Portail "HAL-Francophonie Afrique et Océan Indien"
Not a member yet
43052 research outputs found
Sort by
Rediscovering the lost: eDNA detection of freshwater decapods on Réunion Island
No full textInternational audienceFreshwater ecosystems on tropical oceanic islands host unique biodiversity. On Réunion Island, freshwater decapod crustaceans are key indicators of ecosystem health, yet their distribution and conservation status remain poorly documented. This study aimed to investigate the presence of the endemic prawn Macrobrachium hirtimanus, historically reported but unconfirmed for decades, while producing the first island-wide molecular inventory of freshwater decapods using environmental DNA (eDNA) metabarcoding. Water samples (4 L) were collected from 19 riverine sites, and eDNA was extracted and amplified using mitochondrial 16S rRNA primers validated for crustacean detection, followed by highthroughput sequencing. Bioinformatics analyses yielded 250,545 reads and 198 operational taxonomic units (OTUs), representing diverse amphidromous freshwater, coastal marine, and terrestrial decapods. Species richness was largely uniform across sites, though Rivière des Roches, Sainte-Marie, and Saint-Denis hosted higher diversity. Beta diversity showed strong spatial structuring among watersheds, driven primarily by species turnover. Widespread taxa included Atyoida serrata, Caridina typus, and Macrobrachium australe, while C. henriettae and Halocaridinides sp. were more localized. M. hirtimanus was not detected, consistent with its current absence, though continued targeted surveys are required before any formal reassessment. Overall, this study demonstrates the utility of eDNA metabarcoding for monitoring freshwater biodiversity and informing conservation planning on tropical islands
Overexpression of sirohydrochlorin ferrochelatase boosts nitrogen and carbon assimilation and overcomes nutrient deficiency in <i>Arabidopsis thaliana</i>
No full textInternational audienceNitrogen (N) deficiency in soil results in the reduction of plant productivity and emission of greenhouse nitrogenous gases from the applied nitrogenous fertilizers and formation of sodic soil. To overcome soil Ndeficiency the rate of N-assimilation was augmented by overexpression of AtSirB coding for sirohydrochlorin ferrochelatase, responsible for Fe insertion to the tetrapyrrole moiety of sirohydrochlorin in Arabidopsis thaliana under the control of 35S promoter for increased synthesis of siroheme. The siroheme is a cofactor for the plastidic enzymes nitrite reductase (NiR) and sulfite reductase (SiR), which reduce nitrite (NO 2 -) and sulfite (SO 3 2-) to ammonium (NH 4 +) and sulfide (S 2-) respectively. Increased gene and protein expression of AtSirB resulted in heightened NiR and SiR gene expression and protein abundance, boosting NiR and nitrate reductases (NR) activities that resulted in increased protein and chlorophyll (Chl) content in Arabidopsis thaliana. Conversely, antisense plants showed decreased protein levels due to reduced NR and NiR activities. AtSirB overexpressors due to their higher protein and Chl contents had increased photosynthesis, and biomass. Under N and sulfur (S) limitations, these overexpressors outperformed wild type (WT) and antisense plants. These results demonstrate the crucial role of AtSirB and siroheme in N and carbon (C) assimilation. Furthermore, they indicate the potential of SirB to enhance crop productivity, alleviate N and S deficiency across different cropping regimes
Unrevealed prokaryotic diversity in a peridotite massif in an underground mine of New Caledonia
No full textInternational audienceThe microbial diversity in an abandoned mine accessing the Tiebaghi peridotite massif in New Caledonia was studied. The site allowed sampling of alkaline water (pH 8.9-9.9) flowing through fractures, with no contamination from the atmosphere, ensuring optimal gas recovery. Two sampling campaigns collected gas samples, revealing variable gas flux. At one site, no bubbling was observed. At the other site, methane (0.11-1.2 mol%), CO 2 (0.054-0.08 mol%), and O 2 (7.5-18.3 mol%) were present, while H 2 was below detection. Methane showed a biogenic δ 13 C signature of -90‰ vs. vPDB (Vienna Pee dee Belemnite). The physico-chemistry indicated an oligotrophic environment with recent oxic meteoric water. Microbial biofilms, formed by microorganisms in the formation waters, included methanogenic archaea mainly from Methanobacteriaceae, likely responsible for methane production. In this oligotrophic environment, oxic waters supported methanotrophs (Methylococcaceae) and methylotrophs (Methylophilaceae), which may structure community dynamics. The presence of nitrogencycle families such as Nitrosococcaceae and Rhodocyclaceae raises questions, given the apparent depletion of reduced nitrogen compounds. The absence of H 2 suggests it may be consumed by hydrogenotrophic prokaryotes (Methanobacteriaceae, Comamonadaceae), reducing detectable levels. This study is the first to detail microbial diversity in the Tiebaghi massif, offering new insights into peridotite-associated microbial communities
