Horonobe Research Institute for the Subsurface Environment

Serpentinization of ultramafic rocks provides molecular hydrogen (H2) that can support lithotrophic metabolism of microorganisms, but also poses extremely challenging conditions, including hyperalkalinity and limited electron acceptor availability. Investigation of two serpentinization-active systems reveals that conventional H2-/CO2-dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, “Ca. Lithacetigenota”, that exclusively inhabits serpentinite-hosted systems and harbors genes encoding alternative modes of H2-utilizing lithotrophy. Rather than CO2, these putative metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein—the glycine reductase. A survey of microbiomes shows that glycine reductases are diverse and nearly ubiquitous in serpentinite-hosted environments. “Ca. Lithacetigenota” glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation by Terrabacteria for gaining energy from geogenic H2 even under hyperalkaline, CO2-poor conditions. Unique non-CO2-reducing metabolisms presented here shed light on potential strategies that extremophiles may employ for overcoming a crucial obstacle in serpentinization-associated environments, features potentially relevant to primordial lithotrophy in early Earth.

Abstract To validate and to improve ecological products obtained from satellites, such as a leaf area index (LAI), above‐ground biomass (AGB), and a fraction of photosynthetically active radiation (fAPAR), in‐situ accurate data are indispensable. They must be not a single point‐data but an areal data representing the satellite footprint. Their accuracy needs to be much higher than the required accuracy for the satellite products. The quantitative assessment of their error is necessary for evaluating the satellite products' error from the discrepancy between the satellite products and the in‐situ data. However, such data had not been available. In particular, there had been few data of LAI in a sparse evergreen needle‐leaved forest, because of difficulty of accuracy control of in‐situ observation in such a forest. To overcome the difficulty and to obtain the representative LAI, we made an allometric equation to estimate the leaf mass of Picea glehnii in northern Hokkaido. We report the allometric equations of leaf mass and AGB of P. glehnii , its leaf mass per area (LMA), its leaf life span, its leaf distribution, its crown shapes, its wood specific gravity, and tree locations. We also report LAI, AGB, and fAPAR within the 500 m × 500 m area, which is the footprint scale of the Global Change Observation Mission‐Climate satellite, in a pure and sparse forest of P. glehnii in northern Hokkaido. These precise data are useful for validation of other satellite data, especially with higher spatial resolution, and forest structure modeling. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-06.1/jalter-en . [Correction added on 7 September 2020, after first online publication: JaLTER URL has been updated.]

A series of undrained monotonic and cyclic triaxial tests were performed on silica sand at two initial densities and different confining pressures from 0.1 to 5 MPa to investigate their shear response and crushing behaviour. The influence of particle crushing on the undrained shear strength and pore-water pressure was examined. To clarify the evolution of particle crushing, undrained monotonic and cyclic tests were terminated at several distinctive stages and sieving analysis tests were subsequently performed on the tested specimens. In the undrained monotonic test, specimens exhibited remarkable dilation behaviour and experienced no apparent particle crushing at low confining pressures. An increase in the mean stress suppressed the dilatancy due to a faster increase of the pore-water pressure, giving rise to the occurrence of particle crushing. In the undrained cyclic test, a higher confining pressure and cyclic stress ratio resulted in a much higher relative breakage. At a specific cyclic stress ratio, the relative breakage increased as the cyclic loading progressed. The confining pressure and shear strain amplitude played a significant role in controlling the evolution of particle breakage. The correlation between the relative breakage and plastic work for specimens under isotropic consolidation, undrained monotonic, and cyclic loadings has been validated experimentally.

