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List of works by Thorsten Stoeck

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

scientific article

A Comparison of Different Ciliate Metabarcode Genes as Bioindicators for Environmental Impact Assessments of Salmon Aquaculture

scientific article published on 12 August 2018

A Contribution to the Morphology and Phylogeny of Chlamydodon, with Three New Species from China (Ciliophora, Cyrtophoria).

scientific article

A Proposed Timescale for the Evolution of Armophorean Ciliates: Clevelandellids Diversify More Rapidly Than Metopids

scientific article published on 01 July 2018

A fundamental difference between macrobiota and microbial eukaryotes: protistan plankton has a species maximum in the freshwater-marine transition zone of the Baltic Sea

scientific article published on 13 January 2019

A molecular approach to identify active microbes in environmental eukaryote clone libraries

scientific article

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

scientific article published on 15 July 2013

A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples

scientific article published on 23 January 2006

Aquatic food webs in deep temperate lakes: key species establish through their autecological versatility

scientific article published on 11 December 2020

Assessing Low-Intensity Relationships in Complex Networks

scientific article

Benthic protists: the under-charted majority

scientific article

Beyond the "Code": A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora).

scientific article

CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms

scientific article

Caryotricha minuta (Xu et al., 2008) nov. comb., a unique marine ciliate (Protista, Ciliophora, Spirotrichea), with phylogenetic analysis of the ambiguous genus Caryotricha inferred from the small-subunit rRNA gene sequence

scientific article

Cellular identification of a novel uncultured marine stramenopile (MAST-12 Clade) small-subunit rRNA gene sequence from a norwegian estuary by use of fluorescence in situ hybridization-scanning electron microscopy

scientific article published on 9 February 2007

Cellular identity of an 18S rRNA gene sequence clade within the class Kinetoplastea: the novel genus Actuariola gen. nov. (Neobodonida) with description of the type species Actuariola framvarensis sp. nov.

scientific article

Ciliate diversity and distribution patterns in the sediments of a seamount and adjacent abyssal plains in the tropical Western Pacific Ocean

scientific article published on 12 September 2017

Ciliates and the rare biosphere: a review

scientific article

Ciliates — Protists with complex morphologies and ambiguous early fossil record

scholarly article by Micah Dunthorn published in September 2015

Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys

scientific article

Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity

scientific article

Comparison of three clustering approaches for detecting novel environmental microbial diversity

scientific article published on 25 February 2016

Congruence and indifference between two molecular markers for understanding oral evolution in the Marynidae sensu lato (Ciliophora, Colpodea)

scientific article

Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists

scientific article published on 17 June 2018

Corrigendum to "Description of the Halophile Euplotes qatarensis nov. spec. (Ciliophora, Spirotrichea, Euplotida) Isolated from the Hypersaline Khor Al-Adaid Lagoon in Qatar"

scientific article published on 25 January 2019

Corrigendum: "Morphology and Ontogenesis of Psilotrichides hawaiiensis nov. gen., nov. spec. and Molecular Phylogeny of the Psilotrichidae (Ciliophora, Hypotrichia)" by Heber et al. 2014.

scientific article published on 3 December 2017

Cotterillia bromelicola nov. gen., nov. spec., a gonostomatid ciliate (Ciliophora, Hypotricha) from tank bromeliads (Bromeliaceae) with de novo originating dorsal kineties ⬇️

scientific article published on October 23, 2010

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

scientific article

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

scientific article

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

scientific article

Description of Leptopharynx bromelicola n. sp. and Characterization of the Genus Leptopharynx Mermod, 1914 (Protista, Ciliophora) ⬇️

scientific article published on March 1, 2011

Description of the Halophile Euplotes qatarensis nov. spec. (Ciliophora, Spirotrichea, Euplotida) Isolated from the Hypersaline Khor Al-Adaid Lagoon in Qatar.

scientific article

Diatom diversity through HTS-metabarcoding in coastal European seas

scientific article published in Scientific Reports

Differential thermal adaptation of clonal strains of a protist morphospecies originating from different climatic zones

scientific article published in March 2007

Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea.

