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Zayed, A., Kovacheva, M., Muffler, K., Breiner, H.-W., Stoeck, T. X. & Ulmer, R. (2019) Induction and genetic identification of a callus-like growth developed in the brown alga Fucus vesiculosus. Engineering in Life Science, doi: 10.1002/elsc.201800211.

Li, F., Qu, Z., Luo, D., Filker, S., Hu, X. & Stoeck, T. (2019) 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). Journal of Eukaryotic Microbiology, doi: 10.1111/jeu.12714.

Pitsch, G., Bruni, E. P., Forster, D., Qu, Z., Sonntag, B., Stoeck, T. & Posch, T. (2019) Seasonality of planktonic freshwater ciliates: Are analyses based on V9 regions of the 18S rRNA gene correlated with morphospecies counts? Frontiers in Microbiology (accepted)

Filker, S., Kühner, S., Heckwolf, M., Dierking, J. & Stoeck, T. (2018) A fundamental difference between macrobiotic and microbial eukaryotes: protistan plankton has a species maximum in the fresh-water marine transition zone of the Baltic Sea. Environmental Microbiology, doi: 10.1111/1462-2920.14502.

Piredda, R., Claverie, J.-M., Decelle, J., de Vargas, C., Dunthron, M., Edvardsen, B., Eikrem, W., Forster, D., Kooistra, W. H. C. F., Logares, R., Massana, R., Montresor, M., Not, F., Ogata, H., Pawlowski, J., Romac, S., Stoeck, T. & Zingone, A. (2018) Diatom diversity through HTS-metabarcoding in coastal European seas. Scientific Reports, doi: 10.1038/s41598-018-36345-9.

Cordier, T., Lanzén, A., Apothéloz-Perret-Gentil, L., Stoeck, T. & Pawlowski, J. (2018) Embracing environmental genomics and machine learning for routine biomonitoring. Trends in Microbiology,  doi: 10.1016/j.tim.2018.10.012.

Forster, D., Filker, S., Kochems, R., Breiner, H.-W., Cordier, T., Pawlowski, J. & Stoeck, T. (2018) A comparison of different ciliate meta barcode genes as bioindicators for environmental impact assessments of salmon aquaculture. Journal of Eukaryotic Microbiology (in press).

Stoeck, T., Pan, H., Dully, V., Forster, D. & Jung, T. (2018) Towards an eDNA metabarcode-based performance indicator for full-scale municipal wastewater treatment plants. Water Research, doi: 10.1016/j.watres.2018.07.051.

Cordier, T., Forster, D., Dufresne, Y., Martins, C., Stoeck, T. & Pawlowski, J. (2018) Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring. Molecular Ecology Resources, doi: 10.1111/1755-0998.12926.

Vdacny, P., Rajter, L., Stoeck, T. & Foissner, W. (2018) A proposed timescale for the evolution of armophorean ciliates: clevelandellids diversify more rapidly than metopids. Journal of Eukaryotic Microbiology, doi: 10.1111/jeu.12641.

Lentendu, G., Mahé, F., Bass, D., Rueckert, S., Stoeck, T. & Dunthorn, M. (2018) Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists. Molecular Ecology 27: 2846-2857.

Xu, Y., Stoeck, T., Forster, D., Ma, Z., Zhang, L. & Fan, X. (2018) Environmental status assessment using biological traits analyses and functional diversity indices of benthic ciliate communities. Marine Pollution Bulletin 131: 646-654.

Qu, Z., Groben, R., Marteinsson, V., Agatha, S. & Stoeck, T. (2018) Redescription of Dexiotricha colpidiopsis (Kahl, 1926) Jankowski, 1964 (Ciliophora, Oligohymenophorea) from a hot spring in Iceland with identification key for Dexiotricha species. Acta Protozoologica 57(2).

Qu, Z., Li, L., Lin, X., Stoeck, T., Pan, H., Al-Rasheid, K. A. S. & Song, W. (2018) Diversity of the cyrtophorid genus Chlamydodon (Protista, Ciliophora): its systematics and geographic distribution, with taxonomic descriptions of three species. Systematics and Biodiversity 1-15.

Stoeck, T., Frühe, L., Forster, D., Cordier, T., Martins, C. I. M. & Pawlowski, J. (2018) Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture. Marine Pollution Bulletin 127: 139-149.

Stoeck, T., Kochems, R., Forster, D., Lejzerowicz, F. & Pawlowski, J. (2018) Metabarcoding of benthic ciliate communities shows high potential for environmental monitoring of salmon aquaculture. Ecological Indicators 85: 153-164.

