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Barbier, M.

Publications and source records attributed to Barbier, M..

At least 37 records · Page 2Linked to original sources

Linking intrinsic scales of ecological processes to characteristic scales of biodiversity and functioning patterns

Ecology is a science of scale, which guides our description of both ecological processes and patterns, but we lack a systematic understanding of how process scale and pattern scale are connected. Recent calls for a synthesis between population ecology, community ecology, and ecosystem ecology motivate the integration of phenomena at multiple levels of organization. Furthermore, many studies leave out the scaling of a critical process: species interactions, which may be non-local through movement or foraging and must be distinguished from dispersal scales. Here, we use simulations to explore the consequences of three different process scales (species interactions, dispersal, and the environment) on emergent patterns of biodiversity, ecosystem functioning, and their relationship, in a spatially-explicit landscape and stable equilibrium setting. A major result of our study is that the spatial scales of dispersal and species interactions have opposite effects: a larger dispersal scale homogenizes spatial biomass patterns, while a larger interaction scale amplifies their heterogeneity. Interestingly, the specific scale at which dispersal and interaction scales begin to influence landscape patterns depends on the scale of environmental heterogeneity - in other words, the scale of one process allows important scales to emerge in other processes. This interplay between process scales, i.e., a situation where no single process dominates, can only occur when the environment is heterogeneous and the scale of dispersal small. Finally, contrary to our expectations, we observe that the spatial scale of ecological processes is more clearly reflected in landscape patterns (i.e., distribution of local outcomes) than in global patterns such as Species-Area Relationships or large-scale biodiversity-functioning relationships. Overall we conclude that long-range interactions often act differently and even in opposite ways to dispersal, and that the landscape patterns that emerge from the interplay of long-ranged interactions, dispersal and environmental heterogeneity are not well captured by often-used metrics like the Species-Area Relationship.

ecology↗

Long-term analysis of pertussis vaccine immunity uncovers a memory B cell response to whole cell pertussis immunization that is absent from acellular immunized mice

Over two decades ago acellular pertussis vaccines (aP) replaced whole cell pertussis vaccines (wP) in several countries. Since then, a resurgence in pertussis has been observed, which is hypothesized to be linked to waning immunity. To better understand why waning immunity occurs, we developed a long-term outbred CD1 mouse model to conduct the longest murine pertussis vaccine studies to date, spanning out to 532 days post primary immunization. Vaccine-induced memory results from follicular responses and germinal center formation; therefore, cell populations and cytokines involved with memory were measured alongside protection from challenge. Both aP and wP immunization elicit protection from intranasal challenge and generation of pertussis specific antibody responses in mice. Responses to wP vaccination were characterized by a significant increase in T follicular helper cells in the draining lymph nodes and CXCL13 levels in sera compared to aP mice. In addition, a population of B. pertussis+ memory B cells was found to be unique to wP vaccinated mice. This population peaked post-boost, and was measurable out to day 365 post-vaccination. Anti-B. pertussis and anti-pertussis toxoid antibody secreting cells increased one day after boost and remained high at day 532. The data suggest that follicular responses, and in particular CXCL13 levels in sera, should be monitored in pre-clinical and clinical studies for the development of the next-generation pertussis vaccines.

immunology↗

Mucosal immunization with DTaP confers protection against Bordetella pertussis infection and cough in Sprague-Dawley rats

Pertussis is a respiratory disease caused by the Gram-negative pathogen, Bordetella pertussis (Bp). The transition from a whole cell pertussis vaccine (wP; DTP) to an acellular pertussis vaccine (aP; DTaP; Tdap) correlates with an increase in pertussis cases, despite widespread vaccine implementation and coverage, and it is now appreciated that the protection provided by aP rapidly wanes. To recapitulate the localized immunity observed from natural infection, mucosal vaccination with aP was explored using the coughing rat model of pertussis. Immunity induced by both oral gavage (OG) and intranasal (IN) vaccination of aP in Bp challenged rats over a nine-day infection was compared to intramuscular (IM)-wP and IM-aP immunized rats that were used as positive controls as IM immunization is the current route for wP and aP vaccination. Our data demonstrate that both IN and OG immunization of aP resulted in production of anti-Bp IgG antibody titers similar to IM-wP and IM-aP vaccinated controls post-challenge. IN-aP also induced anti-Bp IgA antibodies in the nasal cavity. Immunization with IM-wP, IM-aP, IN-aP, and OG-aP immunization protected against Bp induced cough, while OG-aP immunization did not protect against respiratory distress. Mucosal immunization (IN-aP and OG-aP) also protected against acute inflammation and decreased bacterial burden in the lung compared to mock vaccinated challenge (MVC) rats. The data presented in this study suggests that mucosal vaccination with aP can induce a mucosal immune response and provide protection against Bp challenge.

