La Rochelle Université

Background DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology. Results Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions. Conclusions This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Bo26ccZX9sY8C76pvHyDeyVideo Abstract

Climate change has marked effects on global weather patterns and oceanic systems, impacting animal behaviour and fitness in potentially profound ways. Despite this, we lack detailed information about species' responses to climatic variation. Using an 11‐year tracking dataset of over 300 individual birds, we explore the consequences of variation in the southern annular mode (SAM) and southern oscillation index (SOI) for individual behaviour and fitness in wandering albatrosses Diomedea exulans breeding in the Southern Indian Ocean. Our results reveal distinct responses between males and females to climatic variation that align with the impacts of each climatic index on the distinct foraging ranges of each sex. In positive SAM phases, linked to poorer foraging conditions in female ranges and better conditions in male ranges, females exhibited behaviour consistent with reduced foraging success: that is, fewer prey capture attempts and more movement between feeding patches. Males, on the other hand, showed no behavioural change. During positive SOI phases, associated with good foraging conditions in both male and female foraging ranges, both sexes showed evidence of more successful foraging, with birds engaging in more search behaviour, and taking shorter trips with fewer prey capture attempts, together indicating increased food intake per unit time. We found limited evidence for a role of individual variation, as measured through differences in personality, suggesting that plastic responses to climate are sufficiently important so as to obscure inter‐individual variation. Supporting this was the finding that individual breeding success was unaffected by climatic variation, suggesting that plastic foraging behaviour allows albatrosses to mitigate climate impacts and maintain reproductive output.

Ecological niche theory predicts coexisting species will segregate spatially, temporally or trophically to limit competition. Few studies have investigated niche segregation in multiple dimensions during the breeding season in sympatric, morphologically similar seabird species. Moreover, these studies showed discrepancies between theoretical predictions and observations. We tested the hypothesis of niche segregation during breeding between 2 sympatric small-sized seabirds, the blue petrel Halobaena caerulea and the thin-billed prion Pachyptila belcheri , by quantifying foraging niche and trophic differences. Combining at-sea GPS and isotopic (stable carbon and nitrogen) data, we assessed spatial, foraging habitat and trophic segregation. We found strong latitudinal and longitudinal segregation between species during incubation. Mean maximum distance from the colony during foraging trips was ~2330 and ~1300 km for blue petrels and thin-billed prions, respectively. Foraging habitat segregation varied during incubation, with blue petrels foraging close to the ice edge and prions foraging in oceanic areas far from ice. Although sample size was low, there was also some evidence for spatial and habitat segregation during chick-rearing, with prions foraging in areas with negative sea surface height anomalies. Trophic segregation was revealed by differences in stable isotopes, with blue petrels feeding on higher trophic level prey than prions (mean plasma δ ¹⁵ N : 9.6 ± 0.4 and 9.0 ± 0.3‰, respectively). Spatial distribution and diet are the primary segregation mechanisms, and patterns of segregation may result from competitive exclusion rather than niche specialization. Spatial and trophic segregation may have evolved to minimize competition, allowing co-existence of these 2 abundant sympatric breeding species.

Recent developments in assessing species-specific seabird bycatch risks have demonstrated that fine-scale approaches are essential tools to quantify interactions with fishing vessels and to understand attraction and attendance behaviours. Matching boat movement with bird tracking data specifically allows us to investigate seabird-fisheries interactions for cryptic species for which on-board information is critically lacking. The sooty albatross Phoebetria fusca overlaps with fisheries throughout its range and is known to be vulnerable to incidental bycatch. Combining radar detectors, GPS and behavioural data from individuals from the Crozet Islands and boat locations during the incubation period, we investigated interactions of sooty albatrosses with fisheries in the southern Indian Ocean. Individuals foraged mostly in sub-tropical international waters, where they only encountered a small number of boats, all reporting to the Automatic Identification System (AIS). The low interaction rate during this period may suggest that sooty albatrosses are not strongly attracted to fishing vessels, and that attraction rates may vary between populations. However, this result should be interpreted with caution due to the low sample size and fishing effort during the study period, as these observations may conceal a higher bycatch risk during intense fishing effort and/or energetically demanding periods. The conservation status of this species requires further data to be collected throughout the annual cycle to provide an accurate assessment of the threat.

