Prof. Jakob Pernthaler
Limnological Station
University of Zürich
Seestrasse 187
CH-8802 Kilchberg
pernthaler@limnol.uzh.ch

phone:
+41 (0)44 63 49210
fax:
+41 (0)44 63 41225
Research Interests
Education
Previous Positions and Research Experience
List of Publications

[ print version ]

Research Interests

I investigate the role and fate of different water column bacteria in freshwater (and marine) habitats in the context of food web structure and substrate availability. My research is targeted to two aspects of microbial ecology. Firstly I study the effects of predator-induced mortality on the composition of microbial assemblages, and in the potential adaptations of microbial species to compensate or to avoid such losses. In this context I have been specifically interested in the identity,activity, biogeography and population dynamics of filamentous aggregate-forming and of gram positive freshwater microbes. Secondly, I have been studying the life strategies of so-called "opportunistic" bacterial species in coastal and freshwater habitats, i.e. bacterial ecotypes that are superior competitors in steep environmental gradients or during rapid changes of growth conditions. These bacteria could potentially qualify as early indicator organisms of water pollution by organic carbon. I am moreover interested in the ecological role of facultatively anaerobic heterotrophic water column bacteria., the similarities and differences in the community composition of freshwater and coastal microbial assemblages, and in the distribution and activities of pelagic microbes in the deep Atlantic Ocean. An emerging subject of interest inspired by the facilities and expertise present at the Limnological Station is the potential role of infochemicals in the relationship between protistan predators and their prey.

Research approaches:

I employ a suite of molecular biological approaches for the identification and staining of common environmental microbes without prior cultivation based upon comparative rRNA gene cloning and sequence analysis. In my laboratory methods have been improved for the determinative whole-cell fluorescence in situ hybridization (FISH) of water column microbes with rRNA-targeted probes. Specifically, the FISH technique was adapted for small slowly-growing bacteria and archaea in oligotrophic offshore or freshwater environments. In addition, we develop and apply image analysis strategies for the rapid quantification of population sizes and biovolumes of FISH-stained microorganisms by automated motorized microscopy. I am moreover interested in cytochemical and autoradiographic techniques to measure the DNA synthesis and specific substrate uptake of individual microbial populations in mixed communities at the single-cell level. This allows to establish a link between the phylogenetic identification of large, environmentally relevant populations of water-column microbes and their growth patterns in situ.


Education

1994 - 1997 PhD thesis at the Department of Zoology and Limnology, University of Innsbruck, titeled: "Protistan grazing and its effects on pelagic bacterial assemblages"; repeated research stays at the Hydrobiological Institut of the Czech Republic, Budweis, and the Technical University of Munich, Germany
1992 - 1994 MSc thesis in Limnology; titeled "Diel vertical migration of planktonic rotifers in a mountain lake"
1986 - 1992 Studies in Biology and Philosophy at the Leopold-Franzens-University of Innsbruck, Austria

Previous Positions and Research Experience

2011 - present Professor at the Institute for Plant Biology at the University of Zurich; Head of the Department of Limnology
2005 - 2011 Assistant Professor at the Institute for Plant Biology at the University of Zurich; Head of the Department of Limnology
1999 - 2005 Head of the Plankton Ecology Group at the Department of Molecular Ecology, Max-Planck-Institute for Marine Microbiology
1997 - 1999 Post-doctoral position at the Max-Planck-Institute for Marine Microbiology, Bremen, Germany

List of Publications

Silva, M., Desmond, P., Derlon, N., Morgenroth, E., and 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.

Silva, M., and Pernthaler, J. (2019). Priming of microcystin degradation in carbon-amended membrane biofilm communities is promoted by oxygen-limited conditions. FEMS microbiology ecology, 95/11.

Krempaska, N., Hornak, K., and Pernthaler, J. (2018). Spatiotemporal distribution and microbial assimilation of polyamines in a mesotrophic lake. Limnology and Oceanography, 63: 816-832.

Losasso, C., Eckert, E., Mastrorilli, E., Villiger, J., Mancin, M., Patuzzi, I., Di Cesare, A., Cibin, V., Barrucci, F., Pernthaler, J., Corno, G., and 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.

Neuenschwander, S., Ghai, R., Pernthaler, J., and Salcher, M. (2018). Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria . ISME Journal, 12: 185-198.

