Fachgebiet Ecology



153. Chen L, Ren Y, Han K, Stoeck T, Jiang J & Pan H.  Re-description and molecular phylogeny of the free-swimming peritrichs Hastatella radians Erlanger, 1890 and H. aesculacantha Jarocki & Jakubowska, 1927 (Ciliophora, Peritrichia) from China. European Journal of Protistology 84: 125891, doi: 10.1016/j.ejop.2022.125891

152. Lian C, Wang Y, Jiang J, Yuan Q, Al-Farraj SA, El-Serehy HA, Song W, Stoeck T & Shao C.  Euplotes huizhouensis nom. nov. (Ciliophora, Euplotida), a replacement name for the junior primary homonym Euplotes tuffraui Lin et al., 2021. European Journal of Protistology 83: 125867, doi: 10.1016/j.ejop.2022.125867

151. Frantal D, Agatha S, Beisser D, Boenigk J, Darienko T, Dirren-Pitsch G, Filker S, Gruber M, Kammerlander B, Nachbaur L, Scheffel U, Stoeck T, Qian K, Pröschold T, Weissenbacher B & Sonntag B. Molecular data reveal a cryptic diversity in the genus Urotricha (Alveolata, Ciliophora, Prostomatida), a key player in freshwater lakes, with remarks on their morphology, food preferences, and distribution. Frontiers in Microbiology (section Aquatic Microbiology) 12: 787290, doi: 10.3389/fmicb.2021.787290


150. Dully V, Rech G, Wilding TA, Lanzén A, MacKichan K, Berrill I & Stoeck T. Comparing sediment preservation methods for genomic biomonitoring of coastal marine ecosystems. Marine Pollution Bulletin 173: 113129, doi: 10.1016/j.marpolbul.2021.113129

149. Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amafitano S, Apothélez-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell´Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontaneli F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Macek I, Sagova-Marecková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A & Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extractions. Science of the Total Environment, doi: 10.1016/j.scitotenv.2021.151783

148. Hanzek N, Udovic MG, Kajan K, Borics G, Várbíró G, Stoeck T, Zutinic P, Orlic S & Stankovic I. Assessing ecological status in karstic lakes through the integration of phytoplankton functional groups, morphological approach and environmental DNA metabarcoding. Ecological Indicators 131: 108166, doi: 10.1016/j.ecolind.2021.108166

147. Zhu C, Liu W, Li X, Xu Y, El-Serehy H, Al-Farraj SA, Ma H, Stoeck T & Yi Z. High salinity gradients and intermediate spatial scales shaped similiar biogeographical and co-occurence patterns of microeukaryotes in a tropical freshwater-saltwater ecosystem. Environmental Microbiology 23: 4778-4796, doi: 10.1111/1462-2920.15668

146. Dully V, Wilding TA, Mühlhaus T & Stoeck T. Identifying the minimum  amplicon sequence depth to adequately predict classes in eDNA-based marine biomonitoring using supervised machine learning. Computational and Structural Biotechnology Journal 19: 2256-2268, doi: 10.1016/j.csbj.2021.04.005

145. Frühe L, Dully V, Forster D, Keeley NB, Laroche O, Pochon X, Robinson SMC, Wilding T & Stoeck T. Global trends of benthic bacterial diversity and community composition along organic enrichment gradients of salmon farms. Frontiers in Microbiology (section Aquatic Microbiology), doi: 10.3389/fmicb.2021.637811

144. Ganser MH, Forster D, Liu W, Lin X, Stoeck T & Agatha S. Genetic diversity in marine planktonic ciliates (Ciliophora, Alveolata) suggests distinct geographical patterns - data from chinese and european coastal waters. Frontiers in Marine Science (section: Marine Evolutionary Biology, Biogeography and Species Diversity), doi:10.3389/fmars.2021.643822

143. Forster D, Qu Z, Pitsch G, Bruni EP, Kammerlander B, Pröschold T, Sonntag B, Posch T & Stoeck T. Lake ecosystem robustness and resilience inferred from a climate-stressed protistan plankton network. Microorganisms 9: 549, doi: 10.3390/microorganisms9030549

142. Qu Z, Pan H, Wang C, Ma H, Stoeck T & Hu X. Gastronautidae Deroux, 1994 and Trithigmostoma Jankowski, 1967: evolutionary links among cyrtophorian ciliates (Protista, Ciliophora, Phyllopharyngea). Frontiers in Marine Science (Marine Evolutionary Biology, Biogeography and Species Diversity), doi: 10.3389/fmars.2021.625644