Zhao, F., Filker, S., Stoeck, T. & Xu, K. (2017) Ciliate diversity and distribution patterns in the sediments of a seamount and adjacent deep-sea plains in the western Pacific Ocean. BMC Microbiology 17, 192.

Pan, H. & Stoeck, T. (2017) Redescription of the halophile ciliate, Blepharisma halophilum Ruinen, 1938 (Ciliophora, Heterotrichea, Heterotrichida) shows that the genus Blepharisma is non-monophyletic. European Journal of Protistology 61: 20-28.

Qu, Z., Pan, H., Lin, X., Li, L., Aleidan, A. M. A., Al-Farraj, S. A., Stoeck, T. & Hu, X. (2017) A contribution to the morphology and phylogeny of Chlamydodon, with three new species from China (Ciliophora, Cyrtophoria). Journal of Eukaryotic Microbiology, doi: 10.1111/jeu.12472.

Filker, S., Forster, D., Weinisch, L., Mora-Ruiz, M., Gonzáles, B., Farías, M. E., Roselló-Móra, R. & Stoeck, T. (2017) Transition boundaries for protistan species turnover in hypersaline waters of different biogeographic regions. Environmental Microbiology 19: 3186-3200.

Warren, A., Patterson, D. J., Dunthorn, M., Clamp, J. C., Achilles-Day, U. E. M., Aescht, E., Al-Farraj, S. A., Al-Quraishy, S., Al-Rasheid, K., Carr, M., Day, J. G., Dellinger, M., El-Serehy, H. A., Fan, Y., Gao, F., Gao, S., Gong, J., Gupta, R., Hu, X., Kamra, K., Langlois, G., Lin, X., Lipscomb, D., Lobban, C. S., Luporini, P., Lynn, D. H., Ma, H., Macek, M., Nikolaeva, S., Ong´ondo, G. O., Pérez-Uz, B., Purushothaman, J., Quintela-Alonso, P., Rotterová, J., Santoferrara, L., Shao, C., Shen, Z., Shi, X., Song, W., Stoeck, T., La Terza, A., Valessi, A., Wang, M., Weisse, T., Wiackowski, K., Wu, L., Xu, K., Yi, Z., Zufall, R. & Agatha, S. (2017) Beyond the "Code": A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora). Journal of Eukaryotic Microbiology 64, 539-554.

Hardge, K., Peeken, I., Neuhaus, S., Krumpen, T., Stoeck, T. & Metfies, K. (2017) Sea ice origin and sea ice retreat as possible drivers of variability in Arctic marine protist composition. Marine Ecology Progress Series 571: 43-57.

Hardge, K., Peeken, I., Neuhaus, S., Lange, B.A., Stock, A., Stoeck, T., Weinisch, L. & Metfies, K. (2017) The importance of sea ice for exchange of habitat-specific protist communities in the Central Arctic Ocean. Journal of Marine Systems 165: 124-138.

Gimmler, A., Korn, R., de Vargas, C., Audi, S. & Stoeck, T. (2016) The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates. Scientific reports, doi: 10.1038/srep33555.

Forster, D., Dunthorn, M., Mahé, F., Dolan, J. R., Audic, S., Bass, D., Bittner, L., Boutte, C., Christen, R., Claverie, J. M., Decelle, J., Edvardsen, B., Egge, E., Eikrem, W., Gobet, A., Kooistra, W. H. C. F., Logares, R., Massana, R., Montresor, M., Not, F., Ogata, H., Pawlowski, J., Pernice, M. C., Romac, S., Shalchian-Tabrizi, K., Simon, N., Richards, T. A., Santini, S., Sarno, D., Siano, R., Vaulot, D., Wincker, P., Zingone, A., de Vargas, C. & Stoeck, T. (2016). Benthic protists: the under-charted majority. FEMS Microbiology Ecology 92(8), fiw120.

Forster, D., Dunthorn, M., Stoeck, T. & Mahé, F. (2016) Comparison of three clustering approaches for detecting novel environmental microbial diversity. PeerJ 4: e1692. doi.org/10.7717/peerj.1692.

Spitz, A., Gimmler, A., Stoeck, T., Zweig, K.A. & Horvat, E.-A. (2016) Assessing Low-Intensity Relationships in Complex Networks. PLoS ONE 11(4):e0152536. doi:10.1371/journal.pone.0152536. (Link)

Filker, S., Sommaruga, R., Vila, I. & Stoeck, T. (2016) Protistan plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns. Molecular Ecology. doi: 10.1111/mec.13633.