scientific article

Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord, Denmark

scientific article published in December 2006

Diversity of the cyrtophorid genus Chlamydodon (Protista, Ciliophora): its systematics and geographic distribution, with taxonomic descriptions of three species

scientific article published in 2018

Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

scientific article published on 16 May 2020

Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring

scientific article published on 13 December 2018

Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture

scientific article published on 6 December 2017

Environmental DNA-based profiling of benthic bacterial and eukaryote communities along a crude oil spill gradient in a coral reef in the Persian Gulf

scientific article published in 2022

Environmental rRNA inventories miss over half of protistan diversity

scientific article

Environmental selection of protistan plankton communities in hypersaline anoxic deep-sea basins, Eastern Mediterranean Sea

scientific article

Environmental status assessment using biological traits analyses and functional diversity indices of benthic ciliate communities

scientific article published on 07 May 2018

Euplotes huizhouensis nom. nov. (Ciliophora, Euplotida), a replacement name for the junior primary homonym Euplotes tuffraui

scholarly article published in 2022

Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection

scientific article (publication date: 8 July 2013)

Evidence for local ciliate endemism in an alpine anoxic lake

scientific article published on 24 February 2007

Fossil Tintinnids

Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation

scientific article

Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

scientific article published on 29 April 2021

High diversity of protistan plankton communities in remote high mountain lakes in the European Alps and the Himalayan mountains

scientific article

Identification of the pathogenic ciliate Pseudocohnilembus persalinus (Oligohymenophorea: Scuticociliatia) by fluorescence in situ hybridization

scientific article published on 22 October 2013

Identifying the minimum amplicon sequence depth to adequately predict classes in eDNA-based marine biomonitoring using supervised machine learning

scientific article published on 26 April 2021

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

scientific article published on 16 August 2019

Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea).

scientific article published on 10 August 2010

Induction and genetic identification of a callus-like growth developed in the brown alga Fucus vesiculosus

scientific article published on 22 March 2019

Intraclass evolution and classification of the Colpodea (Ciliophora).

scientific article published on 18 July 2011

JAGUC--a software package for environmental diversity analyses.

scientific article

Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network

scientific article published in 2021

Living at the Limits: Evidence for Microbial Eukaryotes Thriving under Pressure in Deep Anoxic, Hypersaline Habitats

article

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

scientific article published on 28 June 2015

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

scientific article

Methodology of Protistan Discovery: from rRNA Detection to Quality Scanning Electron Microscope Images ⬇️

scientific article published on November 1, 2003

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

scientific article published on 19 October 2011

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

scientific article

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

scientific article

Microeukaryote community patterns along an O2/H2S gradient in a supersulfidic anoxic fjord (Framvaren, Norway)

scientific article

Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization

scientific article

Molecular Diversity of Fungi from Marine Oxygen-Deficient Environments (ODEs) ⬇️

scientific article published on January 1, 2012

Morphological and Molecular Characterization of Paramecium (Viridoparamecium nov. subgen.) chlorelligerum Kahl (Ciliophora) ⬇️

scientific article published on July 24, 2012

Morphological and Molecular Characterization of Some Peritrichs (Ciliophora: Peritrichida) from Tank Bromeliads, Including Two New Genera: Orborhabdostyla and Vorticellides ⬇️

scientific article published on January 22, 2010

Morphological and molecular characterization of a new protist family, Sandmanniellidae n. fam. (Ciliophora, Colpodea), with description of Sandmanniella terricola n. g., n. sp. from the Chobe floodplain in Botswana

scientific article

Morphological, Phylogenetic and Ecophysiological Characterization of a New Ciliate, Platynematum rossellomorai n. sp. (Oligohymenophorea, Scuticociliatia), Detected in a Hypersaline Pond on Mallorca, Spain

scientific article published on 18 July 2020

Morphology and ontogenesis of Psilotrichides hawaiiensis nov. gen., nov. spec. and molecular phylogeny of the Psilotrichidae (Ciliophora, Hypotrichia).

scientific article

Morphology of Bromeliophrya quadristicha n. spec., an Inhabitant of Tank Bromeliads (Bromeliaceae), and Phylogeny of the Bromeliophryidae (Ciliophora, Tetrahymenida) ⬇️

scientific article published on January 24, 2013

Morphology of four cyrtophorian ciliates (Protozoa, Ciliophora) from Yangtze Delta, China, with notes on the phylogeny of the genus Phascolodon

scientific article published on 25 August 2016

Morphology, Morphogenesis and Molecular Phylogeny of a New Obligate Halophile Ciliate, Schmidtiella ultrahalophila gen. nov., spec. nov. (Ciliophora, Hypotrichia) Isolated from a Volcanic Crater on Sal (Cape Verde Islands)