Silva, M., Blom, J., Yankova, Y., Villiger, J., and Pernthaler, J. (2018). Priming of microbial microcystin degradation in biomass-fed gravity driven membrane filtration biofilms. System. and App. Microbiology, 41:221-231.

Baumgartner, M., Roffler, S., Wicker, T., and Pernthaler, J. (2017). Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment. ISME Journal, 11: 2258-2266.

Pernthaler, J. (2017). Competition and niche separation of pelagic bacteria in freshwater habitats. Environ Microbiol, 19:2133-2150.

Shabarova, T., Kasalický, V., Šimek, K., Nedoma, J., Znachor, P., Posch, T., Pernthaler, J., and Salcher, M.M. (2017). Distribution and ecological preferences of the freshwater lineage LimA (genus Limnohabitans) revealed by a new double hybridisation approach. Environ Microbiol. 19: 1296–1309
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Faltermann, S., Pretot, R., Pernthaler, J., and Fent, K. (2016). Comparative effects of nodularin and microcystin-LR in zebrafish: 1. Uptake by organic anion transporting polypeptide Oatp1d1 (Slco1d1). Aquatic Toxology 171, 69-76.

Hornak, K., Schmidheiny, H., and 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.

Piwosz, K., Kownacka, J., Ameryk, A., Zalewski, M., and Pernthaler, J. (2016). Phenology of cryptomonads and the CRY1 lineage in a coastal brackish lagoon (Vistula Lagoon, Baltic Sea). Journal of Phycology, 52/4, 626-637.

Yankova, Y., Villiger, J., Pernthaler, J., Schanz, F., and 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

Coci, M., Odermatt, N., Salcher, M.M., Pernthaler, J., and Corno, G. (2015) Ecology and distribution of Thaumarchaea in the deep hypolimnion of Lake Maggiore. Archaea 2015: Article ID 590434.
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Garneau, M-È., Posch, T., and 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

Kurmayer, R., Blom, J., Deng, L., and Pernthaler, J. (2015). Integrating phylogeny, geographic niche partitioning and secondary metabolite synthesis in bloom-forming Planktothrix. ISME Journal 9: 909-921.

Neuenschwander, S.M., Pernthaler, J., Posch, T., and Salcher, M.M. (2015). Seasonal growth potential of rare lake water bacteria suggest their disproportional contribution to carbon fluxes. Environ Microbiol 17: 781-795
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Neuenschwander, S.M., Salcher, M.M., and Pernthaler, J. (2015). Fluorescence in situ hybridization and sequential catalysed reporter deposition (2C-FISH) for the flow cytometric sorting of freshwater ultramicrobacteria. Frontiers in Microbiology 6, 247.
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Posch, T., Eugster, B., Pomati, F., Pernthaler, J., Pitsch, G., and Eckert, E. (2015). Network of Interactions Between Ciliates and Phytoplankton During Spring. Frontiers in Microbiology 6, 1289.

