Topic: Groundwater microbiology

Research topic 3: Groundwater Microbiology

To date, little is known about microbial communities, functional diversity, and metabolic processes in the subterranean estuary. Samples will be taken at the same stations as for submarine groundwater biogeochemistry (research topic 2 Groundwater composition) in the intertidal beachface at the recharge zone where seawater is introduced into the beach sediment and at discharge sites where groundwater is released to nearshore waters. To elucidate the active prokaryotic (e.g. nitrate, sulfate, and iron reducers) and eukaryotic (e.g. microphytobenthos and meiofauna) communities and their response to environmental changes, we apply next generation sequencing of ribosomal RNA. Additionally, denaturing gradient gel electrophoresis (DGGE) and quantitative PCR of key-genes for the respective metabolic processes are performed. We also plan small scale surveys across the beach face and around seep sites using hyperspectral imaging to detect microphytobenthos and measure its spatial distribution and temporal variability as a function of submarine groundwater discharge (SGD) composition and flux. To evaluate the microbial metabolism in beach sediments, we are also conducting measurements of oxygen consumption, N cycling (nitrification, denitrification), and Fe release (Fe reduction) in flow-through reactor and slurry experiments.

Project Microbial community

PD Dr. Bert Engelen (ICBM, Paleomicrobiology)

PhD student
M. Sc. Julius Degenhardt (ICBM Paleomicrobiology)


In this part of the project, we want to investigate the impact of microbial activities on the presence of different nutrients and redox-sensitive elements at the study site Spiekeroog beach. The overall goal is to correlate the influence of the SGD on microbial activities, their community composition, carbon mineralization and geochemical cycling within the beach system.

Community analysis using next generation sequencing
To date there are very few studies investigating microbial diversity in sandy beaches and subterranean estuaries. Most of them were performed before the revolutionary development of next generation sequencing. Also, so far most studies have been performed on pore waters, neglecting the bulk sediments. By using Illumina sequencing of the 16S rRNA genes and transcripts on samples obtained at the same stations at different time points during the year, we aim to get a detailed understanding of microbial community dynamics on a spatial and seasonal scale.
By comparing samples taken from areas influenced by SGD with samples lacking this influence we will be able to see adaptations of the microbial community to freshwater influence and changing nutrient and redox conditions.

Understanding and quantification of iron and sulfate reduction dynamics
Since aerobic degradation of organic matter occurs only within the uppermost centimeters of the sediment, sub-oxic processes like manganese and iron reduction, and anoxic processes like sulfate reduction become important for organic matter degradation. It has been shown already, that regardless of e.g. sulfate availability in some subterranean estuaries both processes occur while in some sulfate reduction seems insignificant. With rate measurements of sulfate- and iron reduction in incubation experiments we want to determine the role of these processes within our area of investigation. By mimicking tidal cycles, we will also try to understand iron and sulfate reduction on a very fine scale.


Presentations at national and international symposia
Degenhardt J, Ahrens J, Engelen B (2018) The impact of groundwater seepage on benthic microbial community structures of a sandy beach. VAAM, Wolfsburg, Germany.

Degenhardt J, Ahrens J, Geskowiak J, Waska H, Engelen B (2018) The impact of groundwater seepage on benthic microbial community structures of a sandy beach subsurface. ISME, Leipzig, Germany. 

Project Oxygen and Nitrogen Cycling

Dr. Hannah Marchant (MPI-MM, Department of Biogeochemistry)
Dr. Soeren Ahmerkamp (MPI-MM, Department of Biogeochemistry)


This part of the project focuses on the consumption of oxygen in the sediment and how this is linked to the cycling of nitrogen compounds such as ammonium and nitrate. The tidal induced changes of the sea level drive specific water circulation patterns on beaches. With the falling tide, sea water - rich in oxygen and nitrate - is percolated through the beach sand sustaining an active microbial community. At the same time, groundwater from the subterranean estuary is discharged at the beach; this old water, poor in oxygen but rich in reduced nitrogen in the form of ammonium, forms a unique microbial transition zone. The overall goal of this project is to investigate the microbes that thrive in this dynamic habitat, their respiration and their contribution to global biogeochemical fluxes.


Oxygen consumption and microphytobenthos
Recent technological advances have made it possible to study oxygen penetration depths and consumption rates in sands at greater resolution than ever before. A pioneering benthic lander system called Lance-a-lot is deployed on the beach to study how oxygen penetration depths change as the tide comes in and out. The results of this work will enable us to gain a greater understanding of circulation and microbial processes on beaches. In close collaboration with Janek Greskowiak and Nele Grünenbaum (research topic 1), the measurements are used to develop a transport-reaction model which will improve our mechanistical understanding of the water circulation and subsequently advance the quantification of biogeochemical fluxes.
This part of the project also focuses on a barely understood part of the beach microbial community – the microphytobenthos. Microphytobenthos are photosynthetic organisms that live on the surface of sand and are mainly comprised of diatoms. A hyperspectral camera installed on the lander system will give us insights into the distribution and migration of these oxygen producing organisms that might also be an important source of organic matter.


Nitrogen cycling
Beaches sit at the interface between the land and the ocean therefore play an important role in removing nitrogen compounds such as ammonium and nitrate before they reach the open ocean. Understanding such removal is vital considering that nowadays these inputs are largely driven by anthropogenic activities. In the surface layer of the beach where there is still oxygen, groups of microorganisms carry out nitrification – which results in the conversion of ammonium to nitrate. When oxygen becomes limiting this nitrate is reduced by other organisms either to nitrogen gas or back to ammonium. This part of the project aims to understand where and at what rates these processes occur on the beach and in collaboration with the subproject Microbiology we also aim to identify the microbes that are carrying out these processes. 

(Stand: 20.06.2024)  | 
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