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Introduction
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October 2013 - October 2013
January 2009 - December 2009
January 2002 - October 2008
Publications
Publications (81)
Background
The mechanisms shaping the rare microbial biosphere and its role in ecosystems remain unclear. We developed an approach to study ecological patterns in the rare biosphere and use it on a vast collection of marine microbiomes, sampled in coastal ecosystems at a regional scale. We study the assembly processes, and the ecological strategies...
Green seawater discolorations caused by the marine dinoflagellate Lepidodinium chlorophorum are frequently observed during summer along southern Brittany coasts (NE Atlantic, France). Here, the ecology of L. chlorophorum is studied during a non-bloom period using high-throughput sequencing metabarcoding of environmental DNA (eDNA) samples for the d...
Despite theoretical expectations, marine microeukaryote population are often highly structured and the mechanisms behind such patterns remain to be elucidated. These organisms display huge census population sizes, yet genotyping usually requires clonal strains originating from single cells, hindering proper population sampling. Estimating allelic f...
Blooms of the marine dinoflagellate Lepidodinium chlorophorum cause green seawater discolorations affecting the recreational use and the tourism economy along southern Brittany (NE-Atlantic, France). Hypoxic conditions associated with phytoplankton biomass recycling are suspected to cause fauna mortalities. An in situ monitoring was performed in 20...
Blooms of the toxic benthic dinoflagellate Ostreopsis cf. ovata can induce ecological and human health issues in certain temperate areas. In order to prevent these negative effects, long-term monitoring studies of O. cf. ovata blooms have been conducted in several impacted areas to have a comprehensive understanding of bloom dynamics and efficient...
The coastal oceans can be highly variable, especially near ocean fronts. The Ushant Front is the dominant oceanographic feature in the Iroise Sea (NE Atlantic) during summer, separating warm stratified offshore waters from cool vertically-mixed nearshore waters. Mesozooplankton community structure was investigated over an annual cycle to examine re...
The Bay of Brest (BB) is a mixed, tide-dominated estuarine system. The shore terraces of this bay are occupied by modern free-living (calcareous) coralline algae locally termed “maerl”, organized in bed-like morphologies (rhodolith deposits). Cores retrieved from around the bay reveal fossilized primitive maerl beds of Holocene age, interbedded in...
To evaluate the stability and resilience1 of coastal ecosystem communities to perturbations that occurred during the Anthropocene,2 pre-industrial biodiversity baselines inferred from paleoarchives are needed.3,4 The study of ancient DNA (aDNA) from sediments (sedaDNA)5 has provided valuable information about past dynamics of microbial species6-8 a...
High biomasses of the marine dinoflagellate Lepidodinium chlorophorum cause green seawater discolorations along Southern Brittany (NE Atlantic, France). The viscosity associated to these phenomena has been related to problems in oyster cultivation. The harmful effect of L. chlorophorum might originate from the secretion of Extracellular Polymeric S...
Oceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample. However, an increasing number of theoretical approaches hypothesize that these processes affect phytoplankton diversity which have cascading effects on regional ecosystems. In 2015, we targeted the Iroise Sea (France) and evidenced the setting up of...
In a future scenario of increasing temperatures in North‐Atlantic waters, the risk associated with the expansion of the harmful, benthic dinoflagellate Ostreopsis cf. siamensis has to be evaluated and monitored. Microscopy observations and spatio‐temporal surveys of environmental DNA (eDNA) were associated with Lagrangian particle dispersal simulat...
A recently published study analyzed the phylogenetic relationship between the genera Centrodinium and Alexandrium, confirming an earlier publication showing the genus Alexandrium as paraphyletic. This most recent manuscript retained the genus Alexandrium, introduced a new genus Episemicolon, resurrected two genera, Gessnerium and Protogonyaulax, an...
Harmful algal blooms are caused by specific members of microbial communities. Understanding the dynamics of these events requires comparing the strategies developed by the problematic species to cope with environmental fluctuations to the ones developed by the other members of the community. During three consecutive years, the meta-transcriptome of...
As critical primary producers and recyclers of organic matter, the diversity of marine protists has been extensively explored by high-throughput barcode sequencing. However, classification of short metabarcoding sequences into traditional taxonomic units is not trivial, especially for lineages mainly known by their genetic fingerprints. This is the...
A recently published study analyzed the phylogenetic relationship between the genera Centrodinium and Alexandrium, confirming an earlier publication showing the genus Alexandrium as paraphyletic. This most recent manuscript retained the genus Alexandrium, introduced a new genus Episemicolon, resurrected two genera, Gessnerium and Protogonyaulax, an...