As apex predators, cetaceans play an essential ecological role in marine ecosystems. Fluctuations in the abundance of these top predators linked to human activities can have detrimental consequences for the entire ecosystem. Cetaceans face numerous anthropogenic threats that can have both short and long-term effects. To ensure their conservation, it is necessary to identify changes in seasonal distributions at small and large scales. We aimed to model the seasonal distribution of the most abundant cetacean species in the European Atlantic waters and the Mediterranean Sea by assembling datasets collected over 16 years of surveys using a standardised line-transect protocol. Data were homogenised, detection functions fitted and effective strip widths estimated. We extracted environmental variables integrated over the water column, which we transformed using a principal component analysis (PCA). The dimensions of the PCA were then integrated as explanatory variables in a generalised additive model, taking seasonal and spatial effects into account to predict the seasonal cetacean distribution. We were able to highlight changes in the spatial distribution and/or density of cetaceans throughout the year at a large scale, considering environmental extrapolation areas to predict where environmental variables were sampled during the surveys. For minke (Balaenoptera acutorostrata) and fin (B. physalus) whales, densities varied over the seasons but not the distribution, suggesting a seasonal migration outside the survey areas. For common dolphins (Delphinus delphis), bottlenose dolphins (Tursiops truncatus) and harbour porpoises (Phocoena phocoena), densities varied little but distributions did over the seasons. Finally, pilot whales (Globicephala spp), Risso’s (Grampus griseus) and striped (Stenella coeruleoalba) dolphins showed little seasonal variation in their distribution. Using monthly dynamic environmental variables at depth and PCA dimensions in habitat models, we produced maps of the seasonal distribution of cetaceans in the Mediterranean Sea and the European Atlantic waters to help fill gaps in our knowledge of cetacean distribution.

Theobroma cacao L., commonly known as cocoa, has been an integral part of human culture and diet for thousands of years. However, recent scientific research has highlighted its potential therapeutic properties, particularly in the treatment of cancer and inflammatory diseases. This comprehensive review analyzes the anti-inflammatory and anticancer effects of Theobroma cacao extracts combined with nanoparticles using in vitro and in vivo studies. Its diverse biological activity can be attributed to its rich phytochemical profile, including polyphenols, flavonoids, and alkaloids. In vitro studies have found that cocoa extracts, alone or in combination with nanoparticles, inhibit cancer cell proliferation, induce apoptosis and modulate key signaling pathways in various cancer cell lines. The extracts have also been found to reduce tumor growth and enhance the efficacy of conventional chemotherapeutic agents, potentially reducing their side effects, in vivo. Its anti-inflammatory properties are based on its ability to modulate inflammatory mediators, inhibit NF-κB signaling, and regulate macrophage polarization. These effects have been observed in both cellular and animal models of inflammation. This review opens up new possibilities for future research and therapeutic applications, highlighting the potential of Theobroma cacao as a valuable complementary approach in the treatment and prevention of cancer and inflammatory diseases.

The efficacy of biomass pretreatment methods is critical for enhancing the yield of fermentable sugars, essential for bioethanol production. In this study, a pretreatment approach utilizing impregnation of alfa) fibers (Stipa tenacissima in sulfuric acid or sodium hydroxide diluted catalyst solutions with concentrations ranging from 0.5 to 3% (w/w). This step was coupled to a thermomechanical treatment using “Intensive Vacuum associated with Heat Moisture Treatment” (IV-HMT) technique, developed in our laboratory. The target was to optimize the solubilization of hemicelluloses, removal of lignin, and enhancement of enzymatic hydrolysis. Chemical composition and microstructure alterations were assessed through ABET specific surface area, SEM observations, XRD, and FTIR analysis. Enzymatic hydrolysis efficacy was evaluated by quantifying reducing sugar yields initially (R0h) and after 24 hours (R24h) using DNS method, with glucose and xylose yields quantified by HPLC. Results demonstrated significant disruption of the recalcitrant structure of alfa fibers, with hemicelluloses removal reaching 76.6% and 73.4%, and lignin removal reaching 28.8% and 71.8% for H2SO4 and NaOH, respectively. ABET increased around 7-fold with H2SO4 but decreased with alkali, most probably due to calcium carbonate precipitation. The overall reducing sugars yield increased from 31% (raw) to 89.9% and 82.7% for pretreated samples with H2SO4 (1%) or NaOH (3%), respectively, combined with IV-HMT processing. Maximum glucose production was 66.3 g/L and 58.8 g/L with H2SO4 (1%) and NaOH (3%), respectively. IV-HMT can be regarded as an environmentally friendly approach allowing for a reduced energy consumption and a minimal utilization of chemicals. Graphical Abstract

