Revisiting Mt Fuji's groundwater origins with helium, vanadium and environmental DNA tracers

Mt Fuji’s extensive freshwater springs and aquifers supply residents, agriculture and industry, yet water quality and quantity have been declining. The current hydrogeological model posits three aquifers (Surficial, Shin-Fuji, Ko-Fuji) with mainly laminar flow and negligible vertical exchange; springs are thought to be fed exclusively by shallow Surficial and Shin-Fuji aquifers. This model conflicts with Fuji’s complex, tectonically active setting atop a rare trench–trench–trench triple junction, its permeable basaltic stratigraphy, and atypical microbial signatures in springs. Classic tracers (groundwater levels, major ions, stable isotopes) show a shared meteoric origin and similar hydrochemistry across waters, obscuring vertical interactions and failing to explain observed water quality declines. The study’s objective is to test and revise the prevailing model by determining whether deep Ko-Fuji groundwater substantially upwells into shallow aquifers and springs, particularly along the FKFZ, using unconventional tracers (He isotopes, V, and microbial eDNA).

Prior hydrogeological work around Fuji has relied on shallow groundwater levels, major ions and stable water isotopes (δ2H, δ18O) to infer recharge elevations, seasonality and flow paths. However, similar hydrochemistry and overlapping meteoric signatures limit these tools’ ability to resolve vertical exchange in mountainous volcanic systems. Earlier studies documented Fuji’s basaltic geology, high permeability relative to andesitic arc volcanoes, and vanadium enrichment due to long water–basalt contact, making Fuji’s rivers among the most V-enriched globally. Deep thermal waters from ~1,500 m in the basement show warm, mineralized Ca–Cl and Na–Cl–SO4 types due to seawater inclusions, whereas springs and shallow groundwater are cold, fresh Ca–HCO3 and meteoric in origin. Initial microbial eDNA studies (Segawa et al.; Sugiyama et al.) identified thermophilic and extremophile prokaryotes (notably Parvarchaea) associated with Ko-Fuji aquifer conditions and typhoon-driven increases in suspended Archaea, suggesting potential for microbiological tracers of deep flow. He isotope studies in Japan and volcanic regions globally show mantle and crustal radiogenic He can trace deep fluid contributions and fault-mediated transport. Vanadium has long been measured around Fuji, with concentrations reflecting prolonged rock–water interaction and residence times. Collectively, literature indicates the need for multi-tracer approaches to detect deep–shallow mixing in Fuji’s complex, faulted setting.

Study focus: Springs and artesian wells along Mt Fuji’s southwestern foot across and along the FKFZ, plus key southeastern springs, spanning upstream to downstream flow paths. Sites include Shibakawa, Jimbanotaki, Shiraitonotaki, Fujinishiki (spring and brewery well), Aoki artesian well, Yoshimaike, Wakutamaike (SW), and Mishuku, Tomizawa, Kakitagawa (SE). A regional dataset (>350 sites, >9,500 data points) from literature was compiled for context.

• Classic tracers: Major ions measured by ion chromatography (Dionex ICS-3000); stable isotopes (δ2H, δ18O) by cavity ring-down spectroscopy (Picarro L2120-i), normalized to VSMOW; typical errors ±0.2‰ (δ2H) and ±0.05‰ (δ18O).
• Vanadium and Sr isotopes: Water filtered (0.22 µm), acidified; V quantified by atomic absorption spectrophotometry (Hitachi Z-3700), typical error ±4%. 87Sr/86Sr values compiled from literature.
• Dissolved gases and noble gas isotopes: On-site dissolved gas analysis by portable gas equilibrium–membrane inlet mass spectrometry (GE-MIMS) measuring He, 40Ar, Kr, N2, O2, CO2, H2, CH4 in near real time; uncertainty ±1–3%. High-resolution noble gas isotope analyses (He, Ne; 3He/4He, 20Ne/4He) on copper-tube samples at ETH Zurich with <1% concentration and <0.5% isotope ratio errors. End-member mixing considered among atmospheric (air-saturated water), mantle (MORB-like), and crustal radiogenic sources to partition He origins.
• Microbial eDNA: Ten liters filtered (0.22 µm Sterivex), DNA extracted (lysozyme/proteinase K; phenol–chloroform–isoamyl alcohol), quantified (NanoVue). V3–V4 16S rRNA amplicons (universal 341F/805R) sequenced (Illumina MiSeq, 2×300 bp). OTUs clustered at 97% similarity (QIIME) and taxonomically assigned (Greengenes v13.8). Archaeal community composition emphasized, with focus on Parvarchaea candidate orders YLA114 and WCHD3-30; alpha diversity (Shannon index) computed. eDNA datasets deposited at DDBJ (DRA013474).
• Data analysis: Triple-tracer comparisons (V vs He vs archaeal eDNA fractions and diversity) to test for linear mixing relationships indicative of deep–shallow groundwater mixing. Spatial mapping of tracers and isotopes; evaluation of correlations between V, δ18O, He concentrations, He isotope ratios, and archaeal indicators; comparison with thermal waters and fumaroles as end-members; contextualization with tectonic structures (FKFZ).

