Biology subjects

Pouzadoux, J.

Publications and source records attributed to Pouzadoux, J..

6 recordsLinked to original sources

bioRxiv2026

Decoupling epigenetic variation from genetic variation reveals complementary dimensions of coral eco-evolutionary dynamics

Understanding how intraspecific diversity is structured is essential for predicting the eco-evolutionary trajectories of populations, especially under rapid environmental change. While such diversity has been extensively studied from a genetic perspective, much less is known about the distribution and ecological relevance of epigenetic variation within natural populations. To address this question, we focused on two species of reef-building corals belonging to distinct functional groups, Pocillopora acuta and Acropora hyacinthus, sampled across the South Pacific (New Caledonia, Fiji, French Polynesia). Using genome-wide Enzyme-Methyl sequencing, we jointly analyzed genetic (SNPs) and DNA methylation (CpGs) variation, while explicitly disentangling genetically associated from genetically independent epigenetic variation. Genetic and epigenetic structure showed contrasting spatial patterns, reflecting distinct temporal and ecological components of population dynamics. Genetic structure was strongest between archipelagos and followed an isolation-by-distance pattern consistent with long-term evolutionary processes. In contrast, epigenetic variation converged between colonies from different archipelagos. At finer spatial scales within archipelago, genetically independent epigenetic variation exhibited stronger structure than both genetic and genetically associated epigenetic variation, likely reflecting local environmental conditions. Together, our results show that genetic and epigenetic variation provide complementary insights into the eco-evolutionary processes shaping intraspecific diversity.

evolutionary biology↗

bioRxiv2024

Vibrio are a potential source of novel colistin-resistance genes in European coastal environments

Colistin is a widespread last resort antibiotic for treatment of multidrug-resistant bacteria. The recent worldwide emergence of colistin resistance (Col-R) conferred by mcr-1 in human pathogens has raised concern, but the putative sources and reservoirs of novel mcr genes in the marine environment remain underexplored. We observed a high prevalence of Col-R, particularly in Vibrio isolated from European coastal waters by using a unique stock of specific-pathogen-free (SPF) oysters as a bioaccumulator. The high sequence diversity found in the mcr/eptA gene family was geographically structured, particularly for three novel eptA gene variants, which were restricted to the Mediterranean (France, Spain) and occurred as a dgkA-eptA operon controlled by the RstA/RstB two component system. By analyzing 29427 Vibrionaceae genome assemblies, we showed that this mechanism of intrinsic resistance is prevalent and specific to the Harveyi clade, which includes strains of Vibrio parahaemolyticus and Vibrio alginolyticus causing infections in humans. The operon conferred colistin-resistance when transferred to sensitive non-Vibrio strains. While mcr-and arn-based Col-R mechanisms were also identified, the widespread presence of eptA gene variants in Vibrio suggests they play a key role in intrinsic resistance to colistin. Beyond these ancient eptA gene copies having evolved with the Vibrio lineage, we also identified mobile eptA paralogues that have been recently transferred between and within Vibrio clades. This highlights Vibrio as a potential source of Col-R mechanisms, emphasizing the need for enhanced surveillance to prevent colistin-resistant infections in coastal areas.

microbiology↗

bioRxiv2024

Diversity and functional specialization of oyster immune cells uncovered by integrative single cell level investigations

Mollusks are a major component of animal biodiversity and play a critical role in ecosystems and global food security. The Pacific oyster, Crassostrea (Magallana) gigas, is the most farmed bivalve mollusk in the world and is becoming a model species for invertebrate biology. Despite the extensive research on hemocytes, the immune cells of bivalves, their characterization remains elusive. Here we were able to extensively characterize the diverse hemocytes and identified at least seven functionally distinct cell types and three hematopoietic lineages. A combination of single-cell RNA sequencing, quantitative cytology, cell sorting, functional assays and pseudo-time analyses was used to deliver a comprehensive view of the distinct hemocyte types. This integrative analysis enabled us to reconcile molecular and cellular data and identify distinct cell types performing specialized immune functions, such as phagocytosis, reactive oxygen species production, copper accumulation, and expression of antimicrobial peptides. This study emphasized the need for more in depth studies of cellular immunity in mollusks and non-model invertebrates and set the ground for further comparative immunology studies at the cellular level.