Metallic trace elements (MTEs) constitute a major source of chemical pollution and represent a threat to aquatic ecosystems and organisms. Important variation in contamination may exist at a local scale in relation to the environment (hydrosystem, trophic ressources) and individual traits (age, sex). Heretofore, the factors influencing MTEs exposure of freshwater reptiles in temperate regions are not fully understood. Freshwater turtles have a relatively high trophic position and a long lifespan, thus being potentially highly exposed due to bioaccumulation and bioamplification processes. We investigated MTE blood concentrations from two populations of the European Pond Turtle Emys orbicularis in the Camargue wetland (France). These populations, monitored since 1997, differ in their habitat and exposure (irrigation versus drainage canal). In this study, we detected 7 MTEs (Cu, Fe, Hg, Mn, Pb, Se, and Zn) which levels depended on site and individual characteristics. Hg was positively related to body size and age, indicating an increase of exposure in older individuals. We found differences between males and females with the interaction with body size for Pb and Se and with age for Pb. Nitrogen and carbon stable isotopes varied only marginally between individuals and were poorly associated with MTEs concentrations, showing that trophic position might not explain MTEs contamination for these populations. At the individual level, Hg, Pb, Se blood values were repeatable over years. Further studies should concentrate on potential ecophysiological effects to such exposure, especially since we recently evidenced that these populations of E. orbicularis are highly exposed to organic contaminants, which can lead to synergistic effects.

This article proposes a theoretical approach to the development of Western commercial ports from the Industrial Revolution onwards. It is based both on a bibliographical corpus devoted to port history and on personal research into the main French ports of the nineteenth century. This work was based on two main sources: firstly, the Annales des Ponts et Chaussées, which recorded the experiments and theoretical work carried out by the engineers of this government body; and secondly, the Actes législatifs et Dépenses concernant les Travaux de Navigation Intérieure et Maritime de 1814 à 1900, a document published by the Ministry of Public Works which provides information on the budgets allocated to the main French ports. This reflection shows that since the nineteenth century the development of ports has been subject to a permanent adjustment process, with four main characteristics: disruptive innovation, spatial adaptation, selective adaptation and one-way adaptation.

Since 2011, holopelagic Sargassum have been massively stranding in the coastal environments of the Caribbean Islands inducing damages to coastal ecosystems, public health and the economy. To limit the risks associated with Sargassum stranding, floating barriers with nets can be placed in front of sensitive areas, to divert Sargassum away from the coast. To evaluate the potential transfer of metallic trace element (MTE) from Sargassum to adjacent marine life, seagrasses (Halophila stipulacea, Thalassia testidinum) and urchin (Lytechinus variegatus) were sampled, both close (0 m) and far (200 m) from barriers installed during 4 years in two bays: Baie Cayol (BC) and Cap Est (CE) in Martinique (FWI). A bay without barriers Baie-Tresor (BT) was also sampled in order to compare the effects of Sargassum accumulated in a natural environment versus an environment with floating barriers. The short-term effects of barriers were evaluated by measuring the evolution of MTE after four days, in the algae (Dictyota spp.), located close to Sargassum accumulations. All sampling was realized during two periods of active (July 2021) and reduced (January 2022) Sargassum stranding. The measured concentrations of 19 metal(loid)s trace elements revealed that the proximity of Sargassum to the barriers did not increase MTE concentration. The absence of increase in MTE was observed all sites (BT, BC and CE) and during periods of limited and important Sargassum stranding. Similarly, translocations of Dictyota close to Sargassum accumulations did not reveal any increase in MTE concentrations in the algae after 4 days. The present study suggests that the use of barriers to manage Sargassum stranding would not constitute an important threat of MTE contamination of marine environments.

The construction industry is responsible for significant environmental damage, which can be countered by adopting sustainable practices. This can be achieved using eco-friendly building materials and implementing waste management strategies. Geopolymer concrete is an example of a green building material that uses waste materials like silica fume, fly ash, and glass to reduce environmental impact. Geopolymer is an inorganic material made by mixing aluminosilicate precursor with an alkaline activator such as sodium silicate and potassium hydroxide solution. This work uses hospital waste glass to produce geopolymer mortars and assesses the calorimetric heat exchange released when the material is manufactured to determine its sustainability. This study used hospital glass waste to partially replace Metakaolin and a sodium silicate-based alkali activator in a geopolymer matrix. The mass substitution of Metakaolin with hospital glass waste varied between 0, 5, and 10 %. The mechanical properties were assessed by conducting a compressive test on day 90, followed by a calorimetric study that evaluated the heat change inside the geopolymerization reaction. The samples demonstrated great compressive strength results, reaching a value of 45 MPa for 10% mass substitution at day 90. The calorimetric analysis proved that the increase in strength was due to increased heat evolution inside the matrix, thus increasing the geopolymerization reaction. In conclusion, this work highlighted the importance of using hospital glass waste as a sustainable solution in the material construction sector as it provides new sites on the feasibility of using this recyclable hospital waste in producing eco-green material.

