Unraveling the Diversity of Eukaryotic Microplankton in a Large and Deep Perialpine Lake Using a High Throughput Sequencing Approach

Responses to local and global stressors in the large southern perialpine lakes: Present status and challenges for research and management

(2020) Nico Salmaso et al.   JOURNAL OF GREAT LAKES RESEARCH

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass

(2019) Vincent Caruso et al.   mSystems

Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts?

(2019) Gianna Pitsch et al.   Frontiers in Microbiology

Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline

(2019) Charlie Pauvert et al.   Fungal Ecology

Diat.barcode, an open-access curated barcode library for diatoms

(2019) Frédéric Rimet et al.   Scientific Reports

Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes

(2019) Nico Salmaso   Frontiers in Microbiology

Annual Protist Community Dynamics in a Freshwater Ecosystem Undergoing Contrasted Climatic Conditions: The Saint-Charles River (Canada)

(2019) Perrine Cruaud et al.   Frontiers in Microbiology

Plankton dynamics across the freshwater, transitional and marine research sites of the LTER-Italy Network. Patterns, fluctuations, drivers

(2018) Giuseppe Morabito et al.   SCIENCE OF THE TOTAL ENVIRONMENT

High planktonic diversity in mountain lakes contains similar contributions of autotrophic, heterotrophic and parasitic eukaryotic life forms

(2018) Rüdiger Ortiz-Álvarez et al.   Scientific Reports

European large perialpine lakes under anthropogenic pressures and climate change: present status, research gaps and future challenges

(2018) Nico Salmaso et al.   HYDROBIOLOGIA

Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics

(2018) Alejandra Escobar-Zepeda et al.   Scientific Reports

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

(2018) Jacob T. Nearing et al.   PeerJ

Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units

(2018) Sydney I. Glassman et al.   mSphere

How quantitative is metabarcoding: A meta‐analytical approach

(2018) Philip D. Lamb et al.   MOLECULAR ECOLOGY

Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

(2018) Lotus A. Lofgren et al.   MOLECULAR ECOLOGY

Are We Overestimating Protistan Diversity in Nature?

(2018) David A. Caron et al.   TRENDS IN MICROBIOLOGY

Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta

(2017) Margot Tragin et al.   ENVIRONMENTAL MICROBIOLOGY

Ongoing ecological shifts in a large lake are driven by climate change and eutrophication: evidences from a three-decade study in Lake Garda

(2017) Nico Salmaso et al.   HYDROBIOLOGIA

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

25 years of serving the community with ribosomal RNA gene reference databases and tools

(2017) Frank Oliver Glöckner et al.   JOURNAL OF BIOTECHNOLOGY

Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake

(2017) Nico Salmaso et al.   MICROBIAL ECOLOGY

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error

(2017) Chundi Wang et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

(2017) Luisa W. Hugerth et al.   Frontiers in Microbiology

Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

(2016) Caterina R. Giner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional ecology of aquatic phagotrophic protists – Concepts, limitations, and perspectives

(2016) Thomas Weisse et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Molecular diversity of plankton in a tropical crater lake switching from hyposaline to subsaline conditions: Lake Oloidien, Kenya

(2016) Wei Luo et al.   HYDROBIOLOGIA

Protistan community analysis: key findings of a large-scale molecular sampling

(2016) Lars Grossmann et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom

(2016) David M. Needham et al.   Nature Microbiology

Benthic diatoms and phytoplankton to assess nutrients in a large lake: Complementarity of their use in Lake Geneva (France–Switzerland)

(2015) Frédéric Rimet et al.   ECOLOGICAL INDICATORS

Expansion of bloom-forming Dolichospermum lemmermannii (Nostocales, Cyanobacteria) to the deep lakes south of the Alps: Colonization patterns, driving forces and implications for water use

(2015) Nico Salmaso et al.   HARMFUL ALGAE

Marked seasonality and high spatial variability of protist communities in shallow freshwater systems