Fotedar, R., Stoeck, T., Filker, S., Agatha, S., Fell, J., Al Marri, M. & Jiang, J. (2016) Description of the Halophile Euplotes qatarensis nov. spec. (Ciliophora, Spirotrichea, Euplotida) Isolated from the Hypersaline Khor Al-Adaid Lagoon in Qatar. Journal of Eukaryotic Microbiology. doi: 10.1111/jeu.12305.

Oikonomou, A., Filker, S., Breiner, H.W. and Stoeck, T. (2015) Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany). Environ Microbiol 17(6), 2144-2157.

Massana, R., Gobet, A., Audic, S., Bass, D., Bittner, L., Boutte, C., Chambouvet, A., Christen, R., Claverie, J.M., Decelle, J., Dolan, J.R., Dunthorn, M., Edvardsen, B., Forn, I., Forster, D., Guillou, L., Jaillon, O., Kooistra, W.H., Logares, R., Mahe, F., Not, F., Ogata, H., Pawlowski, J., Pernice, M.C., Probert, I., Romac, S., Richards, T., Santini, S., Shalchian-Tabrizi, K., Siano, R., Simon, N., Stoeck, T., Vaulot, D., Zingone, A. and de Vargas, C. (2015) Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environ Microbiol. doi: 10.1111/1462-2920.12955.

Mahe, F., Mayor, J., Bunge, J., Chi, J., Siemensmeyer, T., Stoeck, T., Wahl, B., Paprotka, T., Filker, S. and Dunthorn, M. (2015) Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys. J Eukaryot Microbiol 62(3), 338-345.

Kammerlander, B., Breiner, H.W., Filker, S., Sommaruga, R., Sonntag, B. and Stoeck, T. (2015) High diversity of protistan plankton communities in remote high mountain lakes in the European Alps and the Himalayan mountains. FEMS Microbiol Ecol 91(4). doi: 10.1093/femsec/fiv010.

Gimmler, A. and Stoeck, T. (2015) Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization. Environ Microbiol Rep 7(4), 679-686.

Forster, D., Bittner, L., Karkar, S., Dunthorn, M., Romac, S., Audic, S., Lopez, P., Stoeck, T. and Bapteste, E. (2015) Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms. BMC Biol 13, 16.

Filker, S., Gimmler, A., Dunthorn, M., Mahe, F. and Stoeck, T. (2015) Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds. Extremophiles 19(2), 283-295.

Oikonomou, A., Pachiadaki, M., and Stoeck, T. (2014) Protistan grazing in a meromictic freshwater lake with anoxic bottom water. FEMS Microbiol Ecol., 87(3):691-703.

Stoeck, T., Filker, S., Edgcomb, V., Orsi, W., Yakimov, M.M., Pachiadaki, M., Breiner, H.-W., LaCono, V., and Stock, A. (2014) Living at the limits: Evidence for microbial eukaryotes thriving under pressure in deep anoxic, hypersaline habitats. Advances in Ecology, Volume 2014, Article ID 532687 (dx.doi.org/10.1155/2014/532687).

Filker, S., Kaiser, M., Rossello-Mora, R., Dunthorn, M., Lax, G., and Stoeck, T. (2014) "Candidatus Haloectosymbiotes riaformosensis" (Halobacteriaceae), an archaeal ectosymbiont of the hypersaline ciliate Platynematum salinarum. Syst Appl Microbiol. pii: S0723-2020(14)00022-8 (doi: 10.1016/j.syapm.2014.01.001).

Pachiadaki, M.G., Taylor, C., Oikonomou, A., Yakimov, M.M., Stoeck, T., and Edgcomb, V. (2014)  In situ grazing experiments apply new technology to gain insights into deep-sea microbial food webs. Deep Sea Research. doi:10.1016/j.dsr2.2014.10.019.

Logares, R., Audic, S., Bass, D., Bittner, L., Boutte, C., Christen, R. et al. (2014) Patterns of Rare and Abundant Marine Microbial Eukaryotes. Curr Biol., 24(8):813-21.

Dunthorn, M., Hall, M., Foissner, W., Stoeck, T., and Katz, L. (2014) Broad taxon sampling of ciliates using mitochondrial small subunit ribosomal DNA. Acta Protozoologica 53:207-213.

Dunthorn, M., Stoeck, T., Clamp, J., Warren, A., and Mahé, F. (2014) Ciliates and the Rare Biosphere: a Review. J Euk Microbiol., 61(4):404–409.

