Biology subjects

Duperron, S.

Publications and source records attributed to Duperron, S..

10 recordsLinked to original sources

bioRxiv2026

The influence of nutrient enrichment and fish addition on microbial communities in water and fish guts during mesocosm experiments conducted in a tropical freshwater lagoon (Lagoon Aghien, Cote dIvoire)

Freshwater ecosystems in the intertropical zone have received considerably less scientific attention than those in temperate regions, with the notable exception of a few large and iconic lakes, such as Lake Victoria. Consequently, the diversity, functioning, and pollution sensitivity of microbial communities in these systems remain poorly understood. To investigate the short-term responses of microbial communities to nutrient enrichment and fish addition, we conducted in situ mesocosm experiments at two stations in a freshwater lagoon near Abidjan (Cote dIvoire). Phosphorus enrichment, either alone or in combination with nitrogen, led to a consistent increase in bacterial abundance across mesocosms, suggesting a potential phosphorus limitation of bacterial growth by these nutrients and consequently a potential competition for this resource between bacteria and microphytoplankton. In contrast, picophytoplankton abundances showed no clear or consistent response to nutrient enrichment, suggesting that other ecological processes may play a more important role in regulating these communities. High-throughput Illumina sequencing revealed contrasting patterns in the relative abundance of cyanobacterial and chloroplast-associated reads, depending on both nutrient enrichment and fish addition. These results, consistent with those obtained by cell counting in a previous study, suggest a potential top-down control of cyanobacteria by fish in Lagoon Aghien. In addition, nutrient (phosphorus and nitrogen combined) enrichment and fish addition significantly affected the amplicon sequence variant (ASV) composition of bacterial communities. Overall, these findings provide new insights into the drivers shaping microbial community structure in tropical freshwater ecosystems and are discussed in the context of previously published data on phytoplankton dynamics from the same experimental system.

ecology↗

bioRxiv2025

Higher trophic status leads to more diverse and divergent microeukaryote communities over time in urban lakes from the Greater Paris (France)

Effects of trophic status on lake microeukaryote community dynamics remain underexplored. Spanning oligotrophic to hypereutrophic conditions, peri-urban lakes located in the Greater Paris region (France) offer unique opportunities to compare these dynamics along a eutrophication gradient. Here, community composition was characterized using 18S rRNA gene metabarcoding, and analyzed in the context of environmental parameters and chlorophyll a-derived trophic status throughout an 18-month sampling period. Microeukaryote assemblages were dominated by Cryptophyceae, Spirotrichea, Chrysophyceae, and Chlorophyceae, with mixotrophic and heterotrophic taxa dominating across all lakes. Taxa richness peaked at intermediate trophic levels, consistent with the intermediate disturbance hypothesis. Beta-diversity and network analyses revealed increasing community modularity, reduced connectivity, and enhanced temporal variability with higher trophic status. In lakes reaching the hypereutrophic status, communities diverged progressively over time, suggesting the onset of regime shifts. Conversely, oligo-to mesotrophic lakes maintained more connected and stable assemblages. These findings demonstrate that eutrophication fosters more diverse and increasingly divergent microeukaryote communities, underscoring its role as a central driver of microbial community restructuring in urban freshwater systems.

microbiology↗

bioRxiv2024

Distinct ecotoxicological impairs induced by different Microcystis genotypes to Medaka fish

One of the most prevalent and notorious bloom-forming freshwater cyanobacterial genus is Microcystis, whom toxicological impairs yet remain incompletely investigated. Based on our previous studies, we hypothesize that some emerging Microcystis metabolites, in addition to microcystins (MCs), are of (eco)toxicological concerns and should be further investigated. To this end, we explore the ecotoxicological potential of different Microcystis genotypes producing various bio-active metabolite cocktails, particularly cyanopeptides of different structural families including MCs, cyanopeptolins, microginins, anabaenopetins, aeruginosins or microcyclamides, on embryo/larvae and adult Medaka fish model. Embryo and larvae exposures to the extracts of the four distinct Microcystis genotypes - comprising two MC-producing (PMC 728.11 and 807.12) and two non-MC-producing (PMC 810.12 and 826.12) strains - showed that PMC 810.12 and 826.12 respectively producing microginins, aeruginosins and microcyclamides exhibit early toxicity and teratogenicity, while PMC 728.11 presented rather larvae toxicity on hatched larvae, in agreement with its high MC content. In addition, we conducted a 4-days microcosm experiment with adult female Medaka exposed to environmental concentrations of these four Microcystis strain cultures to document the microbiome and metabolome responses. Fishes exposed to PMC 728.11 exhibited microbiota dysbiosis signature, while exposure to PMC 826.12 perturbated the fish digestion process inducing even more pronounced microbial and metabolic alterations. The two other strains provoked more moderate perturbations. These findings highlight toxic effects on fish exposed to both MC-as well as non-MC-producing cyanobacteria, suggesting complex interplay and effects of undocumented cyanobacterial bio-active and toxic compounds basides MCs during blooms of Microcystis.

