Solo Blog

What is it like to conduct your thesis in SoS?

May 15th, 2024

In this blog, Stijn Eggenkamp, Master’s Student Earth, Surface, and Water at Utrecht University shares his experience with the platform after successfully completing his master’s thesis.

We are aiming to deepen our understanding of biomass growth dynamics in porous media. Specifically, how biomass growth affects soil permeability at the micro-scale.  The implications of this research extend to broadening our knowledge of the interplay between hydrology and microbiology in soil systems.

Stijn’s master thesis contributes to an interdisciplinary collaboration involving the Hydrogeology Group at Utrecht University, where he conducted his master’s thesis under supervision of Amir Raoof, hydrology department at Utrecht University and Eiko Kuramae, biology department at Utrecht University and NIOO-KNAW Wageningen.

From my part, I gained a lot of insight into the theory of microbiology and how to do good quality microbiological research. It is different from earth science research because, for example, in microbiology research the experiment has to be repeated at least twice to validate the result, which is not mandatory in earth science. SoS offers such rich learning opportunities in collaborative experimental work across the involved disciplines.

Picture of a microfluidic under the Confocal Laser Scanning Microscope.

How was the research conducted?

A microfluidic device was created by using x-ray tomography, a non-destructive visualisation technique, using a sample from a slow sand filter in the soil. The microfluidic device was inoculated with a mix of a nutrient solution (TSB) and a biofilm-producing bacteria (Pseudomonas sp. RA12). The microfluidic is closed off and the bacteria is grown up inside an incubator. The experiments showed that it is possible to create biomass inside the pores of the microfluidic domain. The research also involved creating and improving the method for growing a bacterial solution within a microfluidic device. The main aim of the research was to measure and visualize how permeability reduces over time inside a microfluidic due to the growth of biomass.

Schematic of the microfluidic design (3cm x 1cm, and a depth of 60μm) used in this research.

An application of a biofilm producing bacteria is to improve the soil conditions so plants can grow better in drier soils. The produced biofilm reduces the permeability of the soil, allowing plants to take up more water before it infiltrates deeper into the soil, where the plant roots cannot reach. This is because the biofilm slows the drainage of rainwater.  Furthermore, the biofilm producing bacteria provides nutrients for plant growth and increases the soil moisture content, making the soil more drought resistant.

Permeability measurements, biofilm visualization, and confocal laser scanning microscopy were utilized to conduct a comprehensive experiment assessing the permeability reduction over time due to bacterial growth. After 144 hours at the optimal growth temperature of 28°C, the permeability decreased by 67.7%. This means that with the biofilm growth, the water is retained much longer in the soil.

Microscopy images of biomass growth after 6 days made using Confocal Laser Scanning Microscope under 400X magnification . Biofilms are blocking the pores and thereby reducing the permeability of the sample.

Besides measuring the permeability reduction, the Confocal Laser Scanning Microscope was used to visualize the stained biofilm structures at 400x magnification and their distribution within the microfluidic environment. Confocal imaging over five-time steps revealed the dynamic stages of Pseudomonas sp. RA12 biofilm formation in a soil microfluidics, emphasizing the concentration of biofilm development in pore throats and the size of the formed biofilm over time. This study advances our fundamental understanding of biomass growth dynamics in porous media.

To complement the experimental findings, the results of Stijn’s master thesis have been used for numerical simulations to show how biofilm growth impacts water flow velocity in soil.

All the conducted research will soon be published in an article, linked here when it is live.

While biofilm affects flow of water, we cannot see water streamlines during experiments as water is transparent. So, we use numerical simulation to simulate and visualize water flow with and without biomass to show how biomass growth impacts water flow velocity in soil.

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