Zhan, Z., Stoeck, T., Dunthorn, M. and Xu, K. (2014) Identification of the pathogenic ciliate Pseudocohnilembus persalinus (Oligohymenophorea: Scuticociliatia) by fluorescence in situ hybridization. Eur J Protistol 50(1):16-24.

Stoeck, T., Breiner, H.W., Filker, S., Ostermaier, V., Kammerlander, B. and Sonntag, B. (2014) A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology. Environ Microbiol 16(2):430-444.

Stief, P., Fuchs-Ocklenburg, S., Kamp, A., Manohar, C.S., Houbraken, J., Boekhout, T., de Beer, D. and Stoeck, T. (2014) Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea. BMC Microbiol 14(1):35.

Manohar, C.S., Boekhout, T., Muller, W.H. and Stoeck, T. (2014) Tritirachium candoliense sp. nov., a novel basidiomycetous fungus isolated from the anoxic zone of the Arabian Sea. Fungal Biol 118(2): 139-149.

Heber, D., Stoeck, T. and Foissner, W. (2014) Morphology and Ontogenesis of Psilotrichides hawaiiensis nov. gen., nov. spec. and Molecular Phylogeny of the Psilotrichidae (Ciliophora, Hypotrichia). J Eukaryot Microbiol., 61(3):260-77.

Foissner, W., Filker, S. and Stoeck, T. (2014a) Schmidingerothrix salinarum nov. spec. is the Molecular Sister of the Large Oxytrichid Clade (Ciliophora, Hypotricha). J Eukaryot Microbiol 61(1):61-74.

Foissner, W., Bourland, W.A., Wolf, K.W., Stoeck, T. and Dunthorn, M. (2014b) New SSU-rDNA sequences for eleven colpodeans (Ciliophora, Colpodea) and description of Apocyrtolophosis nov. gen. Eur J Protistol 50(1):40-46.

Dunthorn, M., Otto, J., Berger, S.A., Stamatakis, A., Mahe, F., Romac, S., de Vargas, C., Audic, S., Consortium, B., Stock, A., Kauff, F. and Stoeck, T. (2014) Placing environmental next generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. Mol Biol Evol., 31:993-1009.

Vdacny, P., Breiner, H.W., Yashchenko, V., Dunthorn, M., Stoeck, T. and Foissner, W. (2014) The Chaos Prevails: Molecular Phylogeny of the Haptoria (Ciliophora, Litostomatea). Protist 165(1):93-111.

Stoeck, T., Przybos, E. and Dunthorn, M. (2014) The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates. Mol Ecol Resour., 14(3):458-68.

Foissner, W., Jung, J.H., Filker, S., Rudolph, J. and Stoeck, T. (2014) Morphology, ontogenesis and molecular phylogeny of Platynematum salinarum nov. spec., a new scuticociliate (Ciliophora, Scuticociliatia) from a solar saltern. Eur J Protistol., 50(2):174-84.

Stock, A., Edgcomb, V., Orsi, W., Filker, S., Breiner, H.W., Yakimov, M.M. and Stoeck, T. (2013) Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection. BMC Microbiol 13:150.

Foissner, W. and Stoeck, T. (2013) Morphology of Bromeliophrya quadristicha n. spec., an inhabitant of Tank Bromeliads (Bromeliaceae), and phylogeny of the Bromeliophryidae (Ciliophora, Tetrahymenida). J Eukaryot Microbiol., 60(3):223-34.

Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., de Vargas, C., Decelle, J., Del Campo, J., Dolan, J.R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W.H., Lara, E., Le Bescot, N., Logares, R., Mahe, F., Massana, R., Montresor, M., Morard, R., Not, F., Pawlowski, J., Probert, I., Sauvadet, A.L., Siano, R., Stoeck, T., Vaulot, D., Zimmermann, P. and Christen, R. (2013) The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res 41(D1):D597-D604.

Stock, A., Filker, S., Yakimov, M.M. and Stoeck, T. (2013) Polyextremophiles - Microorganisms and macroorganisms living under multiple forms of stress. Seckbach, J., Oren, A. and Stan-Lotter, H. (eds), Springer, pp. 499-515.

Filker, S., Stock, A., Breiner, H.W., Edgcomb, V., Orsi, W., Yakimov, M.M. and Stoeck, T. (2012) Environmental selection of protistan plankton communities in hypersaline anoxic deep-sea basins, Eastern Mediterranean Sea. Microbiologyopen, 2(1):54-63 (doi: 10.1002/mbo3.56).