scientific article published on 08 February 2019

Morphology, Ontogenesis and Molecular Phylogeny of Neokeronopsis (Afrokeronopsis) aurea nov. subgen., nov. spec. (Ciliophora: Hypotricha), a New African Flagship Ciliate Confirms the CEUU Hypothesis ⬇️

scientific article

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

scientific article

Morphology, ultrastructure, molecular phylogeny, and autecology of Euplotes elegans Kahl, 1932 (Hypotrichida; Euplotidae) isolated from the anoxic Mariager Fjord, Denmark

scientific article published in March 2007

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

scientific article

Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts

scientific article published in 2024

New SSU-rDNA sequences for eleven colpodeans (Ciliophora, Colpodea) and description of Apocyrtolophosis nov. gen.

scientific article

Novel Eukaryotic Lineages Inferred from Small-Subunit rRNA Analyses of Oxygen-Depleted Marine Environments ⬇️

scientific article published on May 1, 2003

Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea).

scientific article

Patterns of rare and abundant marine microbial eukaryotes

scientific article

Phylogenetic placement of the Cyrtolophosididae Stokes, 1888 (Ciliophora; Colpodea) and neotypification of Aristerostoma marinum Kahl, 1931.

scientific article

Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context

scientific article published on 27 January 2014

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

scientific article published on 5 December 2008

Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany).

scientific article published on 11 December 2014

Protistan diversity in the Arctic: a case of paleoclimate shaping modern biodiversity?

scientific article

Protistan grazing in a meromictic freshwater lake with anoxic bottom water.

scientific article published on 5 December 2013

Re-description and molecular phylogeny of the free-swimming peritrichs Hastatella radians Erlanger, 1890 and H. aesculacantha Jarocki & Jakubowska, 1927 (Ciliophora, Peritrichia) from China

scientific article published in June 2022

Redescription of Dexiotricha colpidiopsis (Kahl, 1926) Jankowski, 1964 (Ciliophora, Oligohymenophorea) from a Hot Spring in Iceland with Identification Key for Dexiotricha species

scientific article published on 14 December 2018

Redescription of the halophile ciliate, Blepharisma halophilum Ruinen, 1938 (Ciliophora, Heterotrichea, Heterotrichida) shows that the genus Blepharisma is non-monophyletic

scientific article

Repeated sampling reveals differential variability in measures of species richness and community composition in planktonic protists

scientific article

Report of the 2020 meeting of the German Society for Protozoology

scientific article published on 06 April 2020

Rigidothrix goiseri nov. gen., nov. spec. (Rigidotrichidae nov. fam.), a new "flagship" ciliate from the Niger floodplain breaks the flexibility-dogma in the classification of stichotrichine spirotrichs (Ciliophora, Spirotrichea).

scientific article

Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study

scientific article published on 01 November 2020

Sample pooling obscures diversity patterns in intertidal ciliate community composition and structure

scientific article

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

scientific article published on December 10, 2013

Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts?

article

Small subunit rRNA phylogenies show that the class nassophorea is not monophyletic (Phylum Ciliophora).

scientific article published in July 2009

Small-subunit rRNA Phylogenies Suggest That Epalxella antiquorum (penard, 1922) corliss, 1960 (ciliophora, odontostomatida) is a member of the plagyopylea

scientific article

Spatio-temporal patterns of zooplankton in a main-stem dam affected tributary: a case study in the Xiangxi River of the Three Gorges Reservoir, China

scientific article published on 08 July 2019

Spatio-temporal variations in protistan communities along an O/HS gradient in the anoxic Framvaren Fjord (Norway).

scientific article

Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes

scientific article published on 13 April 2020

Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring

scientific article published on 03 August 2018

Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms

scientific article published on 24 February 2015

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy

scientific article

The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates

scientific article

The chaos prevails: molecular phylogeny of the Haptoria (Ciliophora, Litostomatea).

scientific article published in December 2013

The importance of sea ice for exchange of habitat-specific protist communities in the Central Arctic Ocean

The search finds an end: colpodidiids belong to the Class Nassophorea (ciliophora)

scientific article

Towards an eDNA metabarcode-based performance indicator for full-scale municipal wastewater treatment plants

article

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

scientific article published on 2 June 2017

Tritirachium candoliense sp. nov., a novel basidiomycetous fungus isolated from the anoxic zone of the Arabian Sea.

scientific article

Widespread Occurrence of Two Planktonic Ciliate Species (Urotricha, Prostomatida) Originating from High Mountain Lakes

scientific article published in 2022

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