microbiology↗

Re-investigating the coughing rat model of pertussis to understand Bordetella pertussis pathogenesis

Bordetella pertussis (Bp) is a highly contagious bacterium that is the causative agent of whooping cough (pertussis). Currently, acellular pertussis vaccines (aP; DTaP; Tdap) are used to prevent pertussis disease. However, it is clear that the aP vaccine efficacy quickly wanes, resulting in the re-emergence of pertussis. Furthermore, recent work performed by the CDC suggest that current circulating strains are genetically distinct from strains of the past. Emergence of genetically diverging strains combined with waning aP vaccine efficacy call for re-evaluation of current animal models of pertussis. In this study, we used the rat model of pertussis to compare two genetically divergent strains Tohama 1 and D420. We intranasally challenged seven-week-old Sprague-Dawley rats with 108 viable Tohama 1 and D420 and measured the hallmark signs/symptoms of Bp infection such as neutrophilia, pulmonary inflammation, and paroxysmal cough using whole body plethysmography. Onset of cough occurred between 2-4 days after Bp challenge averaging five coughs per fifteen minutes, with peak coughing occurring at day eight post infection averaging upward of thirteen coughs per fifteen minutes. However, we observed an increase of coughs in rats infected with clinical isolate D420 through 12 days post challenge. The rats exhibited increased bronchial restriction following Bp infection. Histology of the lung and flow cytometry confirm both cellular infiltration and pulmonary inflammation. D420 infection induced higher production of anti-Bp IgM antibodies compared to Tohama 1 infection. The coughing rat model provides a way of characterizing disease manifestation differences between Bp strains.

immunology↗

Burkholderia collagen-like protein 8, Bucl8, is a unique outer membrane component of a tetrapartite efflux pump in Burkholderia pseudomallei and Burkholderia mallei

Bacterial efflux pumps are an important pathogenicity trait because they extrude a variety of xenobiotics. Our laboratory previously identified in silico Burkholderia collagen-like protein 8 (Bucl8) in the Tier one select agents Burkholderia pseudomallei and Burkholderia mallei. We hypothesize that Bucl8, which contains two predicted tandem outer membrane efflux pump domains, is a component of a putative efflux pump. Unique to Bucl8, as compared to other outer membrane proteins, is the presence of an extended extracellular region containing a collagen-like (CL) domain and a non-collagenous C-terminus (Ct). Molecular modeling and circular dichroism spectroscopy with a recombinant protein, corresponding to this extracellular CL-Ct portion of Bucl8, demonstrated that it adopts a collagen triple helix, whereas functional assays screening for Bucl8 ligands identified binding to fibrinogen. Bioinformatic analysis of the bucl8 gene locus revealed it resembles a classical efflux-pump operon. The bucl8 gene is co-localized with downstream fusCDE genes encoding fusaric acid (FA) resistance, and with an upstream gene, designated as fusR, encoding a LysR-type transcriptional regulator. Using RT-qPCR, we defined the boundaries and transcriptional organization of the fusR-bucl8-fusCDE operon. We found exogenous FA induced bucl8 transcription over 80-fold in B. pseudomallei, while deletion of the entire bucl8 locus decreased the MIC of FA 4-fold in its isogenic mutant. We furthermore showed that the Bucl8 pump expressed in the heterologous Escherichia coli host confers FA resistance. On the contrary, the Bucl8 pump did not confer resistance to a panel of clinically-relevant antimicrobials in Burkholderia and E. coli. We finally demonstrated that deletion of the bucl8-locus drastically affects the growth of the mutant in L-broth. We determined that Bucl8 is a component of a novel tetrapartite efflux pump, which confers FA resistance, fibrinogen binding, and optimal growth. Author SummaryBurkholderia pseudomallei and Burkholderia mallei are highly infectious and multidrug resistant bacteria that are classified by the National Institute of Allergy and Infectious Diseases as Tier one select agents partly due to the intrinsic multidrug resistance associated with expression of the efflux pumps. To date, only few efflux pumps predicted in Burkholderia spp. have been studied in detail. In the current study we introduce Bucl8, an outer membrane component of an unreported putative efflux pump with a unique extended extracellular portion that forms a collagen triple helix and binds fibrinogen. We demonstrate Bucl8s role in fusaric acid resistance by defining its operon via bioinformatic and transcriptional analyses, as well as by employing loss-of-function and gain-of-function genetic approaches. Our studies also implicate the Bucl8-associated pump in metabolic and physiologic homeostasis. Understanding how Bucl8 efflux pump contributes to Burkholderia pathology will foster development of pump inhibitors targeting transport mechanism or identifying potential surface-exposed vaccine targets.

