Studying Ecosystems in the Benthic Zone

Northern basin of Tauranga Harbour, New Zealand

The bottom of any body of water, marine or freshwater, is called the benthic zone. This ecological region includes the sediment surface and sub-surface layers and provides diverse habitats. At the sediment-water interface many biological, physical, and geochemical processes take place, which make this region so interesting for biological and ecological studies.

The benthic zone is inhabited by microorganisms, plants, and aquatic macroinvertebrates, like polychaetes, crustaceans, and insects or their larval forms. These organisms are referred to as the Benthos and they are crucial for aquatic ecosystems. They not only break down organic matter, but also serve as a food source for other aquatic species and therefore play an important role in nutrient cycling. They even contribute to pollutant removal from sediments and the overlaying water column.
Like many other ecosystems, the benthic zone is threatened by human activity. Waste, pollutants, and fertilizer are introduced as runoff in bodies of water, while land use and climate change increase the amount of terrestrial sediments that reach the benthic zone. It is important to study the effects of human interference on benthic species to understand and preserve this ecosystem. Furthermore, benthic species can serve as an early indicator for declining water quality.
The turbidity of the overlaying water column and the amount of light that reaches the sediment-water interface, as well as the pH and oxygenation of surface sediments is important for the activity of benthic species. Having appropriate measurement systems to analyse these parameters in sediment samples can give valuable information about microbial oxygen demand, stressors for burrowing polychaetes or geochemical processes taking place in this highly active zone.

Microprofiling gives the opportunity to analyze gradients and gradient development in µm resolution. Microsensors with tiny tips can be introduced in sediments in defined step sizes with micromanipulators. This way different layers and boundaries can be identified. PreSens offers special profiling microsensors and micromanipulator set-ups that are robust and can be used for lab or field applications. PreSens microprofiling set-ups have already been successfully applied in benthic research projects:
Application Note: O2, pH and CO2 Dynamics in Salt Marsh Tidal Ponds
Microprofiling Set-Ups



Fluorescence imaging is another method that can provide information on biogeochemical and microbial processes in the benthic zone. Sensor foils are attached to transparent surfaces and brought in contact with the sediment sample. The sensor foils are read out with special cameras. They allow to create 2-dimensional oxygen, pH and CO2 maps of a certain region of interest, identify biogeochemical gradients and follow changes in analyte distributions over time. With the PreSens VisiSens Imaging Systems even the activity of larger animals in the benthic zone can be investigated:
Application Note: Benthic Disturbance-Recovery Dynamics in a Changing Coastal Ocean



Another method to investigate the benthic zone is to determine oxygen demand in closed sample incubations. Microbial or organismic activity often depends on the amount of light that can reach the sediment surface and is therefore often influenced by effects of climate change and human impact on bodies of water. Optical sensor spots or sensor stripes offer an easy tool for measuring in certain depths of a sediment sample and the overlying water column without any interference of the sample. Like optical sensor foils the spots can be attached to transparent container walls and are then read out from outside via polymer optical fibers - without any disturbances. PreSens sensor spots and vials with integrated sensor stripes have already been applied in determining the biological oxygen demand and microbial activity in sediment samples and at the sediment-water interface:
Application Note: Determining the Impact of Shoreline Retrogressive Thermokarst Slumping to Tundra Lakes
Application Note: Monitoring Oxygen Dynamics at the Sediment-Water Interface


Hydrodynamic conditions also greatly influence the benthic zone and the amount and distribution of nutrients in the sediment surface layers. PreSens offers a special oxygen measurement system, an optical oxygen amplifier with microoptode that delivers oxygen measurements at 10 Hz frequency. The oxygen meter can directly be connected to a Nortek Vector. This way non-invasive eddy covariance measurements on land and in shelf waters can be performed. This system has for example been applied to assess the impact of salmon farming on the benthic zone:
Application Note: Measuring Benthic Impacts of Salmon Farming


When sampling sediment core pore water, it is important not to disturb the sediment layers. When extracting pore water from sediment, flow-through cells with integrated optical sensor can be used to directly measure O2, pH or CO2 during the sampling process. This method was used to determine O2 and pH in different layers of marine sediments:
Application Note: Assessing the Impact of pH Fluxes between the Sediment-Water Interface on the Overlaying Water Column off Namibia

Optical sensors come in very different and even miniaturized designs so minimally invasive or even contactless measurements are possible. This makes optical sensors ideally suited for these research applications. Have a look at our PreSens set-ups that might help to improve your research results!

Microprofiling in Sediments with Optical Microsensors

PreSens offers complete automated or manual microprofiling systems that are ideally suited to measure gradients in sediment core samples or out in the field. Robust optical pH and oxygen profiling microsensors can be inserted in the sample in µm steps with our manual or automated micromanipulators. Measure gradients at the sediment water interface with high resolution!

For further microprofiling set-ups visit our Microprofiling page!

2-dimensional Imaging of Spatio-Temporal Gradients in Sediments

Fluorescence imaging with optical sensor foils allows to assess gradient development of oxygen, pH and CO2 distributions in sediment samples over time. The sensor foils can be attached to the inside wall of transparent flume tanks or core chambers and can be read out non-invasively from the outside with the VisiSens camera systems. The 2-dimensional visualization of gradient development and parameter distributions can give valuable information about biogeochemical processes, microbial or animal activity in the benthic zone. Imaging systems for oxygen, pH or CO2, as well as a multiparameter imaging systems, that allow to record all parameters in one image are available.

For further imaging set-ups visit our Imaging page!

Non-invasive Measurements in Sediment Samples

Optical sensor spots can be integrated in transparent flume tanks or core chambers at different positions and allow assessing oxygen, pH and CO2 levels non-invasively. The sensors are read out from the outside via polymer optical fibers without disturbing the sediment layers. This way microbial activity or biological oxygen demand (BOD) can be determined in different depths and in real time. The sensor spots can be combined with small benchtop oxygen meters or portable devices, so measurements in the lab, as well as in the field can be conducted. With PreSens multi-channel meters even simultaneous measurements of oxygen, pH and CO2 in different areas are possible.

  • OXY-4 SMA + Polymer Optical Fiber + Sensor Spots + PreSens Measurement Studio 2
    O2 Configuration
  • OXY-1 SMA + Polymer Optical Fiber + Vial Adapter + SensorVial + PreSens Measurement Studio 2
    O2 Configuration
  • OXY-4 SMA + Polymer Optical Fiber + Vial Adapter + SensorVial + PreSens Measurement Studio 2
    O2 Configuration

Porewater Analysis

Optical sensors integrated in flow-through cells offer the opportunity to measure O2, pH or CO2 while extracting pore water from a sediment core without the exposure to ambient air. The flow-through cells can be integrated in hoses used for extraction and the sensor and respective parameter can be read out with compact fiber optical meters.

High Resolution O2 Measurements for Eddy Covariance Systems

The OXY Flux is designed for non-invasive eddy covariance measurements. The microsensor has a tip size of 30 µm, so there is only minimal flow disturbance. It delivers precise on-the-spot measurements. The inexpensive sensor can easily be exchanged. The OXY Flux is the solution to expand your eddy covariance measurement set-up.


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