Environmental DNA (eDNA) analysis of microbial communities in a particular region’s water cycle can lead to a better understanding of why pollution is worse in some spots than others. It can also help local officials implement sustainable water management policies and practices.

In combination with the evaluation of other natural tracers, for example, noble gases, the microbial data obtained via eDNA analysis provides important glimpses into the flow, circulation, and functioning of complex groundwater systems.

“It’s a vast toolbox that’s new to our field of research,” said Oliver Schilling, PhD, professor of hydrogeology at the University of Basel and at Eawag, the Swiss Federal Institute of Aquatic Science and Technology. Quantitative hydrogeology maps out where and how quickly new groundwater will accumulate.

Starting in 2018, Schilling conducted various measurements on Mount Fuji in Japan to determine where spring water comes from—where the groundwater flows through before it arrives back at the surface and forms the hundreds of pristine natural springs which are scattered around Mt. Fuji. His results (“Revisiting Mt. Fuji’s groundwater origins with helium, vanadium and eDNA tracers”) appear in the just-published first edition of Nature Water.

The water mountain

“Known locally as the water mountain, for millennia Japan’s iconic Mt. Fuji has provided safe drinking water to millions of people via a vast network of groundwater and freshwater springs. Groundwater, which is recharged at high elevations, flows down Fuji’s flanks within three basaltic aquifers, ultimately forming countless pristine freshwater springs among Fuji’s foothills,” the investigators wrote.

“Here we challenge the current conceptual model of Fuji being a simple system of laminar groundwater flow with little to no vertical exchange between its three aquifers. This model contrasts strongly with Fuji’s extreme tectonic instability due to its unique location on top of the only known continental trench–trench–trench triple junction, its complex geology, and its unusual microbial spring water communities.

Study findings provide evidence for prevailing deep circulation and a previously unknown deep groundwater contribution to Mt. Fuji’s freshwater springs. [CasarsaGuru/Getty Images]
“On the basis of a unique combination of microbial environmental DNA, vanadium, and helium tracers, we provide evidence for prevailing deep circulation and a previously unknown deep groundwater contribution to Fuji’s freshwater springs. The most substantial deep groundwater upwelling has been found along Japan’s most tectonically active region, the Fujikawa-kako Fault Zone.

“Our findings broaden the hydrogeological understanding of Fuji and demonstrate the vast potential of combining environmental DNA, on-site noble gas, and trace element analyses for groundwater science.”

It was thanks to a Japanese colleague that Schilling arrived at the idea of examining microbial eDNA in the region.

“He told me about water sources on Mount Fuji that exhibit noteworthy signatures, namely that the eDNA contained in the water shows the presence of organisms that can only grow at a depth of 500 to 1,000 meters,” he recalls, noting that this is an indicator that some of the source water comes from deep groundwater. “This was the first indication that microbial eDNA might provide some clues as to the groundwater’s flow trajectory when combined with other, independent tracers such as noble gases.”

Along with eDNA, the hydrogeologist also analyzed two groundwater tracers with higher incidences due to Mount Fuji’s unique geological setting: the noble gas helium and the trace element vanadium. “All three natural tracers tell the same story: there is systematic deep circulation of the water within Mount Fuji. Such analyses are the key to understanding the system,” Schilling concluded.

Potential findings for Switzerland, too

This new application of tracers can be used to examine groundwater systems all over the world. In Switzerland, for example, it can be applied to determine where the water comes from that is pumped out of the ground for drinking water.

“A large proportion of eDNA from cold-loving microbes in the groundwater, for example, would indicate that meltwater from snow and glaciers forms a substantial proportion of the sourced groundwater,” Schilling explained.

With an eye to the future, this means: “If we know the importance of these natural water reserves, we can look for alternatives ahead of time in order to shield affected regions from seasonal water shortages as much as possible,” the hydrogeologist continued. As a result of climate change, in Switzerland glaciers are melting and snow is reducing, which means that these important sources of water for streams and groundwater are slowly disappearing. This will negatively affect water availability, particularly in the more and more frequent hot and dry summer months.

One possibility to prevent severe water shortages in summer would be to collect more rainwater in reservoirs during the winter, for example by artificially enhancing groundwater reservoirs or adapting how above-ground reservoirs are managed. “The analysis of microbiological eDNA offers us a new tool for better calibrating the hydrological models used in groundwater management,” Schilling said.

This in turn is an important part of making realistic prognoses for water quality and availability and allows a sustainable, long-term planning for the management of groundwater, our most valuable and abundant source of drinking water.