Publications

ZORA Publication List

Publications

• 2025

  • Golaz, D. (2025). Elucidation of the Molecular Mechanisms Underlying the Adaptation of the Nitrogen-Fixing Symbiont $\textit{Paraburkholderia phymatum}$ in Simulated Microgravity (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-279957
  • Andrei, A.-S., Grossart, H.-P., & Pernthaler, J. (2025). Europe’s water law needs genomic resolution Nature Water, 3, 963–964. https://doi.org/10.1038/s44221-025-00488-7
  • Blanco Ramírez, S. (2025). Potential Value of Different Citizen Science Approaches for Water Quality Observations (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-279243
  • Schalch-Schuler, M. C. (2025). Lake Warming and Microbial Food Web Dynamics in Spring: A Focus on Ciliates (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-278140
  • Paszti, S. (2025). Identification of Colonization Factors in $\textit{Burkholderia}$ by Applying Genome-Wide Mutant Profiling (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-270799

• 2024

  • Malfertheiner, L. (2024). Unraveling Aspects of Community Structure in Microbiomes – From Small Ribozymes to Global Ecological Trends (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-267118
  • Schalch-Schuler, M., Bassin, B., Dirren, G., Waller, K., Hofer, C., Pernthaler, J., Andrei, A.-S., & Posch, T. (2024). The planktonic freshwater ciliate Balanion planctonicum (Ciliophora, Prostomatea): A cryptic species complex or a “complex species”? Journal of Eukaryotic Microbiology, 72, e13084. https://doi.org/10.1111/jeu.13084
  • Labouyrie, M. P. (2024). Soil Biodiversity Assessment across Europe (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-264346
  • Serra Moncadas, L., Hofer, C., Bulzu, P.-A., Pernthaler, J., & Andrei, A.-S. (2024). Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis Nature Communications, 15, 3421. https://doi.org/10.1038/s41467-024-47767-7
  • Boukheloua, R., Mukherjee, I., Park, H., Šimek, K., Kasalický, V., Ngochera, M., Grossart, H.-P., Picazo-Mozo, A., Camacho, A., Cabello-Yeves, P. J., Rodriguez-Valera, F., Callieri, C., Andrei, A.-S., Pernthaler, J., Posch, T., Alfreider, A., Sommaruga, R., Hahn, M. W., Sonntag, B., … et al. (2024). Global freshwater distribution of Telonemia protists The ISME Journal, 18, wrae177. https://doi.org/10.1093/ismejo/wrae177
  • Rain-Franco, A., Le Moigne, A., Serra Moncadas, L., Silva, M. O. D., Andrei, A.-S., & Pernthaler, J. (2024). Dispersal shapes compositional and functional diversity in aquatic microbial communities MSystems, 9, e0140324. https://doi.org/10.1128/msystems.01403-24

• 2023

  • Pernthaler, J., Krempaska, N., & Le Moigne, A. (2023). Small-scale spatial beta diversity of bacteria in the mixed upper layer of a lake Environmental Microbiology, 25, 1847–1859. https://doi.org/10.1111/1462-2920.16399
  • Le Moigne, A., Randegger, F., Gupta, A., Petchey, O. L., & Pernthaler, J. (2023). Stochasticity causes high β-diversity and functional divergence of bacterial assemblages in closed systems Ecology, 104, e4005. https://doi.org/10.1002/ecy.4005
  • Straub, H. J. (2023). Should I stay or should I flow: Pseudomonas aeruginosa biofilm formation under flow in a microfluidic platform (Dissertation, University of Zurich)
  • Shilling, R. E. (2023). Inhibition of BerB within B. cenocepacia H111 single cells and its consequences on the macrolony (Dissertation, University of Zurich)

