Dr. Soeren Ahmerkamp

I lead the newly established research group Physical Microbiology, which operates at the interface of biophysics, microbiology, and biogeochemistry. Our goal is to understand the mechanisms that govern carbon and nutrient transformations in marine systems, particularly where physical transport processes interact with microbial activity.

To achieve this, we pursue an integrative approach that tightly links modeling, observation, and experimentation: from numerical simulations (e.g., large-eddy simulations, transport–reaction models, and porous media), to in situ observations using self-developed platforms such as the benthic observatory LanceALot and the STB lander, and controlled laboratory experiments in flow-through reactors and microfluidic systems.

This combination allows us to mechanistically resolve key processes while simultaneously quantifying their relevance for natural systems, with the aim of developing a consistent understanding of how physical and microbial dynamics jointly shape biogeochemical cycles.

My main research areas are, C- and N-cycle in:

• Sandy sediments
• Seagrass
• Marine Aggregates
• Reef-building corals
• Beaches and Coastal Waters

My research is part of the project Shallow Water Processes and Transitions to the Baltic Scale as well as the IOW research programme 2024-2033 "Perspectives of Coastal Seas". A large portion of my research is conducted at the Reallabor Nienhagen.

I co-lead the Novo Nordisk-funded synergy project MATIC: Multiscale Approach on Coral Resilience together with Klaus Koren (Aarhus University) and Lars Behrendt (Uppsala University).

Publications

h-index: 27, i-10 index: 30, Link to Google Scholar

Selected publications (only lead and corresponding authorships):

Jalaluddin, F. M., Ahmerkamp, S., Marchant, H. K., Meyer, V., Koren, K., & Kuypers, M. M.. Microenvironments on individual sand grains enhance nitrogen loss in coastal sediments. Scientific Reports, 15(1), 16384. (2025)

Ahmerkamp, S., Cesar Pacherres, Mare Mosshammer, Mathilde Godefroid, Michael Wind-Hansen, Marcel Kuypers, Klaus Koren, Lars Behrendt, Michael Kühl. Novel Approach for Lifetime-Proportional Luminescence Imaging Using Frame Straddling. ACS sensors (2024).

Flintrop*, Clara, Soeren Ahmerkamp*, Nasrollah Moradi, Isabell Klawonn, Jöran März, Cora Hörstmann, Rainer Kiko, Arzhang Khalili, Hans-Peter Grossart, Xosé A. Álvarez-Salgado, Javíer Arístegui Ruiz, Morten H. Iversen. "Rethinking sinking: Imaging the flow fields of natural marine aggregates to derive sinking velocity." BioRxiv (2023).

Ahmerkamp*, Soeren, Farooq Moin Jalaluddin*, Yuan Cui*, Douglas R. Brumley, Cesar O. Pacherres, Jasmine Berg, Roman Stocker, Marcel M. M. Kuypers, Klaus Koren, Lars Behrendt. “SensPIV: simultaneous visualization of flow fields and oxygen concentrations to unravel metabolic exchange fluxes.” Cell Reports Methods. (2022)

Pacherres*, Cesar O., Soeren Ahmerkamp*, Klaus Koren, Claudio Richter and Moritz Holtappels: “Ciliary flows in corals ventilate target areas of high photosynthetic oxygen production.” Current Biology, 32(19), 4150-4158. (2022) *Shared first author

Ahmerkamp*, Soeren, Bo Liu*, Kolja Kindler*, Joeran Maerz, Roman Stocker, Marcel M. M. Kuypers, and Arzhang Khalili. "Settling of highly porous and impermeable particles in linear stratification: implications for marine aggregates." Journal of Fluid Mechanics 931. (2022)

Karthäuser*, Clarissa, Soeren Ahmerkamp*, Hannah K. Marchant, Laura A. Bristow, Helena Hauss, Morten H. Iversen, Rainer Kiko, Joeran Maerz, Gaute Lavik, and Marcel M. M. Kuypers. "Small sinking particles control anammox rates in the Peruvian oxygen minimum zone." Nature Communications 12, no. 1 (2021): 1-12. *Shared first author

Ahmerkamp, Soeren, Marchant, Hannah, Peng, Chao, Probandt, David, Littmann, Sten, Kuypers, Marcel, & Holtappels, Moritz. "The effect of sediment grain properties and porewater flow on microbial abundance and respiration in permeable sediments." Scientific Reports, 10(1), (2020), 3573.

Ahmerkamp, Soeren, Christian Winter, Knut Krämer, Dirk de Beer, Felix Janssen, Jana Friedrich, Marcel M. M. Kuypers, and Moritz Holtappels. "Regulation of benthic oxygen fluxes in permeable sediments of the coastal ocean." Limnology and Oceanography 62, no. 5 (2017): 1935-1954.

Ahmerkamp, Soeren, Christian Winter, Felix Janssen, Marcel M. M. Kuypers, and Moritz Holtappels. "The impact of bedform migration on benthic oxygen fluxes." Journal of Geophysical Research: Biogeosciences 120, no. 11 (2015): 2229-2242.

Science Impressions