microbiology↗

FastTrack, A Strategy to Shorten Time to Degree

Recent reports express concern about the sustainability of the biomedical research enterprise in its current form. Recurring concerns include the predictability and sustainability of funding for research, regulatory burden and training the next generation in the biomedical workforce. One specific concern is the duration of training periods during pre-doctoral and post-doctoral studies. This article addresses the issue of time-to-degree (TTD) for doctorates. Many reports stress the importance of shortening the TTD, but provide no recommendations to achieve this goal. Herein, factors potentially affecting TTD are discussed and one mechanism that harmonizes undergraduate and graduate programs is proposed as a strategy to reduce the TTD.

scientific communication and education↗

Can biomass distribution across trophic levels predict trophic cascades?

The biomass distribution across trophic levels (biomass pyramid), and cascading responses to perturbations (trophic cascades), are archetypal representatives of the interconnected set of static and dynamical properties of food chains. A vast literature has explored their respective ecological drivers, sometimes generating correlations between them. Here we instead reveal a fundamental connection: both pyramids and cascades reflect the dynamical sensitivity of the food chain to changes in species intrinsic rates. We deduce a direct relationship between cascades and pyramids, modulated by what we call trophic dissipation - a synthetic concept that encodes the contribution of top-down propagation of consumer losses in the biomass pyramid. Predictable across-ecosystem patterns emerge when systems are in similar regimes of trophic dissipation. Data from 31 aquatic mesocosm experiments demonstrate how our approach can reveal the causal mechanisms linking trophic cascades and biomass distributions, thus providing a road map to deduce reliable predictions from empirical patterns.

ecology↗

Synchrony and perturbation transmission in trophic metacommunities

In a world where natural habitats are ever more fragmented, the dynamics of meta-communities is essential to properly understand species responses to perturbations. If species populations fluctuate asynchronously, the risk of their simultaneous extinction is low, thus reducing the species regional extinction risk. We propose a metacommunity model consisting of two food chains connected by dispersal to study the transmission of small perturbations affecting populations in the vicinity of an equilibrium. We show that perturbing a species in one patch can lead to asynchrony between patches if the perturbed species is not the most affected by dispersal. Dispersal affects rare species the most, thus making biomass distribution critical to understand the response of trophic metacommunities to perturbations. We further partition the effect of each perturbation on species synchrony when several independent perturbations are applied. Our approach allows disentangling and predicting the responses of simple trophic metacommunities to perturbations, thus providing a theoretical foundation for future studies considering more complex spatial ecological systems.

