LEG and Rhode Island Red RIR). Animals were reared in the same conditions from hatching to 42 d of age, and animals from different genetic lines were mixed. Animals were vaccinated at 22 d of age and their humoral vaccine response against NDV was assessed by hemagglutination inhibition assay and ELISA from blood samples collected at 15, 19, and 21 d after vaccination. The immune parameters studied were the 3 immunoglobulins subtypes A, M, and Y and the blood cell composition was assessed by flow cytometry. The composition of the cecal microbiota was assessed at the end of the experiment by analyzing amplified 16S rRNA gene sequences to obtain amplicon sequence variants (ASV). The 4 lines showed significantly different levels of NDV vaccine response at the 3 measured points, with, logically, a higher response of the genetically selected ND3 line, and intermediate and low responses for the unselected CTR control line and for the 2 commercial lines, respectively. The ND3 line displayed also a higher proportion of immunoglobulins (IgA, IgM, and IgY). The RIR line showed the most different blood cell composition. The 4 lines showed significantly different microbiota characteristics: composition, abundances at all taxonomic levels, and correlations between genera and vaccine response. The tested genetic lines differ for immune parameters and gut microbiota composition and functions. These phenotypic differences can be attributed to genetic differences between lines. Causal relationships between both types of parameters are discussed and will be investigated in further studies.
The gut microbiota is known to play an important role in energy harvest and is likely to affect feed efficiency. In this study, we used 16S metabarcoding sequencing to analyse the caecal microbiota ...of laying hens from feed-efficient and non-efficient lines obtained by divergent selection for residual feed intake. The two lines were fed either a commercial wheat-soybean based diet (CTR) or a low-energy, high-fibre corn-sunflower diet (LE). The analysis revealed a significant line x diet interaction, highlighting distinct differences in microbial community composition between the two lines when hens were fed the CTR diet, and more muted differences when hens were fed the LE diet. Our results are consistent with the hypothesis that a richer and more diverse microbiota may play a role in enhancing feed efficiency, albeit in a diet-dependent manner. The taxonomic differences observed in the microbial composition seem to correlate with alterations in starch and fibre digestion as well as in the production of short-chain fatty acids. As a result, we hypothesise that efficient hens are able to optimise nutrient absorption through the activity of fibrolytic bacteria such as Alistipes or Anaerosporobacter, which, via their production of propionate, influence various aspects of host metabolism.
Managing Salmonella enterica Enteritidis (SE) carriage in chicken is necessary to ensure human food safety and enhance the economic, social and environmental sustainability of chicken breeding. ...Salmonella can contaminate poultry products, causing human foodborne disease and economic losses for farmers. Both genetic selection for a decreased carriage and gut microbiota modulation strategies could reduce Salmonella propagation in farms. Two-hundred and twenty animals from the White Leghorn inbred lines N and 6.sub.1 were raised together on floor, infected by SE at 7 days of age, transferred into isolators to prevent oro-fecal recontamination and euthanized at 12 days post-infection. Caecal content DNA was used to measure individual Salmonella counts (ISC) by droplet digital PCR. A RNA sequencing approach was used to measure gene expression levels in caecal tonsils after infection of 48 chicks with low or high ISC. The analysis between lines identified 7516 differentially expressed genes (DEGs) corresponding to 62 enriched Gene Ontology (GO) Biological Processes (BP) terms. A comparison between low and high carriers allowed us to identify 97 DEGs and 23 enriched GO BP terms within line 6.sub.1, and 1034 DEGs and 288 enriched GO BP terms within line N. Among these genes, we identified several candidate genes based on their putative functions, including FUT2 or MUC4, which could be involved in the control of SE infection, maybe through interactions with commensal bacteria. Altogether, we were able to identify several genes and pathways associated with differences in SE carriage level. These results are discussed in relation to individual caecal microbiota compositions, obtained for the same animals in a previous study, which may interact with host gene expression levels for the control of the caecal SE load.
Improving the digestive efficiency of broiler chickens (Gallus gallus) could reduce organic waste, increase the use of alternative feed not used for human consumption and reduce the impact of feed in ...production costs. By selecting chicken lines divergently for their digestive efficiency, we showed previously that digestive efficiency is under genetic control and that the two resulting divergent lines, D+ (high digestive efficiency or "digestibility +") and D- (low digestive efficiency or "digestibility -"), also differ for the abundance of specific bacteria in their caeca. Here we perform a more extensive census of the bacteria present in the digestive microbiota of 60 chickens selected for their low apparent metabolizable energy corrected for nitrogen balance (AMEn-) or high (AMEn+) digestive efficiency in a D+ x D- F8 progeny of 200 individuals. We sequenced the 16S rRNA genes of the ileal, jejunal and caecal microbiotas, and compared the compositions and predicted functions of microbiotas from the different intestinal segments for 20 AMEn+ and 19 AMEn- birds. The intestinal segment of origin was the main factor structuring the samples. The caecal microbiota was the most impacted by the differences in digestive efficiency, with 41 bacterial species with abundances differing between highly and poorly efficient birds. Furthermore, we predicted that the caecal microbiota of efficient birds might be enriched in genes contributing to the degradation of short chain fatty acids (SCFA) from non-starch polysaccharides. These results confirm the impact of the genetic selection led on digestibility on the caecal microbiota taxonomic composition. They open the way toward the identification of specific, causal genes of the host controlling variations in the abundances of bacterial taxons.