141. Kulas A, Gulin V, Kepcija RM, Zutinic P, Peric MS, Orlic S, Kajan K, Stoeck T, Lentendu G, Canjevac I, Martinic I & Udovic MG. Ciliates (Alveolata, Ciliophora) as biodindicators of environmental pressure: a karstic river case. Ecological Indicators 124: 107430, doi: 10.1016/j.ecolind.2021.107430

140. Lian C, Wang Y, Jiang J, Yuan Q, Al-Farraj SA, El-Serehy HA, Song W, Stoeck T & Shao C. Systematic positions and taxonomy of two new ciliates found in China: Euplotes tuffrai sp. nov. and E. shii sp. nov. (Alveolata, Ciliophora, Euplotida). Systematics and Biodiversity, doi: 10.1080/14772000.2020.1865472

139. Zhu R, Qu Z, Zhang Q, Filker S, Stoeck T, Li F & Hu X. A new record of Oxytricha granulifera granulifera Foissner & Adam, 1983 (Protozoa, Ciliophora, Oxytrichidae) from a hot spring in Iceland, with notes on its abnormal form during cultivation. Frontiers in Marine Science, doi:10.3389/fmars.2021.621349

138. Pröschold T, Rieser D, Darienko T, Nachbaur L, Kammerlander B, Qian K, Pitsch G, Bruni EP, Qu Z, Forster D, Rad-Menendez C, Posch T, Stoeck T & Sonntag B. An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea). Scientific Reports, accepted

137. Mareckova M, Boenigk J, Bouchez A, Cermakova K, Chonova T, Cordier T, Eisendle U, Elersek T, Fazi S, Fleituch T, Frühe L, Gajdosova M, Graupner N, Haegerbaeumer A, Kelly AM, Kopecky J, Leese F, Noges P, Orlic S, Panksep K, Pawlowski J, Petrusek A, Piggott J, Rusch J, Salis R, Schenk J, Simek K, Stovicek A, Strand D, Vasquez M, Vralstad T, Zlatkovic S, Zupancic M & Stoeck T. Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. Water Research 191: 116767, doi: 10.1016/j.watres.2020.116767

136. Qu Z, Forster D, Bruni E, Frantal D, Kammerlander B, Nachbauer L, Pitsch G, Posch T, Pröschold T, Teubner K, Sonntag B & Stoeck T. Aquatic food webs in deep temperate lakes: key species establish through their autecological versatility. Molecular Ecology, doi: 10.1111/mec.15776

135. Dong J, Fan X, Zhang T, Al-Farraj SA, Stoeck T, Ma H & Li L. Ultrastructural features of an abundant and ubiquitous marine ciliate, Uronychia binucleata (Protista, Ciliophora, Euplotida). Frontiers in Marine Science (Marine Evolutionary Biology, Biogeography and Species Diversity), doi: 10.3389/fmars.2020.604487

134. Dully V, Balliet H, Frühe L, Däumer M, Thielen A, Gallie S, Berril I & Stoeck T. Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture - An inter-laboratory study. Ecological Indicators, doi: 10.1016/j.ecolind.2020.107049

133. Cordier T, Alonso-Sáez L, Apothéloz-Perret-Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer A, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J & Lanzén A. Ecosystem monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap. Molecular Ecology, doi: 10.1111/mec.15472

132. Frühe L, Cordier T, Dully V, Breiner HW, Lentendu G, Pawlowski J, Martins C, Wilding TA & Stoeck T. Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes. Molecular Ecology, doi: 10.1111/mec15434

131. Forster D, Lentendu G, Filker S, Dubois E, Wilding T & Stoeck T. Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants. Environmental Microbiology 21: 4109-4124, doi: 10.1111/1462-2920.14764

130. Li X, Huang J, Filker S, Stoeck T, Bi Y, Yu Y & Song W. 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. Science China Life Science 62, doi: 10.1007/s11427-018-9523-0

129. Zayed A, Kovacheva M, Muffler K, Breiner HW, Stoeck T & Ulmer R. 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

128. Pitsch G , Bruni EP, Forster D, Qu Z, Sonntag B, Stoeck T & Posch T. Seasonality of planktonic freshwater ciliates: Are analyses based on V9 regions of the 18S rRNA gene correlated with morphospecies counts? Frontiers in Microbiology 10: 248