Fine-Grained Assignment of Unknown Marine eDNA Sequences Using Neural Networks
No full textInternational audienceEnvironmental DNA (eDNA) metabarcoding is an innovative tool that is transforming ecological research. It offers a simple and effective method for simultaneously detecting numerous species across a wide range of environments. The method relies on assigning DNA sequences sampled from the environment to taxa, which is straightforward for species that have already been sequenced and are represented in reference databases. However, existing bioinformatics tools often fail to deliver accurate, fine-grained assignments when target species are absent from these databases. This limitation arises from handcrafted classification thresholds that do not account for nucleotide positional information. Here, we propose a deep neural architecture specifically designed to exploit both nucleotide identity and positional patterns in short TELEO sequences. Using an in-silico validation framework based on NCBI genbank sequences, we compare our approach with several state-of-the-art bioinformatics tools (Obitools, Kraken2, Lolo), as well as alternative sequence embedding methods, under controlled conditions. Our approach yields significantly higher classification accuracy at the genus and family levels, achieving average accuracies of 94.7% at the genus level and 86.5% at the family level, substantially outperforming the tested reference-based pipelines. The method remains robust with limited training data and shows improved performance when nucleotide positional information is preserved through sequence alignment. These results demonstrate the potential of AI-powered eDNA metabarcoding to complement existing taxonomic assignment tools, particularly in contexts where reference databases are incomplete or species-level resolution is not achievable, thereby supporting biodiversity monitoring and ecosystem management
<i>Glossina</i> from the Republic of the Congo: species identification by MALDI-TOF MS and research of associated micro-organisms
No full textInternational audienceHuman African trypanosomiasis (HAT) and Animal African trypanosomiasis (AAT), transmitted by Glossina species, remain major health and economic burdens in Africa. Accurate vector identification is essential for effective control strategies. However, current identification methods of Glossina species based on morphological and/or molecular techniques have several limitations that often hinder reliable species-level classification. This study assessed matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as an alternative or complementary approach to morphological and molecular methods for Glossina species identification and explored its ability to detect infection status. A total of 265 tsetse flies were collected and morphologically classified into the Glossina palpalis group (n = 200) and the Glossina fuscipes group (n = 65), later confirmed by molecular analysis as Glossina palpalis palpalis and Glossina fuscipes quanzensis, respectively. Spectra were generated from wings, legs, and thoraxes to identify the most suitable body parts. For G. p. palpalis, high-quality spectra were obtained from wings (98.0%), legs (96.5%), and thoraxes (93.5%); for G. f. quanzensis, corresponding values were 89.2%, 87.7%, and 72.3%. Blind testing showed that 89.5% of spectra for G. p. palpalis and 95.2% for G. f. quanzensis matched morphological identification, with 87.0% and 94.6%, respectively, reaching relevant score thresholds. Molecular screening detected Trypanosoma congolense DNA in nine specimens, but MALDI-TOF MS spectra could not distinguish infected from uninfected flies. These findings demonstrate that MALDI-TOF MS is a rapid, reliable tool for Glossina species identification, particularly using wings and legs, but is unsuitable for infection status determination.La trypanosomiase humaine africaine (THA) et la trypanosomiase animale africaine (TAA), transmises par des espèces de Glossina , constituent toujours un fardeau sanitaire et économique majeur en Afrique. L’identification précise du vecteur est essentielle à l’efficacité des stratégies de lutte. Cependant, les méthodes d’identification actuelles des espèces de Glossina , basées sur des techniques morphologiques et/ou moléculaires, présentent plusieurs limitations