ecology↗

A macro-ecological approach to predators’ functional response

AO_SCPLOWBSTRACTC_SCPLOWPredation often deviates from the law of mass action: many micro- and meso-scale experiments have shown that consumption saturates with resource abundance, and decreases due to interference between consumers. But does this observation hold at macro-ecological scales, spanning many species and orders of magnitude in biomass? If so, what are its consequences for large-scale ecological patterns and dynamics? We perform a meta-analysis of predator-prey pairs of mammals, birds and reptiles, and show that predation losses appear to increase, not as the product of predator and prey densities following the Lotka-Volterra (mass action) model, but rather as the square root of that product. This suggests a phenomenological power-law expression of the effective cross-ecosystem functional response. We discuss whether the same power-law may hold dynamically within an ecosystem, and assuming that it does, we explore its consequences in a simple food chain model. The empirical exponents fall close to the boundary between regimes of donor and consumer limitation. Exponents on this boundary are singular in multiple ways. First, they maximize predator abundance and some stability metrics. Second, they create proportionality relations between biomass and productivity, both within and between trophic levels. These intuitive relations do not hold in general in mass action models, yet they are widely observed empirically. These results provide evidence of mechanisms limiting predation across multiple ecological scales. Some of this evidence was previously associated with donor control, but we show that it supports a wider range of possibilities, including forms of consumer control. As limiting consumption counter-intuitively allows larger populations, it is worthwhile to reconsider whether the observed functional response arises from microscopic mechanisms, or could hint at selective pressure at the population level. This article has been peer-reviewed and recommended by Peer Community In Ecology (DOI: 10.24072/pci.ecology.100051)

developmental biology↗

Elevated levels of interleukin-27 in early life compromise protective immunity during neonatal sepsis

Neonates are at increased risk for bacterial sepsis as a result of immature immunity. We established that the immune suppressive cytokine interleukin (IL)-27 is elevated in early life. In the present work, we hypothesized that increased levels of IL-27 may predispose the neonatal population to more severe infection during sepsis. In a neonatal sepsis model, systemic IL-27 levels continued to rise during infection. Peripheral tissue analysis revealed systemic IL-27 expression, while myeloid cell profiling identified Gr-1 and F4/80-expressing cells as the most abundant producers of IL-27 during infection. Increased IL-27 levels were consistent with increased mortality that was improved in WSX-1-/- mice that lack a functional IL-27 receptor. Infected WSX-1-/- pups exhibited improved weight gain and reduced morbidity. IL-27 signaling in WT mice promoted increased bacterial burdens and systemic inflammation compared to WSX-1-/- neonates. This was consistent with more efficient bacterial killing by Ly6B.2+ myeloid cells and macrophages from WSX-1-deficient compared to wild-type neonates. Live animal imaging further supported a more severe and disseminated infection in WT neonates. This is the first report to describe the impact of elevated early life IL-27 on the host response in neonates while also defining the cell and tissue sources of cytokine. IL-27 is frequently associated with suppressed inflammation. In contrast, our findings demonstrate that IL-27 promotes inflammation during neonatal sepsis by directly compromising control of bacteria that drive the inflammatory response. Collectively, our results suggest that IL-27 represents a therapeutic target to limit susceptibility and improve infectious outcomes in neonatal sepsis.\n\nIMPORTANCEA number of differences in the neonatal immune response compared with adults have been well described. However, a mechanistic understanding of what needs to be overcome in the neonate to generate a more protective immune response during acute bacterial infection has been limited. The work described here helps fill the gap of what is necessary to overcome in order to achieve improved host response to infection. To further the novelty, IL-27 has not previously been attributed to dysfunction or deficiency in neonatal immunity. Our results enhance the understanding of IL-27 biology in the neonatal population while providing evidence that elevated IL-27 levels limit a protective immune response and are detrimental during neonatal sepsis. Strategies aimed at targeting circulating IL-27 concentrations early in life have the potential to improve control of bacterial infection in neonates.

immunology↗

Ecotone formation through ecological niche construction: the role of biodiversity and species interactions