(2015) Marianne Simon et al.   ISME Journal

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

(2015) Johan Decelle et al.   Molecular Ecology Resources

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Two New Freshwater Woloszynskioids Asulcocephalium miricentonis gen. et sp. nov. and Leiocephalium pseudosanguineum gen. et sp. nov. (Suessiaceae, Dinophyceae) Lacking an Apical Furrow Apparatus

(2015) Kazuya Takahashi et al.   PROTIST

Network of Interactions Between Ciliates and Phytoplankton During Spring

(2015) Thomas Posch et al.   Frontiers in Microbiology

Occurrence and mass development of Mougeotia spp. (Zygnemataceae) in large, deep lakes

(2014) Kálmán Tapolczai et al.   HYDROBIOLOGIA

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Discovery of aKatablepharissp. in the Columbia River estuary that is abundant during the spring and bears a unique large ribosomal subunit sequence element

(2014) Peter Kahn et al.   MicrobiologyOpen

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

(2013) Dong-Lei Sun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phytoplankton configuration in six deep lakes in the peri-Alpine region: are the key drivers related to eutrophication and climate?

(2013) Nicole Gallina et al.   AQUATIC ECOLOGY

Harmful Cyanobacterial Blooms: Causes, Consequences, and Controls

(2013) Hans W. Paerl et al.   MICROBIAL ECOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates

(2013) Jun Gong et al.   PROTIST

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Beyond the Plankton Ecology Group (PEG) Model: Mechanisms Driving Plankton Succession

(2012) Ulrich Sommer et al.   Annual Review of Ecology Evolution and Systematics

Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes

(2012) Jean-François Mangot et al.   ENVIRONMENTAL MICROBIOLOGY

Plankton dynamics under different climatic conditions in space and time

(2012) LISETTE N. DE SENERPONT DOMIS et al.   FRESHWATER BIOLOGY

The Polychytriales ord. nov. contains chitinophilic members of the rhizophlyctoid alliance

(2012) Joyce E. Longcore et al.   MYCOLOGIA

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

Diversity and distribution of cyanobacterial toxins in the Italian subalpine lacustrine district

(2012) Leonardo Cerasino et al.   OCEANOLOGICAL AND HYDROBIOLOGICAL STUDIES

Plankton Microorganisms Coinciding with Two Consecutive Mass Fish Kills in a Newly Reconstructed Lake

(2012) Andreas Oikonomou et al.   TheScientificWorldJOURNAL

Biophysical Aspects of Resource Acquisition and Competition in Algal Mixotrophs

(2011) Ben A. Ward et al.   AMERICAN NATURALIST

Prorocentrum rivalis sp. nov. (Dinophyceae) and its phylogenetic affinities inferred from analysis of a mixed morphological and LSU rRNA data set

(2011) David Delmail et al.   BIOLOGIA

Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations

(2010) Jon Bråte et al.   BMC MICROBIOLOGY

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

(2010) Jon Bråte et al.   ISME Journal

Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

(2010) VIOLA NOLTE et al.   MOLECULAR ECOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

(2010) RALPH MEDINGER et al.   MOLECULAR ECOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Long-term phytoplankton community changes in a deep subalpine lake: responses to nutrient availability and climatic fluctuations

(2009) NICO SALMASO   FRESHWATER BIOLOGY

Quantification of Diatom and Dinoflagellate Biomasses in Coastal Marine Seawater Samples by Real-Time PCR

(2008) A. Godhe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Rapid shifts in dominant taxa among microbial eukaryotes in estuarine ecosystems

(2008) P Vigil et al.   AQUATIC MICROBIAL ECOLOGY

Biomonitoring of Lake Garda: Identification of ciliate species and symbiotic algae responsible for the “black-spot” bloom during the summer of 2004

(2008) Sandra Pucciarelli et al.   ENVIRONMENTAL RESEARCH