ecology↗

bioRxiv2024

A summer in the Greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential

With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lakes within a relatively restricted area. Here, a four-month time-series was carried out during summertime to monitor planktonic microbial communities of nine lakes located within a [~]70 km radius around Paris (Ile-de-France, France) of comparable morphologies, yet distinct trophic statuses (mesotrophic to hypereutrophic). The contribution of the trophic status and intra-summer variations were investigated on prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). Sampled lakes harbored highly distinct and diverse prokaryotic communities. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. The trophic status appears as the main driver of both community structure and functional potential. When focusing on function involved in biogeochemical cycles, responses to phosphorus limitation (mostly polyphosphate-related processes) were highlighted between trophic statuses. Hypereutrophic lakes communities displayed the highest contrast and heterogeneity over time, suggesting a regime shift compared to lakes of lower trophic status. This study explores the influence of eutrophication on lakes microbiome ecology, by comparing for the first time the planktonic microbial communities and their functional potential of lakes of distinct trophic status in close vicinity over a summer season.

microbiology↗

bioRxiv2023

Multi-omics analyses from a single sample: Prior metabolite extraction does not alter the 16S rRNA-based characterization of prokaryotic community in a diversity of sample types

Massive sequencing of the 16S rRNA gene has become a standard first step to describe and compare microbial communities from various samples. Parallel analysis of high numbers of samples makes it relevant to the statistical testing of the influence of natural or experimental factors and variables. However, these descriptions fail to document changes in community or ecosystem functioning. Non-targeted metabolomics are a suitable tool to bridge this gap, yet extractions protocols are different. In this study, prokaryotic community compositions are documented by 16S rRNA sequencing after direct DNA extraction, or after metabolites extraction followed by DNA extraction. Results obtained using the V3-V4 region on non-axenic cultures of cyanobacteria, lake water column, biofilm, gut of wild and lab-reared fish, indicate that prior extraction of metabolites does not influence the obtained image of prokaryotic communities. This validates sequential extraction of metabolites followed by DNA as a way to combine 16S rRNA sequencing with metabolome characterization from a single sample. This approach has the potential to complement community structure characterization with a proxy of their functioning, without the uncertainties associated with the use of separate samples.

microbiology↗

bioRxiv2023

Bacterial microbiota of Ostreobium, the coral-isolated chlorophyte ectosymbiont, at contrasted salinities

Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve the calcium carbonate skeletons of coral colonies, in shallow-water reef environments of contrasted salinities. Their bacterial composition and plasticity in response to salinity remain unknown. Here, we analyzed the bacteria associated with coral-isolated Ostreobium strains from two distinct rbcL lineages, representative of IndoPacific environmental phylotypes, that had been pre-acclimatized (>9months) to three ecologically-relevant reef salinities: 32.9, 35.1 and 40.2 psu. Bacterial phylotypes were visualized at filament scale by CARD-FISH in algal tissue sections, localized to the surface, within filaments or in the algal mucilage. Ostreobium-associated communities, characterized by bacterial 16S rRNA metabarcoding of cultured thalli and corresponding supernatants, were structured by host genotype more than salinity and partly overlapped with those of environmental (Ostreobium-colonized) coral skeletons. Alphaproteobacteria dominated the thalli communities, enriched in Kiloniellaceae or Rhodospirillaceae depending on algal genotype. A small core microbiota composed of 7 ASVs ([~]1.5% of thalli ASVs, 19%-36% cumulated proportions), shared by multiple cultures of both Ostreobium genotypes and persistent across 3 salinities, included putative intracellular Amoebophilus and Rickettsiales bacteria. This novel knowledge on the taxonomic diversity of Ostreobium bacterial associates paves the way to functional interaction studies within the coral holobiont.

genetics↗

bioRxiv2022

Gut microbiota and holobiont metabolome composition of the Medaka fish (Oryzias latipes) are affected by a short exposure to the cyanobacterium Microcystis aeruginosa

Blooms of toxic cyanobacteria are a common stress encountered by aquatic fauna. Evidence indicates that long-lasting blooms affect fauna-associated microbiota. Because of their multiple roles, host-associated microbes are nowadays considered relevant to ecotoxicology, yet the respective timing of microbiota versus functional changes in holobionts response needs to be clarified. The response of gut microbiota and holobionts metabolome to exposure to a dense culture of Microcystis aeruginosa was investigated as a microcosm-simulated bloom in the model fish species Oryzias latipes (medaka). Both gut microbiota and gut metabolome displayed significant composition changes after only 2 days of exposure. A dominant symbiont, member of the Firmicutes, plummeted whereas various genera of Proteobacteria and Actinobacteriota increased in relative abundance. Changes in microbiota composition occurred earlier and faster compared to metabolome composition, suggesting that the microbiota drives the holobionts response. Liver and muscle metabolome were much less affected than guts, supporting that gut and associated microbiota are in the front row upon exposure. This study highlights that even short cyanobacterial blooms, that are increasingly frequent, trigger changes in microbiota composition and holobiont metabolome. It emphasizes the relevance of multi-omics approaches to explore organisms response to an ecotoxicological stress. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/499308v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@112a904org.highwire.dtl.DTLVardef@16589forg.highwire.dtl.DTLVardef@1146629org.highwire.dtl.DTLVardef@3f25e4_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- A 2-day exposure to a simulated M. aeruginosa bloom is enough to sharply decrease the Firmicute/Proteobacteria ratio in the gut of Oryzias latipes fish. - The exposure induced changes in metabolome composition after 2 days in the gut and 4 days in the liver. - The gut bacterial microbiota response occurred faster than metabolomes; we hypothesize that changes in gut microbiota may drive the gut metabolome compositional changes.