Rapid changes in species composition, also known as ecotones, can result from various causes including rapid changes in environmental conditions, or physiological thresholds. The possibility that ecotones arise from ecological niche construction by ecosystem engineers has received little attention. In this study, we investigate how the diversity of ecosystem engineers, and their interactions, can give rise to ecotones. We build a spatially explicit dynamical model that couples a multispecies community and its abiotic environment. We use numerical simulations and analytical techniques to determine the biotic and abiotic conditions under which ecotone emergence is expected to occur, and the role of biodiversity therein. We show that the diversity of ecosystem engineers can lead to indirect interactions through the modification of their shared environment. These interactions, which can be either competitive or mutualistic, can lead to the emergence of discrete communities in space, separated by sharp ecotones where a high species turnover is observed. Considering biodiversity is thus critical when studying the influence of species-environment interactions on the emergence of ecotones. This is especially true for the wide range of species that have small to moderate effects on their environment. Our work highlights new mechanisms by which biodiversity loss could cause significant changes in spatial community patterns in changing environments.

ecology↗

Can endogenous fluctuations persist in high-diversity ecosystems?

When can complex ecological interactions drive an entire ecosystem into a persistent non-equilibrium state, where species abundances keep fluctuating without going to extinction? We show that high-diversity spatially-extended systems, in which conditions vary somewhat between spatial locations, can exhibit chaotic dynamics which persist for extremely long times. We develop a theoretical framework, based on dynamical mean-field theory, to quantify the conditions under which these fluctuating states exist, and predict their properties. We uncover parallels with the persistence of externally-perturbed ecosystems, such as the role of perturbation strength, synchrony and correlation time. But uniquely to endogenous fluctuations, these properties arise from the species dynamics themselves, creating feedback loops between perturbation and response. A key result is that the fluctuation amplitude and species diversity are tightly linked, in particular fluctuations enable dramatically more species to coexist than at equilibrium in the very same system. Our findings highlight crucial differences between well-mixed and spatially-extended systems, with implications for experiments and their ability to reproduce natural dynamics. They shed light on the maintenance of biodiversity, and the strength and synchrony of fluctuations observed in natural systems.

ecology↗

Distribution and abundance of bottlenose dolphin (Tursiops truncatus) over the French Mediterranean continental shelf

The Mediterranean bottlenose dolphin (Tursiops truncatus) sub-population is listed as vulnerable by the International Union for Conservation of Nature. This species is strictly protected in France and the designation of Special Areas of Conservation (SAC) is required under the European Habitat Directive. However, little information is available about the structure, dynamic and distribution of the population in the French Mediterranean waters. We collected photo-identification data over the whole French Mediterranean continental shelf all year round between 2013 and 2015. We sighted 151 groups of bottlenose dolphins allowing the individually photo-identification of 1,060 animals. The encounter rate distribution showed the presence of bottlenose dolphins over the whole continental shelf all year round. Using capture-recapture methods, we estimated for the first time the size of the bottlenose dolphin resident population at 557 individuals (95% confidence interval: 216-872) along the French Mediterranean continental coast. Our results were used in support of the designation of a new dedicated SAC in the Gulf of Lion and provide a reference state for the bottlenose dolphin monitoring in the French Mediterranean waters in the context of the Marine Strategy Framework Directive.

ecology↗

How indirect interactions shape long-term invasion dynamics in complex ecological communities

Many facets of ecological theory rely on the analysis of invasion processes, and general approaches exist to understand the early stages of an invasion. However, predicting the long-term transformations of communities following an invasion remains a challenging endeavour. We propose an analytical method that uses community structure and invader dynamical features to predict when these impacts can be large, and show it to be applicable across a wide class of dynamical models. Our approach reveals that short-term invasion success and long-term consequences are two distinct axes of variation controlled by different properties of both invader and resident community. Whether a species can invade is controlled by its invasion fitness, which depends on environmental conditions and direct interactions with resident species. But whether this invasion will cause significant transformations, such as extinctions or a regime shift, depends on a specific measure of indirect feedbacks that may involve the entire resident community. Our approach applies to arbitrarily complex communities, from few competing phenotypes in adaptive dynamics to large nonlinear food webs. It hints at new questions to ask as part of any invasion analysis, and suggests that long-term indirect interactions are key determinants of invasion outcomes.

ecology↗

Characterizing the innate and adaptive responses of immunized mice to Bordetella pertussis infection using in vivo imaging and transcriptomic analysis