127. Li F, Qu Z, Luo D, Filker S, Hu X & Stoeck T. 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

126. Filker S, Kühner S, Heckwolf M, Dierking J & Stoeck T. 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 21: 603-617, doi: 10.1111/1462-2920.14502

125. Piredda R, Claverie JM, Decelle J, de Vargas C, Dunthorn M, Edvardsen B, Eikrem W, Forster D, Kooistra WHCF, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Romac S, Sarno D, Stoeck T & Zingone A. Diatom diversity through HTS-metabarcoding in coastal European seas. Scientific Reports 8, 18059

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

123. Forster D, Filker S, Kochems R, Breiner HW, Cordier T, Pawlowski J & Stoeck T. A comparison of different ciliate meta barcode genes as bioindicators for environmental impact assessments of salmon aquaculture. Journal of Eukaryotic Microbiology, doi: 10.1111/jeu.12670

122. Stoeck T, Pan H, Dully V, Forster D & Jung T. Towards an eDNA metabarcode-based performance indicator for full-scale municipal wastewater treatment plants. Water Research 144: 322-331

121. Cordier T, Forster D, Dufresne Y, Martins C, Stoeck T & Pawlowski J. Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring. Molecular Ecology Resources 18: 1381-1391

120. 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 66: 167-181

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

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

117. Qu Z, Groben R, Marteinsson V, Agatha S & Stoeck T. 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: 96-106

116. Qu Z, Li L, Lin X, Stoeck T, Pan H, Al-Rasheid KAS & Song W. Diversity of the cyrtophorid genus Chlamydodon (Protista, Ciliophora): its systematics and geographic distribution, with taxonomic descriptions of three species. Systematics and Biodiversity 16:497-511

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

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

113. Zhao F, Filker S, Stoeck T & Xu K. 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

112. Pan H & Stoeck T. 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

111. Qu Z, Pan H, Lin X, Li L, Aleidan AMA, Al-Farraj SA, Stoeck T & Hu X. A contribution to the morphology and phylogeny of Chlamydodon, with three new species from China (Ciliophora, Cyrtophoria). Journal of Eukaryotic Microbiology 65: 236-249

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

109. Warren A, Patterson DJ, Dunthorn M, Clamp JC, Achilles-Day UEM, Aescht E, Al-Farraj SA., Al-Quraishy S, Al-Rasheid K, Carr M, Day JG, Dellinger M, El-Serehy HA., Fan Y, Gao F, Gao S, Gong J, Gupta R, Hu X, Kamra K, Langlois G, Lin X, Lipscomb D, Lobban CS, Luporini P, Lynn DH, Ma H, Macek M, Nikolaeva S, Ong´ondo GO, PérezUz 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. Beyond the "Code": A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora). Journal of Eukaryotic Microbiology 64: 539-554

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

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

106. Pan H, Wang L, Jiang J & Stoeck T. Morphology of four cyrtophorian ciliates (Protozoa, Ciliophora) from Yangtze Delta, China, with notes on the phylogeny of the genus Phascolodon. European Journal of Protistology 56: 134-146

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

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

103. Forster D, Dunthorn M, Stoeck T & Mahé F. Comparison of three clustering approaches for detecting novel environmental microbial diversity. PeerJ 4: e1692

102. Spitz A, Gimmler A, Stoeck T, Zweig KA & Horvat EA. Assessing Low-Intensity Relationships in Complex Networks. PLoS ONE 11(4):e0152536

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

100. Fotedar R, Stoeck T, Filker S, Agatha S, Fell J, Al Marri M & Jiang J. 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 63: 578-590

99. Pachiadaki MG, Taylor C, Oikonomou A, Yakimov MM, Stoeck T & Edgcomb V. In situ grazing experiments apply new technology to gain insights into deep-sea microbial food webs. Deep-Sea Research Part II: Topical Studies in Oceanography 129: 223-231

98. Dunthorn M, Lipps JH, Dolan JR, Abboud-Abi Saab M, Hecht E, Bachy C, Barria de Cal MS, Berger H, Bourland WA, Choi JK, Clamp J, Doherty M, Gao F, Gentekaki E, Gong J, Hu X, Huang J, Kamiyama T, Johnson MD, Kammerlander B, Kim SY, Kim YO, la Terza A, … & Agatha S. Ciliates - Protists with complex morphologies and ambiguous early fossil record. Marine Micropaleontology 119: 1-6