Pawlowski, J., Audic, S., Adl, S., Bass, D., Belbahri, L., Berney, C., Bowser, S.S., Cepicka, I., Decelle, J., Dunthorn, M., Fiore-Donno, A.M., Gile, G.H., Holzmann, M., Jahn, R., Jirku, M., Keeling, P.J., Kostka, M., Kudryavtsev, A., Lara, E., Lukes, J., Mann, D.G., Mitchell, E.A., Nitsche, F., Romeralo, M., Saunders, G.W., Simpson, A.G., Smirnov, A.V., Spouge, J.L., Stern, R.F., Stoeck, T., Zimmermann, J., Schindel, D. and de Vargas, C. (2012) CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol 10(11):e1001419.

Kreutz, M., Stoeck, T. and Foissner, W. (2012) Morphological and molecular characterization of Paramecium (Viridoparamecium nov. subgen.) chlorelligerum Kahl (Ciliophora). J Eukaryot Microbiol 59(6):548-563.

Dunthorn, M., Katz, L.A., Stoeck, T. and Foissner, W. (2012a) Congruence and indifference between two molecular markers for understanding oral evolution in the Marynidae sensu lato (Ciliophora, Colpodea). Eur J Protistol 48(4):297-304.

Dunthorn, M., Klier, J., Bunge, J. and Stoeck, T. (2012b) Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity. J Eukaryot Microbiol 59(2):185-187.

Jebaraj, C.S., Forster, D., Kauff, F. and Stoeck, T. (2012) Molecular Diversity of Fungi from Marine Oxygen-Deficient Environments (ODEs). Prog Mol Subcell Biol 53:189-208.

Engel, M., Behnke, A., Bauerfeld, S., Bauer, C., Buschbaum, C., Volkenborn, N. and Stoeck, T. (2012a) Sample pooling obscures diversity patterns in intertidal ciliate community composition and structure. FEMS Microbiol Ecol 79(3):741-750.

Stock, A., Breiner, H.W., Pachiadaki, M., Edgcomb, V., Filker, S., La Cono, V., Yakimov, M.M. and Stoeck, T. (2012) Microbial eukaryote life in the new hypersaline deep-sea basin Thetis. Extremophiles 16(1):21-34.

Engel, M., Behnke, A., Klier, J., Buschbaum, C., Volkenborn, N. and Stoeck, T. (2012b) Effects of the bioturbating lugworm Arenicola marina on the structure of benthic protistan communities. Mar Ecol Prog Ser 471:87-99.

Lipps, J.H., Dunthorn, M. and Stoeck, T. (2012) Biology and ecology of tintinnid ciliates: models for marine plankton. Dolan, J., Montagnes, D., Agatha, S., Coats, W. and Stoecker, D. (eds), pp. 186-197, Blackwell-Wiley.

Dunthorn, M., Stoeck, T., Wolf, K., Breiner, H.W. and Foissner, W. (2012c) Diversity and endemism of ciliates inhabiting Neotropical phytotelmata. . Syst Biodiv 10:195-205.

Forster, D., Behnke, A. and Stoeck, T. (2012) Meta-analyses of environmental sequence data identify anoxia and salinity as parameters shaping ciliate communities. Syst Biodiv 10:277-288.

Stoeck, T. and Behnke, A. (2012) Anoxia: Paleontological Strategies and Evidence for Eukaryote Survival. . Altenbach, A., Bernhard, J. and Seckbach, J. (eds), Springer.

Edgcomb, V. and Stoeck, T. (2012) Massively parallel tag sequencing unveils the complexity of marine protistan communities in oxygen-depleted habitats. , Wiley-VCH.

Nebel, M.E., Wild, S., Holzhauser, M., Huttenberger, L., Reitzig, R., Sperber, M. and Stoeck, T. (2011a) JAGUC--a software package for environmental diversity analyses. J Bioinform Comput Biol 9(6):749-773.

Foissner, W., Stoeck, T., Agatha, S. and Dunthorn, M. (2011a) Intraclass evolution and classification of the Colpodea (Ciliophora). J Eukaryot Microbiol 58(5):397-415.

Foissner, W., Wolf, K.W., Yashchenko, V. and Stoeck, T. (2011b) Description of Leptopharynx bromelicola n. sp. and characterization of the genus Leptopharynx Mermod, 1914 (Protista, Ciliophora). J Eukaryot Microbiol 58(2):134-151.

Behnke, A., Engel, M., Christen, R., Nebel, M., Klein, R.R. and Stoeck, T. (2011) Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environ Microbiol 13(2):340-349.

