Cédric Berney

Cédric Berney
Station Biologique de Roscoff · Adaptation et Diversité en Milieu Marin - UMR 7144 CNRS UPMC

PhD

About

295
Publications
47,705
Reads
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7,451
Citations
Additional affiliations
April 2014 - present
Station Biologique de Roscoff
Position
  • PostDoc Position
April 2010 - December 2013
Natural History Museum, London
Position
  • PostDoc Position
October 2005 - March 2009
University of Oxford
Position
  • PostDoc Position
Education
October 2000 - June 2005
University of Geneva
Field of study
  • Biology

Publications

Publications (295)
Article
Full-text available
Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chem...
Preprint
Nucleic acid based studies of marine biodiversity often focus on Kingdom-level diversity. Such approaches often largely miss diversity of less studied groups, likely to harbour many unknown lineages which are likely playing significant ecological roles. Among these elusive groups are Endomyxa (Rhizaria), a ubiquitous, but understudied lineage compr...
Article
Full-text available
The salinity barrier that separates marine and freshwater biomes is probably the most important division in biodiversity on Earth. Those organisms that successfully performed this transition had access to new ecosystems while undergoing changes in selective pressure, which often led to major shifts in diversification rates. While these transitions...
Article
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Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18 S -V9) from abyssal and lower bathyal surficial sediments and euphotic...
Preprint
Full-text available
A bstract EukProt is a database of published and publicly available predicted protein sets selected to represent the breadth of eukaryotic diversity, currently including 993 species from all major supergroups as well as orphan taxa. The goal of the database is to provide a single, convenient resource for gene-based research across the spectrum of e...
Preprint
Full-text available
Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated 1,2 . The most prominent global biogeography of marine plankton was derived by Longhurst ³ based on p...
Article
This revision of the classification of eukaryotes follows that of Adl et al., 2012[J. Euk. Microbiol.59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted,environmental sampling in the intervening ye...
Article
Full-text available
This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening...
Article
Full-text available
Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain er...
Article
Full-text available
Rhizarian ‘Novel Clade 10′ (NC10) is frequently detected by 18S rRNA gene sequencing studies in freshwater planktonic samples. We describe a new genus and two species of eukaryovorous biflagellate protists, Aquavolon hoantrani n. gen. n. sp., and A. dientrani n. gen. n. sp., which represent the first morphologically characterized members of NC10, h...
Article
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Some protists with microsporidian‐like cell biological characters, including Mitosporidium, Paramicrosporidium, and Nucleophaga, have SSU rRNA gene sequences that are much less divergent than canonical Microsporidia. We analysed the phylogenetic placement and environmental diversity of microsporidian‐like lineages that group near the base of the fu...
Preprint
Full-text available
Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain er...
Article
Full-text available
Class Ascetosporea (Rhizaria; Endomyxa) comprises many parasites of invertebrates. Within this group, recent group-specific environmental DNA (eDNA) studies have contributed to the establishment of the new order Mikrocytida, a new phylogeny and characterisation of Paramyxida, and illuminated the diversity and distribution of haplosporidians. Here w...
Data
Table S1. Aquavolonida sequences in GenBank. Table S2. Sequences of the PCR primers used in this study. Video S1. Aquavolon dientrani swimming. Video can be accessed at https://yadi.sk/mail/?hash=jsf7XwEScPTOsgvjNRSf5UTcbJ9iAjh6mG6I4cGmALw%3D
Article
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We performed high throughput 18S rDNA V9 region sequencing analyses of micro-eukaryote communities at seven sites with depths ranging from 0-1450 m in the southern part of Lake Baikal. We show that micro-eukaryotic diversity differed according to water column depth and sediment depth. Chrysophytes and perkinsids were diverse in subsurface samples,...
Article
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The bewildering organismal and functional complexity of microbial eukaryotes has long fascinated protistologists but exceeded the capacity of this research community to comprehensively study it. Lacking the critical mass for a strong scientific discipline, protistologists remain largely divided into various sub-communities (protozoology versus phyc...
Article
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High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities...
Article
Full-text available
p>Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades u...
Article
We describe four new species of Flabellula, Leptomyxa and Rhizamoeba and publish new SSU rRNA gene and actin gene sequences of leptomyxids. Using these data we provide the most comprehensive SSU phylogeny of leptomyxids to date. Based on the analyses of morphological data and results of the SSU rRNA gene phylogeny we suggest changes in the systemat...
Article
Full-text available
Clubroot disease caused by Plasmodiophora brassicae is one of the most important diseases of cultivated brassicas. P. brassicae occurs in pathotypes which differ in the aggressiveness towards their Brassica host plants. To date no DNA based method to distinguish these pathotypes has been described. In 2011 polymorphism within the 28S rDNA of P. bra...
Article
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The colonies of Microcystis, one of the most common bloom-forming cyanobacteria worldwide, harbor a diverse community of microorganisms. Among these, naked amoebae feeding on Microcystis cells can strongly influence natural Microcystis population dynamics. In this study, we investigated the species diversity of these amoebae based on 26 Microcystis...
Article
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Paramyxida is an order of rhizarian protists that parasitise marine molluscs, annelids and crustaceans. They include notifiable pathogens (Marteilia spp.) of bivalves and other taxa of economic significance for shellfish production. The diversity of paramyxids is poorly known, particularly outside of commercially important hosts, and their phylogen...
Article
Full-text available
High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities...
Article
Full-text available
Symbiotic partnerships between heterotrophic hosts and intracellular microalgae are common in tropical and subtropical oligotrophic waters of benthic and pelagic marine habitats. The iconic example is the photosynthetic dinoflagellate genus Symbiodinium that establishes mutualistic symbioses with a wide diversity of benthic hosts, sustaining highly...
Article
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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...
Article
Amoebae able to form cytoplasmic networks or displaying a multiply branching morphology remain very poorly studied. We sequenced the small-subunit ribosomal RNA gene of 15 new amoeboid isolates, 14 of which are branching or network-forming amoebae (BNFA). Phylogenetic analyses showed that these isolates all group within the poorly-known and weakly-...
Data
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Article
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Amoebozoa is a key phylum for eukaryote phylogeny and evolutionary history, but its phylogenetic validity has been questioned since included species are very diverse: amoebo-flagellate slime-moulds, naked and testate amoebae, and some flagellates. 18S rRNA gene trees have not firmly established its internal topology. To rectify this we sequenced cD...
Article
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Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental se...
Article
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Microcell parasites have independently evolved in several eukaryotic lineages and are increasingly recognized as important and emerging pathogens of diverse hosts, including species of economic importance subject to international legislation concerning the trading of aquatic animals [1-3]. The microcell Mikrocytos mackini causes Denman Island disea...
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##Assembly-Data-START## Assembly Method :: mira v. 3.4 Sequencing Technology :: Illumina ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: mira v. 3.4 Sequencing Technology :: Illumina ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: mira v. 3.4 Sequencing Technology :: Illumina ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: mira v. 3.4 Sequencing Technology :: Illumina ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: mira v. 4.6 Sequencing Technology :: Illumina ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: mira v. 4.6 Sequencing Technology :: Illumina ##Assembly-Data-END##
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##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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Article
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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...
Article
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Haplosporidians are rhizarian parasites of mostly marine invertebrates. They include the causative agents of diseases of commercially important molluscs, including MSX disease in oysters. Despite their importance for food security, their diversity and distributions are poorly known. We used a combination of group-specific PCR primers to probe envir...
Article
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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...
Data
##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: BioEdit v. 7.0.9.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##