Main Research Topics

River Ecology

We try to understand the functioning of large rivers. Our group is running a large research laboratory on the River Rhine which allows the study of the biology of running water animals in situ in flow channels and exposed substrates independent of the water level. A current topic is the analysis of the grazing of plankton by benthic organisms that can have a strong impact on the composition and functioning of the river system. Both the temperature and water level can strongly influence the intensity of the benthic control, giving rise to the hypothesis that the bentho-pelagic coupling in connection with small changes in the climate could generate large changes in the ecosystem composition and function. We aim to explain and predict the benthic impact on the development of different plankton groups in response to changing climate conditions in a large river ( Rhine ). By identifying temperature generated mismatches in the balance between the grazing rates of benthic consumers (mussels, insect larvae, sponges and biofilm communities) the numerical responses of selected grazers towards warming is investigated in experiments and field studies.
A very significant problem for the functioning of large rivers is the introduction of neozoans, novel communities are established which completely changed the matter flux in the River Rhine. The following important invasive species are currently investigated regarding their impact on the matter flux such as food selectivity, temperature response and effects of bioturbation: chinese midden crab (Eriocheir sinensis), asian clam (Corbicula spp.), polychaet worm Hypania invalida and freshwater sponges.
Of special interest are interactions between macrofauna organisms and plankton communities as well as biofilm communities.
These biofilms form another focus of our investigations in the River Rhine. Natural surface-attached communities are composed of bacteria, algae, fungi, and “animals” (protozoans and small metazoans). Consequently, we as ecologists consider biofilms as “complex communities of microbiota". We investigate unicellular grazers (protozoans) in controlling the structure of biofilm-dwelling bacteria communities under natural and semi-natural conditions. Biofilms can be analyzed "in situ" in micro-chambers (‘flow cells’) and inoculated by the discharge of either natural water from the River Rhine (the grazer composition can be manipulated by size fractionation) or by field isolates of complex bacterial communities in combination with the controlled addition of specific grazers. These different approaches allow to test the effects of natural grazer communities with different complexities. We could show that biofilms significantly influence the structure of the surrounding plankton community.

Arndt, H.,  Schmidt-Denter, K., Auer, B. & Weitere, M. (2003). Protozoans and biofilms. In: Fossil and Recent Biofilms (Krumbein, W.E., Paterson, D.M. & Zavarzin, G.A., Eds.) Kluwer Academic Publ., Dordrecht., p. 173-189

Arndt,H., Borcherding, J. & Kureck, A. (eds.)(2002):  Ecological Studies of Large Rivers. Internat. Rev. Hydrobiol. 87 (2 & 3): 137-348

Becker, G. (in press) Interactions between scrapers and periphyton.  In: Central European stream ecosystems: The long term study of the Breitenbach, Wagner, R., Marxsen, J., Zwick, P., Cox, E. (Eds), Wiley-VCH, Weinheim. ISBN 978-3-527-32952-

Kureck A. (1996) The life cycle and emergence of Ephoron virgo, a large potamal mayfly that has returned to the River Rhine. Arch. Hydrobiol. Suppl., Large Rivers 10;113:319-323

Vohmann, A., Borcherding, J., Kureck, A., Bij de Vaate, A., Arndt, H. & Weitere, M. (2010): Strong body mass decrease of the invasive clam Corbicula fluminea during summer. Biological Invasions 12: 53-64

Vohmann, A., Mutz, M., Arndt, H., Weitere, M. (2009): Grazing impact and phenology of the freshwater sponge Ephydatia muelleri and the bryozoans Plumatella emarginata and Fredericella sultana under experimental warming. Freswater Biology 54: 1078-1092

Weitere, M., Vohmann, A., Schulz, N., Linn, C., Dietrich, D. Arndt, H. (2009): Linking environmental warming to the fitness of the invasive clam Corbicula fluminea. Global Change Biology, 15: 2838-2851