immunology↗

bioRxiv2024

Microbial education plays a crucial role in harnessing the beneficial properties of microbiota for infectious disease protection in Crassostrea gigas

BackgroundRecently, the frequency and severity of marine diseases have increased in association with global changes, and molluscs of economic interest are particularly concerned. Among them, the Pacific oyster (Crassostrea gigas) production faces challenges from several diseases such as the Pacific Oyster Mortality Syndrome (POMS) or vibriosis. Various strategies such as genetic selection or immune priming have been developed to fight some of these infectious diseases. The microbial education, which consist of exposing the host immune system to beneficial microorganisms during early life stages is a promising approach against diseases. This study explores the concept of microbial education using controlled and pathogen-free bacterial communities and assesses its protective effects against POMS and Vibrio aestuarianus infections, highlighting potential applications in oyster production. ResultsWe demonstrate that it is possible to educate the oyster immune system by adding microorganisms during the larval stage. Adding culture based bacterial mixes to larvae protects only against the POMS disease while adding whole microbial communities from oyster donors protects against both POMS and vibriosis. The efficiency of the immune protection depends both on oyster origin and on the composition of the bacterial mixes used for exposure. No preferential protection was observed when the oysters were stimulated with their sympatric strains. We further show that the added bacteria were not maintained in the oyster microbiota after the exposure, but this bacterial addition induced long term changes in the microbiota composition and oyster immune gene expression. ConclusionOur study reveals successful immune system education of oysters by introducing beneficial micro-organisms during the larval stage. We improved the long-term resistance of oysters against critical diseases (POMS disease and Vibrio aestuarianus infections) highlighting the potential of microbial education in aquaculture.

microbiology↗

bioRxiv2023

Cooperation and cheating orchestrate Vibrio assemblages and polymicrobial synergy in oysters infected with OsHV-1 virus

Polymicrobial diseases significantly impact the health of humans and animals but remain understudied in natural systems. We recently described the Pacific Oyster Mortality Syndrome (POMS), a polymicrobial disease that impacts oyster production and is prevalent worldwide. Analysis of POMS-infected oysters on the French North Atlantic coast revealed that the disease involves co-infection with the endemic ostreid herpesvirus 1 (OsHV-1) and virulent bacterial species such as Vibrio crassostreae. However, it is unknown whether consistent Vibrio populations are associated with POMS in different regions, how Vibrio contribute to POMS, and how they interact with the OsHV-1 virus during pathogenesis. We resolved the Vibrio population structure in oysters from a Mediterranean ecosystem and investigated their functions in POMS development. We find that Vibrio harveyi and Vibrio rotiferianus are the predominant species found in OsHV-1-diseased oysters and show that OsHV-1 is necessary to reproduce the partition of the Vibrio community observed in the field. By characterizing the interspecific interactions between OsHV-1, V. harveyi and V. rotiferianus, we find that only V. harveyi synergizes with OsHV-1. When co-infected, OsHV-1 and V. harveyi behave cooperatively by promoting mutual growth and accelerating oyster death. V. harveyi showed high virulence potential in oysters and dampened host cellular defenses, making oysters a more favorable niche for microbe colonization. We next investigated the interactions underlying the co-occurrence of diverse Vibrio species in diseased oysters. We found that V. harveyi harbors genes responsible for the biosynthesis and uptake of a key siderophore called vibrioferrin. This important resource promotes the growth of V. rotiferianus, a cheater that efficiently colonizes oysters during POMS without costly investment in host manipulation nor metabolite sharing. By connecting field-based approaches, laboratory infection assays and functional genomics, we have uncovered a web of interdependencies that shape the structure and function of the POMS pathobiota. We showed that cooperative behaviors contribute to synergy between bacterial and viral co-infecting partners. Additional cheating behaviors further shape the polymicrobial consortium. Controlling such behaviors or countering their effects opens new avenues for mitigating polymicrobial diseases.

microbiology↗

bioRxiv2016

A dense brown trout (Salmo trutta) linkage map reveals recent chromosomal rearrangements in the Salmo genus and the impact of selection on linked neutral diversity

High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socio-economically important species heavily impacted by human activities. A total of 3,977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species Salmo salar revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3,721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity ({pi}) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high density linkage map provides a useful genomic resource for future aquaculture, conservation and eco-evolutionary studies in brown trout.

genomics↗