Salcher, M.M, Neuenschwander, S.M., Posch, T., and Pernthaler, J. (2015). The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign. ISME Journal 9: 2442-2453.
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Takeuchi, Y., Chaffron, S. Salcher, M.M., Shimizu-Inatsugia, R., Kobayashia, M.J., Diway, B, von Mering, C, Pernthaler, J., and Shimizu, K.K. (2015) Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. Syst Appl Microbiol. 38:330-339
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Faltermann S, Zucchi S, Kohler E, Blom JF, Pernthaler J, Fent K (2014) Molecular effects of the cyanobacterial toxin cyanopeptolin (CP 1020) occurring in algal blooms: Global transcriptome analysis in zebrafish embryos. Aquatic Toxicology 149: 33-39
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Kohler E, Grundler V, Häussinger D, Kurmayer R, Gademann K, Pernthaler J, Blom JF (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
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Kohler E, Villiger J, Posch T, Derlon N, Shabarova T, Morgenroth E, Pernthaler J, Blom JF (2014) Biodegradation of microcystins during gravity-driven membrane (GDM) ultrafiltration. Plos One 9: e111794
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Derlon, N., Koch, N., Eugster, B., Posch, T., Pernthaler, J., Pronk, W., and Morgenroth, E. (2013). Activity of metazoa governs biofilm structure formation and enhances permeate flux during Gravity-Driven Membrane (GDM) filtration. Water Res 47, 2085-2095.
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Eckert, E.M., Baumgartner, M., Huber, I.M., and Pernthaler, J. (2013) Grazing resistant freshwater bacteria profit from chitin and cell-wall-derived organic carbon. Environ Microbiol online early DOI: 10.1111/1462-2920.12083
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Garneau, M-E., Posch, T., Hitz, G., Pomerleau, F., Pradalier, C., Siegwart, R., and Pernthaler, J. (2013) Short-term displacement of Planktothrix rubescens (cyanobacteria) in a pre-alpine lake observed using an autonomous sampling platform. Limnol Oceanogr 58, 1892–1906.
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Piwosz, K., Salcher, M.M., Zeder, M., Ameryk, A., and Pernthaler, J. (2013). Seasonal dynamics and activity of typical freshwater bacteria in brackish waters of the Gulf of Gdańsk. Limnol Oceanogr 58:817-826
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Salcher, M.M., Posch, T., Pernthaler, J. (2013) In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake. ISME Journal 7:896-907
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Shabarova, T., Widmer, F., and Pernthaler, J. (2013) Mass effects meet species sorting: Transformations of microbial assemblages in epiphreatic subsurface karst water pools. Environ Microbiol online early
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Eckert, E.M., Salcher, M.M., Posch, T., Eugster, B., and Pernthaler, J. (2012) Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom. Environ Microbiol 14:794-806
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Hitz, G., Pomerleau, F., Garneau, M.E., Pradalier, C., Posch, T., Pernthaler, J., and Siegwart, R.Y. (2012) Autonomous Inland Water Monitoring. Design and Application of a Surface Vessel. IEEE Robotics & Automation Magazine 19(1), 62-72.

Horňák, K., Zeder, M., Blom, J. F., Posch, T., and Pernthaler, J. (2012). Suboptimal light conditions negatively affect the heterotrophy of Planktothrix rubescens but are beneficial for accompanying Limnohabitans spp. Environ Microbiol 14, 765-778.
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Posch, T., Koester, O., Salcher, M.M., and Pernthaler, J. (2012) Harmful filamentous cyanobacteria favoured by reduced water turnover with lake warming. Nature Climate Change 2:809-813
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Salcher, M.M., Pernthaler J., Frater N., Posch T. (2011). Vertical and longitudinal distribution patterns of differnt bacterioplankton populations in a canyon-shaped, deep prealpine lake. Limnol Oceanogr 56:2027-2039.
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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). ISMEJ 5:1242-1252.
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Takeuchi, Y., Salcher, M.M., Ushio, M., Shimizu-Inatsugi, R., Kobayashi, M.J., Diway, B., Von Mering, C., Pernthaler, J., Shimizu, K.K. (2011). Enzyme Activity in the Dissolved and Particulate Fraction of the Fluid from Four Pitcher Plant Species of the Genus Nepenthes. PLoS ONE 6:9
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Van den Wyngaert, S., Salcher, M.M., Pernthaler, J., Zeder, M., and 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.
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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. Microsc Microanal. 2011 Oct;17(5):799-809.
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Alonso-Saez, L., Pinhassi, J., Pernthaler, J., and Gasol, J.M. (2010). Leucine-to-carbon empirical conversion factor experiments: does bacterial community structure have an influence? Environmental Microbiology 12, 2988-2997.

Blom, J.F., Hornak, K., Simek, K., and Pernthaler, J. (2010). Aggregate formation in a freshwater bacterial strain induced by growth state and conspecific chemical cues. Environmental Microbiology 12, 2486-2495.

Blom, J.F., Zimmermann, Y.S., Ammann, T., and 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.

Blom, J.F., and Pernthaler, J. (2010). Antibiotic effects of three strains of chrysophytes (Ochromonas, Poterioochromonas) on freshwater bacterial isolates. Fems Microbiology Ecology 71, 281-290.

Chaffron, S., Rehrauer, H., Pernthaler, J., and von Mering, C. (2010). A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Research 20, 947-959.

Piwosz, K., and 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.

Salcher, M.M., Pernthaler, J., and Posch, T. (2010). Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake. Limnology and Oceanography 55, 846-856.
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Shabarova, T., and Pernthaler, J. (2010). Karst pools in subsurface environments: collectors of microbial diversity or temporary residence between habitat types. Environmental Microbiology 12, 1061-1074.