Weitere, M., Scherwass, A., Sieben, K.-T., Friedrich, G., Arndt, H. (2005). Planctonic Food Web Structure and Potential Carbon Flow in the Lower River Rhine with a Focus on the Role of the Protozoans. River Research and Applications: 21, 535-549

Additional selected publications:

Ackermann, B., Esser, M., Scherwaß, A., Arndt, H. (2011) Long-term dynamics of microbial biofilm communities of the River Rhine with special references to ciliates. Int. Revue Hydrobiol. 96:1-19

Bergfeld, T., Scherwass, A., Ackermann,B., Arndt;H. and Schöl,A. (2009): Comparison of the components of the planktonic food web in three large rivers (Rhine, Moselle and Saar)". River Research and Applications: 25 (10): 1232-1250

Boenigk, J. & Arndt, H. (2002) Bacterivory by heterotrophic flagellates: community structure and feeding strategies. Antonie van Leeuwenhoek 81: 465-480

Kathol, M., Norf, H., Arndt, H., Weitere, M. (2009): Effects on temperature increase on the grazing within river biofilms under semi-natural conditions. AME 52: 283-296

Kureck A. (1992) Neue Tiere im Rhein. Die Wiederbesiedlung des Stroms und die Ausbreitung der Neozoen. Naturwissenschaften 79:533-40

Norf, H., Arndt, H., Weitere, M. (2009): Responses of biofilm-dwelling ciliate communities to planctonic and benthic resource enrichment. Microbial Ecology 57: 678-700

Norf, H., Arndt, H., Weitere, M. (2009): Effects of resource supplements on mature ciliate biofilms: an empirical test using a new type of flow cell. Biofouling 25 (6): 769-778

Risse-Buhl, U., Scherwass, A., Schlüssel, A., Arndt, A., Kröwer, S., Küsel, K. (2009): Detachment and mortality of surface-associated ciliates at increased flow velocities. AME 55: 209-218

Scherwass, A., T. Bergfeld, A. Schoel, M. Weitere und H. Arndt (2010): Changes in the plankton community along the length of the River Rhine: Lagrangian sampling during a spring situation. JJ. Plankt. Res. 32 (4): 491-502

Stief, P. & Becker, G. (2005). Structuring of epilithic biofilms by the caddisfly Tinodes rostocki: photosynthetic activity and photopigment distribution in and beside larval retreats. Aquatic Microbial Ecology 38:71-79

Weitere, M. & Arndt, H. (2002): Top-down effects on pelagic heterotrophic nanoflagellates (HNF) in a large river (River Rhine): Do losses to the benthos play a role? Freshw. Biol. 47: 1437-1450

Weitere, M. & Arndt, H. (2002): Water discharge regulated bacteria/ heterotrophic nanoflagellates (HNF) interactions in the water column of the River Rhine. Microb. Ecol. 44: 19-29

Wey, J.K., Norf, H., Arndt, H., Weitere, M. (2009): Role of dispersal in shaping communities of ciliates and heterotrophic flagellates within riverine biofilms. Limnol. Oceanogr. 54(5): 1615-1626

Marine Biology

Marine systems form the largest part of the biosphere. Deep-sea bottom (depths larger than 1000m) covers more than the half of the earth surface. It is amazing how little we know about the biological processes and the biodiversity in this important ecosystem. We took part in several deep-sea expeditions to study the diversity of unicellular eukaryotes as the by far most productive component among marine eukaryotes. The research on unicellular eukaryotes is challenging since nearly nothing is known about their contribution to tha deep-sea marine life. Recent studies were aimed to recognize possible relationships between the primary production in the water column and the benthic biodiversity. Moreover, possible biogeographic barriers between the different deep-sea basins in the Atlantic and Mediterranean were analyzed. An additional goal is to prove whether there exists a latitudinal diversity gradient along transects within deep-sea basins. In approximately 5,000m depth, the organismic biodiversity of all size classes (from nano- up to megafauna) is surprisingly high. Each single sample contains a lot of new species and even new families. We co-operate especially with the Senckenberg Museum in Frankfurt/M. and Wilhelmshaven (Prof. Martinez, Prof. Türkay) and the Free University of Berlin (Prof. Hausmann). The methods we apply are isolation and cultivation of deep-sea protists, the morphological analysis and molecular identification of species, the establishment of clone libraries of uncultivated samples and the study of the specific ecology of deep-sea protists using laboratory experiments. In addition, we are interested in the global distribution of marine protists in surface waters from the Arctic to the Tropics.