• Classic tracers indicate shared meteoric origin and similar Ca–HCO3 chemistry in springs and shallow groundwater, offering limited discrimination of vertical exchange.
• Helium evidence for deep inputs: Using 3He/4He and 20Ne/4He ratios with end-member mixing, mantle He contributions were estimated at ~20% in Aoki well (Ko-Fuji deep groundwater) and Yoshimaike spring, ~12% in Wakutamaike, and ~5% in Shiraitonotaki (sample no. 1). High mantle He contributions coincide with high total dissolved He, especially at sites on the FKFZ (Yoshimaike, Wakutamaike), implying significant deep groundwater upwelling into springs.
• Exceptional He anomaly at Wakutamaike: Total He is three orders of magnitude higher than other springs, with ~83% radiogenic He, closely matching deep thermal water signatures near Lake Tanuki, suggesting hydraulic connection and transport through FKFZ fracture networks of Misaka-Tenshu basement groundwater.
• Vanadium enrichment with residence time: V concentrations correlate with δ18O (lighter, higher-elevation recharge shows higher V) and with He. Highest V observed in deep Ko-Fuji groundwater at Aoki well (221.0 µg l−1). Yoshimaike spring shows markedly elevated V (87.5 µg l−1) among southwestern springs, consistent with deep groundwater admixture and longer residence times.
• Microbial eDNA signatures of depth: Parvarchaea dominate Ko-Fuji deep groundwater (Aoki: 95% of archaeal eDNA). In southwestern springs, Parvarchaea fractions increase downstream (e.g., Shibakawa ~20% to Yoshimaike ~80%). In the southeastern sub-basin, Parvarchaea are also high at Tomizawa (~77%) and present at Kakitagawa (~37%). Typhoon observations support WCHD3-30 and YLA114 as suspended-depth tracers.
• Triple-tracer correlations: Nearly linear relationships among V, He, and archaeal eDNA fractions (YLA114 and YLA114+WCHD3-30), and between V, He and archaeal alpha diversity, indicate physical mixing of deep Ko-Fuji groundwater with shallow waters, increasing along flow paths and faults.
• Revised hydrogeological model: Contrary to the laminar, non-mixing paradigm, substantial upwelling of Ko-Fuji deep groundwater occurs along FKFZ faults, fissures and clinkers, with an additional Misaka-Tenshu deep groundwater component feeding Wakutamaike. The upwelling rate and spatial extent are greater than previously assumed, notably in the densely populated southwestern sub-basin.

The multi-tracer approach reconciles the discrepancy between Fuji’s complex tectono-volcanic setting and the overly simplistic laminar flow model. Classic tracers alone cannot resolve vertical interactions due to uniform meteoric signatures and similar hydrochemistry across aquifers. In contrast, He isotopes directly reveal deep fluid contributions, V reflects prolonged water–rock interaction and residence times, and archaeal eDNA (Parvarchaea YLA114 and WCHD3-30) uniquely indicates environmental conditions associated with deep Ko-Fuji aquifer waters. The strong, near-linear co-variation of these independent tracers, combined with spatial patterns aligned with the FKFZ, provides compelling evidence for widespread deep–shallow mixing and focused upwelling along active faults. The findings update the conceptual model by incorporating significant vertical exchange, including a distinct Misaka-Tenshu deep source to Wakutamaike, thereby explaining anomalous He and V enrichments and microbial patterns. These insights are crucial for water resource management, as deep upwelling pathways can influence water quality, vulnerability to contamination, and response to seismic or climatic perturbations.

Combining on-site noble gas analysis, noble gas isotopes, vanadium geochemistry and next-generation microbial eDNA profiling enabled detection of substantial upwelling of Ko-Fuji deep groundwater into shallow aquifers and springs of Mt Fuji, especially along the FKFZ. The results overturn the prevailing non-mixing, laminar flow paradigm, propose a revised conceptual model with robust vertical exchange, and identify an additional Misaka-Tenshu deep groundwater contribution at Wakutamaike. This triple-tracer framework demonstrates a powerful, generalizable strategy for disentangling complex groundwater systems where classic tracers are ambiguous. Future work should quantify upwelling rates, extend spatial coverage, and integrate time-series monitoring to assess variability related to tectonic activity and climate-driven hydrological changes.

• Classic tracers (major ions, stable isotopes) are inherently limited for detecting vertical exchange in Fuji’s setting; while addressed by unconventional tracers, their integration relies on mixing assumptions and end-member characterization.
• Elevated V in springs could theoretically arise from longer shallow flow paths or reduced permeability zones, necessitating independent confirmation—which the study provides via He and eDNA; nonetheless, quantitative partitioning among processes remains uncertain.
• The presence of mantle He could reflect direct mantle gas input; corroboration using additional tracers was required and applied, but precise source apportionment and fluxes are not directly measured.
• Hydrogeological properties and dynamics of the FKFZ remain incompletely characterized; upwelling rates and temporal variability (e.g., seismic events, extreme rainfall) were not quantified in this study.
• Sampling focused on key springs and wells; broader spatial and temporal sampling would improve generalizability and allow system-wide mass-balance constraints.