97. Oikonomou A, Filker S, Breiner HW & Stoeck T. Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany). Environmental Microbiology 17: 2144-2157

96. Massana R, Gobet A, Audic S, Bass D, Bittner L, Boutte C, Chambouvet A, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Forn I, Forster D, Guillou L, Jaillon O, Kooistra WH, Logares R, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Probert I, Romac S, Richards T, Santini S, Shalchian-Tabrizi K, Siano R, Simo N, Stoeck T, Vaulot D, Zingone A & de Vargas C. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environmental Microbiology 10: 4035-4049

95. Mahé F, Mayor J, Bunge J, Chi J, Siemensmeyer T, Stoeck T, Wahl B, Paprotka T, Filker S & Dunthorn M. Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys. Journal of Eukaryotic Microbiology 62: 338-345

94. Kammerlander B, Breiner HW, Filker S, Sommaruga R, Sonntag B & Stoeck T. High diversity of protistan plankton communities in remote high mountain lakes in the European Alps and the Himalayan mountains. FEMS Microbiology Ecology, doi: 10.1093/femsec/fiv010

93. Gimmler A & Stoeck T. Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization. Environmental Microbiology Reports 7: 679-686

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

91. Filker S, Gimmler A, Dunthorn M, Mahé F & Stoeck T. Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds. Extremophiles 19: 283-295

90. Oikonomou A, Pachiadaki M & Stoeck, T. Protistan grazing in a meromictic freshwater lake with anoxic bottom water. FEMS Microbiology Ecology 87: 691-703

89. Stoeck T, Filker S, Edgcomb V, Orsi W, Yakimov MM, Pachiadaki M, Breiner HW, LaCono V & Stock A. Living at the limits: Evidence for microbial eukaryotes thriving under pressure in deep anoxic, hypersaline habitats. Advances in Ecology, Volume 2014, Article ID 532687

88. Filker S, Kaiser M, Rossello-Mora R, Dunthorn M, Lax G & Stoeck T. "Candidatus Haloectosymbiotes riaformosensis" (Halobacteriaceae), an archaeal ectosymbiont of the hypersaline ciliate Platynematum salinarum. Systematics and Applied Microbiology 37: 244-251

87. Logares R, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Gobet A, Kooistra WH, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Stoeck T, Santini S, Siano R, Winker P, Zingone A, Richards TA, de Vargas C & Massana R. Patterns of Rare and Abundant Marine Microbial Eukaryotes. Current Biology 24: 813-821

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

85. Dunthorn M, Stoeck T, Clamp J, Warren A & Mahé F. Ciliates and the Rare Biosphere: a Review. Journal of Eukaryotic Microbiology 61: 404–409

84. Zhan Z, Stoeck T, Dunthorn M & Xu K. Identification of the pathogenic ciliate Pseudocohnilembus persalinus (Oligohymenophorea: Scuticociliatia) by fluorescence in situ hybridization. European Journal of Protistology 50: 16-24

83. Stoeck T, Breiner HW, Filker S, Ostermaier V, Kammerlander B & Sonntag B. A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology. Environmental Microbiology 16: 430-444

82. Stief P, Fuchs-Ocklenburg S, Kamp A, Manohar CS, Houbraken J, Boekhout T, de Beer D & Stoeck T. Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea. BMC Microbiology 14: 35

81. Manohar CS, Boekhout T, Muller WH & Stoeck T. Tritirachium candoliense sp. nov., a novel basidiomycetous fungus isolated from the anoxic zone of the Arabian Sea. Fungal Biology 118: 139-149

80. Heber D, Stoeck T & Foissner W. Morphology and Ontogenesis of Psilotrichides hawaiiensis nov. gen., nov. spec. and Molecular Phylogeny of the Psilotrichidae (Ciliophora, Hypotrichia). Journal of Eukaryotic Microbiology 61: 260-277

79. Foissner W, Filker S & Stoeck T. Schmidingerothrix salinarum nov. spec. is the Molecular Sister of the Large Oxytrichid Clade (Ciliophora, Hypotricha). Journal of Eukaryotic Microbiology 61: 61-74

78. Foissner W, Bourland WA, Wolf KW, Stoeck T & Dunthorn M. New SSU-rDNA sequences for eleven colpodeans (Ciliophora, Colpodea) and description of Apocyrtolophosis nov. gen. European Journal of Protistology 50: 40-46