Arndt, H., Hausmann, K., Wolf, M. (2003). Deep-sea heterotrophic nanoflagellates of the Eastern Mediterranean Sea: qualitative and quantitative aspects of their pelagic and benthic occurence. Mar. Ecol. Progr. Ser. 256: 45-56

Hausmann, K., Selchow, P., Scheckenbach, F., Weitere, M., Arndt, H. (2006). Cryptic Species in a Morphospecies Complex of Heterotrophic Flagellates: the Case Study of Caecitellus spp. Acta Protozoologica 45: 415-431

Nitsche, F. & Arndt, H. (2008): A new choanoflagellate species from Taiwan: Morphological and molecular biological studies of Diplotheca elongata nov. spec. and D. costata. Europ. J. Protistol. 44: 220-226

Nitsche F., Weitere M., Scheckenbach F., Hausmann K., Wylezich C., Arndt H. (2007): Deep sea records of choanoflagellates with a description of two new species. Acta Protozool. 46 (2): 99-106

Scheckenbach, F., Hausmann, K., Wylezich, C., Weitere, M., Arndt, H. (2010): Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor. PNAS 107(1): 115-120

Scheckenbach F, Wylezich C, Mylnikov AP, Weitere M, Arndt H. (2006). Molecular comparisons of freshwater and marine isolates of the same morphospecies of heterotrophic flagellates. Appl Environ. Microb. 72 (10): 6638-6643

Scheckenbach F., Wylezich C., Weitere M., Hausmann K. & Arndt H. (2005). Molecular identity of strains of heterotrophic flagellates isolated from surface waters and deep-sea sediments of the South Atlantic based on SSU rDNA. Aquat. Microb. Ecol. 38(3): 239-247


Fish Ecology

Ecological studies on fish are mainly carried out in the Ecological Research Station of the Institute for Zoology. The surrounding area with oxbow lakes and gravel pit lakes as well as the adjacent River Rhine and its tributaries offer a unique arena for field studies in fish ecology. On the ground of the field station outdoor mesocosms and indoor aquaria systems allow detailed autecological and behavioural studies as well as studies on the community level. Based on extensive international co-operation, different topics of research were in our focus in recent years, including (1) the early piscivory of juvenile European perch (Perca fluviatilis, from 28 mm TL onwards) and its consequence for the functioning of fish populations in lakes, (2) the study migratory fishes, mainly North Sea houting (Coregonus oxyrinchus ) and European eel (Anguilla anguilla), (3) the influence of connectivity of ephemeral floodplain waters on the fish communities of the River Rhine, (4) the invasion of Gobiid species from the Danube to the Rhine system and their consequences for the fish communities at the Lower Rhine, and (5) on eco-evolutionary links in population ecology, sexual selection, life-history evolution, context-dependent reproductive decisions, behavioural adaptations to changing ecological contexts, and dynamics of sexual-asexual coexistence. In addition to actual research at the Ecological Research Station in Rees-Grietherbusch, a large project on the downstream migration of European Atlantic Salmon Smolts and European Silver Eel at different hydropower stations at different rivers in Germany (Unkemühle at the River Sieg, Kuhlemühle at the River Diemel, Gengenbach at the River Kinzig) is conducted in close cooperation with the Norwegian Institute for Nature Research (NINA, Trondheim, Finn Økland, Eva Thorstad, Torgeir Havn).