The southern oceans are home to a large variety of organisms, including many endemic species. High levels of endemism are due in part to non-physical barriers limiting gene flow in marine species. The sooty albatross Phoebetria fusca is an endangered seabird breeding on seven island groups in Atlantic and Indian Oceans. We sequenced the mitochondrial control region (55 birds) and genotyped 10 microsatellite markers (88 birds) to examine the population genetics of sooty albatrosses from Tristan da Cunha and Gough Island (Atlantic Ocean), and Marion Island, Île de la Possession (Crozet) and Amsterdam Island (Indian Ocean), which together support > 99% of the global population. We also analysed the bill sulcus colouration and quantified stable isotope composition of body feathers of breeding adults from Gough and Marion Islands. Both genetic markers identified two clusters separating sooty albatrosses breeding in the Atlantic and Indian Ocean basins. Standardized colour analysis also separated populations in the two ocean basins and revealed the sulcus of sooty albatrosses on Gough Island is significantly more yellow than individuals on Marion Island. Stable isotope analysis of body feathers showed significantly higher δ¹³C values from Marion sooty albatrosses compared to Gough conspecifics, indicating different moulting areas. Sooty albatrosses breeding on islands in the two ocean basins differ from each other in their genetics, morphology and ecological preferences. Accordingly, it is recommended that separate conservation management plans be implemented for sooty albatrosses breeding in each ocean basin to prevent the loss of evolutionarily significant units.

Background Adoptive cell therapy (ACT) has revolutionized cancer treatment. However, optimizing its design for consistent long-term benefits remains challenging. Mechanisms determining ACT efficacy are not fully understood, making experimentally explaining immune-tumor interactions difficult. Multiple aspects contribute to pharmacological variances, such as cellular heterogeneity and dynamic tumor microenvironment (TME). While widely used to investigate these perturbations, cell-line and animal models are resource-heavy, cross-sectional, and provide limited data granularity, hindering the translation to clinical practices. In silico modeling can flank in vivo/vitro experiments by providing additional insights and cost-effective hypothesis testing, though accuracy, complexity, and interpretability vary. To systematically evaluate ACT variables and bridge biological mechanisms with experimental observations, we hypothesized that a data-informed, rule-based microscale model can simulate cell population dynamics in ACT and thereby predict differential tumor control effects. Given the scarcity of computational models on natural killer cells, in this project, we developed ABMACT to understand, simulate, and predict TME dynamics in Chimeric Antigen Receptor Natural Killer (CAR-NK) ACT for B cell lymphoma. Methods Agent-based models (ABM) are well-suited to emulate spatial interactions at the single-cell level and retain stochasticity, flexibility, and interpretability. ABMs encode the biological rules of individual cells and simulate the collective behaviors of cell populations over time. ABMACT integrated data from in vitro/vivo experiments and scRNA-seq to capture variable cytotoxicity in NK cells, delineate NK cell fate transitions, and predict tumor control. We validated our models on a Raji-NK cell coculturing mouse model experiments¹ and benchmarked it against other modeling methods such as ordinary differential equations (ODE). Results By cross-evaluating multiple NK cell characteristics and dosages, we found that NK cell proliferation rate most significantly influenced time to tumor clearance, followed by effector-to-target ratio, and serial killing capacity. Higher baseline cytotoxicity, proliferation rate, serial killing capacity, and lower death rate in the CD19IL15 CAR-NK group accelerated tumor reduction. ABMACT substantially outperforms ODE models in the accuracy and interpretability of NK cell dynamics. In addition, ABMACT allows investigations of multiple dosing, which can help optimize ACT treatment schedules and dosages. Conclusions By developing ABMACT, we provide a computational framework for testing the impact of CAR-NK ACT design and conditions on long-term tumor control and patient responses. Integrating biological knowledge with multi-modal data, ABMACT offers mechanistic explanations of immune-tumor interactions. In silico models reduce the need for extensive laboratory work and can adapt to other cell types and ACTs, aiding hypothesis generation and testing for ACT design and personalized treatment planning. Reference • Li L, et al. Loss of metabolic fitness drives tumor resistance after CAR-NK cell therapy and can be overcome by cytokine engineering. Sci Adv 2023; 9 :eadd6997.