Peat from highly organic soil is abundant in Northern Hokkaido, Japan. In the past, peat was used in various applications in Japan, such as an artificial culture of soil, as a fertilizer for gardening, and as an energy resource. However, peat is not used by the modern energy and manufacturing sectors in Japan because it has a high moisture content and low calorific value, which lowers its value as a resource considering its material characteristics and handling difficulties. Furthermore, large amounts of peat are generated at the construction sites in this area, and they are difficult to be reused at their generation sites because peat is a very soft soil and not suitable for construction work. Recently, many Japanese research institutions have been carrying out research and development on renewable energy resources including biomass energy. In Hokkaido, there are many biogas plants for methanizing biomass derived from livestock excrement or food waste. Thus, peat which is high in organic matter could potentially be used as an energy resource. In this study, we investigated the potential of utilizing peat as an energy resource for biogenic methane production in regional cities of Northern Hokkaido, while considering both its material characteristics and resource circulation. Batch tests using a hydrogen peroxide solution were performed on peat and silty soil to estimate the quantity of low-molecular-weight organic acids and the producing potential for biogenic methane gas. The oxidative decomposition of the peat produced a high yield of low-molecular-weight organic acids that were used as substrates for methanogenic microorganisms. In addition, a novel resource circulation method was proposed for peat in order to use it as an energy resource. Moreover, the energy resources problem in Northern Hokkaido was discussed in association with geographical parameters and the construction recycling system in Japan.

As one of the application of coal resources, domestic and overseas industries have been focusing on the recovery of methane from coal resources by methanogens using low-molecular weight acids or hydrogen that are converted from the organic matter in coal. For this application, it is essential to enhance the extraction of organic matter from low-rank coal (lignite) and maximize the conversion rate to consumable substrates for methanogen. In this study, we focused on the effects of chelating and reducing agents on the extraction of organics and metals from low-rank coal. Citric acid (chelating and reducing agent) and EDTA (chelating agent) were chosen as typical solvents. In the presence of citric acid, the Fe (II) concentration was correlated with the concentration of extracted organics as well as the total Fe. By contrast, the Fe (II) concentration was constantly at a low level for each EDTA concentration and pH. The absorbance (280 nm) of both solutions was almost the same when the total Fe concentrations were similar, regardless of the concentrations of Fe (II) , Al, Mg and Ca. These results indicated that organics from lignite were extracted with the leaching of Fe (III) and that the effects of reduction on the extraction of organics were insignificant. Excitation emission matrix spectra analysis suggested that humic acid was the main component of the extracted organics from lignite. The amount of acetic acid and formic acid released from 1g of lignite was calculated to be in the range 0.14 to 0.25 mg, and it was observed no correlation of the released amount with the citric acid /EDTA concentrations. Further research to obtain substrates such as low-molecularweight acids from the extracted organic materials is necessary for methane production using methanogens.

本研究では，二酸化炭素（CO2）地中貯留におけるキャップロックのシール性能を評価するために，水で飽和させた泥質岩試料にCO2を注入し，その閾値圧力，力学特性および浸透率を測定する室内実験を行った。岩石試料は，第四紀更新統上総層群下部の大田代層の泥質岩円柱試料（直径：50 mm，高さ：125 mm）を用いた。測定試料にはひずみゲージや圧電素子を貼付し，CO2注入後のひずみやP波速度の変化を測定しながら，CO2が泥質岩試料へ浸透し始める注入圧力（閾値圧力）を求めた。地下深部の温度・圧力条件を考慮し，封圧12～18 MPa，間隙圧10MPa，温度40℃の条件下で測定試験を実施した。超臨界CO2の注入実験と比較検討するために，温度のみ20℃に変えた液体CO2注入実験も行った。その結果，閾値圧力は液体CO2注入時では，封圧12～18MPaの条件下で3MPa，超臨界CO2注入時では，封圧12MPa条件下で1MPa，封圧15，18MPa条件下で2MPaであった。一方，力学特性を調べる三軸圧縮試験では，超臨界CO2を注入した場合，封圧12MPa 条件下では脆性破壊を示すが，封圧が15MPaと18MPaの条件下では延性破壊を示した。力学特性試験で得られたヤング率とポアソン比は，封圧の増加に伴って減少したほか，超臨界CO2注入によって水で飽和した試料に比べてそれぞれ約21～24%，28～35%小さくなった。また，ピーク強度以降の超臨界CO2の有効浸透率は軸圧載荷前に比べ約10～30μDの増加が認められた。本研究で得られたキャップロックの閾値圧力，力学特性および浸透率の測定結果は，CO2地中貯留の安全性評価に重要な知見を提供できると考えられる。