Zeder, M., Kohler, E., and Pernthaler, J. (2010). Automated Quality Assessment of Autonomously Acquired Microscopic Images of Fluorescently Stained Bacteria. Cytometry Part A 77A, 76-85.

Zeder, M., Van den Wyngaert, S., Koester, O., Felder, K.M., and 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.

Alonso, C., Zeder, M., Piccini, C., Conde, D., and Pernthaler, J. (2009). Ecophysiological differences of betaproteobacterial populations in two hydrochemically distinct compartments of a subtropical lagoon. Environmental Microbiology 11, 867-876.

Buck, U., Grossart, H.-P., Amann, R., and Pernthaler, J. (2009). Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake. Environmental Microbiology 11, 1854-1865.

Piccini, C., Conde, D., Pernthaler, J., and 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.

Schattenhofer, M., Fuchs, B.M., Amann, R., Zubkov, M.V., Tarran, G.A., and Pernthaler, J. (2009). Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean. Environmental Microbiology 11, 2078-2093.

Schmidt, S., Blom, J.F., Pernthaler, J., Berg, G., Baldwin, A., Mahenthiralingam, E., and Eberl, L. (2009). Production of the antifungal compound pyrrolnitrin is quorum sensing-regulated in members of the Burkholderia cepacia complex. Environmental Microbiology 11, 1422-1437.

Zeder, M., Peter, S., Shabarova, T., and 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.

Zeder, M., and Pernthaler, J. (2009). Multispot Live-Image Autofocusing for High-Throughput Microscopy of Fluorescently Stained Bacteria. Cytometry Part A 75A, 781-788.

Allers, E., Niesner, C., Wild, C., and Pernthaler, J. (2008). Microbes enriched in seawater after addition of coral mucus. Applied and Environmental Microbiology 74, 3274-3278.

Fazi, S., Amalfitano, S., Piccini, C., Zoppini, A., Puddu, A., and Pernthaler, J. (2008). Colonization of overlaying water by bacteria from dry river sediments. Environmental Microbiology 10, 2760-2772.

Salcher, M.M., Pernthaler, J., Zeder, M., Psenner, R., and Posch, T. (2008). Spatio-temporal niche separation of planktonic Betaproteobacteria in an oligo-mesotrophic lake. Environmental Microbiology 10, 2074-2086.
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Allers, E., Gomez-Consarnau, L., Pinhassi, J., Gasol, J.M., Simek, K., and Pernthaler, J. (2007). Response of Alteromonadaceae and Rhodobacteriaceae to glucose and phosphorus manipulation in marine mesocosms. Environmental Microbiology 9, 2417-2429.

Alonso, C., Warnecke, F., Amann, R., and Pernthaler, J. (2007). High local and global diversity of Flavobacteria in marine plankton. Environmental Microbiology 9, 1253-1266.

Alonso-Saez, L., Balague, V., Sa, E.L., Sanchez, O., Gonzalez, J.M., Pinhassi, J., Massana, R., Pernthaler, J., Pedros-Alio, C., and 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.

Fazi, S., Amalfitano, S., Pizzetti, H., and Pernthaler, J. (2007). Efficiency of fluorescence in situ hybridization for bacterial cell identification in temporary river sediments with contrasting water content. Systematic and Applied Microbiology 30, 463-470.

Vila-Costa, M., Pinhassi, J., Alonso, C., Pernthaler, J., and Simo, R. (2007). An annual cycle of dimethylsulfoniopropionate-sulfur and leucine assimilating bacterioplankton in the coastal NW Mediterranean. Environmental Microbiology 9, 2451-2463.

Alonso, C., and Pernthaler, J. (2006). Concentration-dependent patterns of leucine incorporation by coastal picoplankton. Applied and Environmental Microbiology 72, 2141-2147.

Alonso, C., and Pernthaler, J. (2006). Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters. Environmental Microbiology 8, 2022-2030.

Piccini, C., Conde, D., Alonso, C., Sommaruga, R., and Pernthaler, J. (2006). Blooms of single bacterial species in a coastal lagoon of the southwestern Atlantic Ocean. Applied and Environmental Microbiology 72, 6560-6568.

Alonso, C., and Pernthaler, J. (2005). Incorporation of glucose under anoxic conditions by bacterioplankton from coastal North Sea surface waters. Applied and Environmental Microbiology 71, 1709-1716.

