Fachbereich Geowissenschaften

Slow Microbial Transformations in Oligotrophic Aquifers

What are the controlling factors of biogeochemical reactions in aquifers at characteristic time scales of years?

PhD Researcher: Bijendra Man Bajracharya
Supervisors: Olaf Cirpka (University of Tübingen), Chuanhe Lu (University of Tübingen), Philippe van Capellen (University of Waterloo)


Most natural aquifers are oligotrophic in nature, therefore are poor in nutrients and exhibit low microbial densities. These are important reservoirs of drinking water. Understanding the dynamics of intrinsic microbial transformations and the inherent oxygen-consuming processes is of vital importance as it can have a tremendous effect on the water quality, and thus on the drinking water supply to many of the world’s communities. Changing the residence times or the composition of infiltrating water will change the distribution of redox zones within aquifers, which may affect the quality of extracted groundwater.

If we closely observed the oligotrophic aquifer system, we realize that there are two constraints in the system. There is slow and small release of natural organic matter in the system. NOM can be a complex molecular compound and cannot be taken by organism so extracellular hydrolysis is required to produce smaller, monomeric molecules which may take considerable period of time. Moreover, even there is sufficient amount of substrates in the system; there is slow kinetic uptake of these nutrients by the microbes which may be due to inaccessibility. This inaccessibility can rises due to biochemical state, spatial variation, occlusion of organic matter, sorption and complexation reaction etc.

It is believed that these microbial communities can sustain solely by the energy supplied by water-rock chemistry.

The microbial activities are very sensitive to the physical and chemical conditions of the medium (e.g. temperature, ionic concentration, DOC concentration and quality, and pH etc.). Hence, they use dormancy as a survival strategy. Only a fraction of the microbial population is active at any given time. As environmental conditions change, previously active microorganisms may switch to an inactive or dormant state, while dormant ones may become active.

Definitely there is a minimum levels and fluxes of energy that environment must sustain in order to support life. Additionally, the mineral matrix should store a sufficiently large energy potential, but also that the potential be transferred in a biologically accessible form to the interior of cells, where it can drive energy-conserving metabolism.


For the accurate understanding, we established two hypotheses.

  1. Limitation stems only from restricted supply of organic or inorganic electron donors, most likely from the sediment matrix
  2. Microbial transformation kinetics is additionally controlled by thermodynamic constraints inherent in the ecosystem

We will first develop models of mineral dissolution and natural-organic-matter disaggregation and couple them to one-dimensional bio-reactive transport models. Furthermore, we will modify the bioreactive transport codes to include thermodynamic constraints and multiple electron-donor utilization, and simulate the same systems as before. Both mass transfer kinetics and thermodynamic constraints will be formulated temperature dependent.


  • Bajracharya, B., Lu, C., Cirpka, O.A. (2014): Modeling substrate-bacteria-grazer interactions coupled to substrate transport in groundwater. Water Resour. Res. 50, 4149–4162, doi: 10.1002/2013WR015173