Bleeker, K., de Jong, K., van Kessel, N., Hinde. C.A., Nagelkerke, L.A.J. (2017): Evidence for ontogenetically and morphologically distinct alternative reproductive tactics in the invasive Round Goby Neogobius melanostomus. PLOS ONE 12(4): e0174828. doi: 10.1371/journal.pone.0174828

Havn, T.B., , Økland, F., Teichert, M.A.K., Heermann, L. , Borcherding, J. , Sæther, S.A., Tambets, M., Diserud, O.H., Thorstad, E.B. (2017): Movements of dead fish in rivers. Anim. Biotelemetry (2017). DOI 10.1186/s40317-017-0122-2

Thorstad, E.B., Havn, T.B., Saether, S.A., Heerman, L., Teichert, M.A.K., Diserud, G.H., Tambets, M., Borcherding, J., Odland, F. (2017): Survival and behaviour of Atlantic salmon smolts passing a run-of-river hydropower facility with a movable bulb turbine. Fish. Manag. Ecol. 2017: 1-9. DOI: 10.1111/fme.12216

Adrian-Kalchauser, I., Hirsch, P.E., Behrmann-Godel, J, Guyen,A.N., Watzlawczyk, S., Gertzen,S., Borcherding, J., Burkhardt-Holm, P. (2016): The invasive bighead goby Ponticola kessleri displays large-scale genetic similarities and small-scale genetic differentiation in relation to shipping patterns. Molecular Ecology 25: 1925-1943

Vallon, M., Anthes, N., Heubel, K.U. (2016): Water mold infection but not paternity induces selective filial cannibalism in a goby. Ecology and Evolution 6(20):7221-7229

Vallon, M., Grom, C., Kalb, N., Sprenger, N., Anthes, N., Lindström, K., Heubel, K.U.(2016): You eat what you are: Personality-dependent filial cannibalism in a fish with paternal care. Ecology and Evolution 6(5): 1340-1352

Borcherding, J., Breukelaar, A.W., Winter, H.V., König, U. (2014): Spawning migration and larval drift of anadromous North Sea houting (Coregonus oxyrinchus) in the River IJssel, the Netherlands. Ecology of Freshwater Fish 23: 161-170

Dierking, J., Phelps, L., Praebel, K., Ramm, G., Prigge, E., Borcherding, J., Brunke, M. & Eizaguirre, C. (2014): Anthropogenic hybridization between endangered migratory and commercially harvested stationary whitefish taxa (Coregonus spp.). Evolutionary Applications 7: 1068-1083

Borcherding, J., Dolina, M., Heermann, L., Knutzen, P., Krüger, S., Matern, S., van Treeck, R. & Gertzen, S. (2013): Feeding and niche differentiation in three invasive gobies in the Lower Rhine, Germany. Limnologica 43: 49-58

Scharbert, A., Borcherding, J. (2013): Relationships of hydrology and life-history strategies on the spatio-temporal habitat utilisation of fish in European temperate river floodplains. Ecological Indicators 29: 348-360

Magnhagen, C., Hellström, G., Borcherding, J., Heynen, M. (2012): Boldness in two perch populations–long-term differences and the effect of predation pressure. Journal of Animal Ecology 81: 1311-1318

Borcherding, J., Beeck, P., DeAngelis, D. L., Scharf, W. R. (2010): Match or mismatch: the influence of phenology on size-dependent life history and divergence in population structure. Journal of Animal Ecology 79(5): 1101-1112


Additional selected publications:

Borcherding, J., Heynen, M., Jäger-Kleinicke, T., Winter, H.V., Eckmann, R. (2010): Re-establishment of the North Sea houting in the River Rhine. Fisheries Management and Ecology 17: 291-293

Heermann, L., Eriksson, L.-O., Magnhagen, C., Borcherding, J. (2009): Size-dependent energy storage and winter mortality of perch. Ecology of Freshwater Fish 18: 560-571

Heynen, M., Heermann, L., Borcherding, J. (2011): Does the consumption of divergent resources influence risk taking behaviour in juvenile perch (Perca fluviatilis L.)? Ecology of Freshwater Fish 20: 1–4

Klein Breteler, J.K., Borcherding, J., Breukelaar, A., Jörgens, L., Staas, S., de Laak, G., Ingendahl, D. (2007): Assessment of population size and migration routes of silver eel in the River Rhine based on a 2-year combined mark-recapture and telemetry study. ICES Journal of Marine Science 64: 1450-1456

Molecular Ecology

Molecular methods are used in our group at the moment to study the phylogeny of protists and metazoans, the diversity of phylotypes, populations genetics, microevolutionary processes and gene expression patterns. Actually, protists are in the major focus of our studies. Despite many decades of study, their diversity in natural ecosystems is still rather poorly known, as is the extent to which many of these species are distributed on our planet. Protists are still a white area for research, many new interesting species can be detected and even important new genera and families are still undiscovered. These ‘unknown, uncultured phylotypes’ represent species, genera and higher-level taxa of protists that have not yet been described based on morphological criteria, and which have not yet been studied regarding their ecology. Some of these taxa are very important regarding the matter flux in their habitats. In the deep sea, groundwater and polar regions, the largest habitats of the biosphere, nanoprotists show an enormous up to now undiscoverd diversity with important functions for the stabilty of the ecosystems. Methods applied in our group at the moment are single cell PCR, establishment of clone libraries, 454 sequencing of protist communities, microsatellite analyses, etc.

Nitsche, F. & Arndt, H. (2008): A new choanoflagellate species from Taiwan: Morphological and molecular biological studies of Diplotheca elongata nov. spec. and D. costata. Europ. J. Protistol. 44: 220-226

Scheckenbach, F., Hausmann, K., Wylezich, C., Weitere, M., Arndt, H. (2010): Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor. PNAS 107(1): 115-120

Scheckenbach F, Wylezich C, Mylnikov AP, Weitere M, Arndt H. (2006). Molecular comparisons of freshwater and marine isolates of the same morphospecies of heterotrophic flagellates. Appl Environ. Microb. 72 (10): 6638-6643 

Scheckenbach F., Wylezich C., Weitere M., Hausmann K. & Arndt H.(2005): Molecular identity of strains of heterotrophic flagellates isolated from surface waters and deep-sea sediments of the South Atlantic based on SSU rDNA. Aquat. Microb. Ecol. 38(3): 239-247

Wylezich C., Nies G., Mylnikov A. P., Tautz D. & Arndt H. (2010): An evaluation of the use of LSU rRNA D1-D5 region for DNA based taxonomy of eukaryotic protists. Protist 161: 342-352

Wylezich C., Mylnikov A. P., Weitere M. & Arndt H. (2007): Distribution and phylogenetic relationships of freshwater thaumatomonads with a description of the new species Thaumatomonas coloniensis n. sp.  J. Eukaryot. Microbiol. 54(4): 347-357

Addidional selected publications:

Quintela Alonso, P., Nitsche, F. and Arndt, H. (2011): Molecular characterization and revised systematics of Microdiaphanosoma arcuatum (Ciliophora, Colpodea). Journal of Eukaryotic Microbiology 58: 114-119

Hausmann K, Selchow P, Scheckenbach F, Weitere M, Arndt H. (2006). Cryptic Species in a Morphospecies Complex of Heterotrophic Flagellates: The case study of Caecitellus spp.  Acta Protozool. 45, 415-431

Loquay N., Wylezich C. & Arndt H. (2009): Composition of groundwater nanoprotist communities in different aquifers based on aliquot cultivation and genotype assessment of cercomonads. Fund. Appl. Limnol. 174 (3):261-269

Theoretical ecology and chaos research

Spiral chaos

Finding out why natural population densities change over time and vary depending on location is one of the central goals of ecology.  The recognition that even simple ecological systems have the potential for chaotic behaviour has made chaos a topic of considerable interest among theoretical ecologists. However, there is still a lack of experimental evidence to demonstrate that chaotic behaviour occurs in the real world of coexisting populations in multi-species systems.
We study the dynamics of defined predator-prey systems in controlled systems (e.g. chemostats) as model systems to understand the role of chaotic and other intrinsic dynamics in the "real world". In the course of a long series of autecological studies of protists in chemostats and batch systems we arrived at a defined chemostat system consisting of multi-species–systems which can be studied regarding the different types of dynamic behaviour, stable coexistence, limit cycles and even chaos.
Apart from the intuitive understanding that external (extrinsic) stimuli (such as temperatures) influence the variability of abundances, we hope to understand the internal (intrinsic) characteristics of a population which give rise to population dynamics with large and (at certain parameter ranges) even chaotic fluctuations of abundances even under constant and predictable conditions. We are just at the beginning to understand the role of intrinsic fluctuations in nature and are on the way to study the type and properties of chaotic attractors in experimental systems.

Becks, L., Hilker, F., Malchow, H., Jürgens, K., Arndt, H. (2005). Experimental demonstration of chaos in a microbial food web. Nature 435, 1226-1229

Becks, L. and H. Arndt (2008): Transitions from stable equilibria to chaos, and back, in an experimental food web. Ecology 89 (11): 3222-3226

Additional selected publications:

Stauffer, D., Arndt, H. (2005). Simulation and experiment of extinction or adaptation of biological species after temperature changes. Int. J. Mod. Phys. C. 16 (3), 389-392



Polar Research


As polar regions are severely affected by global warming, the effects of rising temperatures in aquatic systems can be studied. The defined spatial and temporal separation of the polar regions offers the opportunity to study potential speciation and population genetics of protists.  In polar regions, heterotrophic nanoflagellates are major consumers of bacteria and contribute significantly to the carbon flux from DOC via bacteria to larger organisms such as ciliates and metazoans. Heterotrophic flagellate biomass may greatly exceed bacterial biomass in the sea ice. According to our recent molecular biological and morphological studies of Antarctic and Arctic nanofauna, morphological investigations reveal only limited taxonomic resolution for these tiny organisms (mainly 2-8µm cell size). Many morphotypes contain several genotypes with sometimes high evolutionary distances (p-distances of SSU rDNA). We study the role of endemism in polar waters, the discrepancies and overlaps between morphotypes, genotypes and ecotypes of selected taxa to draw conclusions regarding the possible effects of small changes in temperature on the sensitive Antarctic and Arctic ice biota. We take samples from Antarctic and Arctic sites, establish cultures of unicelluar organisms and analyse them combining morphological, molecular biological and ecological methods. Knowing more about the role of biodiversity of the most important bacterivorous components of Antarctic and Arctic ecosystems will support our understanding of ecological processes in polar regions. In addition, we investigate the global distribution of nanoprotists and analyze their potential global distribution. Bachelor, Master and Ph.D. students are incorporated in the project in laboratory and field work. The global distribution and the ways of distribution are studied using ice and snow as archives and air as transport media. Among our sampling sites are Svålbard (Spitsbergen), Greenland and Iceland in the North as well as the Antarctic Peninsula in the South. In the lab we use molecular (single cell PCR, 454 sequencing), morphological (high resolution video-enhanced microscopy, electron microscopy) and cultivation methods to analyse the samples.

Dietrich, D., Arndt, H. (2004): Benthic heterotrophic flagellates in an Antarctic melt water stream. Hydrobiologia, 529: 59-70

Nitsche F., Weitere M., Scheckenbach F., Hausmann K., Wylezich C., Arndt H. (2007): Deep sea records of choanoflagellates with a description of two new species. Acta Protozool. 46 (2): 99-106

River Ecology

Ecological Rhine Station Cologne
Lab at the Ecological Rhine Station
Ephoron virgo

Marine Biology

Fish Ecology


chaos research


Polar Research