A5074791594- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Environmental DNA in Biodiversity Studies
- Genomics and Phylogenetic Studies
- Medical Imaging Techniques and Applications
- Methane Hydrates and Related Phenomena
- Plant Pathogens and Fungal Diseases
- Radiomics and Machine Learning in Medical Imaging
- Botanical Research and Chemistry
- Mycorrhizal Fungi and Plant Interactions
- Gene expression and cancer classification
- Legume Nitrogen Fixing Symbiosis
- Plant Virus Research Studies
- Forest Ecology and Biodiversity Studies
- Bioinformatics and Genomic Networks
- Genetic and Environmental Crop Studies
- Mathematical Biology Tumor Growth
- Insect and Arachnid Ecology and Behavior
- Parasitic Infections and Diagnostics
- Algorithms and Data Compression
- Geological Studies and Exploration
- Biomedical Text Mining and Ontologies
- Marine Biology and Ecology Research
- Polysaccharides Composition and Applications
- Gut microbiota and health
Centre de Coopération Internationale en Recherche Agronomique pour le Développement
2016-2025
Biologie et Génétique des Interactions Plante-Parasite
2019-2025
Institut de Recherche pour le Développement
2017-2025
Institut Agro Montpellier
2017-2025
L'Institut Agro
2020-2025
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2020-2025
Université de Montpellier
2017-2025
Plant Health Institute de Montpellier
2021-2023
Centre Occitanie-Montpellier
2021-2023
Agropolis International
2018-2023
VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing preparing metagenomics, genomics population nucleotide sequence data. It designed as alternative to the widely used USEARCH (Edgar, 2010) which code not publicly available, algorithm details are only rudimentarily described, a memory-confined 32-bit version freely available academic use.When searching sequences, uses fast heuristic based on words shared by query target sequences in order quickly identify...
The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack taxonomically curated reference data sets for targeted genes. Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with taxonomy. mainly consists nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi organelles (mitochondrion, plastid...
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted not accounted for the full range size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone communities collected across tropical temperate oceans during circumglobal Tara Oceans expedition. analyzed 18S ribosomal DNA sequences intermediate plankton-size spectrum smallest unicellular eukaryotes (protists, >0.8 micrometers) to small...
Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues first nearly identical amplicons iteratively using a local threshold, then clusters' internal structure abundances refine its results. This fast, scalable, independent approach reduces the influence of parameters produces robust operational taxonomic units.
Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global thresholds input-order dependency. v1 worked with an initial phase used iterative single-linkage local threshold (d), followed by the internal abundance structures clusters to break chained OTUs. Here present v2, which has two important features: (1) new algorithm for d = 1 allows computation time scale linearly...
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns diversity and underlying drivers remain poorly known, precluding projections responses global changes. Here we investigate latitudinal gradients predictors plankton across archaea, bacteria, eukaryotes, major virus clades using both molecular imaging data from Tara Oceans. We show a decline for most groups toward poles, mainly driven by decreasing...
Although protists are critical components of marine ecosystems, they still poorly characterized. Here we analysed the taxonomic diversity planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) ribonucleic (RNA) from three size fractions (pico-, nano- micro/mesoplankton), as well dissolved DNA surface sediments were used templates for tag pyrosequencing V4 region 18S ribosomal DNA. Beta-diversity analyses split...
Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity abundance many marine environments, especially the upper water column. Here, we use a dual approach involving high-throughput tag sequencing from both RNA templates fluorescent cell counts to evaluate relative of across samples taken six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered multiple for detailed analysis. This...
Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated performance recently released state-of-the-art open-source software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST USEARCH) QIIME, hierarchical methods mothur, USEARCH's most recent algorithm,...
Abstract 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 environmental diversity of lineages group near base fungal radiation show they in a clade metchnikovellids microsporidians, to exclusion Rozella line what is currently known their morphology biology. These results scope...
Summary Dinoflagellates (Alveolata) are one of the ecologically most important groups modern phytoplankton. Their biological complexity makes assessment their global diversity and community structure difficult. We used massive V 9 18 S rDNA sequencing from 106 size‐fractionated plankton communities collected across world's surface oceans during T ara O ceans expedition (2009–2012) to assess patterns pelagic dinoflagellate structuring over taxonomic ecological scales. Our data analyses...
Nucleotide positions in the hypervariable V4 and V9 regions of small subunit (SSU)-rDNA locus are normally difficult to align usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons these all that available answer ecological evolutionary questions rely on inferences. With ciliates, we asked how inclusion or regions, regardless alignment quality, affects tree topologies using distinct methods (including PairDist is introduced here). Results...
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists received relatively little attention. We therefore hypothesize that current surveys only skimmed the surface of in marine sediments, which may harbor greater than environments. tested this by analyzing sequences hypervariable V4 18S rRNA from and communities sampled European coastal regions. Despite a similar number OTUs both realms, richness estimations indicated we recovered at...
Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost solely relying on 18S rRNA gene. As are extremely diverse, many primers and primer pairs have been developed. To cover a relevant representative fraction protist community given study system, an informed choice is necessary, no pair can target all protists equally well. such, smart very difficult even for experts there few online resources available to list existing...
Abstract Motivation Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) are free of arbitrary global thresholds. Here, present swarm v3 to address issues contemporary datasets growing towards tera-byte sizes. Results When compared with previous versions, has modernized C++ source code, reduced memory footprint by up 50%, optimized CPU-usage and multithreading (more than 7 times faster default...
Abstract. Biological communities populating the Mediterranean Sea, which is situated at northern boundary of subtropics, are often claimed to be particularly affected by global warming. This indicated, for instance, introduction (sub)tropical species fish or invertebrates that can displace local species. raises question whether microbial similarly affected, especially in Levantine basin where sea surface temperatures have significantly risen over last 25 years (0.50 ± 0.11 °C average per...
Metabarcoding is a powerful tool for exploring microbial diversity in the environment, but its accurate interpretation impeded by diverse technical (e.g. PCR and sequencing errors) biological biases intra-individual polymorphism) that remain poorly understood. To help interpret environmental metabarcoding datasets, we investigated intracellular of V4 V9 regions 18S rRNA gene from Acantharia Nassellaria (radiolarians) using 454 pyrosequencing. Individual cells radiolarians were isolated, PCRs...
Marine planktonic organisms that undertake active vertical migrations over their life cycle are important contributors to downward particle flux in the oceans. Acantharia, globally distributed heterotrophic protists unique building skeletons of celestite (strontium sulfate), can produce reproductive cysts covered by a heavy mineral shell sink rapidly from surface deep waters. We combined phylogenetic and biogeochemical analyses explore ecological significance this strategy. Phylogenetic...
Abstract Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the carbon cycle, and their exceptional fossil record serves as basis for biochronostratigraphy past climate reconstructions. A major worldwide sampling effort over last two decades has resulted establishment of multiple large collections cryopreserved individual planktonic samples. Thousands 18S r DNA partial sequences...
Abstract Heterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using approach of combined DNA metabarcoding cultivation-based surveys 11 deep-sea regions, we show that protist communities, mostly overlooked current foodweb models, are highly specific, locally diverse have...