2025

51 Abad-Recio I, Rubel V, Filker S, Garate L, Stoeck T, Logares R & Lanzén A

The Basque Coast Estuarine Sediment Gene Catalogue.

Scientific Data (accepted)

50 Lazrak K, Nothof M, Filker S, El Bouaidi W, Berger E & Loudiki M

49 Oster S, Bollinger E, Schreiner VC, Schmitt T, Filker S*, Bundschuh M* (*shared authorship)

48 Bollinger E, Mayer J, Lai FY, Schulz R, Filker S*, Bundschuh M* (*shared authorship)

47 Schnurr J, Feckler A, Filker S, Zubrod JP, Mayer J, Schützenmeister K, Jungkunst HF & Bundschuh M

Fungicides affect the structure and function of soil microorganisms and the physiology of four riparian tree species - evidence from a pot experiment.

Ecotoxicology and Environmental Safety 302: 118641, doi: 10.1016/j.ecoenv.2025.118641

46 Rubel V, Filker S, Lanzén A, Abad IL & Stoeck T

Exploiting taxonomic information from metagenomes to infer bacterial bioindicators and environmental quality at salmon aquaculture installations.

Marine Pollution Bulletin 218: 118173, doi: 10.1016/j.marpolbul.2025.118173

45 Lazrak K, Tazart Z, Nothof M, Filker S, Hakkoum Z, Kaczmarek N, Berger E, Mouhri K & Loudiki M

Assessment of the short-term salinity effect on algal biofilm through field transfer in the Drâa river (Southeastern Morocco) using metabarcoding and morphological analyses.

Environmental Monitoring and Assessment 197: 424, doi: 10.1007/s10661-025-13842-9

2024

44 Bollinger E, Schwilden P, Lai FY, Schulz R, Bundschuh M & Filker S

Higher temperatures exacerbate effects of antibiotics on methanogenesis in freshwater sediment.

Communications Earth & Environment 5: 647, doi: 10.1038/s43247-024-01828-3

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

Parasitic taxa are key to the vertical stratification and community variation of pelagic ciliates from the surface to the abyssopelagic zone.

Environmental Microbiome 19: 85, doi: 10.1186/s40793-024-00630-0

42 Lazrak K, Nothof M, Tazart, Filker S, Berger E, Mouhri K & Loudiki M

Salt stress responses of microalgae biofilm communities under controlled microcosm conditions.

Algal Research 78 : 103430, doi: 10.1016/j.algal.2024.103430

41 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 222: 103216, doi: 10.1016/j.pocean.2024.103216

2023

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

2022

38 Spanner C, Darienko T, Filker S, Sonntag B & 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

2021

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

2020

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

30th 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

2019

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

2018

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 halophilic, heterotrophic ciliate Schmidingerothrix salinarum.

PLoS Biology 16: e2003892

2017

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

2016

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

2015

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

2014

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

2013

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

2012

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

2011

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

2020

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
Wiley

2013

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

2020

Filker S & Stoeck T
Report of the 2020 meeting of the German Society for Protozoology.
European Journal of Protistology 75: 125702, doi: 10.1016/j.ejop.2020.125702

2014

Stoeck T, Filker S & Weinisch L
DNA sequencing in microbial diversity research.
In: BIOspektrum. Springer, pp. 528-530. doi: 10.1007/s12268-014-0478-2