77. Dunthorn M, Otto J, Berger SA, Stamatakis A, Mahé F, Romac S, de Vargas C, Audic S, BioMarKs Consortium, Stock A, Kauff F & Stoeck T. Placing environmental next generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. Molecular Biology and Evolution 31: 993-1009

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

75. Stoeck T, Przybos E & Dunthorn M. The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates. Molecular Ecology Resources 14: 458-468

74. Foissner W, Jung JH, Filker S, Rudolph J & Stoeck T. Morphology, ontogenesis and molecular phylogeny of Platynematum salinarum nov. spec., a new scuticociliate (Ciliophora, Scuticociliatia) from a solar saltern. European Journal of Protistology 50: 174-84

73. Stock A, Edgcomb V, Orsi W, Filker S, Breiner HW, Yakimov MM & Stoeck T. Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection. BMC Microbiology 13: 150

72. Foissner W & Stoeck T. Morphology of Bromeliophrya quadristicha n. spec., an inhabitant of Tank Bromeliads (Bromeliaceae), and phylogeny of the Bromeliophryidae (Ciliophora, Tetrahymenida). Journal of Eukaryotic Microbiology 60: 223-234

71. 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 JR, Dunthorn M, Edvardsen B, Holzmann M, Kooistra WH, Lara E, Le Bescot N, Logares R, Mahe F, Massana R, Montresor M, Morard R, Not F, Pawlowski J, Probert I, Sauvadet AL, Siano R, Stoeck T, Vaulot D, Zimmermann P & Christen R. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Research 41: D597-D604

70. Filker S, Stock A, Breiner HW, Edgcomb V, Orsi W, Yakimov MM & Stoeck T. Environmental selection of protistan plankton communities in hypersaline anoxic deep-sea basins, Eastern Mediterranean Sea. Microbiologyopen, 2: 54-63

69. Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, Bowser SS, Cepicka I, Decelle J, Dunthorn M, Fiore-Donno AM, Gile GH, Holzmann M, Jahn R, Jirku M, Keeling PJ, Kostka M, Kudryavtsev A, Lara E, Lukes J, Mann DG, Mitchell EA, Nitsche F, Romeralo M, Saunders GW, Simpson AG, Smirnov AV, Spouge JL, Stern RF, Stoeck T, Zimmermann J, Schindel D & de Vargas C. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biology 10: e1001419

68. Kreutz M, Stoeck T & Foissner W. Morphological and molecular characterization of Paramecium (Viridoparamecium nov. subgen.) chlorelligerum Kahl (Ciliophora). Journal of Eukaryotic Microbiology 59: 548-563

67. Dunthorn M, Katz LA, Stoeck T & Foissner W. Congruence and indifference between two molecular markers for understanding oral evolution in the Marynidae sensu lato (Ciliophora, Colpodea). European Journal of Protistology 48: 297-304

66. Dunthorn M, Klier J, Bunge J & Stoeck T. Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity. Journal of Eukaryotic Microbiology 59: 185-187

65. Engel M, Behnke A, Bauerfeld S, Bauer C, Buschbaum C, Volkenborn N & Stoeck T. Sample pooling obscures diversity patterns in intertidal ciliate community composition and structure. FEMS Microbiology Ecology 79: 741-750

64. Stock A, Breiner HW, Pachiadaki M, Edgcomb V, Filker S, La Cono V, Yakimov MM & Stoeck T. Microbial eukaryote life in the new hypersaline deep-sea basin Thetis. Extremophiles 16: 21-34

63. Engel M, Behnke A, Klier J, Buschbaum C, Volkenborn N & Stoeck. Effects of the bioturbating lugworm Arenicola marina on the structure of benthic protistan communities. Marine Ecology Progress Series 471: 87-99

62. Dunthorn M, Stoeck T, Wolf K, Breiner HW & Foissner W. Diversity and endemism of ciliates inhabiting Neotropical phytotelmata. Systematics and Biodiversity 10: 195-205

61. Forster D, Behnke A & Stoeck T. Meta-analyses of environmental sequence data identify anoxia and salinity as parameters shaping ciliate communities. Systematics and Biodiversity 10: 277-288

60. Nebel ME, Wild S, Holzhauser M, Huttenberger L, Reitzig R, Sperber M & Stoeck T. JAGUC--a software package for environmental diversity analyses. Journal of Bioinformatics and Computational Biology 9: 749-773

