5:15 PM - 7:15 PM
[MZZ42-P12] Methane and hydrogen dependent deep biosphere at the boundary between the North American and the Eurasian Plates: Hydrogeological controls on prokaryotic ecology
Keywords:Deep biosphere, Methane-oxidizing bacteria, Suwa Basin, Pull-apart basin, Itoigawa-Shizuoka Tectonic Line
Subsurface biosphere hosts diverse prokaryotes whose metabolic activities are largely unexplored. In particular, interactions between subsurface prokaryotes and environmental characteristics are not well constrained. Therefore, revealing impacts of geochemical and geological backgrounds on subsurface ecosystems is crucial to elucidate their functions in biogeochemical cycles. In this context, we investigated CH4– and H2–dependent deep biosphere in the Suwa Basin, Japan (36.0°N, 138.1°E).
The Suwa Basin consists of a sedimentary layer and an underlying bedrock layer of andesite and granodiorite [1]. The basin offers an ideal setting to study interactions between environmental features and subsurface microbiology as it lies at boundary between the North American and the Eurasian Plates. Due to its unique location, these features are tightly related with subsurface ecosystems by preparing distinctive ecological niches and supplying substrates from deep regions. Indeed, a previous study reported active CH4 emission from the sedimentary layer, suggesting CH4–dependent subsurface biosphere [2]. However, the diversity and distribution of subsurface ecosystems in the basin remain uncharacterized.
Here, we performed geochemical and microbiological analyses on three types of water samples: groundwater from the sedimentary layer (10–100 m below ground level), hot spring water from the bedrock layer (–1,000 mbgl), and mountain spring water. Subsurface microbial community analysis was conducted based on 16S rRNA gene sequencing. Concentrations of ions and trace elements were measured by ion chromatography (IC) and inductively coupled plasma mass spectrometry (ICP–MS). For gas samples associated with water samples, concentrations and isotopic compositions (δ13C and δD) were measured for CH4, CO2, and H2 by isotope ratio mass spectrometry (IRMS). Furthermore, 14C contents were measured for dissolved inorganic carbon (DIC) using acceleration mass spectrometry (AMS) [3].
Isotopic profiles of CH4 and CO2 from the sedimentary layer indicated a primary microbial origin, namely fermentation and CO2 reduction with H2 [4]. In contrast, gas samples of hot spring sites contained H2, with isotopic compositions (-736‰ VSMOW) suggesting an origin related to fault activity. The aerobic methane-oxidizing bacteria (MOB) were abundant in groundwater from the sedimentary layer (10–100 mbgl), whereas methanogens were not significant. These results suggest the presence of an ecological niche for methanogens in deeper, reducing environments. The hot spring samples were dominated by hyperthermophilic hydrogenotrophs, consistent with H2 in gas phase. 14C–DIC analysis revealed the significant influx of young groundwater with high redox potential from mountainous areas surrounding the basin, which may be critical for flourishing of MOB at 10–100 mbgl of the sedimentary layer rather than methanogens. This is consistent with reported water isotope compositions (δD and δ18O) which indicated meteoric water–origin of the groundwater [5]. Additionally, the Li/Na ratios of groundwater suggest the recharge of deeply derived hydrothermal fluids into the sedimentary layer. As faults act as conduits for vertical material transport, the unique geological setting of Suwa Basin may support prokaryotic growth in the sedimentary layer through an enhanced nutrient supply (e.g., H2) from deep fluids. These findings provide new insights into subsurface CH4–related microbial ecology and the hydrogeological factors that control it. In this presentation, the impacts of hydrogeochemistry on subsurface prokaryotic ecology will be further discussed [6].
Acknowledgements
This study was performed by the official collaboration agreement through the joint research project between JAMSTEC and Shinshu Univ. The authors are grateful to Drs. N. Ohkouchi and N. O. Ogawa for constructive advice and the development of the chemistry laboratory at JAMSTEC. The authors thank Drs. T. Aze, Y. Ando, S. Izawa (AORI) for technical assistance of radiocarbon analysis. We wish to thank Dr. S. Kawagucci (JAMSTEC) for the support of stable isotope analysis, Ms. Y. Yoshikawa (JAMSTEC) for technical support for inorganic analysis, and Dr. M. Sunamura (U. Tokyo) for the assistance of diversity analysis of microbial community.