Foissner, W. and Stoeck, T. (2011) Cotterillia bromelicola nov. gen., nov. spec., a gonostomatid ciliate (Ciliophora, Hypotricha) from tank bromeliads (Bromeliaceae) with de novo originating dorsal kineties. Eur J Protistol 47(1):29-50.

Jebaraj, C.S., Kauff, F., Forster, D. and Stoeck, T. (2011) Biology of Marine Fungi – revisited. . Whalley, A. and Sarma, V.V.R. (eds), pp. 189-208, Springer.

Dolan, J. and Stoeck, T. (2011) Repeated sampling reveals differential variability in measures of species richness and community composition in planktonic protists Environ Microbiol Reports 3:661-666.

Nebel, M., Pfabel, C., Dunthorn, M. and Stoeck, T. (2011b) Delimiting operational taxonomic units for assessing ciliate environmental diversity using SSU rRNA gene sequences. Environ Microbiol Reports 3:145-158.

Foissner, W., Blake, N., Wolf, K., Breiner, H.W. and Stoeck, T. (2010) Morphological and Molecular Characterization of Some Peritrichs (Ciliophora: Peritrichida) from Tank Bromeliads, Including Two New Genera: Orborhabdostyla and Vorticellides. Acta Protozool 48(4):291-319.

Yi, Z., Dunthorn, M., Song, W. and Stoeck, T. (2010) Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea). Mol Phylogenet Evol 57(2):937-941.

Stoeck, T., Bass, D., Nebel, M., Christen, R., Jones, M.D., Breiner, H.W. and Richards, T.A. (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol 19 Suppl 1:21-31.

Behnke, A., Barger, K.J., Bunge, J. and Stoeck, T. (2010a) Spatio-temporal variations in protistan communities along an O/HS gradient in the anoxic Framvaren Fjord (Norway). FEMS Microbiol Ecol 72(1):89-102.

Jebaraj, C.S., Raghukumar, C., Behnke, A. and Stoeck, T. (2010) Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation. FEMS Microbiol Ecol 71(3):399-412.

Stoeck, T. and Stock, A. (2010) The protistan gap in the eukaryotic tree of life. . Palaeodiversity 3:151-154.

Dunthorn, M., Lipps, J.H. and Stoeck, T. (2010) Reassessment of the putative ciliate fossils Eotintinnopsis, Wujiangella, and Yonyangella from the Neoproterozoic Doushantuo Formation in China. Acta Protozool 49:139-144.

Stoeck, T. and Edgcomb, V. (2010) Handbook of Hydrocarbon and Lipid Microbiology. Timmis, K.N., McGenity, T., van der Meer, J.R. and de Lorenzo, V. (eds), pp. 2423-2434, Springer.

Behnke, A., Engel, M., Edgcomb, V. and Stoeck, T. (2010b) Handbook of Hydrocarbon and Lipid Microbiology. . Timmis, K.N., McGenity, T., van der Meer, J.R. and de Lorenzo, V. (eds), pp. 3884-3904.

Stoeck, T., Behnke, A., Christen, R., Amaral-Zettler, L., Rodriguez-Mora, M.J., Chistoserdov, A., Orsi, W. and Edgcomb, V.P. (2009) Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biol 7:72.

Foissner, W. and Stoeck, T. (2009) 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. J Eukaryot Microbiol 56(5):472-483.

Gong, J., Stoeck, T., Yi, Z., Miao, M., Zhang, Q., Roberts, D.M., Warren, A. and Song, W. (2009) Small subunit rRNA phylogenies show that the class nassophorea is not monophyletic (Phylum Ciliophora). J Eukaryot Microbiol 56(4):339-347.

Miao, M., Shao, C., Jiang, J., Li, L., Stoeck, T. and Song, W. (2009) 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. Int J Syst Evol Microbiol 59(Pt 2):430-438.

Dunthorn, M., Eppinger, M., Schwarz, M.V., Schweikert, M., Boenigk, J., Katz, L.A. and Stoeck, T. (2009) Phylogenetic placement of the Cyrtolophosididae Stokes, 1888 (Ciliophora; Colpodea) and neotypification of Aristerostoma marinum Kahl, 1931. Int J Syst Evol Microbiol 59(Pt 1), 167-180.

Edgcomb, V., Orsi, W., Leslin, C., Epstein, S.S., Bunge, J., Jeon, S., Yakimov, M.M., Behnke, A. and Stoeck, T. (2009) Protistan community patterns within the brine and halocline of deep hypersaline anoxic basins in the eastern Mediterranean Sea. Extremophiles 13(1), 151-167.