Besides from the well-known intracellular “paralytic shellfish toxins (PST)”, A. minutum produces uncharacterized exudates which have been implicated in ichtyotoxic, hemolytic and allelochemical activities, but the nature of these extracellular toxins remain unknown. The aim of the Phycotox GDR project ALAsKA was to verify that candidate A. minutum...
During their life cycle, Alexandrium minutum and Scrippsiella donghaienis can produce resistant and revivable cysts that can accumulate in marine sediments for hundreds of years. Our working hypothesis assumes that these two genera have "recorded" their adaptation to ecosystem changes in these cells preserved in the form of cysts. From these revive...
The study of protistan functional diversity is crucial to understand the dynamics of oceanic ecological processes. We combined the metabarcoding data of various coastal ecosystems and a newly developed trait‐based approach to study the link between taxonomic and functional diversity across marine protistan communities of different size‐classes. Env...
Parasites are key drivers of phytoplankton bloom dynamics and related aquatic ecosystem processes. Yet, the dearth of morphological and molecular information hinders the assessment of their diversity and ecological role. Using single-cell techniques, we characterise morphologically and molecularly, intracellular parasitoids infecting four potential...
Studying the coupling between functions and taxonomy is a major challenge of microbiology. The objectives are to understand the structure, dynamics and influence of micro-organisms communities on their environment. We analysed the coupling between functional and taxonomic diversity in communities of marine protists across coastal ecosystems. We use...
Dinoflagellates are part of the marine plankton and about 200 species produce a cyst (dinocyst) during their life cycle, these organic-walled sexually-produced cysts being fossilizable in sediments for hundreds of millions of years. Over the past 40–50 years, dinocysts have led to major advances on Mesozoic-Cenozoic research, in terms of biostratig...
Protists (microbial eukaryotes) are diverse, major components of marine ecosystems, and are fundamental to ecosystem services. In the last 10 years, molecular studies have highlighted substantial novel diversity in marine systems including sequences with no taxonomic context. At the same time, many known protists remain without a DNA identity. Sinc...
Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high‐throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and...
A citizen monitoring program (Phenomer) of marine water discolorations caused by high biomass phytoplankton development (Harmful Algal Blooms, HABs) was conducted in 2013, 2014 and 2015 in the coastal waters of Brittany (France). This project aimed to explore the feasibility of acquiring scientifically valuable data on water discolorations phenomen...
The sand-dwelling dinoflagellate genera Adenoides and Pseudadenoides are morphologically very close but distinct in their molecular phylogeny. We established three cultures by isolating single cells from sand samples collected in intertidal zones of Qingdao (Yellow Sea), Dongshan (South China Sea) and Brittany (English Channel, North Atlantic, Fran...
Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and...
Seventy-five diatoms strains isolated from the Beaufort Sea (Canadian Arctic) in the summer of 2009 were characterized by light and electron microscopy (SEM and TEM) as well as 18S and 28S rRNA gene sequencing. These strains group into 20 genotypes and 17 morphotypes and are affiliated with the genera Arcocellulus, Attheya, Chaetoceros, Cylindrothe...
Within the framework of research aimed at using genetic methods to evaluate harmful species distribution and their impact on coastal ecosystems, a portion of the ITS1rDNA of Alexandrium minutum was amplified by real-time PCR from DNA extracts of superficial (1–3 cm) sediments of 30 subtidal and intertidal stations of the Bay of Brest (Brittany, Fra...
Understanding divergence in the highly dispersive and seemingly homogeneous pelagic environment for organisms living as free drifters in the water column remains a challenge. Here, we analyzed the transcriptome wide mRNA sequences, as well as the morphology of 18 strains of Alexandrium minutum, a dinoflagellate responsible for Harmful Algal Blooms...
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbour greater diversity than planktonic environments. We t...
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We te...
The multiannual dynamic of the cyst-forming and toxic marine dinoflagellate Alexandrium minutum was studied over a time scale of about 150 years by a paleoecological approach based on ancient DNA (aDNA) quantification and cyst revivification data obtained from two dated sediment cores of the Bay of Brest (Brittany, France). The first genetic traces...
A new non-toxic Pseudo-nitzschia species belonging to the P. pseudodelicatissima complex, P. arctica, was isolated from different areas of the Arctic. The erection of P. arctica is mainly supported by molecular data, since the species shares identical ultrastructure with another species in the complex, P. fryxelliana, and represents a new case of c...
Dinoflagellates (Alveolata) are one of the ecologically most important groups of modern phytoplankton. Their biological complexity makes assessment of their global diversity and community structure difficult. We used massive V9 18SrDNA sequencing from 106 size-fractionated plankton communities collected across the world's surface oceans during the...
