121 research outputs found
"Tu vois, sur cette photographie, c'est moi" - L'identité : questions, critères et représentations
No full textCe billet prend le parti de ne pas s'inscrire a priori dans une perspective disciplinaire, ni dans la pensée d'un auteur donné : il est issu d'une séance organisée avec Bachar Cheaib dans le cadre du laboratoire Junior "Enquête sur l'homme vivant", qui souhaitait constituer un point de départ, sous formes de questionnements issus de parcours ou de supports, à d'autres séances et des lectures interdisciplinaires pour essayer de comprendre, justement, comment différentes disciplines posent et c..
"Tu vois, sur cette photographie, c'est moi" - L'identité : questions, critères et représentations
No full textCe billet est publié en parallèle sur le site du Laboratoire Junior "Enquête sur l'homme vivant". Ce billet prend le parti de ne pas s'inscrire a priori dans une perspective disciplinaire, ni dans la pensée d'un auteur donné : il est issu d'une séance organisée avec Bachar Cheaib dans le cadre du laboratoire Junior "Enquête sur l'homme vivant", qui souhaitait constituer un point de départ, sous formes de questionnements issus de parcours ou de supports, à d'autres séances et des lectures inte..
Étude de l’évolution contemporaine de systèmes microbiens environnementaux et hôtes associés dans un contexte d’écotoxicologie
No full textLes microbes ou micro-organismes sont les producteurs primaires des services écosystémiques pour les cycles biogéochimiques de la terre et les systèmes biologiques. Les xénobiotiques marquent une nouvelle ère anthropogénique « l’anthropocène », et ils représentent une source de sélection artificielle de la structure et de la composition de la biodiversité microbienne. Par conséquent, les perturbations anthropogéniques sont néfastes pour les systèmes microbiens et induisent des changements adaptatifs ou des dommages dans leurs répertoires génotypiques. L’assemblage des communautés microbiennes durant la résistance et la résilience est gouverné par des processus éco-évolutifs. Ce travail découle de l’intersection transdisciplinaire de l’écotoxicologie, l’écologie microbienne, la métagénomique et la bioinformatique. L’objectif de ce travail consiste à étudier les signatures adaptatives de la résistance et de la résilience microbienne selon deux modèles. Le premier est environnemental (E) composé d’un bassin versant lacustre contaminé par des métaux lourds. Le deuxième modèle est hôte-associé (HA), constitué d’un système expérimental d’exposition de la Perchaude (Perca flavescens) au chlorure de cadmium selon deux régimes constant et graduel. Trois nouveautés résument les travaux de cette thèse de doctorat. Premièrement, le phénomène de découplage taxon-fonction a été démontré pour la première fois, dans le système E sous un gradient sélectif de pollution, et au sein du microbiote cutané dans le système HA durant sa période de résilience. Deuxièmement, des altérations significatives de la diversité taxonomiques et fonctionnelles mettent en évidence des signatures adaptatives du résistome et de l’érosion des fonctions métaboliques dans le système E. Quant au système HA, le stress métallique a augmenté la prévalence significative de souches pathogènes et des opportunistes avec une dysbiose cutanée de la perchaude accompagnée par une réduction de sa capacité de résistance à une colonisation bactérienne massive. Troisièmement, la modélisation de l’assemblage bactérien de microbiote du système HA montre des rôles confondus de l’ontogenèse et de la force de sélection durant la période de résistance. La persistance des effets à long terme de la sélection durant le stade de résilience a été expliquée par une augmentation inattendue de la bioaccumulation du cadmium dans les tissus hépatiques de l’hôte. En conclusion, nos travaux montrent que l’adaptation des répertoires métagénomiques peut être décelée par le phénomène de redondance fonctionnelle observée à l’échelle de découplage taxon-fonction, ce qui reflète potentiellement une stratégie adaptative par transfert horizontal de gènes partagés entre les communautés microbiennes environnementales sous perturbation graduelle. Dans le système HA, l’assemblage de microbiote montre un gradient de processus neutres et non neutres. Enfin, la dérive taxonomique serait une force écologique non négligeable plus importante dans le système environnemental que dans le système intestinal durant et après la perturbation.Microbes or microorganisms are the primary producers of ecosystem services for biogeochemical cycles of the earth and biological systems. Xenobiotics mark a new anthropogenic era, "the Anthropocene," and they represent a source of artificial selection of the structure and composition of microbial biodiversity. As a result, anthropogenic disturbances are detrimental to microbial systems and induce adaptive changes or damage in their metagenomic repertories. During resistance and recovery, the ecological processes governing the assembly of microbial communities cannot be dissociated from those of microbial evolution. This work stems from the transdisciplinary intersection of ecotoxicology, microbial ecology, metagenomics and bioinformatics. The main goal is to understand the adaptive signatures of microbial resistance and resilience in two models. The first is environmental (E) composed of a lake-bound watershed contaminated by heavy metals. The second model is hostassociated (HA), consisting of an experimental system of perch (Perca flavescens) intoxicated with cadmium using two steady and gradual regimes. Three novelties summarize the work of this doctoral thesis. Firstly, the phenomenon of taxon-function decoupling has been demonstrated for the first time, in the E system under selective pollution gradient, and second, within the cutaneous microbiota in the HA system during its recovery stage. Third, the microbiota assembly modelling in the HA system suggested mixed effects of ontogenesis, and selective pressure during the period of resistance and recovery. The increase in cadmium bioaccumulation in liver tissues of perch can argue the persistence of the long-term effects of selection during the recovery stage. In conclusion, our work showed that the adaptation of microbial metagenomic repertories could be revealed through functional and taxonomic redundancy patterns observed at the scale of taxon-function decoupling. The gap between functional and taxonomic diversity reflects an adaptive strategy by horizontal gene transfer among environmental communities microbial under gradual disruption In the HA system, the microbiota assembly shows a gradient of neutral and non-neutral processes. Finally, the taxonomic drift is a significant ecological force, more effective in the environmental system than in the intestinal system during and after the disruption
Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations
No full textBackground:
The eco-evolutionary processes ruling post-disturbance microbial assembly remain poorly studied, particularly in host-microbiome systems. The community recovery depends not only on the type, duration, intensity, and gradient of disturbance, but also on the initial community structure, phylogenetic composition, legacy, and habitat (soil, water, host). In this study, yellow perch (Perca flavescens) juveniles were exposed over 90 days to constant and gradual sublethal doses of cadmium chloride. Afterward, the exposure of aquaria tank system to cadmium was ceased for 60 days. The skin, gut and water tank microbiomes in control and treatment groups, were characterized before, during and after the cadmium exposure using 16s rDNA libraries and high throughput sequencing technology (Illumina, Miseq).