Alexander, E., Stock, A., Breiner, H.W., Behnke, A., Bunge, J., Yakimov, M.M. and Stoeck, T. (2009) Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin. Environ Microbiol 11(2), 360-381.

Stock, A., Bunge, J., Jürgens, K. and Stoeck, T. (2009) Protistan diversity in the suboxic and anoxic waters of the Gotland Deep (Baltic Sea) as revealed by 18S rRNA clone libraries. Aquat Microb Ecol 55, 267-284.

Zhenzhen, Y., Song, W., Stoeck, T., Al-Rasheid, K., Al-Khedairy, A., Gong, J., Ma, H. and Chen, Z. (2009) Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information. Zoological J Linnean Society, UK 157, 227-236.

Jeon, S., Bunge, J., Leslin, C., Stoeck, T., Hong, S. and Epstein, S.S. (2008) Environmental rRNA inventories miss over half of protistan diversity. BMC Microbiol 8, 222.

Foissner, W. and Stoeck, T. (2008) Morphology, Ontogenesis and Molecular Phylogeny of Neokeronopsis (Afrokeronopsis) aurea nov. subgen., nov. spec. (Ciliophora: Hypotricha), a New African Flagship Ciliate Confirms the CEUU Hypothesis. Acta Protozool 47(1), 1-33.

Stoeck, T., Jost, S. and Boenigk, J. (2008) Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions. Int J Syst Evol Microbiol 58(Pt 3), 716-724.

Breiner, H.W., Foissner, W. and Stoeck, T. (2008) The search finds an end: colpodidiids belong to the Class Nassophorea (ciliophora). J Eukaryot Microbiol 55(2), 100-102.

Stoeck, T., Foissner, W. and Lynn, D.H. (2007a) Small-subunit rRNA Phylogenies Suggest That Epalxella antiquorum (penard, 1922) corliss, 1960 (ciliophora, odontostomatida) is a member of the plagyopylea. J Eukaryot Microbiol 54(5), 436-442.

Stoeck, T., Kasper, J., Bunge, J., Leslin, C., Ilyin, V. and Epstein, S. (2007b) Protistan diversity in the Arctic: a case of paleoclimate shaping modern biodiversity? PLoS One 2(8), e728.

Schwarz, M.V.J., Zuendorf, A. and Stoeck, T. (2007) Morphology, ultrastructure, molecular phylogeny, and autecology of Euplotes elegans Kahl, 1932 (Hypotrichida; Euplotidae) isolated from the anoxic Mariager Fjord, Denmark. J Eukaryot Microbiol 54(2), 125-136.

Stoeck, T., Bruemmer, F. and Foissner, W. (2007c) Evidence for local ciliate endemism in an alpine anoxic lake. Microb Ecol 54(3), 478-486.

Boenigk, J., Jost, S., Stoeck, T. and Garstecki, T. (2007) Differential thermal adaptation of clonal strains of a protist morphospecies originating from different climatic zones. Environ Microbiol 9(3), 593-602.

Kolodziej, K. and Stoeck, T. (2007) 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. Appl Environ Microbiol 73(8), 2718-2726.

Stoeck, T., Zuendorf, A., Breiner, H.W. and Behnke, A. (2007d) A molecular approach to identify active microbes in environmental eukaryote clone libraries. Microb Ecol 53(2), 328-339.

Schwarz, M.V. and Stoeck, T. (2007) Euplotes pseudoelegans n. sp. (Hypotrichida; Euplotidae): description of a new species previously misidentified as Euplotes elegans Kahl, 1932. Acta Protozool 46, 193-200.

Zuendorf, A., Bunge, J., Behnke, A., Barger, K.J. and Stoeck, T. (2006) Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord, Denmark. FEMS Microbiol Ecol 58(3), 476-491.

Foissner, W. and Stoeck, T. (2006) 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). Eur J Protistol 42(4), 249-267.

Jeon, S.O., Bunge, J., Stoeck, T., Barger, K.J., Hong, S.H. and Epstein, S.S. (2006) Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column. Appl Environ Microbiol 72(10), 6578-6583.

Behnke, A., Bunge, J., Barger, K., Breiner, H.W., Alla, V. and Stoeck, T. (2006) Microeukaryote community patterns along an O2/H2S gradient in a supersulfidic anoxic fjord (Framvaren, Norway). Appl Environ Microbiol 72(5), 3626-3636.

Stoeck, T., Hayward, B., Taylor, G.T., Varela, R. and Epstein, S.S. (2006) A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157(1), 31-43.