Beardsley, C., Knittell, K., Amann, R., and Pernthaler, J. (2005). Quantification and distinction of aplastidic and plastidic marine nanoplankton by fluorescence in situ hybridization. Aquatic Microbial Ecology 41, 163-169.

Fazi, S., Amalfitano, S., Pernthaler, J., and Puddu, A. (2005). Bacterial communities associated with benthic organic matter in headwater stream microhabitats. Environmental Microbiology 7, 1633-1640.

Herndl, G.J., Reinthaler, T., Teira, E., van Aken, H., Veth, C., Pernthaler, A., and Pernthaler, J. (2005). Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Applied and Environmental Microbiology 71, 2303-2309.

Mindl, B., Sonntag, B., Pernthaler, J., Vrba, J., Psenner, R., and Posch, T. (2005). Effects of phosphorus loading on interactions of algae and bacteria: reinvestigation of the 'phytoplankton-bacteria paradox' in a continuous cultivation system. Aquatic Microbial Ecology 38, 203-213.

Pernthaler, A., and Pernthaler, J. (2005). Diurnal variation of cell proliferation in three bacterial taxa from coastal North Sea waters. Applied and Environmental Microbiology 71, 4638-4644.

Pernthaler, A., and Pernthaler, J. (2005). Simultaneous fluorescence in situ hybridization of mRNA and rRNA for the detection of gene expression in environmental microbes. In Environmental Microbiology, pp. 352-+.

Pernthaler, J. (2005). Predation on prokaryotes in the water column and its ecological implications (vol 3, pg 537, 2005). Nature Reviews Microbiology 3.

Pernthaler, J. (2005). Predation on prokaryotes in the water column and its ecological implications. Nature Reviews Microbiology 3, 537-546.

Pernthaler, J., and Amann, R. (2005). Fate of heterotrophic microbes in pelagic habitats: Focus on populations. Microbiology and Molecular Biology Reviews 69, 440-+.

Salcher, M.M., Pernthaler, J., Psenner, R., and Posch, T. (2005). Succession of bacterial grazing defense mechanisms against protistan predators in an experimental microbial community. Aquatic Microbial Ecology 38, 215-229.
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Warnecke, F., Sommaruga, R., Sekar, R., Hofer, J.S., and Pernthaler, J. (2005). Abundances, identity, and growth state of actinobacteria in mountain lakes of different UV transparency. Applied and Environmental Microbiology 71, 5551-5559.

Peplies, J., Lau, S.C.K., Pernthaler, J., Amann, R., and Glockner, F.O. (2004). Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environmental Microbiology 6, 638-645.

Pernthaler, J., Zollner, E., Warnecke, F., and Jurgens, K. (2004). Bloom of filamentous bacteria in a mesotrophic lake: Identity and potential controlling mechanism. Applied and Environmental Microbiology 70, 6272-6281.

Sekar, R., Fuchs, B.M., Amann, R., and Pernthaler, J. (2004). Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Applied and Environmental Microbiology 70, 6210-6219.

Teira, E., Reinthaler, T., Pernthaler, A., Pernthaler, J., and Herndl, G.J. (2004). Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and archaea in the deep ocean. Applied and Environmental Microbiology 70, 4411-4414.

Warnecke, F., Amann, R., and Pernthaler, J. (2004). Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environmental Microbiology 6, 242-253.

Beardsley, C., Pernthaler, J., Wosniok, W., and Amann, R. (2003). Are readily culturable bacteria in coastal North Sea waters suppressed by selective grazing mortality? Applied and Environmental Microbiology 69, 2624-2630.

Burkert, U., Warnecke, F., Babenzien, D., Zwirnmann, E., and Pernthaler, J. (2003). Members of a readily enriched beta-proteobacterial clade are common in surface waters of a humic lake. Applied and Environmental Microbiology 69, 6550-6559.

Pernthaler, J., Pernthaler, A., and Amann, R. (2003). Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization. Applied and Environmental Microbiology 69, 2631-2637.

Sekar, R., Pernthaler, A., Pernthaler, J., Warnecke, F., Posch, T., and Amann, R. (2003). An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Applied and Environmental Microbiology 69, 2928-2935.

Warnecke, F., Pernthaler, J., Sekar, R., and Amann, R. (2003). Diversity of freshwater Actinobacteria and their detection by fluorescence in situ hybridization (FISH). Abstracts of the General Meeting of the American Society for Microbiology 103, N-087.