qui entravent souvent une classification fiable au niveau de l’espèce. Cette étude a évalué la spectrométrie de masse MALDI-TOF comme approche alternative ou complémentaire aux méthodes morphologiques et moléculaires pour l’identification des espèces de Glossina et a exploré sa capacité à détecter le statut infectieux. Au total, 265 mouches tsé-tsé ont été collectées et classées morphologiquement en deux groupes : Glossina palpalis ( n = 200) et Glossina fuscipes ( n = 65). L’identification de ces espèces a été confirmée ultérieurement par analyse moléculaire, respectivement comme Glossina palpalis palpalis et Glossina fuscipes quanzensis . Des spectres ont été générés à partir des ailes, des pattes et du thorax afin d’identifier les parties du corps les plus pertinentes. Pour G. p. palpalis , des spectres de haute qualité ont été obtenus à partir des ailes (98,0 %), des pattes (96,5 %) et du thorax (93,5 %). Pour G. f. quanzensis , les valeurs correspondantes étaient de 89,2 %, 87,7 % et 72,3 %. Des tests à l’aveugle ont montré que 89,5 % des spectres de G. p. palpalis et 95,2 % de ceux de G. f. quanzensis correspondaient à l’identification morphologique, avec respectivement 87,0 % et 94,6 % atteignant les seuils de score pertinents. Le criblage moléculaire a détecté l’ADN de Trypanosoma congolense dans neuf spécimens, mais les spectres MALDI-TOF MS n’ont pas permis de distinguer les mouches infectées des non infectées. Ces résultats démontrent que la spectrométrie de masse MALDI-TOF est un outil rapide et fiable pour l’identification des espèces de Glossina , notamment à partir des ailes et des pattes, mais qu’elle ne convient pas à la détermination du statut infectieux
Assessment of biophysical properties of mango purées from whole-fruit NIRS of different varieties
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/616408/) * Autres projets (id;sigle;titre): ;SADUR;(FRA) Systèmes Alimentaires Durables en milieu insulaire//International audienceThis work combined multi-variety, multi-ripening stages with non-destructive Near-Infrared Spectra (NIRS) modeling to predict processed mango purée quality traits. 2083 fruits were analyzed by non-destructive texture and NIRS measurements, and then processed into 240 purées. The quality traits of 61 representative purées were characterized. The performance of partial least-square regression (PLS) models was evaluated to predict the purées' dry matter (DM), total soluble solids (TSS), pH, titratable acidity (TA), color (L∗, a∗, b∗), rheological parameters (flow indices n, consistency index K, flow point ɣf, elastic and viscous moduli (G'LVE and G"LVE)), and granulometric parameters (statistical diameters D [3; 2] and D [4; 3]). Cogshall purées had the highest n, and the lowest G'LVE, G"LVE and D [3; 2] values. Modelling highlighted that ripening was the only factor modulating D [3; 2], whereas ɣf was variety-dependent. The fruit NIRS PLS models with RPD value > 2.5 for DM, G'LVE, while G"LVE and ɣf demonstrated good/excellent performance. For TSS, b∗, D [3;2] and D [4;3] satisfactory quantitative prediction was obtained (2 < RPD <2.5). Finally, NIRS presented poor predictive performance for pH, AT, L∗, a∗, n and k. These findings should be extended to other varieties and production systems to achieve higher representativity and genericity
Weak adversarial networks for solving 2D incompressible Navier-Stokes-Brinkman equations
No full textThe use of neural networks has shown significant potential to reduce the computational costs associated with the dynamics of industrial computational fluids. Weak adversarial networks (WAN) leverage weak solution theory to transform the problem of solving PDEs into a Min-Max optimization problem, which is then solved by training a generative adversarial network. Although this method has been successfully applied to two-dimensional (2D) Navier-Stokes (NS) equations, previous work says nothing about the Navier-Stokes-Brinkman (NSB) equations. In this study, we first leverage the stream function to introduce the biharmonic 1 formulation of NSB equations. Then, we extend the WAN framework to solve NS equations in porous media (WAN2DNSB) and provide free surface flow as a numerical experiment. Our results demonstrate the stability and accuracy of the proposed method, highlighting its advantages over the traditional Physic-Informed Neural Networks (PINNs) algorithm, particularly for problems lacking strong solutions. This work contributes to the growing research on AI-driven numerical methods for complex fluid dynamics problems, offering a promising approach for industrial applications
Tree water status behavior of two common European urban species using dendrometric measurements and remote sensing imagery.
