A5089898426- Microbial Community Ecology and Physiology
- Environmental DNA in Biodiversity Studies
- Protist diversity and phylogeny
- Geology and Paleoclimatology Research
- Marine Biology and Ecology Research
- Isotope Analysis in Ecology
- Genomics and Phylogenetic Studies
- Methane Hydrates and Related Phenomena
- Paleontology and Stratigraphy of Fossils
- Identification and Quantification in Food
- Coral and Marine Ecosystems Studies
- Marine and coastal plant biology
- Marine and environmental studies
- Marine Ecology and Invasive Species
- Evolution and Paleontology Studies
- Parasite Biology and Host Interactions
- Marine and coastal ecosystems
- Aquatic Invertebrate Ecology and Behavior
- Parasitic Infections and Diagnostics
- Coastal wetland ecosystem dynamics
- Plant and Fungal Species Descriptions
- Polar Research and Ecology
- Myxozoan Parasites in Aquatic Species
- Diatoms and Algae Research
- Species Distribution and Climate Change
University of Geneva
2016-2025
Polish Academy of Sciences
2019-2025
Instytut Oceanologii Polskiej Akademii Nauk
2019-2024
L.A.C. (Switzerland)
2024
Sopot University of Applied Science
2024
Przedsiębiorstwo Badań i Doradztwa
2022
University of Urbino
2021
Stazione Zoologica Anton Dohrn
2021
Université Grenoble Alpes
2021
University of Kaiserslautern
2021
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...
Abstract This revision of the classification eukaryotes, which updates that Adl et al. [ J. Eukaryot. Microbiol . 52 (2005) 399], retains an emphasis on protists and incorporates changes since 2005 have resolved nodes branches in phylogenetic trees. Whereas previous was successful re‐introducing name stability to classification, this provides a for lineages were then still unresolved. The supergroups withstood hypothesis testing with some modifications, but despite progress, problematic at...
Abstract This revision of the classification eukaryotes follows that Adl et al., 2012 [ J. Euk. Microbiol . 59(5)] and retains an emphasis on protists. Changes since have improved resolution many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling intervening years has massively increased genetic information at hand. Consequently, discovered novel clades, exciting new genera uncovered a massive species level...
Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, ecology; this Community Page describes a resource 700 transcriptomes marine microbial help understand role in the world's oceans.
A group of protist experts proposes a two-step DNA barcoding approach, comprising universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity microbial eukaryotes.
BackgroundResolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, accumulation molecular data led to a new understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, composition these large assemblages and their remain controversial.Methodology/Principle FindingsHere, we report sequencing expressed sequence tags (ESTs) for two species belonging supergroup Rhizaria present...
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...
Tagging amplicons with tag sequences appended to PCR primers allow the multiplexing of numerous samples for high-throughput sequencing (HTS). This approach is routinely used in HTS-based diversity analyses, especially microbial ecology and biomedical diagnostics. However, amplicon library preparation subject pervasive sample sequence cross-contaminations as a result switching events referred mistagging. Here, we sequenced seven libraries prepared using various designs order measure magnitude...
The deep ocean below 200 m water depth is the least observed, but largest habitat on our planet by volume and area. Over 150 years of exploration has revealed that this dynamic system provides critical climate regulation, houses a wealth energy, mineral, biological resources, represents vast repository diversity. A long history deep-ocean observation led to initial concept for Deep-Ocean Observing Strategy (DOOS), under auspices Global Ocean System (GOOS). Here we discuss scientific need...
Abstract Environmental diversity surveys are crucial for the bioassessment of anthropogenic impacts on marine ecosystems. Traditional benthic monitoring relying morphotaxonomic inventories macrofaunal communities is expensive, time-consuming and expertise-demanding. High-throughput sequencing environmental DNA barcodes (metabarcoding) offers an alternative to describe biological communities. However, whether metabarcoding approach meets quality standards remains be tested. Here, we compared...
Abstract The measurement of species diversity represents a powerful tool for assessing the impacts human activities on marine ecosystems. Traditionally, impact fish farming coastal environment is evaluated by monitoring dynamics macrobenthic infaunal populations. However, taxonomic sorting and morphology‐based identification macrobenthos demand highly trained specialists are extremely time‐consuming costly, making it unsuitable large‐scale biomonitoring efforts involving numerous samples....
The last decade brought a spectacular development of so-called environmental (e)DNA studies. In general, "environmental DNA" is defined as DNA isolated from samples, in contrast to genomic that extracted directly specimens. However, the variety different sources eDNA and range taxonomic groups are targeted by studies large, which has led some discussion about breadth concept. particular, there recent trend restrict use term "eDNA" macro-organisms, not physically present samples. this paper,...
Diatoms are widely used as bioindicators for the assessment of water quality in rivers and streams. Classically, diatom biotic indices based on relative abundance morphologically identified species weighted by their autoecological value. Obtaining such is time-consuming, costly, requires excellent taxonomic expertise, which not always available. Here we tested possibility to overcome these limitations using a next-generation sequencing (NGS) approach identify quantify diatoms found...
Monitoring biodiversity is essential to assess the impacts of increasing anthropogenic activities in marine environments. Traditionally, biomonitoring involves sorting and morphological identification benthic macro-invertebrates, which time-consuming taxonomic-expertise demanding. High-throughput amplicon sequencing environmental DNA (eDNA metabarcoding) represents a promising alternative for monitoring. However, an important fraction eDNA sequences remains unassigned or belong taxa unknown...
Deep-sea sediments represent the largest but least known ecosystem on earth. With increasing anthropogenic pressure, it is now a matter of urgency to improve our understanding deep-sea biodiversity. Traditional morpho-taxonomic studies suggest that ocean floor hosts extraordinarily diverse benthic communities. However, due both its remoteness and lack expert taxonomists, assessing diversity very challenging task. Environmental DNA (eDNA) metabarcoding offers powerful tool complement studies....
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 (18S-V9) abyssal and lower bathyal surficial sediments euphotic aphotic ocean pelagic layers distinguish plankton diversity in material. Based 1685 samples collected throughout world ocean, show that DOS is at threefold...