Royal Netherlands Institute for Sea Research
PhD student
Universiteit Utrecht
Prof. dr. Karline Soetaert
  • numerical simulation
  • partial differential equations
  • biogeochemical cycles
  • reactive-transport modeling
  • scientific software (R)

MSc. Qi Liu

PhD student

Modeling effects of microorganisms on environment under fluctuating physical conditions

    - create new sediment biogeochemistry predictive software combining state-of-the-art mechanistic model and high spatio-temporal resolution data


My PhD project lies within the interface between physical (hydrodynamics, irradiance, thermodynamics), biological (photosynthesis, respiration, nutrient absorption) and geochemical (aerobic and anaerobic mineralization, nitrification, denitrification) processes in the dynamic intertidal systems, coupled with mathematical modeling and scientific software development.  Specifically, primary producers like microphytobenthos experience temperature and nutrients fluctuations driven by tide and radiation, which eventually influence sediment biogeochemical cycles through MPB ecophysiological activities. To enhance our predictive capacity in the future scenarios of environment change, high spatial and temporal resolution data need to be collected to establish a new class of model which combine biogeochemistry and microbiology explicitly. 

  • Sediment temperature under variable physical conditions

Temperature has a great influence on the rate of physiological and biochemical reactions of organisms in the earth system. Recently more and more extreme weather such as heat waves are threatening natural ecosystems. Sediment temperature on intertidal flat may change significantly in a short time period due to the changes of irradiance, tidal inundation and other conditions. The aim is to establish a one-dimensional numerical model of water-sediment system to simulate the response of water-sediment temperature to changes in external physical conditions.

  • Oxygen dynamics influenced by microbial activities

Light and temperature control microbial primary production and respiration, and further determine oxygen profiles in the sediment. However, the effect of oxygen availability especially oscillations at a smaller temporal and spatial scales on biogeochemical cycles remains unclear. We set up microsensors to capture the rate data of microbial physiological and biochemical reactions under different physical conditions in the lab. On this basis, we established a mathematical model of microbial photosynthesis and respiration. Coupled with the temperature physical mode, we can gain more insight into how light and temperature affects the production and respiration reactions of microorganisms and thus the elemental cycles in nature.

  • Controlling influence of MPB on biogeochemical cycles

Because the composition processes depend on oxygen to different degrees, oxygen availability will affect geochemical reactions by cascades and feedbacks. When tidal flat is exposed, the accumulated nutrients and high radiation induced high production, which produces more OM and deepen oxic layer, therefore also increase the nitrification-dinitrification coupled process; on the other hand, when sediment surface is inundated, the decreased light will cause less production and aerobic mineralization, on the contrary the anoxic mineralization increases. The previous models can not balance the different temporal and spatial scales of geochemical and microbial processes, neither can they predict the effect of transient redox oscillation on biogeochemical cycles, while our model will try to fill this gap.

  • Upscale the model to predict C, N, Si and P cycling at estuarine scale

This new generation of coupled physical-biological-geochemical model will be used to construct and upscale the elements cycles of intertidal systems, especially under the background of global warming and sea-level rise, which will give us insights on the role of estuaries on global biogeochemical cycles.


Education background
2021-       Ph.D.   Royal NIOZ & Utrecht University   

Physical-microbiological-geochemical modeling, thesis: "Impact of microphytobentos on C, N, P and Si cycling in dynamic intertidal systems"

2018-2021   MSc.    Beijing Normal University        

Hydrodynamic-biogeochemical coupled modeling, thesis: "Simulating response of aquatic ecosystem in the Yellow River Estuary under change of water and sediment"

2014-2018   BSc.    Dalian University of Technology

Major in hydraulic engineering, minor in mathematical modeling, thesis: "Attribution and optimal allocation of upstream N and P pollutants for estuarine ecological objectives"



Research gate

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