Bordetella pertussis (B. pertussis) is the causative agent of pertussis (whooping cough). Since the 1990s, pertussis has re-emerged in the United States despite an estimated 95% vaccine coverage. Our goal was to characterize neutrophil responses and gene expression profiles of murine lungs in the context of vaccination and B. pertussis challenge. We utilized a bioluminescent neutrophil mouse model (NECre luc) to track neutrophil recruitment. NECre luc mice were immunized with whole cell vaccine (WCV), acellular vaccine (ACV), or a truncated adenylate cyclase toxoid (RTX) vaccine. Neutrophil recruitment was measured in live mice across time and corroborated by flow cytometry and other data. WCV immunized mice showed signs of neutrophilia in response to B. pertussis challenge. Mice immunized with either ACV or WCV cleared the challenge infection; however immunization with RTX alone was not protective. RNA sequencing revealed distinctive gene expression profiles for each immunization group. We observed an increase in expression of genes associated with responses to infection, and changes in expression of distinct genes in each vaccine group, providing a complex view of the immune response to B. pertussis infection in mice. This study suggests that combination of immunological analysis with transcriptomic profiling can facilitate discovery of pre-clinical correlates of protection for vaccine development.

immunology↗

Diffuse cliques maintain biodiversity in species-rich ecological communities

The coexistence of many competing species is a long-standing puzzle in ecology. Classic niche theory explains coexistence by trade-offs between a few essential species traits. Here we study an unexplored frontier of this theory: we assume that coexistence is intrinsically high-dimensional, arising from many traits and trade-offs at once. Species interactions then appear almost random, but their disorder hides a diffuse statistical structure: competitors that become successful start by subtly favoring each other, and partitioning their impacts on other species. We validate our quantitative predictions using data from grassland biodiversity experiments. We conclude that a high biodiversity can be attained through a pattern of collective organization that cannot be understood at the species level, but exhibits the fingerprint of high-dimensional interactions.

ecology↗

Pyramids and cascades: a synthesis of food chain functioning and stability

Food chain theory is one of the cornerstones of ecology, providing many of its basic predictions, such as biomass pyramids, trophic cascades and predator-prey oscillations. Yet, ninety years into this theory, the conditions under which these patterns may occur and persist in nature remain subject to debate. Rather than address each pattern in isolation, we propose that they must be understood together, calling for synthesis in a fragmented landscape of theoretical and empirical results. As a first step, we propose a minimal theory that combines the long-standing energetic and dynamical approaches of food chains. We chart theoretical predictions on a concise map, where two main regimes emerge: across various functioning and stability metrics, one regime is characterized by pyramidal patterns, the other by cascade patterns. The axes of this map combine key physiological and ecological variables, such as metabolic rates and self-regulation. A quantitative comparison with data sheds light on conflicting theoretical predictions and empirical puzzles, from size spectra to causes of trophic cascade strength. We conclude that drawing systematic connections between various existing approaches to food chains, and between their predictions on functioning and stability, is a crucial step in confronting this theory to real ecosystems.

ecology↗

Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia

Bacterial factors favoring the unprecedented multidrug-resistant tuberculosis (MDR-TB) epidemic in the former Soviet Union remain unclear.\n\nWe utilized whole genome sequencing and Bayesian statistics to analyze the evolutionary history, temporal emergence of resistance and transmission networks of MDR-MTBC strains from Karakalpakstan, Uzbekistan (2001-2006).\n\nOne MTBC-clone (termed Central Asian outbreak, CAO) with resistance mediating mutations to eight anti-TB drugs existed prior the worldwide introduction of standardized WHO-endorsed directly observed treatment, short-course (DOTS). DOTS implementation in Karakalpakstan in 1998 likely selected for these CAO-strains, comprising 75% of sampled MDR-TB strains in 2005/2006. CAO-strains were also identified in a previously published cohort from Samara, Russia (2008-2010). Similarly, transmission success and resistance development was linked to mutations compensating fitness deficits associated with rifampicin resistance.\n\nThe genetic make-up of these outbreak clades threatens the success of both empirical and standardized guideline driven MDR-TB therapies, including the newly WHO-endorsed short MDR-TB regimen in Uzbekistan.

evolutionary biology↗