• 2022

  • Dirren-Pitsch, G., Bühler, D., Salcher, M. M., Bassin, B., Le Moigne, A., Schuler, M., Pernthaler, J., & Posch, T. (2022). FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates Frontiers in Microbiology, 13, 1070232. https://doi.org/10.3389/fmicb.2022.1070232
  • Zhu, B., Karwautz, C., Andrei, A.-S., Klingl, A., Pernthaler, J., & Lueders, T. (2022). A novel Methylomirabilota methanotroph potentially couples methane oxidation to iodate reduction MLife, 1, 323–328. https://doi.org/10.1002/mlf2.12033
  • Hofer, C. (2022). Long-Read MinION data for microbial community analysis (Master’s thesis, University of Zurich) https://doi.org/10.5167/uzh-255853
  • Le Moigne, A. (2022). Emergent complexity in microbial community assembly: insights from taxonomic and functional properties (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-222715
  • Purtschert-Montenegro, G. (2022). Identification of a novel bacterial killing nanomachine in Pseudomonas putida IsoF (Dissertation, University of Zurich)
  • Kalawong, R. (2022). Influence of putisolvin on membrane vesicle and nanotube formation in Pseudomonas putida IsoF (Dissertation, University of Zurich)
  • Gschwend, F. (2022). Next-generation soil quality monitoring : metabarcoding of soil bacterial and fungal communities for long-term soil quality monitoring. (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-230423

• 2021

  • Krempaska, N., Horňák, K., Silva, M. O. D., & Pernthaler, J. (2021). Spatial microheterogeneity and selective microbial consumption of dissolved free amino acids in an oligomesotrophic lake Limnology and Oceanography, 66, 3728–3739. https://doi.org/10.1002/lno.11912
  • Gualdi, S. (2021). Identification of fitness determinants in Burkholderia cenocepacia H111 by transposon sequencing (Dissertation, University of Zurich)

• 2020

  • Silva, M. O. D., & Pernthaler, J. (2020). Biomass addition alters community assembly in ultrafiltration membrane biofilms Scientific Reports, 10, 11552. https://doi.org/10.1038/s41598-020-68460-x
  • Le Moigne, A., Bartosiewicz, M., Schaepman‐Strub, G., Abiven, S., & Pernthaler, J. (2020). The biogeochemical variability of Arctic thermokarst ponds is reflected by stochastic and niche‐driven microbial community assembly processes Environmental Microbiology, 22, 4847–4862. https://doi.org/10.1111/1462-2920.15260
  • Piwosz, K., Shabarova, T., Pernthaler, J., Posch, T., Šimek, K., Porcal, P., & Salcher, M. M. (2020). Bacterial and eukaryotic small-subunit amplicon data do not provide a quantitative picture of microbial communities, but they are reliable in the context of ecological interpretations MSphere, 5, 00052–20. https://doi.org/10.1128/msphere.00052-20

• 2019

  • Silva, M. O. D., & Pernthaler, J. (2019). Priming of microcystin degradation in carbon-amended membrane biofilm communities is promoted by oxygen-limited conditions FEMS Microbiology Ecology, 95, 157–157. https://doi.org/10.1093/femsec/fiz157
  • Eckert, E. M., Di Cesare, A., Malki, L.-S., Villiger, J., Pernthaler, J., Callieri, C., Bertoni, R., & Corno, G. (2019). Seasonality of the antibiotic resistance gene blaCTX-M in temperate Lake Maggiore Hydrobiologia, 843, 143–153. https://doi.org/10.1007/s10750-019-04043-w
  • Silva, M. O. D., Desmond, P., Derlon, N., Morgenroth, E., & Pernthaler, J. (2019). Source Community and Assembly Processes Affect the Efficiency of Microbial Microcystin Degradation on Drinking Water Filtration Membranes Frontiers in Microbiology, 10, 843–843. https://doi.org/10.3389/fmicb.2019.00843
  • Pitsch, G. (2019). Ciliates in freshwater ecosystems : insights from morphological and molecular approaches. (Dissertation, University of Zurich)

