Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds

Molecular Phylogeny and Ontogeny of a New Ciliate Genus,Paracladotricha salinan. g., n. sp. (Ciliophora, Hypotrichia)

(2014) Chen Shao et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

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

Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum

(2014) Tamar Kis-Papo et al.   Nature Communications

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

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

Morphology, ontogenesis and molecular phylogeny of Platynematum salinarum nov. spec., a new scuticociliate (Ciliophora, Scuticociliatia) from a solar saltern

(2013) Wilhelm Foissner et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Microbial biodiversity in saline shallow lakes of the Monegros Desert, Spain

(2013) Emilio O. Casamayor et al.   FEMS MICROBIOLOGY ECOLOGY

High genetic diversity and novelty in planktonic protists inhabiting inland and coastal high salinity water bodies

(2013) Xavier Triadó-Margarit et al.   FEMS MICROBIOLOGY ECOLOGY

Schmidingerothrix salinarumnov. spec. is the Molecular Sister of the Large Oxytrichid Clade (Ciliophora, Hypotricha)

(2013) Wilhelm Foissner et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia

(2013) Karla B. Heidelberg et al.   Frontiers in Microbiology

Targeted recovery of novel phylogenetic diversity from next-generation sequence data

(2012) Michael D J Lynch et al.   ISME Journal

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

(2012) Ramiro Logares et al.   ISME Journal

Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity

(2012) Micah Dunthorn et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

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

(2012) Dominik Forster et al.   SYSTEMATICS AND BIODIVERSITY

Marine Protistan Diversity

(2011) David A. Caron et al.   Annual Review of Marine Science

Microbial eukaryote life in the new hypersaline deep-sea basin Thetis

(2011) Alexandra Stock et al.   EXTREMOPHILES

Hypervariable regions (V1–V9) of the dinoflagellate 18S rRNA using a large dataset for marker considerations

(2011) Jang-Seu Ki   JOURNAL OF APPLIED PHYCOLOGY

JAGUC — A SOFTWARE PACKAGE FOR ENVIRONMENTAL DIVERSITY ANALYSES

(2011) MARKUS E. NEBEL et al.   Journal of Bioinformatics and Computational Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Characterization of halotolerant Bicosoecida and Placididea (Stramenopila) that are distinct from marine forms, and the phylogenetic pattern of salinity preference in heterotrophic stramenopiles

(2010) Jong Soo Park et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2010) Anke Behnke et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2010) Anna Engelbrektson et al.   ISME Journal

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

(2010) Jon Bråte et al.   ISME Journal

Microbial community structure across the tree of life in the extreme Río Tinto

(2010) Linda A Amaral-Zettler et al.   ISME Journal

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

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences

(2010) Markus Nebel et al.   Environmental Microbiology Reports

Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology

(2009) D. A. Caron et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Community structure and seasonal dynamics of planktonic ciliates along salinity gradients

(2009) Yanli Lei et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11)

(2009) R. Logares et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogeny of euglyphid testate amoebae (Cercozoa: Euglyphida) suggests transitions between marine supralittoral and freshwater/terrestrial environments are infrequent

(2009) Thierry J. Heger et al.   MOLECULAR PHYLOGENETICS 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

Ultrastructure and Molecular Phylogeny of two Heterolobosean Amoebae, Euplaesiobystra hypersalinica gen. et sp. nov. and Tulamoeba peronaphora gen. et sp. nov., Isolated from an Extremely Hypersaline Habitat

(2009) Jong Soo Park et al.   PROTIST

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin

(2008) Eva Alexander et al.   ENVIRONMENTAL MICROBIOLOGY

Communities structure of the planktonic halophiles in the solar saltern of Sfax, Tunisia

(2008) Jannet Elloumi et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Protistan community patterns within the brine and halocline of deep hypersaline anoxic basins in the eastern Mediterranean Sea

(2008) Virginia Edgcomb et al.   EXTREMOPHILES

Morphology and Molecular Phylogeny ofTrimyema koreanumn. sp., a Ciliate from the Hypersaline Water of a Solar Saltern

(2008) BYUNG CHEOL CHO et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Abundance and biomass of prokaryotic and eukaryotic microorganisms coupled with environmental factors in an arid multi-pond solar saltern (Sfax, Tunisia)

(2008) Jannet Elloumi et al.   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM