44. Lazrak K, Nothof MTazart, Filker SBerger E, Mouhri K & Loudiki M

Salt Stress Responses of Microalgae Biofilm Communities under Controlled Microcosm Conditions  

Algal Research (accepted)


43. Li L, Zhao F, Filker S, Liu W, Zhao R, Wan Y & Xu K

Microeukaryotes have unexpected importance in cold seep food webs through predation and parasitism

Progress in Oceanography (accepted)


42. Kaczmarek N, Benlasri M, Schäfer RB, Aabid A, Nothof M, Lazrak K, Ghamizi M, Berger E

Macroinvertebrate community responses to salinity around non‑saline–saline confluences in the Draa River basin, Morocco

Hydrobiologia, doi: 10.1007/s10750-023-05445-7



41. Kaczmarek N, Mahjoubi I, Benlasri M, Nothof M, Schäfer RB, Frör O, Berger E

Water quality, biological quality, and human well-being: Water salinity and scarcity in the Draa River basin, Morocco.

Ecological Indicators 148: 11050


40. Leontidou K, Abad-Recio IL, Rubel V, Filker S, Däumer M, Thielen A, Lanzén A & Stoeck T

Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection. 

Environmental Microbiology, doi: 10.1111/1462-2920.16530


39. Rozman U, Filker S & Kalčíková G

Monitoring of biofilm development and physico-chemical changes of floating microplastics at the air-water interface.

Environmental Pollution 322: 121157, doi: 10.1016/j.envpol.2023.121157



38. Spanner C, Sonntag B, Filker S & Pröschold T

Morphological diversity and molecular phylogeny of five Paramecium bursaria (Alveolata, Ciliophora, Oligohymenophora) syngens and the identification of their algal endosymbionts.

Scientific Reports 322: 121157, doi: 10.1016/j.envpol.2023.121157


37. Qu Z, Pan H, Gong J, Wang C, Filker S & Hu X

Historical review of studies on Cyrtophorian Ciliates (Ciliophora, Cyrtophoria) from China.

Microorganisms 10: 1325, doi: 10.3390/microorganisms10071325


36. Sonntag B, Frantal D, Kammerlander B, Darienko T, Filker S, Stoeck T, Gruber M & Pröschold T

Widespread occurence of two planktonic ciliate species (Urotricha, Prostomatida) originating from high mountain lakes.

Diversity 14: 362, doi: 10.3390/d14050362



35. 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/fmcib.2021.787290


34. Bollinger E, Zubrod J, Lai FY, Ahrens L, Filker S, Lohrke A & Bundschuh M

Antibiotics as a silent driver of climate change? A case study investigating methane production in freshwater sediments.

Ecotoxicology and Environmental Safety 228: 113025, doi: 10.1016/j.ecoenv.2021.113025


33. Laborenz J, Bykov YS, Knöringer K, Räschle M, Filker S, Prescianotto-Baschong C, Spang A, Tatsuta T, Langer T, Storchová Z, Schuldiner M & Herrmann JM

The ER protein Ema19 facilitates the degradation of non-imported mitochondrial precursor proteins

Molecular Biology of the Cell 32: 664-674, doi: 10.1091/mbc.E20-11-0748


32. Zhu R, Qu Z, Zhang Q, Filker S, Stoeck T, Li F & Hu X

A new revord of Oxytrichia 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 8: 63, doi: 10.3389/fmars.2021.621349


31. Zhao F, Filker S, Wang C & Xu K

Bathymetric gradient shapes the community composition rather than the species richness of deep-sea benthic ciliates

Science of the Total Environment 755: 142623, doi:10.1016/j.scitotenv.2020.142623

30. Qu Z, Weinisch L, Fan X, Katzenmeier S, Stoeck T & Filker S

Morphological, phylogenetic and ecophysiological characterization of a new ciliate, Platynematum rosellomorai n. sp. (Oligohymenophorea, Scuticociliatia), detected in a hypersaline pond on Mallorca, Spain

Protist 171: 125751, doi: 10.1016/j.protis.2020.125751


29. Santoferrara L, Burki F, Filker S, Logares R,  Dunthorn M & McManus G

Perspectives from ten years of protist studies by high-throughput metabarcoding

Journal of Eukaryotic Microbiology, doi: 10.1111/jeu.12813


28. Zhao F, Filker S, Xu K, Huang P & Zheng S

Microeukaryote communities exhibit phyla-specific distance-decay patterns and an intimate link between sea water and sediment habitats in the Western Pacific Ocean.

Deep-Sea Research Part I: Oceanographic Research Papers, doi: 10.1016/j.dsr.2020.103279



27. Forster D, Lentendu G, Filker S, Dubois E, Wilding T & Stoeck T

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

Environmental Microbiology, doi: 10.1111/1462-2920.14764


26. Zhao F, Filker S, Xu K, Li J, Zhou T & Huang P

Effects of intragenomic polymorphism in the SSU rRNA gene on estimating microeukaryotic diversity: a test for ciliates using single-cell high-throughput DNA sequencing. 

Limnology and Oceanography: Methods, doi: 10.1002/lom3.10330


25. 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 Sciences 62, doi: 10.1007/s11427-018-9523-9


24. 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 freshwater‐marine transition zone of the Baltic Sea.

Environmental Microbiology, doi: 10.1111/1462-2920.14502


23. 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


22. Zhao F & Filker S

Characterization of protistan plankton diversity in ancient salt evaporation ponds located in a volcanic crater on the island Sal, Cape Verde.

Extremophiles 22: 943-954


21. 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


20. Weinisch L, Kirchner I, Grimm M, Kühner S, Pierik A, Roselló-Móra R & Filker S

Glycine betaine and ectoine are the major compatible solutes used by four different halophilic heterotrophic ciliates.

Microbial Ecology, doi: 10.1007/s00248-018-1230-0


19. Weinisch L, Kühner S, Roth R, Grimm M, Roth T, Netz DJA, Pierik A & Filker S

Identification of osmoadaptive strategies in the halophile, heterotrophic ciliate Schmidingerothrix salinarum.

PLoS Biology 16: e2003892


18. Zhao, F., Filker, S., Xu, K., Huang, P. & Zheng, S

Patterns and drivers of vertical distribution of the ciliate community from the surface to the abyssopelagic zone in the Western Pacific Ocean.

Frontiers in Microbiology 8: 2559


17. 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


16. Filker S, Forster D, Weinisch L, Mora Ruiz M, González B, Farías M, Rosselló-Móra R & Stoeck T

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

Environmental Microbiology 19: 3186-3200


15. 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


14. 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, doi: 10.1111/jeu.12305


13. Kammerlander B, Breiner HW, Filker S, Sommaruga R, Sonntag B & Stoeck T

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

FEMS Microbiology Ecology, doi: 10.1093/femsec/fiv010


12. Filker S, Gimmler A, Dunthorn M, Mahé F & Stoeck T

Deep sequencing uncovers high and substantial novel diversity in protistan plankton of solar saltern ponds.

Extremophiles 19: 283-295


11. Mahé F, Mayor 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


10. 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


9. Filker S, Stoeck T, 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


8. Filker S, Kaiser M, Roselló-Móra R, Dunthorn M, Lax G & Stoeck T

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

Systematic and Applied Microbiology 37: 244-251


7. 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: 174-184


6. 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


5. Stoeck T, Breiner HW, Filker S, Ostermaier V, Kammerlander B & Sonntag B

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

Environmental Microbiology 16: 430-444


4. Stock A, Edgcomb V, Orsi W, Filker S, Breiner HW, Yakimov MM & Stoeck T

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

BMC Microbiolgy 13: 150


3. 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.

Microbiolgyopen 2: 54-63


2. Stock A, Breiner HW, Pachiadaki M, Edgcomb V, Filker S, LaCono V, Yakimov MM & Stoeck T

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

Extremophiles 16: 21-34


1. Edgcomb V, Orsi W, Breiner HW, Stock A, Filker S, Yakimov MM & Stoeck T

Novel active kinetoplastids associated with hypersaline anoxic basins in the Eastern Mediterranean deep-sea.

Deep Sea Research Part 1: Oceanographic Research Papers 58: 1040-1048


2. Filker S

Candidatus Halectosymbiota

In: Bergey´s Manual of Systematics of Archaea and Bacteria.

Editors: Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P, Rainey FA & Whitman WB




1. 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