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Physical Microbiology

Our newly established research group, Physical Microbiology, works at the interface of biophysics, microbiology, and biogeochemistry. We investigate how physical transport processes interact with microbial activity to shape carbon and nutrient cycling in marine environments. Our research bridges scales, from individual cells and their immediate surroundings to regional ecosystems, to understand how microscale interactions influence larger-scale biogeochemical dynamics.

Our approach combines numerical modeling, field observations, and controlled laboratory experiments. We use large-eddy simulations and reactive transport models, including models of porous media, alongside in situ measurements with platforms developed by our team, such as the benthic observatory LanceALot and the STB lander. Experiments in flow-through reactors and microfluidic systems allow us to isolate mechanisms under controlled conditions, while stable-isotope tracing coupled with nanoscale secondary ion mass spectrometry (NanoSIMS) reveals carbon and nutrient uptake at the level of individual cells.

By connecting these approaches across scales, we aim to uncover the mechanisms linking physical transport and microbial activity, quantify their importance in natural environments, and determine how they jointly shape marine biogeochemical cycles.

Projects

HypoWave investigates how short-term fluctuations in oxygen availability affect microbial processes and nitrogen cycling in coastal waters, focusing on low-oxygen events and their effects on microbial activity in marine particles and sediments.

Shore-to-Basin investigates how physical, biological, and biogeochemical processes connect shallow coastal waters with the deeper Baltic Sea, shaping the transport and transformation of carbon, nutrients, and oxygen.

 

Technicians

Anne Köhler
Annett Grüttmüller

Scientists & Students

Dr. Angela Vogts (NanoSIMS)
Dr. Sophie Kache (PostDoc)
Emma Charlotte Clauder (Master Student)

Group Leader

Group Publications

2027

  • Wolf, F., L. A. Schulz, O. Thiele, S. Ahmerkamp, P. Holtermann, K. Attard and M. L. Zettler (2027). Carbon fluxes within an Arctica islandica habitat in the German Baltic Sea. Estuar. Coast. Shelf Sci. 344: 110306, doi: 10.1016/j.ecss.2026.110306

2026

  • Benavides, M., A. Coet, M. Sebastian, A. Vogts, C. Furbo Reeder, E. Cerdan-Garcia, L. Norman, R. Hawley, O. Flanagan, M. C. Lohan, J. E. Hopkins and C. Mahaffey (2026). Particle-associated diazotrophs drive nitrogen fixation in Arctic subsurface waters of the Barents Sea. Nat. Commun. 17: 9, doi: 10.1038/s41467-026-75354-5
  • Feuring, A., C. D. Lawrence, J. Salcedo, M. J. Whitehouse, A. Vogts, L. Zoccarato and I. Klawonn (2026). Fungal parasites infecting N2-fixing cyanobacteria reshape carbon and N2 fixation and trophic transfer. Nat. Commun. 17: 154, doi: 10.1038/s41467-025-67818-x
  • Geersen, J., P. Feldens, L. Rollwage, L. M. Baumann, K. Krämer, P. Westfeld, S. Krastel, S. Ahmerkamp, F. Tauber and J. S. von Deimling (2026). Ship wake-induced water column mixing and meter-scale seabed erosion in the Baltic Sea. Nat. Commun. 17: 1350, doi: 10.1038/s41467-026-68875-6
  • Godefroid, M., F. Otero-Ferrer, M. Wind-Hansen, L. Behrendt, I. Ransquin, E. Soler-Onís, F. Espino, S. Littmann and S. Ahmerkamp (2026). Ciliary flow and morphology shape mass transport at the surface and within gastrovascular cavities of black corals. Commun. Biol. 9: 876, doi: 10.1038/s42003-026-10531-2
  • Koopmans, D., A. Schaap, V. Meyer, P. Färber, L. Queiss, L. Montilla, S. Loucaides, S. Ahmerkamp and U. Cardini (2026). Benthic Ecosystem Calcification Measured with Coupled pH and O2 Aquatic Eddy Covariance. ACS ES&T Water 6: 2719–2730, doi: 10.1021/acsestwater.5c00481
  • Lange, F., S. Ahmerkamp, A. Akeerath Mundanatt, F. M. Jalaluddin, G. Schulz, D. Voß, O. Zielinski, U. Hanz, G. Lavik, H. K. Marchant, J.-H. Hehemann, T. G. Ferdelman, M. Holtappels and M. M. M. Kuypers (2026). Algal glycans promote microbial turnover of organic matter through stabilization of subtidal permeable sandy sediments. Limnol. Oceanogr. 71: e70350, doi: 10.1002/lno.70350
  • Maerz, J., K. D. Six, S. Ahmerkamp and T. Ilyina (2026). Marine particles and their remineralization buffer future ocean biogeochemistry response to climate warming. Biogeosciences 23: 1897–1929, doi: 10.5194/bg-23-1897-2026
  • Pacherres, C. O., M. S. Dhillon, M. Bilbo, M. Hansen, D. R. Brumley, M. Aranda, S. Ahmerkamp and M. Kühl (2026). Acute temperature effects on cilia beating increase coral deoxygenation. Sci. Adv. 12: eaeg0950, doi: 10.1126/sciadv.aeg0950
  • Souley, S., S. Kache and H. Mahaman (2026). Physico-chemical characterization of the Niger river in Niamey and its impacts on Mormyridae biodiversity. Environ. Res. Commun. 8: 065026, doi: 10.1088/2515-7620/ae76e0
  • Wind-Hansen, M., M. Godefroid, A. Kalinichev, L. Behrendt, S. Ahmerkamp and K. Koren (2026). Flash nanoprecipitation of monodisperse luminescent nanosensors for simultaneous oxygen and flow imaging. Methods Appl. Fluoresc.: online, http://iopscience.iop.org/article/10.1088/2050-6120/aeac9c
  • Zeller, L. M., S. Schorn, L. Nicolas-Asselineau, J. Zopfi, S. Ahmerkamp, C. J. Schubert, F. Lepori, M. M. M. Kuypers, J. S. Graf and J. Milucka (2026). Redox gradients define the ecological niche of ciliates with denitrifying endosymbionts in anoxic lake waters. ISME J. 20: wrag043, doi: 10.1093/ismejo/wrag043

2025

  • Auer, F., S. Ahmerkamp, J. Cueto, C. Winter and M. Holtappels (2025). Extensive Oxygen Consumption in the Intertidal Infiltration Zone of Beach Aquifers—The Impact of Seasonal Input, Filtration Efficiency, and Morphodynamics. J. Geophys. Res. Biogeosciences 130: e2024JG008291, doi: 10.1029/2024JG008291
  • Jalaluddin, F. M., S. Ahmerkamp, H. K. Marchant, V. Meyer, K. Koren and M. M. M. Kuypers (2025). Microenvironments on individual sand grains enhance nitrogen loss in coastal sediments. Sci. Rep. 15: 16384, doi: 10.1038/s41598-025-00755-3
  • Kache, S., I. Liskow, J. Pein, M. Žilius and M. Voss (2025). The role of retention processes in the coastal filter of the Oder River. Estuar. Coast. Shelf Sci. 322: 109325, doi: 10.1016/j.ecss.2025.109325
  • Panthalil, B. S., A. Vogts, M. Benavides, M. J. Harke, C. Hassenrück, A. Subramaniam, J. P. Montoya and M. Voss (2025). Novel pennate diatom symbionts support high N2 fixation rates. ISME Commun. 5: ycaf190, doi: 10.1093/ismeco/ycaf190
  • Voss, M., P. Holtermann, S. Ahmerkamp, D. L. Arévalo Martínez, B. Cahill, M. Chouksey, J. W. Dippner, J. Dutz, P. Feldens, J. Geersen, K. Gentsch, M. Gogina, D. Herlemann, J. Henkel, M. Kanwischer, B. Krebs, A. Kremp, A. Malissery, R. Mars, J. Müller, S. Neubert, H. Osterholz, H. Radtke, G. Rehder, K. Romoth, M. Sass, I. Sassenhagen, O. Schmale, M. v. Thenen, M. v. Weber and O. Zielinski (2025). Coastal zones of the Baltic Sea in the Anthropocene: Current state and the impact of climate change. Estuar. Coast. Shelf Sci. 326: 109504, doi: 10.1016/j.ecss.2025.109504

2024

  • Ahmerkamp, S., C. O. Pacherres, M. Mosshammer, M. Godefroid, M. Wind-Hansen, M. Kuypers, L. Behrendt, K. Koren and M. Kühl (2024). Novel Approach for Lifetime-Proportional Luminescence Imaging Using Frame Straddling. ACS Sensors 9: 5531-5540, doi: 10.1021/acssensors.4c01828
  • Filella, A., J. Umbricht, A. Klett, A. Vogts, T. Vannier, O. Grosso, M. Voss, L. Riemann and M. Benavides (2024). Dissolved organic matter offsets the detrimental effects of climate change in the nitrogen-fixing cyanobacterium Crocosphaera. Limnol. Oceanogr. Lett. 9, 296-306, doi: 10.1002/lol2.10380
  • Umbricht, J., A. Filella, A. Klett, A. Vogts, M. Benavides and M. Voss (2024). Uptake of dissolved inorganic nitrogen and N2 fixation by Crocosphaera watsonii under climate change scenarios. Front. Mar. Sci. 11, doi: 10.3389/fmars.2024.1388214