Predicting animal population trajectories into the future has become a central exercise in both applied and fundamental ecology. Because demographic models classically assume population closure, they tend to provide inaccurate predictions when applied locally to interconnected subpopulations that are part of a larger metapopulation. Ideally, one should explicitly model dispersal among subpopulations, but in practice this is prevented by the difficulty of estimating dispersal rates in the wild. To forecast the local demography of connected subpopulations, we developed a new demographic model (hereafter, the two‐scale model) that disentangles two processes occurring at different spatial scales. First, at the larger scale, a closed population model describes changes in metapopulation size over time. Second, total metapopulation size is redistributed among subpopulations, using time‐varying proportionality parameters. This two‐step approach ensures that the long‐term growth of every subpopulation is constrained by the overall metapopulation growth rate. It implicitly accounts for the interconnectedness among subpopulations and avoids unrealistic trajectories. Using realistic simulations, we compared the performance of this new model with that of a classical closed population model at predicting subpopulations' trajectories over 30 years. While the classical model predicted future subpopulation sizes with an average bias of 30% and produced predictive errors sometimes >500%, the two‐scale model showed very little bias (<3%) and never produced predictive errors >20%. We also applied both models to a real dataset on European shags (Gulosus aristotelis) breeding along the Atlantic coast of France. Again, the classical model predicted highly unrealistic growths, as large as a 200‐fold increase over 30 years for some subpopulations. The two‐scale model predicted very sensible growths, never larger than a threefold increase over the 30‐year time horizon, which is more in accordance with this species' life history. This two‐scale model provides an effective solution to forecast the local demography of connected subpopulations in the absence of data on dispersal rates. In this context, it is a better alternative than closed population models and a more parsimonious option than full‐dispersal models. Because the only data required are simple counts, this model could be useful to many large‐scale wildlife monitoring programs.

Knowledge of how animals respond to weather and changes in their physical environment is increasingly important, given the higher frequency of extreme weather recorded in recent years and its forecasted increase globally. Even species considered to be highly adapted to extremes of weather, as albatrosses are to strong winds, may be disadvantaged by shifts in those extremes. Tracked albatrosses were shown recently to avoid storms and the strongest associated winds. The drivers of this response are so far unknown, though we hypothesize that turbulent storm conditions restrict foraging success, possibly by reducing the detectability or accessibility of food, and albatrosses divert toward more profitable conditions where possible. We tested the impact of the physical environment—wind speed, rainfall, water clarity, and time of day—on feeding activity and success of two species of albatrosses with contrasting foraging strategies. We tracked 33 wandering and 48 black-browed albatrosses from Bird Island (South Georgia) with GPS and immersion loggers, and 19 and 7 individuals, respectively, with stomach-temperature loggers to record ingestions, providing an in-depth picture of foraging behavior. Reduced foraging profitability (probability of prey capture and overall mass) was associated with stormy conditions, specifically strong winds and heavy rain in surface-seizing wandering albatrosses, and the probability of prey capture was reduced in strong winds in black-browed albatrosses. We show that even highly wind-adapted species may frequently encounter conditions that make foraging difficult, giving context to storm avoidance in albatrosses.

Fishes inhabiting the mesopelagic zone of the world's oceans are estimated to account for the majority of the world's fish biomass. They have recently attracted new attention because they are part of the biological carbon pump and have been reconsidered as a contribution to food security. Hence, there is an urgent need to understand how environmental conditions and species interactions shape their assemblages, and how they contribute to the functioning of marine ecosystems. Trait‐based approaches are valuable for addressing these types of questions. However, the biology and ecology of mesopelagic fishes are understudied compared to fishes in shallow and epipelagic waters. Here, we synthesise existing knowledge of traits of mesopelagic fishes and relate them to their role in survival, feeding and growth and reproduction, the key functions that contribute to fitness. Vertical migrations, specialised vision and the use of bioluminescence are among the most striking adaptations to the conditions in the mesopelagic realm. Many traits are interrelated as a result of trade‐offs, which may help to understand selection pressures. While morphological traits are straightforward to observe, major knowledge gaps exist for traits that require frequent sampling, assessment under experimental conditions or age determination. The unique adaptations of mesopelagic fishes need to be included in management strategies as well as fundamental research of the habitat.