• 2018

  • Neuenschwander, S. M., Ghai, R., Pernthaler, J., & Salcher, M. M. (2018). Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria The ISME Journal, 12, 185–198. https://doi.org/10.1038/ismej.2017.156
  • Silva, M. O. D., Blom, J. F., Yankova, Y., Villiger, J., & Pernthaler, J. (2018). Priming of microbial microcystin degradation in biomass-fed gravity driven membrane filtration biofilms Systematic and Applied Microbiology, 41, 221–231. https://doi.org/10.1016/j.syapm.2017.11.009
  • Losasso, C., Eckert, E. M., Mastrorilli, E., Villiger, J., Mancin, M., Patuzzi, I., Di Cesare, A., Cibin, V., Barrucci, F., Pernthaler, J., Corno, G., & Ricci, A. (2018). Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study Frontiers in Microbiology, 9:317. https://doi.org/10.3389/fmicb.2018.00317
  • Krempaska, N., Horňák, K., & Pernthaler, J. (2018). Spatiotemporal distribution and microbial assimilation of polyamines in a mesotrophic lake Limnology and Oceanography, 63, 816–832. https://doi.org/10.1002/lno.10672
  • da Silva, A. M. O. (2018). Removal of microcystins by mature biofilms during water filtration (Dissertation, University of Zurich)

• 2017

  • Granato, E. (2017). Evolution of Cooperation and Virulence in an Opportunistic Pathogen (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-147574
  • Yankova, Y. (2017). Effects of Lake Warming on Cyanobacterial and Algal Bloom Dynamics (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-147585
  • Baumgartner, M., Roffler, S., Wicker, T., & Pernthaler, J. (2017). Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment The ISME Journal, 11, 2258–2266. https://doi.org/10.1038/ismej.2017.87
  • Pernthaler, J. (2017). Competition and niche separation of pelagic bacteria in freshwater habitats Environmental Microbiology, 19, 2133–2150. https://doi.org/10.1111/1462-2920.13742
  • Shabarova, T., Kasalický, V., Šimek, K., Nedoma, J., Znachor, P., Posch, T., Pernthaler, J., & Salcher, M. M. (2017). Distribution and ecological preferences of the freshwater lineage LimA (genus Limnohabitans) revealed by a new double hybridization approach Environmental Microbiology, 19, 1296–1309. https://doi.org/10.1111/1462-2920.13663
  • Butaitė, E. (2017). Pyoverdine production and its social effects in natural communities of Pseudomonas bacteria (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-147572

• 2016

  • Suppiger, A. (2016). Fatty Acid-Based Signalling in the Genus Burkholderia: Distribution, Mechanism, Cross-Linkage (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-129350
  • Dirren, S. (2016). The basal Opisthokonts Nuclearia spp. with associated bacterial symbionts: aspects of diversity and ecology (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-129337
  • Baumgartner, M., Neu, T. R., Blom, J. F., & Pernthaler, J. (2016). Protistan predation interferes with bacterial long‐term adaptation to substrate restriction by selecting for defence morphotypes Journal of Evolutionary Biology, 29, 2297–2310. https://doi.org/10.1111/jeb.12957
  • Schilcher, K. (2016). Antibiotic-Mediated Modulation of Staphylococcus aureus Virulence Factors (Dissertation, University of Zurich)
  • Baumgartner, M. (2016). Experimental Evolution of a Freshwater Isolate with Inducible Aggregate Formation – Genome Streamlining and Variability of Phenotypic Plasticity (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-129331
  • Yankova, Y., Villiger, J., Pernthaler, J., Schanz, F., & Posch, T. (2016). Prolongation, deepening and warming of the metalimnion change habitat conditions of the harmful filamentous cyanobacterium Planktothrix rubescens in a prealpine lake Hydrobiologia, 776, 125–138. https://doi.org/10.1007/s10750-016-2745-3
  • Horňák, K., Schmidheiny, H., & Pernthaler, J. (2016). High-throughput determination of dissolved free amino acids in unconcentrated freshwater by ion-pairing liquid chromatography and mass spectrometry Journal of Chromatography. A, 1440, 85–93. https://doi.org/10.1016/j.chroma.2016.02.045
  • Faltermann, S., Grundler, V., Gademann, K., Pernthaler, J., & Fent, K. (2016). Comparative effects of nodularin and microcystin-LR in zebrafish: 2. Uptake and molecular effects in eleuthero-embryos and adult liver with focus on endoplasmic reticulum stress Aquatic Toxicology, 171, 77–87. https://doi.org/10.1016/j.aquatox.2015.12.001

• 2015

  • Bao, K. (2015). Novel organotypic modelling for the study of periodontal infection (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-117702
  • Neuenschwander, S. (2015). Functional Analysis of Pelagic Freshwater Microbes Based on Targeted Enrichment Approaches (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-117699
  • Mathew, A. (2015). Iron transport strategies of the genus Burkholderia (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-113412
  • Salcher, M. M., Neuenschwander, S. M., Posch, T., & Pernthaler, J. (2015). The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign The ISME Journal, 9, 2442–2453. https://doi.org/10.1038/ismej.2015.55
  • Coci, M., Odermatt, N., Salcher, M. M., Pernthaler, J., & Corno, G. (2015). Ecology and distribution of thaumarchaea in the deep hypolimnion of Lake Maggiore Archaea, 2015, 590434. https://doi.org/10.1155/2015/590434
  • Cárcamo Oyarce, G. (2015). Social behaviors of Pseudomonas putida IsoF (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-117697
  • Takeuchi, Y., Chaffron, S., Salcher, M. M., Shimizu-Inatsugi, R., Kobayashi, M. J., Diway, B., von Mering, C., Pernthaler, J., & Shimizu, K. K. (2015). Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes Systematic and Applied Microbiology, 38, 330–339. https://doi.org/10.1016/j.syapm.2015.05.006
  • Garneau, M.-È., Posch, T., & Pernthaler, J. (2015). Seasonal patterns of microcystin-producing and non-producing Planktothrix rubescens genotypes in a deep pre-alpine lake Harmful Algae, 50, 21–31. https://doi.org/10.1016/j.hal.2015.10.001
  • Neuenschwander, S. M., Salcher, M. M., & Pernthaler, J. (2015). Fluorescence in situ hybridization and sequential catalyzed reporter deposition (2C-FISH) for the flow cytometric sorting of freshwater ultramicrobacteria Frontiers in Microbiology, 6, 247. https://doi.org/10.3389/fmicb.2015.00247

• 2014

  • Kohler, E. (2014). Structural characterization, bioactivity and biodegradation of cyanobacterial toxins (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-105523
  • Kohler, E., Villiger, J., Posch, T., Derlon, N., Shabarova, T., Morgenroth, E., Pernthaler, J., & Blom, J. F. (2014). Biodegradation of microcystins during gravity-driven membrane (GDM) ultrafiltration PLoS ONE, 9, e111794. https://doi.org/10.1371/journal.pone.0111794
  • Kohler, E., Grundler, V., Häussinger, D., Kurmayer, R., Gademann, K., Pernthaler, J., & Blom, J. F. (2014). The toxicity and enzyme activity of a chlorine and sulfate containing aeruginosin isolated from a non-microcystin-producing Planktothrix strain Harmful Algae, 39, 154–160. https://doi.org/10.1016/j.hal.2014.07.003
  • Neuenschwander, S. M., Pernthaler, J., Posch, T., & Salcher, M. M. (2014). Seasonal growth potential of rare lake water bacteria suggest their disproportional contribution to carbon fluxes Environmental Microbiology, 17, 781–795. https://doi.org/10.1111/1462-2920.12520
  • Horňák, K., & Pernthaler, J. (2014). A novel ion-exclusion chromatography–mass spectrometry method to measure concentrations and cycling rates of carbohydrates and amino sugars in freshwaters Journal of Chromatography. A, 1365, 115–123. https://doi.org/10.1016/j.chroma.2014.09.007
  • Alonso-Sáez, L., Zeder, M., Harding, T., Pernthaler, J., Lovejoy, C., Bertilsson, S., & Pedrós-Alió, C. (2014). Winter bloom of a rare betaproteobacterium in the Arctic Ocean Frontiers in Microbiology, 5:425. https://doi.org/10.3389/fmicb.2014.00425
  • Shabarova, T., Villiger, J., Morenkov, O., Niggemann, J., Dittmar, T., & Pernthaler, J. (2014). Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools FEMS Microbiology Ecology, 89, 111–126. https://doi.org/10.1111/1574-6941.12339
  • Schmid, N. (2014). Cell-to-Cell Signaling in Burkholderia cenocepacia H111: An Entangled Web of Chemical Languages (Dissertation, University of Zurich)
  • Eckert, E. M., & Pernthaler, J. (2014). Bacterial epibionts of Daphnia: A potential route for the transfer of dissolved organic carbon in freshwater food webs The ISME Journal, 8, 1808–1819. https://doi.org/10.1038/ismej.2014.39
  • Faltermann, S., Zucchi, S., Kohler, E., Blom, J. F., Pernthaler, J., & Fent, K. (2014). Molecular effects of the cyanobacterial toxin cyanopeptolin (CP1020) occurring in algal blooms: Global transcriptome analysis in zebrafish embryos Aquatic Toxicology, 149, 33–39. https://doi.org/10.1016/j.aquatox.2014.01.018

• 2013

  • Alonso, C., Piccini, C., Unrein, F., Bertoglio, F., Conde, D., & Pernthaler, J. (2013). Environmental dynamics as a structuring factor for microbial carbon utilization in a subtropical coastal lagoon Frontiers in Microbiology, 4:14. https://doi.org/10.3389/fmicb.2013.00014
  • Eckert, E. M., Baumgartner, M., Huber, I. M., & Pernthaler, J. (2013). Grazing resistant freshwater bacteria profit from chitin and cell-wall-derived organic carbon Environmental Microbiology, 15, 2019–2030. https://doi.org/10.1111/1462-2920.12083
  • Piwosz, K., Salcher, M. M., Zeder, M., Ameryk, A., & Pernthaler, J. (2013). Seasonal dynamics and activity of typical freshwater bacteria in brackish waters of the Gulf of Gdańsk Limnology and Oceanography, 58, 817–826. https://doi.org/10.4319/lo.2013.58.3.0817
  • Ammann, T. (2013). Advancement and structural analysis of a subgingival biofilm model system (Dissertation, University of Zurich)
  • Eiler, A., Drakare, S., Bertilsson, S., Pernthaler, J., Peura, S., Rofner, C., Simek, K., Yang, Y., Znachor, P., & Lindström, E. S. (2013). Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach PLoS ONE, 8, e53516. https://doi.org/10.1371/journal.pone.0053516
  • Dengler, V. (2013). Factors affecting antibiotic resistance of staphylococcus aureus (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-89854
  • Piccini, C., Conde, D., Pernthaler, J., & Sommaruga, R. (2013). Photoalteration of macrophyte-derived chromophoric dissolved organic matter induces growth of single bacterial populations in a coastal lagoon Journal of Limnology, 72, 582–591. https://doi.org/10.4081/jlimnol.2013.e49
  • Pernthaler, J. (2013). Freshwater microbial communities In E. Rosenberg, E. DeLong, & S. Lory (Eds.), The Prokaryotes (pp. 97–112). Springer. https://doi.org/10.1007/978-3-642-30123-0_40
  • Shabarova, T., Widmer, F., & Pernthaler, J. (2013). Mass effects meet species sorting: transformations of microbial assemblages in epiphreatic subsurface karst water pools Environmental Microbiology, 15, 2476–2488. https://doi.org/10.1111/1462-2920.12124
  • Corno, G., Villiger, J., & Pernthaler, J. (2013). Coaggregation in a microbial predator–prey system affects competition and trophic transfer efficiency Ecology, 94, 870–881. https://doi.org/10.1890/12-1652.1
  • Derlon, N., Koch, N., Eugster, B., Posch, T., Pernthaler, J., Pronk, W., & Morgenroth, E. (2013). Activity of metazoa governs biofilm structure formation and enhances permeate flux during Gravity-Driven Membrane (GDM) filtration Water Research, 47, 2085–2095. https://doi.org/10.1016/j.watres.2013.01.033
  • Garneau, M.-È., Posch, T., Hitz, G., Pomerleau, F., Pradalier, C., Siegwart, R., & Pernthaler, J. (2013). Short-term displacement of Planktothrix rubescens (cyanobacteria) in a pre-alpine lake observed using an autonomous sampling platform Limnology and Oceanography, 58, 1892–1906. https://doi.org/10.4319/lo.2013.58.5.1892
  • Salcher, M. M., Posch, T., & Pernthaler, J. (2013). In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake The ISME Journal, 7, 896–907. https://doi.org/10.1038/ismej.2012.162

• 2012

  • Posch, T., Köster, O., Salcher, M. M., & Pernthaler, J. (2012). Harmful filamentous cyanobacteria favoured by reduced water turnover with lake warming Nature Climate Change, 2, 809–813. https://doi.org/10.1038/nclimate1581
  • Dieckmann, S. M. (2012). Analysis of novel haemotrophic mycoplasma isolates with main focus on significance of haemotrophic mycoplasma infections in horses (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-60776

• 2011

  • Zeder, M., Kohler, E., Zeder, L., & Pernthaler, J. (2011). A novel algorithm for the determination of bacterial cell volumes that is unbiased by cell morphology Microscopy and Microanalysis, 17, 799–809. https://doi.org/10.1017/S1431927611012104
  • Piwosz, K., & Pernthaler, J. (2011). Enrichment of omnivorous cercozoan nanoflagellates from coastal Baltic Sea waters PLoS ONE, 6, e24415. https://doi.org/10.1371/journal.pone.0024415
  • Salcher, M. M., Pernthaler, J., & Posch, T. (2011). Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria “that rule the waves” (LD12). The ISME Journal, 5, 1242–1252. https://doi.org/10.1038/ismej.2011.8
  • Oggier, D. M. (2011). Effects of pharmaceuticals and personal care products on different developmental stages in fish (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-163990
  • Salcher, M. M., Pernthaler, J., Frater, N., & Posch, T. (2011). Vertical and longitudinal distribution patterns of different bacterioplankton populations in a canyon-shaped, deep prealpine lake Limnology and Oceanography, 56, 2027–2039. https://doi.org/10.4319/lo.2011.56.6.2027
  • Takeuchi, Y., Salcher, M. M., Ushio, M., Shimizu-Inatsugi, R., Kobayashi, M. J., Diway, B., von Mering, C., Pernthaler, J., & Shimizu, K. K. (2011). In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus nepenthes PLoS ONE, 6, e25144. https://doi.org/10.1371/journal.pone.0025144
  • Horňák, K., Zeder, M., Blom, J. F., Posch, T., & Pernthaler, J. (2011). Suboptimal light conditions negatively affect the heterotrophy of Planktothrix rubescens but are beneficial for accompanying Limnohabitans spp Environmental Microbiology, 14, 765–778. https://doi.org/10.1111/j.1462-2920.2011.02635.x
  • Van den Wyngaert, S., Salcher, M. M., Pernthaler, J., & Posch, T. (2011). Quantitative dominance of seasonally persistent filamentous cyanobacteria (Planktothrix rubescens) in the microbial assemblages of a temperate lake Limnology and Oceanography, 56, 97–109. https://doi.org/10.4319/lo.2011.56.1.0097
  • Schreiner, S. A. (2011). Analysis of in vitro growth and characterisation of metabolic pathways of Mycoplasma suis linked to pathogenesis (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-59370
  • Stark, M. (2011). MLTreeMap - maximum likelihood placement of environmental DNA sequence reads into curated reference phylogenies (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-59539