microbiology↗

bioRxiv2021

Disruption of fish gut microbiota composition and holobiont metabolome by cyanobacterial blooms

BackgroundCyanobacterial blooms are one of the most common stress encountered by metazoans living in freshwater lentic systems such as lakes and ponds. Blooms reportedly impair fish health, notably through oxygen depletion and production of bioactive compounds including cyanotoxins. However, in the times of the "microbiome revolution", it is surprising that so little is still known regarding the influence of blooms on fish microbiota. In this study, an experimental approach is used to demonstrate that blooms affect fish microbiome composition and functions, as well as the metabolome of holobionts. To this end, the model teleost Oryzias latipes is exposed to simulated Microcystis aeruginosa blooms of various intensities in a microcosm setting, and the response of bacterial gut communities is evaluated in terms of composition, metagenome-encoded functions and metabolome profiling. ResultsThe gut bacterial community of O. latipes exhibits marked responses to the presence of M. aeruginosa blooms in a dose-dependent manner. Notably, abundant gut-associated Firmicutes almost disappear, while potential opportunists increase. The holobionts gut metabolome displays major changes, while functions encoded in the metagenome of bacterial partners are more marginally affected. Bacterial communities tend to return to original composition after the end of the bloom suggesting post-bloom resilience, and remain sensitive in case of a second bloom, reflecting a highly reactive gut community. ConclusionIn the context of increasingly frequent and intense blooms worldwide, results point to the relevance of accounting for short- and long-term microbiome-related effects in fish ecology, with potential outcomes relevant to conservation biology as well as aquaculture.

microbiology↗

bioRxiv2020

Characterization of cyanobacteria isolated from thermal muds of Balaruc-Les-Bains (France) and description of a new genus and species Pseudochroococcuscouteii

Cyanobacteria are able to synthesize a high diversity of natural compounds that account for their success in the colonization of a variety of ecological niches. Many of them have beneficial properties. The mud from the thermal baths of Balaruc-Les-Bains, one of the oldest thermal baths in France, has long been recognized as a healing treatment for arthro-rheumatic diseases. To characterize the cyanobacteria living in these muds and the metabolites they potentially produce, several strains were isolated from the water column and biofilms of the retention basin and analyzed using a polyphasic approach. Morphological, ultrastructural and molecular (16S rRNA gene and 16S-23S ITS region sequencing) methods were employed to identify nine cyanobacterial strains belonging to the orders Chroococcales, Synechococcales, Oscillatoriales and Nostocales. The combination of morphological and genetic characteristics supported the description of a new genus and species with the type species as Pseudo-chroococcus couteii. The high taxonomic diversity in the muds of the thermal baths of Balaruc-Les-Bains along with literature reports of the potential for bioactive metabolite synthesis of these taxa allowed us to hypothesize that some of the metabolites produced by these strains could contribute to the therapeutic properties of the muds from Thermes de Balaruc-Les-Bains.

microbiology↗

bioRxiv2018

High rates of apoptosis visualized in the symbiont-bearing gills of deep-sea Bathymodiolus mussels

Symbiosis between Bathymodiolus and Gammaproteobacteria enables these deep-sea mussels to live in toxic environments like hydrothermal vents and cold seeps. The quantity of endosymbionts within the gill-bacteriocytes appears to vary according to the hosts environment. We investigated the hypothesis of a control of the endosymbionts density by apoptosis, a programmed cell death. We used fluorometric TUNEL-method and active Caspase-3-targeting antibodies to visualize and quantify apoptotic cells in mussel gills. To avoid artefacts due to depressurization upon specimen recovery from the deep-sea, we compared the apoptotic rates between mussels recovered unpressurised, versus mussels recovered in a pressure-maintaining device, in two species from hydrothermal vents on the Mid-Atlantic Ridge: Bathymodiolus azoricus and B. puteoserpentis. Our results show that pressurized recovery had no significant effect on the apoptotic rate in the gill filaments. Apoptotic levels were highest in the ciliated zone and in the circulating hemocytes, compared to the bacteriocyte zone. Apoptotic gill-cells in B. aff. boomerang from the pockmarks off the Gulf of Guinea, show similar distribution patterns. Deep-sea symbiotic mussels have much higher rates of apoptosis in their gills than the coastal mussel Mytilus edulis without chemolithoautotrophic symbionts. We discuss how apoptosis might be one of the mechanisms that contribute to the adaptation of deep-sea mussels to toxic environments and/or to symbiosis.

zoology↗