Pernthaler, A., Pernthaler, J., Schattenhofer, M., and Amann, R. (2002). Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Applied and Environmental Microbiology 68, 5728-5736.

Pernthaler, A., Pernthaler, J., and Amann, R. (2002). Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Applied and Environmental Microbiology 68, 3094-3101.

Pernthaler, A., Preston, C.M., Pernthaler, J., DeLong, E.F., and Amann, R. (2002). Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea. Applied and Environmental Microbiology 68, 661-667.

Simek, K., Nedoma, J., Pernthaler, J., Posch, T., and Dolan, J.R. (2002). Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 81, 453-463.

Eilers, H., Pernthaler, J., Peplies, J., Glockner, F.O., Gerdts, G., and Amann, R. (2001). Isolation of novel pelagic bacteria from the German bight and their seasonal contributions to surface picoplankton. Applied and Environmental Microbiology 67, 5134-5142.

Pernthaler, A., Pernthaler, J., Eilers, H., and Amann, R. (2001). Growth patterns of two marine isolates: Adaptations to substrate patchiness? Applied and Environmental Microbiology 67, 4077-4083.

Pernthaler, J., Glockner, F.O., Schonhuber, W., and Amann, R. (2001). Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. Methods in Microbiology, Vol 30 30, 207-226.

Pernthaler, J., Posch, T., Simek, K., Vrba, J., Pernthaler, A., Glockner, F.O., Nubel, U., Psenner, R., and Amann, R. (2001). Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture. Applied and Environmental Microbiology 67, 2145-2155.

Posch, T., Jezbera, J., Vrba, J., Simek, K., Pernthaler, J., Andreatta, S., and Sonntag, B. (2001). Size selective feeding in Cyclidium glaucoma (Ciliophora, Scuticociliatida) and its effects on bacterial community structure: A study from a continuous cultivation system. Microbial Ecology 42, 217-227.

Posch, T., Loferer-Krossbacher, M., Gao, G., Alfreider, A., Pernthaler, J., and Psenner, R. (2001). Precision of bacterioplankton biomass determination: a comparison of two fluorescent dyes, and of allometric and linear volume-to-carbon conversion factors. Aquatic Microbial Ecology 25, 55-63.

Simek, K., Pernthaler, J., Weinbauer, M.G., Hornak, K., Dolan, J.R., Nedoma, J., Masin, M., and Amann, R. (2001). Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. Applied and Environmental Microbiology 67, 2723-2733.

Eilers, H., Pernthaler, J., Glockner, F.O., and Amann, R. (2000). Culturability and in situ abundance of pelagic bacteria from the North Sea. Applied and Environmental Microbiology 66, 3044-3051.

Eilers, H., Pernthaler, J., Gloeckner, F.O., and Amann, R. (2000). The marine gammas: Culturability of pelagic bacteria from the North Sea. Abstracts of the General Meeting of the American Society for Microbiology 100, 467.

Eilers, H., Pernthaler, J., and Amann, R. (2000). Succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts. Applied and Environmental Microbiology 66, 4634-4640.

Glockner, F.O., Zaichikov, E., Belkova, N., Denissova, L., Pernthaler, J., Pernthaler, A., and Amann, R. (2000). Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Applied and Environmental Microbiology 66, 5053-+.

Oerther, D.B., Pernthaler, J., Schramm, A., Amann, R., and Raskin, L. (2000). Monitoring precursor 16S rRNAs of Acinetobacter spp. in activated sludge wastewater treatment systems. Applied and Environmental Microbiology 66, 2154-2165.

Jurgens, K., Pernthaler, J., Schalla, S., and Amann, R. (1999). Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. Applied and Environmental Microbiology 65, 1241-1250.

Oerther, D.B., Pernthaler, J., Schramm, A., Amann, R., and Raskin, L. (1999). Monitoring in situ activity of Acinetobacter spp. in activated sludge wastewater treatment systems using oligonucleotide hybridization probes targeting precursor-rRNA. Abstracts of the General Meeting of the American Society for Microbiology 99, 484.

Ravenschlag, K., Sahm, K., Pernthaler, J., and Amann, R. (1999). High bacterial diversity in permanently cold marine sediments. Applied and Environmental Microbiology 65, 3982-3989.

