Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding

Disentangling the mechanisms shaping the surface ocean microbiota

(2020) Ramiro Logares et al.   Microbiome

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

A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes

(2019) Waldan K. Kwong et al.   NATURE

Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

(2019) Dominik Forster et al.   ENVIRONMENTAL MICROBIOLOGY

Towards PacBio‐based pan‐eukaryote metabarcoding using full‐length ITS sequences

(2019) Leho Tedersoo et al.   Environmental Microbiology Reports

Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens

(2019) Kaire Loit et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

(2019) Guillem Salazar et al.   CELL

Current practice in plankton metabarcoding: optimization and error management

(2019) Luciana F Santoferrara   JOURNAL OF PLANKTON RESEARCH

Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework

(2019) Javier del Campo et al.   Frontiers in Microbiology

Intracellular Infection of Diverse Diatoms by an Evolutionary Distinct Relative of the Fungi

(2019) Aurélie Chambouvet et al.   CURRENT BIOLOGY

Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution

(2018) Russell J. S. Orr et al.   BMC EVOLUTIONARY BIOLOGY

Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?

(2018) Mara A. Freilich et al.   ECOLOGY

Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing

(2018) William D. Orsi et al.   ENVIRONMENTAL MICROBIOLOGY

Genome-reconstruction for eukaryotes from complex natural microbial communities

(2018) Patrick T. West et al.   GENOME RESEARCH

The ecology and diversity of microbial eukaryotes in geothermal springs

(2018) Angela M. Oliverio et al.   ISME Journal

16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer)

(2018) Clare Bird et al.   PLoS One

β-Diversity, Community Assembly, and Ecosystem Functioning

(2018) Akira S. Mori et al.   TRENDS IN ECOLOGY & EVOLUTION

A global ocean atlas of eukaryotic genes

(2018) Quentin Carradec et al.   Nature Communications

Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring

(2018) Valentin Vasselon et al.   Methods in Ecology and Evolution

Identification of osmoadaptive strategies in the halophile, heterotrophic ciliate Schmidingerothrix salinarum

(2018) Lea Weinisch et al.   PLOS BIOLOGY

Ubiquitous abundance distribution of non-dominant plankton across the global ocean

(2018) Enrico Ser-Giacomi et al.   Nature Ecology & Evolution

Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments

(2018) Felix Heeger et al.   Molecular Ecology Resources

EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

(2018) Javier del Campo et al.   PLOS BIOLOGY

Quantifying long-term recurrence in planktonic microbial eukaryotes

(2018) Caterina R. Giner et al.   MOLECULAR ECOLOGY

Are We Overestimating Protistan Diversity in Nature?

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

Transition boundaries for protistan species turnover in hypersaline waters of different biogeographic regions

(2017) Sabine Filker et al.   ENVIRONMENTAL MICROBIOLOGY

Biogeography and diversity of Collodaria (Radiolaria) in the global ocean

(2017) Tristan Biard et al.   ISME Journal

Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities

(2017) Wenxue Wu et al.   ISME Journal

UniEuk : Time to Speak a Common Language in Protistology!

(2017) Cédric Berney et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

More protist genomes needed

(2017) Shannon J. Sibbald et al.   Nature Ecology & Evolution

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

(2017) Frédéric Mahé et al.   Nature Ecology & Evolution

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

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

Extreme Diversity of Diplonemid Eukaryotes in the Ocean

(2016) Olga Flegontova et al.   CURRENT BIOLOGY

Comparison of Niskin vs. in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples

(2016) V.P. Edgcomb et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists

(2016) Tommy Harding et al.   Genome Biology and Evolution

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

(2016) Lars Grossmann et al.   ISME Journal

Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?

