New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts

Shedding Light on the Polyphyletic Thecate Amoeba Genus Plagiophrys : Transition of Some of its Species to Rhizaspis (Tectofilosida, Thecofilosea, Cercozoa) and the Establishment of Sacciforma gen. nov. and Rhogostomidae fam. nov. (Cryomonadida, Thecofilosea, Cercozoa)

(2017) Kenneth Dumack et al.   PROTIST

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs

(2016) A. Ö. C. Dupont et al.   ENVIRONMENTAL MICROBIOLOGY

Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists

(2016) David Bass et al.   ENVIRONMENTAL MICROBIOLOGY

Protozoan indicators and extracellular polymeric substances alterations in an intermittently aerated membrane bioreactor treating mature landfill leachate

(2016) Nikolaos Remmas et al.   ENVIRONMENTAL TECHNOLOGY

Local diversity of heathland Cercozoa explored by in-depth sequencing

(2016) Christoffer Bugge Harder et al.   ISME Journal

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

(2016) Lars Grossmann et al.   ISME Journal

High Diversity Revealed in Leaf-Associated Protists (Rhizaria: Cercozoa) of Brassicaceae

(2016) Sebastian Ploch et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria

(2016) Ding He et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Richness and distribution of tropical oyster parasites in two oceans

(2016) KATRINA M. PAGENKOPP LOHAN et al.   PARASITOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Metacommunity analysis of amoeboid protists in grassland soils

(2016) Anna Maria Fiore-Donno et al.   Scientific Reports

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

(2015) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomic census of active protists in soils

(2015) Stefan Geisen et al.   ISME Journal

Estimating Protistan Diversity Using High-Throughput Sequencing

(2015) Sarah K. Hu et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Testate amoeba Rhogostoma minus Belar, 1921, associated with nodular gill disease of rainbow trout, Oncorhynchus mykiss (Walbaum)

(2015) I Dyková et al.   JOURNAL OF FISH DISEASES

Evolutionary Origins of Rhizarian Parasites

(2015) Roberto Sierra et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Rhizaria

(2014) Fabien Burki et al.   CURRENT BIOLOGY

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

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Changes in biocrust cover drive carbon cycle responses to climate change in drylands

(2013) Fernando T. Maestre et al.   GLOBAL CHANGE BIOLOGY

Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians

(2013) Hanna Hartikainen et al.   ISME Journal

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

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

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

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

Global biogeography of highly diverse protistan communities in soil

(2012) Scott T Bates et al.   ISME Journal

Contribution of cryptogamic covers to the global cycles of carbon and nitrogen

(2012) Wolfgang Elbert et al.   Nature Geoscience

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

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Anne Domonell et al.   PEDOBIOLOGIA

Reticulamoeba Is a Long-Branched Granofilosean (Cercozoa) That Is Missing from Sequence Databases

(2012) David Bass et al.   PLoS One

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

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Novel Cultured Protists Identify Deep-branching Environmental DNA Clades of Cercozoa: New Genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia

(2011) Alexis T. Howe et al.   PROTIST

Implementing large-scale and long-term functional biodiversity research: The Biodiversity Exploratories

(2010) Markus Fischer et al.   BASIC AND APPLIED ECOLOGY

Reduction of heteroduplex formation in PCR amplification

(2010) E. Michu et al.   BIOLOGIA PLANTARUM

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

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Evolutionary relationships among marine cercozoans as inferred from combined SSU and LSU rDNA sequences and polyubiquitin insertions

(2010) Chitchai Chantangsi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Phylogeny, Taxonomy, and Astounding Genetic Diversity of Glissomonadida ord. nov., The Dominant Gliding Zooflagellates in Soil (Protozoa: Cercozoa)

(2009) Alexis T. Howe et al.   PROTIST

Biological crusts as a model system for examining the biodiversity–ecosystem function relationship in soils

(2009) Matthew A. Bowker et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

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

(2008) Tim Urich et al.   PLoS One

Phylogeny of Novel Naked Filose and Reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea Revised

(2008) David Bass et al.   PROTIST

Testate amoebae and nutrient cycling: peering into the black box of soil ecology

(2008) David M. Wilkinson   TRENDS IN ECOLOGY & EVOLUTION