Pernthaler, J., Alfreider, A., Sattler, B., Gloeckner, F.O., Amann, R., and Psenner, R. (1998). Structure analysis of bacterial communities in a high mountain lake. In [Munich Contributions to Wastewater Fishery and River Biology

Pernthaler, J., Glockner, F.O., Unterholzner, S., Alfreider, A., Psenner, R., and Amann, R. (1998). Seasonal community and population dynamics of pelagic bacteria and archaea in a high mountain lake. Applied and Environmental Microbiology 64, 4299-4306.

Pernthaler, J., Posch, T., Simek, K., Vrba, J., Psenner, R., and Amann, R. (1998). Protist-induced population shifts in an experimental microbial community. In [Munich Contributions to Wastewater Fishery and River Biology

Pernthaler, J., Alfreider, A., Posch, T., Andreatta, S., and Psenner, R. (1997). In situ classification and image cytometry of pelagic bacteria from a high mountain lake (Gossenkollesee, Austria). Applied and Environmental Microbiology 63, 4778-4783.

Pernthaler, J., Posch, T., Simek, K., Vrba, J., Amann, R., and Psenner, R. (1997). Contrasting bacterial strategies to coexist with a flagellate predator in an experimental microbial assemblage. Applied and Environmental Microbiology 63, 596-601.

Posch, T., Pernthaler, J., Alfreider, A., and Psenner, R. (1997). Cell-specific respiratory activity of aquatic bacteria studied with the tetrazolium reduction method, cyto-clear slides, and image analysis. Applied and Environmental Microbiology 63, 867-873.

Simek, K., Hartman, P., Nedoma, J., Pernthaler, J., Springmann, D., Vrba, J., and Psenner, R. (1997). Community structure, picoplankton grazing and zooplankton control of heterotrophic nanoflagellates in a eutrophic reservoir during the summer phytoplankton maximum. Aquatic Microbial Ecology 12, 49-63.

Simek, K., Vrba, J., Pernthaler, J., Posch, T., Hartman, P., Nedoma, J., and Psenner, R. (1997). Morphological and compositional shifts in an experimental bacterial community influenced by protists with contrasting feeding modes. Applied and Environmental Microbiology 63, 587-595.

Vrba, J., KofronovaBobkova, J., Pernthaler, J., Simek, K., Macek, M., and Psenner, R. (1997). Extracellular, low-affinity beta-N-acetylglucosaminidases linked to the dynamics of diatoms and crustaceans in freshwater systems of different trophic degree. Internationale Revue Der Gesamten Hydrobiologie 82, 277-286.

Alfreider, A., Pernthaler, J., Amann, R., Sattler, B., Glockner, F.O., Wille, A., and Psenner, R. (1996). Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization. Applied and Environmental Microbiology 62, 2138-2144.

Glockner, F.O., Amann, R., Alfreider, A., Pernthaler, J., Psenner, R., Trebesius, K., and Schleifer, K.H. (1996). An in situ hybridization protocol for detection and identification of planktonic bacteria. Systematic and Applied Microbiology 19, 403-406.

Macek, M., Simek, K., Pernthaler, J., Vyhnalek, V., and Psenner, R. (1996). Growth rates of dominant planktonic ciliates in two freshwater bodies of different trophic degree. Journal of Plankton Research 18, 463-481.

Pernthaler, J., Sattler, B., Simek, K., Schwarzenbacher, A., and Psenner, R. (1996). Top-down effects on the size-biomass distribution of a freshwater bacterioplankton community. Aquatic Microbial Ecology 10, 255-263.

Pernthaler, J., Simek, K., Sattler, B., Schwarzenbacher, A., Bobkova, J., and Psenner, R. (1996). Short-term changes of protozoan control on autotrophic picoplankton in an oligo-mesotrophic lake. Journal of Plankton Research 18, 443-462.

Simek, K., Macek, M., Pernthaler, J., Straskrabova, V., and Psenner, R. (1996). Can freshwater planktonic ciliates survive on a diet of picoplankton? Journal of Plankton Research 18, 597-613.

Vrba, J., Simek, K., Pernthaler, J., and Psenner, R. (1996). Evaluation of extracellular, high-affinity beta-N-acetylglucosaminidase measurements from freshwater lakes: An enzyme assay to estimate protistan grazing on bacteria and picocyanobacteria. Microbial Ecology 32, 81-99.