DNA metabarcoding reveals that 200-μ m-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes

Local diversity of heathland Cercozoa explored by in-depth sequencing

(2016) Christoffer Bugge Harder et al.   ISME Journal

Is metabarcoding suitable for estuarine plankton monitoring? A comparative study with microscopy

(2016) David Abad et al.   MARINE BIOLOGY

Decline in water level boosts cyanobacteria dominance in subtropical reservoirs

(2016) Jun Yang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species

(2016) Aitor Albaina et al.   Ecology and Evolution

Spatiotemporal dynamics and determinants of planktonic bacterial and microeukaryotic communities in a Chinese subtropical river

(2015) Yongming Wang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

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

(2015) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2015) Massimo C Pernice et al.   ISME Journal

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China

(2015) Lemian Liu 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

Morphological and Molecular Diversification of Asian Endemic Difflugia tuberspinifera (Amoebozoa, Arcellinida): A Case of Fast Morphological Evolution in Protists?

(2015) Fatma Gomaa et al.   PROTIST

Discrimination of Closely Related Species in Tintinnid Ciliates: New Insights on Crypticity and Polymorphism in the Genus Helicostomella

(2015) Luciana F. Santoferrara et al.   PROTIST

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Open science resources for the discovery and analysis of Tara Oceans data

(2015) Stéphane Pesant et al.   Scientific Data

Determining Microeukaryotic Plankton Community around Xiamen Island, Southeast China, Using Illumina MiSeq and PCR-DGGE Techniques

(2015) Lingyu Yu et al.   PLoS One

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

Dynamics in microbial communities: unraveling mechanisms to identify principles

(2014) Allan Konopka et al.   ISME Journal

REVIEW: The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology

(2014) Helen C. Rees et al.   JOURNAL OF APPLIED ECOLOGY

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

Drastic change in China's lakes and reservoirs over the past decades

(2014) Xiankun Yang et al.   Scientific Reports

Seasonality and disturbance: annual pattern and response of the bacterial and microbial eukaryotic assemblages in a freshwater ecosystem

(2013) Adriane Clark Jones et al.   ENVIRONMENTAL 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

Water Stratification Affects the Microeukaryotic Community in a Subtropical Deep Reservoir

(2013) Zheng Yu et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Patterns in the Composition of Microbial Communities from a Subtropical River: Effects of Environmental, Spatial and Temporal Factors

(2013) Lemian Liu et al.   PLoS One

Eukaryotic versus prokaryotic marine picoplankton ecology

(2012) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

Algae community and trophic state of subtropical reservoirs in southeast Fujian, China

(2012) Jun Yang et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

The Revised Classification of Eukaryotes

(2012) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

A combined sequence-based and fragment-based characterization of microbial eukaryote assemblages provides taxonomic context for the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method

(2012) Diane Y. Kim et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Biodiversity loss and its impact on humanity

(2012) Bradley J. Cardinale et al.   NATURE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Concepts in protistology: Species definitions and boundaries

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

Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness

(2011) Virginia Edgcomb et al.   ISME Journal

Monitoring endangered freshwater biodiversity using environmental DNA

(2011) PHILIP FRANCIS THOMSEN et al.   MOLECULAR ECOLOGY

Two decades of describing the unseen majority of aquatic microbial diversity

(2011) LUCIE ZINGER et al.   MOLECULAR ECOLOGY

Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

(2011) Jan Pawlowski et al.   PLoS One

Persistence of Environmental DNA in Freshwater Ecosystems

(2011) Tony Dejean et al.   PLoS One

Depth matters: Microbial eukaryote diversity and community structure in the eastern North Pacific revealed through environmental gene libraries

(2010) Astrid Schnetzer et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Microbial eukaryotic community in response to Microcystis spp. bloom, as assessed by an enclosure experiment in Lake Taihu, China

(2010) Meijun Chen et al.   FEMS MICROBIOLOGY ECOLOGY

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing

(2010) Man Kit Cheung et al.   ISME Journal

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

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

(2010) Justin Kuczynski et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

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

Species detection using environmental DNA from water samples

(2008) G. F. Ficetola et al.   Biology Letters

FORWARD SELECTION OF EXPLANATORY VARIABLES

(2008) F. Guillaume Blanchet et al.   ECOLOGY