Results:
Our data exhibited long-term bioaccumulation of cadmium salts in the liver even after two months since ceasing the exposure. The gradient of cadmium disturbance had differential effects on the perch microbiota recovery, including increases in evenness, taxonomic composition shifts, as well as functional and phylogenetic divergence. The perch microbiome reached an alternative stable state in the skin and nearly complete recovery trajectories in the gut communities. The recovery of skin communities showed a significant proliferation of opportunistic fish pathogens (i.e., Flavobacterium). Our findings provide evidence that neutral processes were a much more significant contributor to microbial community turnover in control treatments than in those treated with cadmium, suggesting the role of selective processes in driving community recovery.
Conclusions:
The short-term metallic disturbance of fish development has important long-term implications for host health. The recovery of microbial communities after metallic exposure depends on the magnitude of exposure (constant, gradual), and the nature of the ecological niche (water, skin, and gut). The skin and gut microbiota of fish exposed to constant concentrations of cadmium (CC) were closer to the control negative than those exposed to the gradual concentrations (CV). Overall, our results show that the microbial assembly during the community recovery were both orchestrated by neutral and deterministic processes
Image_8_Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient.PDF
No full textAdaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.</p
V-Proximal Trustworthy Banach Spaces
No full textIn a recent work (2016), the first author proved the fuzzy sum rule for the V-proximal subdifferential under some natural assumptions on an equivalent norm of the Banach spaces. In the present paper, we are going to prove that the class of Banach spaces satisfying the fuzzy sum rule is very large and contains all Lp spaces 1<p<∞ as well as the sequence spaces lp1<p<∞, the Sobolev spaces Wp,n1<p<∞, and the Schatten trace ideals Cp1<p<∞
Vascular endothelial growth factor restores delayed tumor progression in tumors depleted of macrophages
No full textGenetic depletion of macrophages in Polyoma Middle T oncoprotein (PyMT)-induced mammary tumors in mice delayed the angiogenic switch and the progression to malignancy. To determine whether vascular endothelial growth factor A (VEGF-A) produced by tumor-associated macrophages regulated the onset of the angiogenic switch, a genetic approach was used to restore expression of VEGF-A into tumors at the benign stages. This stimulated formation of a high-density vessel network and in macrophage-depleted mice, was followed by accelerated tumor progression. The expression of VEGF-A led to a massive infiltration into the tumor of leukocytes that were mostly macrophages. This study suggests that macrophage-produced VEGF regulates malignant progression through stimulating tumor angiogenesis, leukocytic infiltration and tumor cell invasion
Dietary contamination with a neonicotinoid (clothianidin) gradient triggers specific dysbiosis signatures of microbiota activity along the honeybee (Apis mellifera) digestive tract
No full textPesticides are increasing honeybee (Apis mellifera) death rates globally. Clothianidin neonicotinoid appears to impair the microbe–immunity axis. We conducted cage experiments on newly emerged bees that were 4–6 days old and used a 16S rRNA metataxonomic approach to measure the impact of three sublethal clothianidin concentrations (0.1, 1 and 10 ppb) on survival, sucrose syrup consumption and gut microbiota community structure. Exposure to clothianidin significantly increased mortality in the three concentrations compared to controls. Interestingly, the lowest clothianidin concentration was associated with the highest mortality, and the medium concentration with the highest food intake. Exposure to clothianidin induced significant variation in the taxonomic distribution of gut microbiota activity. Co-abundance network analysis revealed local dysbiosis signatures specific to each gut section (midgut, ileum and rectum) were driven by specific taxa. Our findings confirm that exposure to clothianidin triggers a reshuffling of beneficial strains and/or potentially pathogenic taxa within the gut, suggesting a honeybee’s symbiotic defense systems’ disruption, such as resistance to microbial colonization. This study highlights the role of weak transcriptional activity taxa in maintaining a stable honeybee gut microbiota. Finally, the early detection of gut dysbiosis in honeybees is a promising biomarker in hive management for assessing the impact exposure to sublethal xenobiotics
Additional file 6 of Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations
No full textAdditional file 6: Figure S6. Heat trees and stacked bar plots of water and host microbiome structure. This figure summarizes pairwise comparison of the community composition of water and each of the host communities for different treatments (Ctrl, CC and CV). Additionally, stacked bar plots of relative abundance at phylum level are provided for each community (water, skin, gut). The non-grey coloring (which category the branches are upregulated in) indicates significant differences in terms of log median ratios for samples from different habitats (Gut, Skin and Water) as determined by a Wilcox rank-sum test followed by a Benjamini-Hochberg (FDR) correction for multiple testing. The heat trees were built using metacoder and stacked barplots were produced using the Rhea package
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