Stoeck, T., Schwarz, M.V., Boenigk, J., Schweikert, M., von der Heyden, S. and Behnke, A. (2005) 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. Int J Syst Evol Microbiol 55(Pt 6), 2623-2635.

Stoeck, T. and Kröncke, I. (2004) Relationship between structural and functional aspects of microbial and macrofaunal communities in different areas of the North Sea. Mar Ecol Prog Ser 282, 13-31.

Stoeck, T., Fowle, W.H. and Epstein, S.S. (2003a) Methodology of protistan discovery: from rRNA detection to quality scanning electron microscope images. Appl Environ Microbiol 69(11), 6856-6863.

Stoeck, T., Taylor, G.T. and Epstein, S.S. (2003b) Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea). Appl Environ Microbiol 69(9), 5656-5663.

Stoeck, T. and Epstein, S. (2003) Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl Environ Microbiol 69(5), 2657-2663.

Stoeck, T., Kröncke, I. and Garland, J. (2003c) Functional profiles of microbial communities in southern and central North Sea sediments in relation to organic carbon input. . Senckenbergiana Maritima 32, 11-23.

Stoeck, T., Kröncke, I., Duineveld, G.C.D. and Palojärvi, A. (2002) Phospholipid fatty acid profiles at depositional and non-depositional sites in the North Sea. . Mar Ecol Prog Ser 242, 57-70.

Stoeck, T. and Kröncke, I. (2001) Influence of particle mixing on down-core profiles of bacterial biomass in sediments of the German Bight, Oyster Ground and Dogger Bank (North Sea). . Est Coast Shelf Sci 52, 783-795.

Foissner, W., Stoeck, T., Schmidt, H.J. and Berger, H. (2001) Biogeographical differences in a common soil ciliate Gonostomum affine (Stein), as revealed by morphological and RAPD-fingerprint analyses. . Acta Protozool 40, 83-97.

Stoeck, T., Duineveld, G.C.D., Kok, A. and Albers, B.P. (2000a) Nucleic acids and ATP to asses microbial biomass and activity in a marine biosedimentary system. . Mar Biol 137, 1111-1123.

Stoeck, T. and Albers, B.P. (2000) Microbial biomass and activity in vicinity of a mussel bed built up by Mytilus edulis. . Helgol Mar Res 54, 39-46.

Stoeck, T., Welter, H., Seitz-Bender, D., Kusch, J. and Schmidt, H.J. (2000b) ARDRA and RAPD-fingerprinting reject the sibling species concept for the ciliate Paramecium caudatum. . Zool Scripta 29, 75-82.

Stoeck, T., Przybos, E., Kusch, J. and Schmidt, H.J. (2000c) Intra-species differentiation and level of inbreeding of different sibling species of the Paramecium aurelia complex. . Acta Protozool 39, 15-22.

Fokin, S., Stoeck, T. and Schmidt, H.J. (1999a) Rediscovery of Paramecium nephridiatum Gelei, 1925, and its characteristics. . J Eukaryot Microbiol 46, 416-426.

Fokin, S., Stoeck, T. and Schmidt, H.J. (1999b) Paramecium duboscqui Chatton, Brachon 1933-Distribution, ecology and taxonomy. . Eur J Protistol 35, 161-167.

Przybos, E., Fokin, S., Stoeck, T. and Schmidt, H.J. (1999) Occurrence and ecology of Paramecium jenningsi strains. Folia Biologica 47, 53-59.

Stoeck, T. and Albers, B.P. (1999) Microbial biomass and activity in marine sediments with TOC gradient. Senckenbergiana Maritima 29, 145-147.

Poremba, K., Dürselen, C.-D. and Stoeck, T. (1999) Successions of bacterial abundance, activity and survival strategy during the ice-winter of 1996 in parts of the German Wadden Sea and adjacent waters. J Sea Reas 42, 1-10.

Stoeck, T. and Schmidt, H.J. (1998) Fast and Accurate Identification of European Species of the Paramecium aurelia Complex by RAPD-Fingerprints. Microb Ecol 35(3), 311-317.

Stoeck, T., Przybos, E. and Schmidt, H.J. (1998a) A combination of genetics with inter- and intra-strain crosses and RAPD-fingerprints reveal different population structures within the Paramecium aurelia species complex. . Eur J Protistol 34, 348-355.

Stoeck, T., Duineveld, G.C.D., Kok, A. and Albers, B.P. (1998b). VAAM (ed), pp. 47-56, Oldenbourg, München, Wien.

Albers, B.P. and Stoeck, T. (1998). VAAM (ed), pp. 35-44, Oldenbourg, München, Wien.