Although protists are critical components of marine ecosystems they are still poorly characterized. Here we analyzed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental DNA and RNA from three size-fractions (pico-, nano-, and micro/meso-plankton) as well as from dissol...
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during...
4. GdR PHYCOTOX e An interdisciplinary research
network on toxic algae, their toxins and their effects on
marine ecosystems and society
P. Hess a, H. Hegaret b, Z. Amzil a, R. Araaoz c, S. Dragacci d,
V. Fessard e, L. Guillou f, E. Michel-Guillou g, J. Molgó,
S. Pardo h, V. Sechet a, R. Siano i, P. Soudant b, A. Thebault j
a Ifremer, Laboratoire Ph...
The Phenomer Project was launched across Brittany in 213. In addition to communication and outreach objectives, the project aims to explore the possibility of acquiring scientifically valuable data on Harmful Algal Blooms (HAB) with the help of citizens
Background: Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, where most constituent taxa are usually extremely rare. Yet, microbiologists normally do not differentiate between abundant and rare sub-communities, although they may present intrinsic c...
Symbiotic interactions between pelagic hosts and microalgae have received little attention, despite the fact that they are widespread in the photic layer of the world ocean where they play a fundamental role in the ecology of the planktonic ecosystem. Polycystine radiolarians (including the orders Spumellaria, Collodaria and Nassellaria) are plankt...
The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR(2), http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequenc...
Vampire amoebae (vampyrellids) are predators of algae, fungi, protozoa and small metazoans known primarily from soils and in freshwater habitats. They are among the very few heterotrophic naked, filose and reticulose protists that have received some attention from a morphological and ecological point of view over the last few decades, because of th...
A new photosynthetic planktonic marine dino-flagellate, Azadinium dexteroporum sp. nov., is described from the Gulf of Naples (South Tyrrhenian Sea, Mediterranean Sea). The plate formula of the species, Po, cp, X, 4′, 3a, 6″, 6C, 5S, 6‴ and 2″″, is typical for this recently described genus. Azadinium dexteroporum is the smallest rep-resentative of...
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##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Marine phytoplankton, the photosynthetic microorganisms drifting in the illuminated waters of our planet, are extremely diverse, being distributed across major eukaryotic lineages. About 5000 eukaryotic species have been described with traditional morphological methods, but recent environmental molecular surveys are unveiling an ever-increasing div...
During the MALINA cruise (summer 2009), an extensive effort was undertaken to isolate phytoplankton strains from the northeast (NE) Pacific Ocean, the Bering Strait, the Chukchi Sea, and the Beaufort Sea. In order to characterise the main photosynthetic microorganisms occurring in the Arctic during the summer season, strains were isolated by flow c...
Recent advances in laser and video technologies have enabled single particles to be visualized in aqueous solution. Here, we describe a new instrument enabling the analysis of the fluorescence signatures of marine particles directly in seawater: the Video Fluorescence Analyser (VFA). A field of view is produced inside a measurement chamber by a las...
During the MALINA cruise (summer 2009) an extensive effort was undertaken to isolate phytoplankton strains from the North East (NE) Pacific Ocean, the Bering Strait, and the Beaufort Sea. Strains were isolated by flow cytometry sorting (FCS) and pipetting before or after phytoplankton enrichment of seawater samples. Strains were isolated both onboa...
Acantharia (Radiolaria) are widespread and abundant heterotrophic marine protists, some of which can host endosymbiotic eukaryotic microalgae. Although this photosymbiotic association was first described at the end of the 19th century, the diversity of the symbiotic microalgae remains poorly characterized. Here, we examined the identity of the micr...
The section of the Liguro-Provencal basin north of the Bal earic Islands is one of the most productive sites in the whole Mediterranean Sea, with intense phytoplankton bloom lasting about 2 months in late winter-early spring. The phytoplank-ton species composition of the area was investigated using light and electron microscopy to analyze bottle an...
Sequences affiliated to Syndiniales (Marine alveolate, MALV) regularly dominate 18S rDNA genetic libraries of nearly all marine ecosystems investigated so far. Among them, Amoebophryidae (MALV group II) is composed of numerous and genetically distant environmental sequences, where Amoebophrya is the only known and formally described genus. Amoeboph...
The distribution of summer phytoplankton across the Straits of Magellan (SOM) was studied with the aims of tracing differences
among the distinct subregions of the area and contributing to the knowledge of its biodiversity. Samples collected at 25 stations
were observed and counted in light microscopy. Selected samples were observed with transmissi...
The taxonomic status of the free-living stage of the dinoflagellate Gymnodinium béii, symbiont of the foraminifer Orbulina universa, was reassessed on the basis of detailed morpho-genetic analyses. Electron microscopy observations revealed previously undescribed morphological features of the cell that are important for species recognition. The pres...