ABSTRACTWe investigated microbial methanogenesis and community structure based on 16S rRNA gene sequences from a coal seam aquifer located 843–907 m below ground level in northern Japan; additionally, we studied the δ13C and δ2H (δD) of coal‐bed gases and other physicochemical parameters. Although isotopic analysis suggested a thermocatalytic origin for the gases, the microbial activity and community structure strongly implied the existence of methanogenic microbial communities in situ. Methane was generated in the enrichment cultures of the hydrogenotrophic and methylotrophic microorganisms obtained from coal seam groundwater. Methanogen clones dominated the archaeal 16S rRNA gene libraries and were mostly related to the hydrogenotrophic genus Methanoculleus and the methylotrophic genus Methanolobus. Bacterial 16S rRNA gene libraries were dominated by the clones related to the genera Acetobacterium and Syntrophus which have a symbiotic association with methanogens. LIBSHUFF analysis revealed that N2 gas injected into the coal seam (for enhanced methane production) does not affect the coverage of archaeal and bacterial populations. However, amova analysis does provide evidence for a change in the genetic diversity of archaeal populations that are dominated by methanogens. Therefore, N2 injection into the coal seam might affect the cycling of matter by methanogens in situ.

北海道北部の幌延地域に分布する新第三紀の海成堆積物における地下水のpHに影響を与えている水－岩石反応を把握するために，本堆積物の岩石学的特徴と地下水の地球化学的特徴を検討した．その結果，1）本堆積物中の地下浅部における天水の浸透領域では岩石からNaの溶脱が生じており，この溶脱が岩石中のスメクタイト中のNa＋と地下水中の陽イオンとの陽イオン交換反応によること，2）地下浅部における地下水のpHは，Naの溶脱の際に起こるスメクタイト中のNa＋と地下水中のH＋との陽イオン交換反応により規制されており，天水が浸透するとpHが上昇すること，が考えられた．この検討結果は海外における既存のモデルと整合的である．

ABSTRACTWe investigated the diversity and distribution of archaeal and bacterial 16S rRNA gene sequences in deep aquifers of mid‐ to late Miocene hard shale located in the northernmost region of the Japanese archipelago. A major fault in the north‐west–south‐east (NW–SE) direction runs across the studied area. We collected three groundwater samples from boreholes on the south‐west (SW) side of the fault at depths of 296, 374 and 625 m below ground level (m.b.g.l.) and one sample from the north‐east (NE) side of the fault at a depth of 458 m.b.g.l. The groundwater samples were observed to be neutral and weakly saline. The total microbial counts after staining with acridine orange were in the order 105−106 cells mL−1 and 103 cells mL−1 in the aquifers to the SW and to the NE of the fault, respectively. A total of 407 archaeal and bacterial 16S rRNA gene sequences (204 and 203 sequences, respectively) were determined for clone libraries constructed from all groundwater samples. Phylogenetic analyses showed that the libraries constructed from the SW aquifers were generally coherent but considerably different from those constructed from the NE aquifer. All of the archaeal clone libraries from the SW aquifers were predominated by a single sequence closely related to the archaeon Methanoculleus chikugoensis, and the corresponding bacterial libraries were mostly predominated by the sequences related to Bacteroidetes, Firmicutes and δ‐Proteobacteria. In contrast, the libraries from the NE aquifer were dominated by uncultured environmental archaeal clones with no methanogen sequences and by β‐proteobacterial clones with no sequences related to Bacteroidetes and δ‐Proteobacteria. Hence, the possible coexistence of methanogens and sulphate reducers in Horonobe deep borehole (HDB) on the SW side is suggested, particularly in HDB‐6 (374 m.b.g.l.). Moreover, these organisms might play an important geochemical role in the groundwater obtained from the aquifers.