59. Foissner W, Stoeck T, Agatha S & Dunthorn M. Intraclass evolution and classification of the Colpodea (Ciliophora). Journal of Eukaryotic Microbiology 58: 397-415

58. Foissner W, Wolf KW, Yashchenko V & Stoeck T. Description of Leptopharynx bromelicola n. sp. and characterization of the genus Leptopharynx Mermod, 1914 (Protista, Ciliophora). Journal of Eukaryotic Microbiology 58:134-151

57. Behnke A, Engel M, Christen R, Nebel M, Klein RR & Stoeck T. Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environmental Microbiology 13: 340-349

56. Foissner W & Stoeck T. Cotterillia bromelicola nov. gen., nov. spec., a gonostomatid ciliate (Ciliophora, Hypotricha) from tank bromeliads (Bromeliaceae) with de novo originating dorsal kineties. European Journal of Protistology 47: 29-50

55. Dolan J & Stoeck T. Repeated sampling reveals differential variability in measures of species richness and community composition in planktonic protists. Environmental Microbiology Reports 3: 661-666

54. Nebel M, Pfabel C, Dunthorn M & Stoeck T. Delimiting operational taxonomic units for assessing ciliate environmental diversity using SSU rRNA gene sequences. Environmental Microbiology Reports 3: 145-158

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

52. Yi Z, Dunthorn M, Song W & Stoeck T. Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea). Molecular Phylogenetics and Evolution 5: 937-941

51. Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW & Richards TA. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology 19: 21-31

50. Behnke A, Barger KJ, Bunge J & Stoeck T. Spatio-temporal variations in protistan communities along an O/HS gradient in the anoxic Framvaren Fjord (Norway). FEMS Microbiology Ecology 72: 89-102

49. Jebaraj CS, Raghukumar C, Behnke A & Stoeck T. Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation. FEMS Microbiology Ecology 71: 399-412

48. Stoeck T & Stock A. The protistan gap in the eukaryotic tree of life. Palaeodiversity 3: 151-154

47. Dunthorn M, Lipps JH & Stoeck T. Reassessment of the putative ciliate fossils Eotintinnopsis, Wujiangella, and Yonyangella from the Neoproterozoic Doushantuo Formation in China. Acta Protozoologica 49: 139-144

46. Stoeck T, Behnke A, Christen R, Amaral-Zettler L, Rodriguez-Mora MJ, Chistoserdov A, Orsi W & Edgcomb VP. Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biology 7:72

45. Foissner W & Stoeck T. 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. Journal of Eukaryotic Microbiology 56: 472-483

44. Gong J, Stoeck T, Yi Z, Miao M, Zhang Q, Roberts DM, Warren A & Song W. Small subunit rRNA phylogenies show that the class nassophorea is not monophyletic (Phylum Ciliophora). Journal of Eukaryotic Microbiology 56: 339-347.

43. Miao M, Shao C, Jiang J, Li L, Stoeck T & Song W. 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. International Journal of Systematic and Evolutionary Microbiology 59: 430-438

42. Dunthorn M, Eppinger M, Schwarz MV, Schweikert M, Boenigk J, Katz LA & Stoeck T. Phylogenetic placement of the Cyrtolophosididae Stokes, 1888 (Ciliophora; Colpodea) and neotypification of Aristerostoma marinum Kahl, 1931. International Journal of Systematic and Evolutionary Microbiology 59: 167-180

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

40. Alexander E, Stock A, Breiner HW, Behnke A, Bunge J, Yakimov MM & Stoeck T. Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin. Environmental Microbiology 11: 360-381

39. Stock A, Bunge J, Jürgens K & Stoeck T. Protistan diversity in the suboxic and anoxic waters of the Gotland Deep (Baltic Sea) as revealed by 18S rRNA clone libraries. Aquatic Microbial Ecology 55: 267-284

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

37. Jeon S, Bunge J, Leslin C, Stoeck T, Hong S. & Epstein SS. Environmental rRNA inventories miss over half of protistan diversity. BMC Microbiology 8: 222

36. Foissner W & Stoeck T. 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 Protozoologica 47: 1-33

35. Stoeck T, Jost S & Boenigk J. Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions. International Journal of Systematic and Evolutionary Microbiology 58: 716-724

34. Breiner HW, Foissner W & Stoeck T. The search finds an end: colpodidiids belong to the Class Nassophorea (ciliophora). Journal of Eukaryotic Microbiology 55: 100-102