[1] Motojima et al. (1952) Bull Geol Survey Jpn 3:644–649. (in Japanese)
[2] Urai et al. (2022) ACS Earth Space Chem 6:1689–1697
[3] Yokoyama et al. (2019) Nucl Instrum Methods Phys Res B 455:311–316
[4] Milkov and Etiope (2018) Org Geochem 125:109–120
[5] Sakakibara et al. (2025) J Hydrol 653:132790
[6] Nishimura (2025) Univ. Tokyo, Ph.D. thesis
The Suwa Basin consists of a sedimentary layer and an underlying bedrock layer of andesite and granodiorite [1]. The basin offers an ideal setting to study interactions between environmental features and subsurface microbiology as it lies at boundary between the North American and the Eurasian Plates. Due to its unique location, these features are tightly related with subsurface ecosystems by preparing distinctive ecological niches and supplying substrates from deep regions. Indeed, a previous study reported active CH4 emission from the sedimentary layer, suggesting CH4–dependent subsurface biosphere [2]. However, the diversity and distribution of subsurface ecosystems in the basin remain uncharacterized.
Here, we performed geochemical and microbiological analyses on three types of water samples: groundwater from the sedimentary layer (10–100 m below ground level), hot spring water from the bedrock layer (–1,000 mbgl), and mountain spring water. Subsurface microbial community analysis was conducted based on 16S rRNA gene sequencing. Concentrations of ions and trace elements were measured by ion chromatography (IC) and inductively coupled plasma mass spectrometry (ICP–MS). For gas samples associated with water samples, concentrations and isotopic compositions (δ13C and δD) were measured for CH4, CO2, and H2 by isotope ratio mass spectrometry (IRMS). Furthermore, 14C contents were measured for dissolved inorganic carbon (DIC) using acceleration mass spectrometry (AMS) [3].
Isotopic profiles of CH4 and CO2 from the sedimentary layer indicated a primary microbial origin, namely fermentation and CO2 reduction with H2 [4]. In contrast, gas samples of hot spring sites contained H2, with isotopic compositions (-736‰ VSMOW) suggesting an origin related to fault activity. The aerobic methane-oxidizing bacteria (MOB) were abundant in groundwater from the sedimentary layer (10–100 mbgl), whereas methanogens were not significant. These results suggest the presence of an ecological niche for methanogens in deeper, reducing environments. The hot spring samples were dominated by hyperthermophilic hydrogenotrophs, consistent with H2 in gas phase. 14C–DIC analysis revealed the significant influx of young groundwater with high redox potential from mountainous areas surrounding the basin, which may be critical for flourishing of MOB at 10–100 mbgl of the sedimentary layer rather than methanogens. This is consistent with reported water isotope compositions (δD and δ18O) which indicated meteoric water–origin of the groundwater [5]. Additionally, the Li/Na ratios of groundwater suggest the recharge of deeply derived hydrothermal fluids into the sedimentary layer. As faults act as conduits for vertical material transport, the unique geological setting of Suwa Basin may support prokaryotic growth in the sedimentary layer through an enhanced nutrient supply (e.g., H2) from deep fluids. These findings provide new insights into subsurface CH4–related microbial ecology and the hydrogeological factors that control it. In this presentation, the impacts of hydrogeochemistry on subsurface prokaryotic ecology will be further discussed [6].
Acknowledgements
This study was performed by the official collaboration agreement through the joint research project between JAMSTEC and Shinshu Univ. The authors are grateful to Drs. N. Ohkouchi and N. O. Ogawa for constructive advice and the development of the chemistry laboratory at JAMSTEC. The authors thank Drs. T. Aze, Y. Ando, S. Izawa (AORI) for technical assistance of radiocarbon analysis. We wish to thank Dr. S. Kawagucci (JAMSTEC) for the support of stable isotope analysis, Ms. Y. Yoshikawa (JAMSTEC) for technical support for inorganic analysis, and Dr. M. Sunamura (U. Tokyo) for the assistance of diversity analysis of microbial community.
[1] Motojima et al. (1952) Bull Geol Survey Jpn 3:644–649. (in Japanese)
[2] Urai et al. (2022) ACS Earth Space Chem 6:1689–1697
[3] Yokoyama et al. (2019) Nucl Instrum Methods Phys Res B 455:311–316
[4] Milkov and Etiope (2018) Org Geochem 125:109–120
[5] Sakakibara et al. (2025) J Hydrol 653:132790
[6] Nishimura (2025) Univ. Tokyo, Ph.D. thesis