• 2010

  • Zeder, M., Van den Wyngaert, S., Köster, O., Felder, K. M., & Pernthaler, J. (2010). Automated quantification and sizing of unbranched filamentous cyanobacteria by model based object oriented image analysis Applied and Environmental Microbiology, 76, 1615–1622. https://doi.org/10.1128/AEM.02232-09
  • Piwosz, K., & Pernthaler, J. (2010). Seasonal population dynamics and trophic role of planktonic nanoflagellates in coastal surface waters of the Southern Baltic Sea Environmental Microbiology, 12, 364–377. https://doi.org/10.1111/j.1462-2920.2009.02074.x
  • Banu, L. D. (2010). Gene expression in Streptococcus mutans biofilms (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-46739
  • Chaffron, S., Rehrauer, H., Pernthaler, J., & von Mering, C. (2010). A global network of coexisting microbes from environmental and whole-genome sequence data Genome Research, 20, 947–959. https://doi.org/10.1101/gr.104521.109
  • Blom, J. F., & Pernthaler, J. (2010). Antibiotic effects of three strains of chrysophytes (Ochromonas, Poterioochromonas) on freshwater bacterial isolates FEMS Microbiology Ecology, 71, 281–290. https://doi.org/10.1111/j.1574-6941.2009.00800.x
  • Blom, J. F., Horňák, K., Simek, K., & Pernthaler, J. (2010). Aggregate formation in a freshwater bacterial strain induced by growth state and conspecific chemical cues Environmental Microbiology, 12, 2486–2495. https://doi.org/10.1111/j.1462-2920.2010.02222.x
  • Horath, T. D. (2010). Endolithic microbial communities in dolomite (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-163992
  • Alonso-Sáez, L., Pinhassi, J., Pernthaler, J., & Gasol, J. M. (2010). Leucine-to-carbon empirical conversion factor experiments: does bacterial community structure have an influence? Environmental Microbiology, 12, 2988–2997. https://doi.org/10.1111/j.1462-2920.2010.02276.x
  • Felder, K. M. (2010). Analysis of the pathogenesis of severe anaemia of pigs due to Mycoplasma suis infection (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-46815
  • Blom, J. F., Zimmermann, Y. S., Ammann, T., & Pernthaler, J. (2010). Scent of danger: floc formation by a freshwater bacterium is induced by supernatants from a predator-prey coculture Applied and Environmental Microbiology, 76, 6156–6163. https://doi.org/10.1128/AEM.01455-10
  • Chaffron, S. (2010). Tracing microbes and their genes through the environment: diversity, ecology and evolution (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-45544
  • Zeder, M., Kohler, E., & Pernthaler, J. (2010). Automated quality assessment of autonomously acquired microscopic images of fluorescently stained bacteria Cytometry Part A, 77, 76–85. https://doi.org/10.1002/cyto.a.20810
  • Salcher, M. M., Pernthaler, J., & Posch, T. (2010). Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake Limnology and Oceanography, 55, 846–856. https://doi.org/10.4319/lo.2010.55.2.0846
  • Shabarova, T., & Pernthaler, J. (2010). Karst pools in subsurface environments: collectors of microbial diversity or temporary residence between habitat types Environmental Microbiology, 12, 1061–1074. https://doi.org/10.1111/j.1462-2920.2009.02151.x
  • Gröbel, K. (2010). New insights into the pathogenesis of the Mycoplasma suis infection (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-46812