33. Stoeck T, Foissner W & Lynn DH. Small-subunit rRNA Phylogenies Suggest That Epalxella antiquorum (penard, 1922) corliss, 1960 (ciliophora, odontostomatida) is a member of the plagyopylea. Journal of Eukaryotic Microbiology 54: 436-442

32. Stoeck T, Kasper J, Bunge J, Leslin C, Ilyin V & Epstein SS. Protistan diversity in the Arctic: a case of paleoclimate shaping modern biodiversity? PLoS One 2: e728

31. Schwarz MVJ, Zuendorf A & Stoeck T. Morphology, ultrastructure, molecular phylogeny, and autecology of Euplotes elegans Kahl, 1932 (Hypotrichida; Euplotidae) isolated from the anoxic Mariager Fjord, Denmark. Journal of Eukaryotic Microbiology 54: 125-136

30. Stoeck T, Bruemmer F & Foissner W. Evidence for local ciliate endemism in an alpine anoxic lake. Microbial Ecology 54: 478-486

29. Boenigk J, Jost S, Stoeck T & Garstecki T. Differential thermal adaptation of clonal strains of a protist morphospecies originating from different climatic zones. Environmental Microbiology 9: 593-602

28. Kolodziej K & Stoeck T. 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. Applied and Environmental Microbiology 73: 2718-2726

27. Stoeck T, Zuendorf A, Breiner HW & Behnke A. A molecular approach to identify active microbes in environmental eukaryote clone libraries. Microbial Ecology 53: 328-339

26. Schwarz MV & Stoeck T. Euplotes pseudoelegans n. sp. (Hypotrichida; Euplotidae): description of a new species previously misidentified as Euplotes elegans Kahl, 1932. Acta Protozoologica 46, 193-200.

25. Zuendorf A, Bunge J, Behnke A, Barger KJ & Stoeck T. Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord, Denmark. FEMS Microbiology Ecology 58: 476-491

24. Foissner W & Stoeck T. 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). European Journal of Protistology 42: 249-267

23. Jeon SO, Bunge J, Stoeck T, Barger KJ, Hong SH & Epstein SS. Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column. Applied and Environmental Microbiology 72: 6578-6583

22. Behnke A, Bunge J, Barger K, Breiner HW, Alla V & Stoeck T. Microeukaryote community patterns along an O2/H2S gradient in a supersulfidic anoxic fjord (Framvaren, Norway). Applied and Environmental Microbiology 72: 3626-3636

21. Stoeck T, Hayward B, Taylor GT, Varela R & Epstein SS. A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157: 31-43

20. Stoeck T, Schwarz MV, Boenigk J, Schweikert M, von der Heyden S & Behnke A. 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. International Journal of Systematic and Evolutionary Microbiology 55: 2623-2635

19. Stoeck T & Kröncke I. Relationship between structural and functional aspects of microbial and macrofaunal communities in different areas of the North Sea. Marine Ecology Progress Series 282: 13-31

18. Stoeck T, Fowle WH & Epstein SS. Methodology of protistan discovery: from rRNA detection to quality scanning electron microscope images. Applied and Environmental Microbiology 69: 6856-6863

17. Stoeck T, Taylor GT & Epstein SS. Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea). Applied and Environmental Microbiology 69: 5656-5663

16. Stoeck T & Epstein SS Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Applied and Environmental Microbiology 69: 2657-2663

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

14. Stoeck T, Kröncke I, Duineveld GCD & Palojärvi A. Phospholipid fatty acid profiles at depositional and non-depositional sites in the North Sea. Marine Ecology Progress Series 242: 57-70

13. Stoeck T & Kröncke I. Influence of particle mixing on down-core profiles of bacterial biomass in sediments of the German Bight, Oyster Ground and Dogger Bank (North Sea). Estuarine, Coastal and Shelf Science 52: 783-795

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

11. Stoeck T, Duineveld GCD, Kok A & Albers BP. Nucleic acids and ATP to asses microbial biomass and activity in a marine biosedimentary system. Marine Biology 137: 1111-1123

10. Stoeck T & Albers BP. Microbial biomass and activity in vicinity of a mussel bed built up by Mytilus edulis. Helgololand Marine Research 54: 39-46.