No full textInternational audienceWith growing urban populations and rising heatwaves, urban trees are increasingly valued for their cooling benefits through transpiration and shading. However, water stress can limit transpiration, and the effects of urban environment and species-specific traits on tree water status remain understudied. This work investigates how meteorology, soil imperviousness and species influence tree water status behavior, and how vegetation indices derived from remote sensing relate to tree water status, at both seasonal and individual tree scales. Eleven mature Acer platanoides and Tilia x euchlora trees (two common European urban species) growing under varying soil imperviousness levels in a medium-sized French city were monitored. For summer 2023 and spring 2024, two dendrometric indicators of water status - maximum daily shrinkage (MDS) and tree water deficit (TWD) - were calculated, and vegetation index NDVI was extracted from SuperDove imagery. Results show that TWD, more than MDS, effectively assessed tree water status and was closely linked to vapor pressure deficit and relative humidity. Higher soil imperviousness increased water deficit in both seasons, particularly for trees in pits. Acer platanoides exhibited a more isohydric strategy than Tilia x euchlora. NDVI was strongly correlated with TWD in summer 2023 (R² = -0.43), and with MDS in spring 2024 (R² = 0.40). These findings underline the value of dendrometric measurements in urban environments for understanding tree water status, and highlight the potential of very high spatio-temporal resolution satellite data to assess individual tree water status across cities, supporting improved management to maximize the cooling benefits of urban trees
Culturable macroplastic-associated potential human pathogens in coral reef lagoons, Madagascar
No full textInternational audiencePotentially human pathogenic bacteria (PHPBs) have been detected in plastic-associated marine microbiomes, primarily through DNA-based methods. However, data on their culturability and concentrations on plastics remain limited, yet are essential to assess actual health risks. To address this gap, 70 floating macroplastic and 20 seawater samples were collected from two human-impacted reef lagoons in southwestern Madagascar (Atsimo-Andrefana region). PHPBs were cultured from their microbiomes using selective media and quantified. Macroplastics were predominantly polypropylene (34 %) and polyamide (31 %). In increasing order of concentration, four culturable PHPBs, Staphylococcus aureus, Escherichia coli, Enterococcus faecalis, and Vibrio Harveyi clade species, were identified on both macroplastics and in seawater, across all sites and polymer types. Notably, 52 % of macroplastic samples harbored two PHPB species simultaneously, while only 7 % were PHPB-free. Concentrations of all PHPBs were consistently and significantly higher on macroplastics than in seawater, regardless of the measurement unit or polymer type, with the Vibrio Harveyi clade being the most abundant. No significant correlations were observed among PHPB species concentrations, suggesting limited interaction and independent colonization. These findings indicate that floating macroplastics may serve as reservoirs and fomites for viable PHPBs. However, their potential impacts on ecosystems and human health should be interpreted cautiously. We emphasize the need to contextualize PHPB concentration data by considering factors such as exposure pathways, environmental persistence, and bacterial virulence, rather than relying solely on concentration-based comparisons, which may lead to misinterpretation
Contractions of the relativistic quantum LCT group and the emergence of spacetime symmetries
No full textAdvances in the study of relativistic quantum phase space have established the set of Linear Canonical Transformations (LCTs) as a candidate for the fundamental symmetry group associated with relativistic quantum physics. In this framework, for a spacetime of signature , the symmetry of the relativistic quantum phase space is described by the LCT group, isomorphic to the symplectic Lie group , which preserves the canonical commutation relations (CCRs) and treats spacetime coordinates and momenta operators on an equal footing. In this work, we investigate the contraction structure of the Lie algebra associated with the LCT group for signature , clarifying how familiar spacetime symmetry groups emerge from this more fundamental quantum phase space symmetry.Using the Inönü-Wigner group contraction formalism, we examine each limit case corresponding to the possible combinations of asymptotic values of two fundamental length scale parameters associated with the theory, namely a minimum length and a maximum length , which may be identified respectively with the Planck length and the de Sitter radius. We explicitly analyze how contractions of the LCT Lie algebra lead to the physically relevant de Sitter algebra and, in the flat-curvature limit, to the Poincaré algebra of four-dimensional spacetime. This provides an explicit mechanism through which relativistic spacetime symmetry can emerge from a deeper quantum symplectic structure of phase space