• 2009

  • Piccini, C., Conde, D., Pernthaler, J., & Sommaruga, R. (2009). Alteration of chromophoric dissolved organic matter by solar UV radiation causes rapid changes in bacterial community composition Photochemical & Photobiological Sciences, 8, 1321–1328. https://doi.org/10.1039/b905040j
  • Zeder, M., Peter, S., Shabarova, T., & Pernthaler, J. (2009). A small population of planktonic Flavobacteria with disproportionally high growth during the spring phytoplankton bloom in a prealpine lake Environmental Microbiology, 11, 2676–2686. https://doi.org/10.1111/j.1462-2920.2009.01994.x
  • Pernthaler, J., & Posch, T. (2009). Aquatic microbial food webs In G. E. Likens (Ed.), Encyclopedia of Inland Waters ; vol. 3 (pp. 244–251). Elsevier. http://www.elsevierdirect.com/brochures/inlandwaters/index.html
  • Meier, S. (2009). Characterisation of the SoVG homolog in Staphylococcus aureus (Dissertation, University of Zurich)
  • Zeder, M., & Pernthaler, J. (2009). Multi-spot live-image autofocusing for high-throughput microscopy of fluorescently stained bacteria Cytometry Part A, 75, 781–788. https://doi.org/10.1002/cyto.a.20770
  • Zeder, M. (2009). Development of methods and technology for automated high-throughput multi-parameter analysis of single cells by fluorescence microscopy (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-31287
  • Shabarova, T., & Pernthaler, J. (2009). Investigation of bacterioplankton communities in aquatic karst pools in Bärenschacht cave of Bernese Oberland In W. B. White (Ed.), Proceedings of the 15th International Congress of Speleology, Kerrville, Texas, July 19-26, 2009 (pp. 416–421). National Speleological Society. http://www.ics2009.us/pubs.html
  • Buck, U., Grossart, H. P., Amann, R., & Pernthaler, J. (2009). Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake Environmental Microbiology, 11, 1854–1865. https://doi.org/10.1111/j.1462-2920.2009.01910.x
  • Alonso, C., Zeder, M., Piccini, C., Conde, D., & Pernthaler, J. (2009). Ecophysiological differences of betaproteobacterial populations in two hydrochemically distinct compartments of a subtropical lagoon Environmental Microbiology, 11, 867–876. https://doi.org/10.1111/j.1462-2920.2008.01807.x

• 2008

  • Fazi, S., Amalfitano, S., Piccini, C., Zoppini, A., Puddu, A., & Pernthaler, J. (2008). Colonization of overlaying water by bacteria from dry river sediments Environmental Microbiology, 10, 2760–2772. https://doi.org/10.1111/j.1462-2920.2008.01695.x
  • Salcher, M. M., Pernthaler, J., Zeder, M., Psenner, R., & Posch, T. (2008). Spatio-temporal niche separation of planktonic Betaproteobacteria in an oligo-mesotrophic lake Environmental Microbiology, 10, 2074–2086. https://doi.org/10.1111/j.1462-2920.2008.01628.x
  • Allers, E., Niesner, C., Wild, C., & Pernthaler, J. (2008). Microbes enriched in seawater after addition of coral mucus Applied and Environmental Microbiology, 74, 3274–3278. https://doi.org/10.1128/AEM.01870-07
  • Salcher, M. M. (2008). Seasonality of bacterial phylotypes affected by bottom-up and top-down control in Piburger See, Austria (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-13746
  • Caminada, D. (2008). Pharmaceuticals as environmental pollutants : cytotoxicity and biochemical effects in an in vitro model system for aquatic organism. (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-163769
  • Ender, M. (2008). Molecular and functional charactersiation of the Swiss drug clone, a Methicillin-resistenter Staphylococcus aureus (Dissertation, University of Zurich)

• 2007

  • Alonso-Sáez, L., Balagué, V., Sà, E. L., Sanchez-Pernaute, O., González-Navajas, J. M., Pinhassi, J., Massana, R., Pernthaler, J., Pedrós-Alió, C., & Gasol, J. M. (2007). Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH FEMS Microbiology Ecology, 60, 98–112. https://doi.org/10.1111/j.1574-6941.2006.00276.x

• 2006

  • Kunz, P. Y. (2006). Hormonal activity of UV filters in aquatic ecosystems (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-163506