top of page

BactoSense on Mount Fuji

Updated: Dec 5, 2023

How natural hydrological tracers help understand the local aquifer

The picturesque Mount Fuji is a stratovolcano with recognisable steep sides and a conical shape. Annually, 2.2 billion tons of rain and snowfall seep through the multi-layered lava gaps to become clean springs and well water. This water is consumed daily by the local inhabitants. Fish farmers' industries like paper manufacturing, chemicals, electronic equipment, etc. depend on this liquid resource. For this reason, scientists like Prof. Dr. Oliver Schilling are working hard to understand the evolution and behaviour of the aquifer in the region to ensure its safeguarding.

Prof. Dr Schilling is an Assistant Professor of Hydrogeology at the University of Basel and head of the Tracer Hydrogeology group at Eawag. He and his team (Dr. Stephanie Musy, Dr. Yama Tomonaga & PhD student Friederike Currle) combine innovative measuring techniques of natural markers with sophisticated mathematical models to understand the complex hydrogeology of the volcanic groundwater system of Fuji. In this short interview, Prof. Dr. Schilling explains how they use bacteria as a hydrological tracer and implement BactoSense in their research.

BactoSense is being used on Fujiyama to understand the local aquifer with natural hydrologic indicators

In your previous work, you focused on physico-chemical tracers. What more do online bacteria monitoring bring?

In our first study, we searched for patterns that could tell us whether we had a significant contribution of groundwater from a more than 100-metre-deep, confined aquifer to the shallow, unconfined groundwater and springs at the southwestern foot of Mount Fuji. For this, we combined several different tracer techniques, namely the analysis of helium isotopes (to identify deep water enriched with mantle gases), vanadium (to identify deep water with its long and deep flow path), and microbial eDNA (to identify extremophile microbes adapted to life at considerable depths/pressures). Owing to these measurements, we could identify springs and shallow wells that received substantial deep groundwater inflow. Some of the wells most affected by deep groundwater were the larger wells used for drinking water. In our ongoing follow-up study, we want to extend our spatial mapping of deep groundwater upwelling and quantify the temporal variability in deep groundwater inflow into the drinking water well.

As this is one of Japan’s most active seismic regions, we expect seasonal variations in deep groundwater upwelling and changes associated with seismic events such as earthquakes. For this purpose, we employ online flow cytometry alongside online dissolved (noble) gas measurements.

How do you combine eDNA and BactoSense measurement?

We continuously monitor the changes in the microbial composition in the drinking water well with BactoSense. We also conduct repeated spatial measurement campaigns where we sample different springs and wells for many hydrological tracers, including microbial eDNA. The eDNA samples are then analysed on BactoSense via next-generation sequencing to match the flow cytometry fingerprints to metagenomic/phylogenetic information.

BactoSense is designed to be robust and transportable. What is your experience of it in the field?

So far, we had a great experience. Even though we had to transport the instrument with us as ordinary checked baggage on our flights from Switzerland to Japan, owing to a well-padded Peli travel case and the very robust build of BactoSense, we had no problems with the instrument's functionality.

It was set up in the drinking water well house within one day of work and has been running smoothly for over two months. We particularly like the ability to control the instrument remotely.

The water quality of Mount Fuji is declining, as mentioned in your previous publication. Is that also true for bacterial content? How can BactoSense help monitor this phenomenon?

The water quality issues at Mount Fuji are not as much a question of hygiene as of agricultural and industrial pollution and steadily declining water levels in certain areas within the catchment. Nonetheless, due to the intense seismic activity in the region and the increased frequency of torrential rainfall events (we already captured the effect of a 350-mm rainfall event in 48 hours), monitoring of the microbial load by online flow cytometry will undoubtedly become a pivotal technology to guarantee the safety of drinking water also in the Fuji catchment.

Mount Fuji is emblematic. How can your findings be applied to other regions?

Yes, Mount Fuji is emblematic with its nearly perfect conical shape. It is also a quasi-perfect example of a volcanic aquifer system with complex hydrogeology, vigorous seismic activity and extreme meteorological events. It is a good model for other volcanic islands and coastal volcanic regions. Such systems are still seldom studied in hydrogeological terms, and our findings will help to develop monitoring techniques and protocols critical for sustainable and resilient drinking water management in volcanic areas.


The project is a collaborative effort between Prof. Oliver Schilling of the University of Basel and Prof. Yuji Sano of Kochi University in Japan. It is co-funded by the Swiss National Science Foundation and the Japan Society for the Promotion of Science via their Japanese-Swiss Science and Technology program (project IZLJZ2_214048).


bottom of page