(2016) Luciana F Santoferrara et al.   ISME Journal

Temporal variation of Skeletonema community composition from a long-term time series in Narragansett Bay identified using high-throughput DNA sequencing

(2016) KL Canesi et al.   MARINE ECOLOGY PROGRESS SERIES

Strengths and Biases of High-Throughput Sequencing Data in the Characterization of Freshwater Ciliate Microbiomes

(2016) Vittorio Boscaro et al.   MICROBIAL ECOLOGY

Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns

(2016) Sabine Filker et al.   MOLECULAR ECOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Probing the evolution, ecology and physiology of marine protists using transcriptomics

(2016) David A. Caron et al.   NATURE REVIEWS MICROBIOLOGY

Insights into global diatom distribution and diversity in the world’s ocean

(2016) Shruti Malviya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

Temporal variation of Skeletonema community composition from a long-term time series in Narragansett Bay identified using high-throughput DNA sequencing

(2016) KL Canesi et al.   MARINE ECOLOGY PROGRESS SERIES

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

(2015) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

(2015) Noan Le Bescot et al.   ENVIRONMENTAL MICROBIOLOGY

The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.)

(2015) Solenn Mordret et al.   ISME Journal

Metatranscriptomic census of active protists in soils

(2015) Stefan Geisen et al.   ISME Journal

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

(2015) Massimo C Pernice et al.   ISME Journal

Global diversity and biogeography of deep-sea pelagic prokaryotes

(2015) Guillem Salazar et al.   ISME Journal

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa

(2015) S. Geisen et al.   MOLECULAR ECOLOGY

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

(2015) Harriet Alexander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rarity in aquatic microbes: placing protists on the map

(2015) Ramiro Logares et al.   RESEARCH IN MICROBIOLOGY

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods

(2014) Luciana F. Santoferrara et al.   ENVIRONMENTAL MICROBIOLOGY

Evidence of concurrent local adaptation and high phenotypic plasticity in a polar microeukaryote

(2014) Karin Rengefors et al.   ENVIRONMENTAL MICROBIOLOGY

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

(2014) Pier Luigi Buttigieg et al.   FEMS MICROBIOLOGY ECOLOGY

Metacommunity organisation, spatial extent and dispersal in aquatic systems: patterns, processes and prospects

(2014) Jani Heino et al.   FRESHWATER BIOLOGY

Oceanographic structure drives the assembly processes of microbial eukaryotic communities

(2014) Adam Monier et al.   ISME Journal

Ciliates and the Rare Biosphere: A Review

(2014) Micah Dunthorn et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context

(2014) Micah Dunthorn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia

(2014) Luisa W. Hugerth et al.   PLoS One

Intracellular Diversity of the V4 and V9 Regions of the 18S rRNA in Marine Protists (Radiolarians) Assessed by High-Throughput Sequencing

(2014) Johan Decelle et al.   PLoS One

“Candidatus Haloectosymbiotes riaformosensis” (Halobacteriaceae), an archaeal ectosymbiont of the hypersaline ciliate Platynematum salinarum

(2014) Sabine Filker et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

(2014) Laura Wegener Parfrey et al.   Frontiers in Microbiology

A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology

(2013) Thorsten Stoeck et al.   ENVIRONMENTAL MICROBIOLOGY

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

(2013) D. R. Nemergut et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera

(2013) Alexandra A-T. Weber et al.   PLoS One

454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

(2013) Elianne Egge et al.   PLoS One

Eukaryotic versus prokaryotic marine picoplankton ecology

(2012) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

(2012) Charles Bachy et al.   ISME Journal

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

Meta-analyses of environmental sequence data identify anoxia and salinity as parameters shaping ciliate communities

(2012) Dominik Forster et al.   SYSTEMATICS AND BIODIVERSITY

The rise of model protozoa

(2012) David Montagnes et al.   TRENDS IN MICROBIOLOGY

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

Prevalence of partnerships between bacteria and ciliates in oxygen-depleted marine water columns

(2012) William Orsi et al.   Frontiers in Microbiology

Concepts in protistology: Species definitions and boundaries

(2011) Jens Boenigk et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

NOVEL COOPERATION EXPERIMENTALLY EVOLVED BETWEEN SPECIES

(2010) William Harcombe   EVOLUTION

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

Genomic and functional adaptation in surface ocean planktonic prokaryotes

(2010) Shibu Yooseph et al.   NATURE

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

(2010) M. L. Cuvelier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Hypotheses on the role of the protistan rare biosphere in a changing world

(2009) DA Caron et al.   AQUATIC MICROBIAL ECOLOGY

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

(2009) Thorsten Stoeck et al.   BMC BIOLOGY

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY