University of Bath

The influence of breathing sediment on oxygen dynamics and the marine benthos

We study in situ O2 dynamics to understand seasonality in sediment & water column processes in a coastal environment and coinciding effects on aquatic systems.

This study aims to examine benthic flux drivers within two coastal shelf sea environments, off the coast of Plymouth, UK (L4 and Cawsands). In particular, focusing on seasonal variations of organic matter (OM), hydrodynamics, and the corresponding oxygen distributions within marine benthic regions. This thesis also aims to assess and quantify the drivers of benthic oxygen fluxes in shallow-water permeable seagrass sediments using the EC measurements and microprofiler technique under field conditions that include naturally varying light and current flow. With regard to water-column oxygen dynamics and oxygen budgets, this study is focused on;

1) the influence of drivers such as plankton blooms/dumping of dredged spoils on a seasonal benthic oxygen flux, linked to historical water column data at a shelf sea location;

2) assessment of hydrodynamical drivers on benthic oxygen fluxes; and

3) quantification of oxygen dynamics within seagrass beds using EC and microprofiler techniques.

By assessing in situ oxygen dynamics, this thesis aims to improve understanding of seasonality in benthic-pelagic processes in a coastal environment. Results from this thesis will fill a gap in the existing historical (50+ year) dataset to provide the first insight of marine oxygen cycling and benthic oxygen drivers at this site.

Project outline

The main objective of this research was to establish a comprehensive picture of in situ oxygen dynamics within two coastal shelf sea environments off the coast of Plymouth, UK (Cawsands and L4). The eddy correlation (EC) technique, which measures total turbulent oxygen flux 12 cm above the seabed, along with accompanying instruments was used to document drivers of benthic oxygen uptake over a season at L4. Benthic oxygen uptake significantly increased over the five-month period. However, once the drivers of EC oxygen fluxes were assessed, dumping of dredged material showed to be a minor impact on fluxes, and instead the sediment oxygen demand showed variations in keeping with seasonal trends (nutrients, temperature and inputs of organic matter) and hydrodynamics.

Furthermore, an in-depth analysis of hydrodynamic drivers within the L4 site was conducted. In combination with 12 hours of benthic EC data, acoustic Doppler current profiler (ADCP) data, which measures velocities throughout the water column, was obtained. The separation of tidal components, which distinguished contribution from baroclinic (internal) tides were minimal compared to the barotropic (surface) tide. EC oxygen fluxes were seen to have directional differences, which were attributed to the varying sediment types in the north/south directions, as well as varying dissipating levels from each direction due to topographical effects.

Quantification and assessment of the drivers of benthic oxygen flux within a seagrass bed at the Cawsands site was made. By combining the relatively new EC technique with a traditional technique (microprofiler), which measures diffusive point flux, allows for estimates of the benthic oxygen flux drivers.

This thesis investigated benthic-pelagic coupling via in situ profiling and the EC technique which does not currently exist at this long-term coastal monitoring station. Ultimately, results contributed to a more comprehensive analysis of benthic oxygen flux, with particular focus on the influence of drivers within these historically significant coastal environments.


The Eddy Covariance (EC) technique measures aquatic oxygen flux non-invasively by capturing the vertical turbulent fluxes within aquatic boundary layers. Even though the EC technique has been used in aquatic systems for over a decade, it is still under development for this purpose. Measurement of oxygen flux within coastal shelf seas is difficult to achieve using more traditional methods such as chambers and microprofiling. Despite this, only a small number of authors have undertaken EC measurements in shelf seas due to the significant deployment challenges. Nonetheless, by solving these challenges, this thesis has demonstrated that this method can advance our knowledge of oxygen dynamics in shallow shelf seas.

This project describes the first field campaign to investigate benthic-pelagic coupling by using an in situ traditional technique, microprofiling, along with the non-invasive EC technique, at the Western Channel Observatory (WCO), Plymouth, UK (study site). Ultimately, results have contributed to a more comprehensive analysis of water column oxygen budgets, with a particular focus on the influence of benthic oxygen flux drivers in shelf sea environments.