Interactions between the gut microbiota and the immune system may be involved in vaccine and infection responses. In the present study, we studied the interactions between caecal microbiota ...composition and parameters describing the immune response in six experimental inbred chicken lines harboring different MHC haplotypes. Animals were challenge-infected with the infectious bronchitis virus (IBV), and half of them were previously vaccinated against this pathogen. We explored to what extent the gut microbiota composition and the genetic line could be related to the immune response, evaluated through flow cytometry. To do so, we characterized the caecal bacterial communities with a 16S rRNA gene amplicon sequencing approach performed one week after the IBV infectious challenge. We observed significant effects of both the vaccination and the genetic line on the microbiota after the challenge infection with IBV, with a lower bacterial richness in vaccinated chickens. We also observed dissimilar caecal community profiles among the different lines, and between the vaccinated and non-vaccinated animals. The effect of vaccination was similar in all the lines, with a reduced abundance of OTU from the Ruminococcacea UCG-014 and Faecalibacterium genera, and an increased abundance of OTU from the Eisenbergiella genus. The main association between the caecal microbiota and the immune phenotypes involved TCR
expression on TCR
T cells. This phenotype was negatively associated with OTU from the Escherichia-Shigella genus that were also less abundant in the lines with the highest responses to the vaccine. We proved that the caecal microbiota composition is associated with the IBV vaccine response level in inbred chicken lines, and that the TCR
T cells (judged by TCR
expression) may be an important component involved in this interaction, especially with bacteria from the Escherichia-Shigella genus. We hypothesized that bacteria from the Escherichia-Shigella genus increased the systemic level of bacterial lipid antigens, which subsequently mitigated poultry γδ T cells.
In all organisms, life-history traits are constrained by trade-offs, which may represent physiological limitations or be related to energy resource management. To detect trade-offs within a ...population, one promising approach is the use of artificial selection, because intensive selection on one trait can induce unplanned changes in others. In chickens, the breeding industry has achieved remarkable genetic progress in production and feed efficiency over the last 60 years. However, this may have been accomplished at the expense of other important biological functions, such as immunity. In the present study, we used three experimental lines of layer chicken-two that have been divergently selected for feed efficiency and one that has been selected for increased antibody response to inactivated Newcastle disease virus (ND3)-to explore the impact of improved feed efficiency on animals' immunocompetence and, vice versa, the impact of improved antibody response on animals' growth and feed efficiency.
There were detectable differences between the low (R+) and high (R-) feed-efficiency lines with respect to vaccine-specific antibody responses and counts of monocytes, heterophils, and/or T cell population. The ND3 line presented reduced body weight and feed intake compared to the control line. ND3 chickens also demonstrated an improved antibody response against a set of commercial viral vaccines, but lower blood leucocyte counts.
This study demonstrates the value of using experimental chicken lines that are divergently selected for RFI or for a high antibody production, to investigate the modulation of immune parameters in relation to growth and feed efficiency. Our results provide further evidence that long-term selection for the improvement of one trait may have consequences on other important biological functions. Hence, strategies to ensure optimal trade-offs among competing functions will ultimately be required in multi-trait selection programs in livestock.
Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication resulting from consumption of contaminated poultry products. Genetic selection of animals that are more ...resistant to Salmonella carriage and modulation of the gut microbiota are two promising ways to decrease individual Salmonella carriage. The aims of this study were to identify the main genetic and microbial factors that control the level of Salmonella carriage in chickens (Gallus gallus) under controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines N and 6
were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition, using a 16S rRNA gene high-throughput sequencing approach.
Our results confirmed that the N line is more resistant to Salmonella carriage than the 6
line, and that intra-line variability is higher for the 6
line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Among the 617 operational taxonomic units (OTU) observed, more than 390 were differentially abundant between the two lines. Furthermore, within the 6
line, we found a difference in the microbiota taxonomic composition between the high and low Salmonella carriers, with 39 differentially abundant OTU. Using metagenome functional prediction based on 16S data, several metabolic pathways that are potentially associated to microbiota taxonomic differences (e.g. short chain fatty acids pathways) were identified between high and low carriers.
Overall, our findings demonstrate that the caecal microbiota composition differs between genetic lines of chickens. This could be one of the reasons why the investigated lines differed in Salmonella carriage levels under experimental infection conditions.
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