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

Next-Generation Environmental Diversity Surveys of Foraminifera: Preparing the Future

(2016) J. Pawlowski et al.   BIOLOGICAL BULLETIN

Metatranscriptomic census of active protists in soils

(2015) Stefan Geisen et al.   ISME Journal

Concomitant predation on parasites is highly variable but constrains the ways in which parasites contribute to food web structure

(2015) Alyssa R. Cirtwill et al.   JOURNAL OF ANIMAL ECOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The effect of anthropogenic arsenic contamination on the earthworm microbiome

(2014) Daniel Antony Pass et al.   ENVIRONMENTAL MICROBIOLOGY

Two new species of the genus Stenamoeba (Discosea, Longamoebia): Cytoplasmic MTOC is present in one more amoebae lineage

(2014) Stefan Geisen et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes

(2014) Vera G. Fonseca et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach

(2014) Guillaume Lentendu et al.   MOLECULAR ECOLOGY

Acanthamoeba everywhere: high diversity of Acanthamoeba in soils

(2014) Stefan Geisen et al.   PARASITOLOGY RESEARCH

Soil water availability strongly alters the community composition of soil protists

(2014) Geisen Stefan et al.   PEDOBIOLOGIA

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

(2014) Kenan Hadziavdic et al.   PLoS One

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

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

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

(2014) K. S. Ramirez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Discrepancy between Species Borders at Morphological and Molecular Levels in the Genus Cochliopodium (Amoebozoa, Himatismenida), with the Description of Cochliopodium plurinucleolum n. sp.

(2014) Stefan Geisen et al.   PROTIST

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity

(2014) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

Identification of Parasitic Communities within European Ticks Using Next-Generation Sequencing

(2014) Sarah Bonnet et al.   PLoS Neglected Tropical Diseases

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

Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils

(2013) Darren S. Baldwin et al.   MOLECULAR ECOLOGY

Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms

(2013) L. Kermarrec et al.   Molecular Ecology Resources

Barcoding in the dark?: A critical view of the sufficiency of zoological DNA barcoding databases and a plea for broader integration of taxonomic knowledge

(2013) Sebastian Kvist   MOLECULAR PHYLOGENETICS AND EVOLUTION

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic Affiliation of SSU rRNA Genes Generated by Massively Parallel Sequencing: New Insights into the Freshwater Protist Diversity

(2013) Najwa Taib et al.   PLoS One

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

(2013) Alexandra A-T. Weber 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

Amplification primers of SSU rDNA for soil protists

(2013) Sina M. Adl et al.   SOIL BIOLOGY & BIOCHEMISTRY

High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities

(2013) Aibin Zhan et al.   Methods in Ecology and Evolution

Global biogeography of highly diverse protistan communities in soil

(2012) Scott T Bates et al.   ISME Journal

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

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

The Revised Classification of Eukaryotes

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

Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities

(2012) Jae-Hyung Ahn et al.   JOURNAL OF MICROBIOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

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

Community structure of cultivable protists in different grassland and forest soils of Thuringia

(2012) Anne Domonell et al.   PEDOBIOLOGIA

Sequencing our way towards understanding global eukaryotic biodiversity

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

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

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

Epidemiology and Molecular Relationships of Cryptosporidium spp. in People, Primates, and Livestock from Western Uganda

(2012) Stephanie J. Salyer et al.   PLoS Neglected Tropical Diseases

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Concepts in protistology: Species definitions and boundaries

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

Behavioural resistance against a protozoan parasite in the monarch butterfly

(2011) Thierry Lefèvre et al.   JOURNAL OF ANIMAL ECOLOGY

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions

(2010) Anke Behnke et al.   ENVIRONMENTAL MICROBIOLOGY

Grellamoeba robusta gen. n., sp. n., a possible member of the family Acramoebidae Smirnov, Nassonova et Cavalier-Smith, 2008

(2010) Iva Dyková et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

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

Phylogenetic Relationships, Evolution, and Systematic Revision of the Septate Gregarines (Apicomplexa: Eugregarinorida: Septatorina)

(2009) Richard E. Clopton   COMPARATIVE PARASITOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Environmental rRNA inventories miss over half of protistan diversity

(2008) Sunok Jeon et al.   BMC MICROBIOLOGY

Elevated atmospheric CO2affects soil microbial diversity associated with trembling aspen

(2008) Celine Lesaulnier et al.   ENVIRONMENTAL MICROBIOLOGY

Protists are microbes too: a perspective

(2008) David A Caron et al.   ISME Journal

An optimised PCR/T-RFLP fingerprinting approach for the investigation of protistan communities in groundwater environments

(2008) Kathrin Euringer et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

Ultrastructure, SSU rRNA Gene Sequences and Phylogenetic Relationships of Flamella Schaeffer, 1926 (Amoebozoa), with Description of Three New Species

(2008) Alexander Kudryavtsev et al.   PROTIST

Microsporidia Are Natural Intracellular Parasites of the Nematode Caenorhabditis elegans

(2008) Emily R Troemel et al.   PLOS BIOLOGY

Correct identification of species makes the amoebozoan rRNA tree congruent with morphology for the order Leptomyxida Page 1987; with description of Acramoeba dendroida n. g., n. sp., originally misidentified as ‘Gephyramoeba sp.’

(2007) Alexey V. Smirnov et al.   EUROPEAN JOURNAL OF PROTISTOLOGY