9. Stoeck T, Welter H, Seitz-Bender D, Kusch J & Schmidt HJ. ARDRA and RAPD-fingerprinting reject the sibling species concept for the ciliate Paramecium caudatum. Zoologica Scripta 29: 75-82

8. Stoeck T, Przybos E, Kusch J & Schmidt HJ. Intra-species differentiation and level of inbreeding of different sibling species of the Paramecium aurelia complex. Acta Protozoologica 39: 15-22

7. Fokin S, Stoeck T & Schmidt HJ. Rediscovery of Paramecium nephridiatum Gelei, 1925, and its characteristics. Journal of Eukaryotic Microbiology 46: 416-426

6. Fokin S, Stoeck T & Schmidt HJ. Paramecium duboscqui Chatton, Brachon 1933-Distribution, ecology and taxonomy. European Journal of Protistology 35: 161-167

5. Przybos E, Fokin S, Stoeck T & Schmidt HJ. Occurrence and ecology of Paramecium jenningsi strains. Folia Biologica 47: 53-59

4. Stoeck T & Albers, BP. Microbial biomass and activity in marine sediments with TOC gradient. Senckenbergiana Maritima 29: 145-147

3. Poremba K, Dürselen CD & Stoeck T. Successions of bacterial abundance, activity and survival strategy during the ice-winter of 1996 in parts of the German Wadden Sea and adjacent waters. Journal of Sea Research 42: 1-10

2. Stoeck T & Schmidt HJ. Fast and Accurate Identification of European Species of the Paramecium aurelia Complex by RAPD-Fingerprints. Microbial Ecology 35: 311-317

1. Stoeck T, Przybos E & Schmidt HJ. A combination of genetics with inter- and intra-strain crosses and RAPD-fingerprints reveal different population structures within the Paramecium aurelia species complex. European Journal of Protistology 34: 348-355


9. Stock A, Filker S, Yakimov MM & Stoeck T

Deep Hypersaline Anoxic Basins as Model Systems for Environmental Selection of Microbial Plankton.

In: Polyextremophiles - Microorganisms and macroorganisms living under multiple forms of stress.

Editors: Seckbach J, Oren A & Stan-Lotter H

Springer, pp. 499-515


8. Jebaraj CS, Forster D, Kauff F & Stoeck T

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

In: Biology of Marine Fungi: Progress in Molecular and Subcellular Biology, Vol 53.

Editor: Raghukumar C

Springer, pp. 189-208


7. Lipps JH, Dunthorn M & Stoeck T

Fossil Tintinnids.

In: The Biology and Ecology of Tintinnid Ciliates: Models for Marine Plankton.

Editors: Dolan J, Montagnes D, Agatha S, Coats W & Stoecker D

Blackwell-Wiley, pp. 186-197


6. Stoeck T & Behnke A

The Anoxic Framvaren Fjord as a Model System to Study Protistan Diversity and Evolution.

In: Anoxia: Evidence for Eukaryote Survival and Paleontological Strategies.

Editors: Altenbach A, Bernhard J & Seckbach J

Springer, pp. 421-448

5. Edgcomb V & Stoeck T

Massively parallel tag sequencing unveils the complexity of marine protistan communities in oxygen-depleted habitats.

In: Tag-Based Next Generation Sequencing.

Editors: Harbers M, Kahl G

Wiley-VCH, pp. 171-182


4. Stoeck T & Edgcomb V

Role of protists in microbial interactions with hydrocarbons

In: Handbook of Hydrocarbon and Lipid Microbiology.

Editors: Timmis KN, McGenity T, van der Meer JR & de Lorenzo V

Springer, pp. 2423-2434


3. Behnke A, Engel M, Edgcomb V & Stoeck T

Studying the in situ role of protistan communities in hydrocarbon contaminated water samples via community profiling and CARD-FISH

In: Handbook of Hydrocarbon and Lipid Microbiology.

Editors: Timmis KN, McGenity T, van der Meer JR & de Lorenzo V

Springer, pp. 3884-3904


2. Stoeck T, Duineveld G, Kok A & Albers BP

Extraktion und Quantifizierung von Nukleinsäuren aus Sedimenten.

In: Mikrobiologische Charakterisierung aquatischer Sedimente.

Hrsg: VAAM

Oldenburg Verlag, Münschen, Wien, pp. 47-58


1. Albers BP & Stoeck T

Extraktion und Bestimmung von AMP, ADT und ATP.

In: Mikrobiologische Charakterisierung aquatischer Sedimente.

Hrsg: VAAM

Oldenburg Verlag, Münschen, Wien, pp. 36-46

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