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Methods and materials

The deep-water coal-bearing basin off Shimokita lies in the Sanriku Province in a fore-arc basin formed by the subduction of the Pacific plate beneath the North American plate along the Japan Trench (Fig. F1A). Scientific ocean drilling was performed in the basin off Shimokita during Expeditions 902 (D/V Chikyu shakedown Cruise CK06-06; Aoike, 2007) and 337 (see the “Site C0020” chapter [Expedition 337 Scientists, 2013b]), in order to clarify the main factors responsible for the vertical distribution and limits of microbial activity in the deep sedimentary biosphere. Expedition 902 recovered core samples from 0 to 365 meters below seafloor (mbsf) at Site C9001 (41°10.5983′N, 142°12.0328′E; 1180 m water depth), and Expedition 337 drilled deeper at the same location (the site name changed from Site C9001 to Site C0020) to extend the coring depth of Expedition 902. During Expedition 337, core samples were collected from 1276.5 to 2466 mbsf (Fig. F1B).

Sampling for analysis was conducted onshore at the Kochi Core Center, Japan (, where the core samples had been stored as half-cylinders measuring 1–1.5 m in length for 7 y (Expedition 902) and ~1 y (Expedition 337) at 4°C in gas-tight bags (ESCAL) to prevent the evaporation of pore fluids from core sediments during transfer and storage (Aoike, 2007; see the “Methods” chapter [Expedition 337 Scientists, 2013a]). Samples for analysis were obtained by subsampling core samples collected at intervals of approximately 40 m during Expedition 902. For Expedition 337, two samples were collected from every core unit (one unit is approximately 9.5 m long). Discrete core samples were obtained from working halves. Core samples were sliced into 90° sectors measuring <5 mm in thickness (bulk weight = 4–11 g) at room temperature (20°–25°C). Each sample was stored in a zipper storage bag after slicing to prevent the evaporation of pore fluid. All Aw measurements were completed one month after the samples were sliced.

Aw measurements

The water activities of core samples were measured using two commercially available Aw sensors that employed different measurement principles. One method is based on humidity measurements performed using an electric resistance humidity sensor (LabTouch-AW, Novasina, Switzerland), and the other method is based on measuring the dew point using an advanced chilled miller sensor (WP4-T, Decagon Devices, Inc., Pullman, WA, USA). The samples in the zipper storage bags were placed in the laboratory with a room temperature controlled at around 23°C before the Aw measurements. Thin-sliced samples were retrieved from the bags and put in a disposable plastic cup (40 mm in diameter and 12 mm deep). Then, a sample was placed in a sealed measurement chamber that allows heating but not cooling to stabilize the temperature of the samples. Aw measurements were initially conducted by the WP4-T system, then we proceeded to measure by using the LabTouch-AW system. The sample temperature, which was controlled using both sensors, was kept at 25°C for all measurements. Both sample chambers do not apply confining pressure and pore pressure to samples. Therefore, the Aw measured in this study reflects the value under control conditions and not the in situ value (i.e., Brown et al., 2017).

Based on the product specifications, the WP4-T system was more accurate (±0.0004) than the LabTouch-AW system (±0.005) for higher Aw values (>0.964), with the standard deviation of five replicate Aw readings for 24 samples measured with the WP4-T (±0.00067) being less than that obtained with the LabTouch-AW (±0.00089). Temperature control was more accurate with the LabTouch-AW (constant at 25.0°C) than with the WP4-T (24.9°–25.1°C). The differences in Aw values between the two systems were small for higher Aw values (>0.96), with the Aw values from the WP4-T being smaller than those from LabTouch-AW (<0.96; see Fig. F2; Table T1). We therefore used the Aw measurements obtained using the WP4-T system in this study.

Dependence of Aw on salinity and water content

The chemical composition, concentration, and water content of aqueous solutions are all affected by the thermodynamic properties and Aw (or vapor pressure) (Fredlund and Xing, 1994; Aung et al., 2001; Starzak and Mathlouthi, 2006). We therefore selected six core samples to investigate the effect of salinity and water content on Aw. To measure the effect of the NaCl concentration on Aw, pore water was desalinated and replaced with pure water (Elix, Merck Millipore Corporation, Germany) by immersing core samples in 1 L of pure water for several days. The pure water was replaced 3 times to ensure that the core sediments were desalinized. The samples were then fully saturated by pure water (Elix) again using a vacuum pump for 1 day before the start of the experiment. After performing the Aw measurements, the NaCl concentrations of pore water from the same sample were restored by resaturating the core sample in increasing concentrations of NaCl solution in a stepwise manner. In this way, the same sediment materials were reused to investigate the effect of water content on Aw and to conduct the porosity measurements. To measure the dependence of Aw on pore water content, the water content of the same sample was reduced in a stepwise manner by heating the sample at temperatures between 50° and 70°C using a moisture analyzer (MX-50, A&D Co., Ltd., Japan).

Computation of Aw values from pore water chemistry

Aw is generally influenced by the physicochemical characteristics of the interstitial pore water. According to Raoult’s law (Taoukis and Richardson, 2007), Aw for an ideal solution is a function of the mole fraction of the dissolved component, and is defined as follows:

Aw = nw/(nw + ns),


where nw and ns are the total moles of water and solutes, respectively. In this study, the interstitial water chemistry data measured on the ship using whole-round core samples, cuttings, and drilling mud during Expeditions 902 and 337 (Aoike, 2007; see the “Site C0020” chapter [Expedition 337 Scientists, 2013b]) was used in Equation 2 to predict Aw for core samples. However, since there was a disparity in the depth between interstitial water data measured on board and the Aw values measured in this study, pore water chemistry analyses were newly performed on core samples from Expedition 902 and on drilling mud fluid from Expedition 337. Samples for water chemistry analyses during Expedition 902 were obtained from core samples from working halves stored for 7 y. We selected the massive core samples that did not form fractures and tiny cracks for sampling. The exterior (15–20 mm width) of the half-round section was carefully removed to reduce drilling fluid contamination, and then interstitial water was squeezed from peeled sediment. The drilling fluid was collected from the mud tanks at intervals of approximately 50 m during Expedition 337 (see the “Methods” chapter [Expedition 337 Scientists, 2013a]), and then stored in plastic bottles (50–100 cm3) at 4°C in the Kochi Core Center. Therefore, we used these drilling mud samples (gravimetric water content ranges from 0.75 to 0.92). The methodology used for the water chemistry analysis performed in this study was the same as that performed on the ship (see the “Site C0020” chapter [Expedition 337 Scientists, 2013b]). The Aw for pore fluid with a multicomponent of solutes in the core samples was calculated using Geochemist’s Workbench (GWB) (Bethke, 2008) and PHREEQC for Windows (version 2.11; Parkhurst and Appelo, 1999); the calculations of Aw using GWB and PHREEQC are based on the Debye-Hückel equation (Helgeson, 1969) and Raoult’s law, respectively.

Porosity measurements

The porosity and pore water content were calculated from the measured pore and matrix volumes using the same samples as that used for the Aw measurements. Pore volume was calculated from wet and dry weights by drying samples in an oven at 105°C for 24 h), and the matrix volumes of the core sample were measured using a commercial helium gas pycnometer (Pentapycnometer, Quantachrome Instruments, Boynton Beach, FL, USA). Wet weights were measured just before the Aw measurement, and dry weight measurements were conducted after the Aw measurements. The matrix volume was measured using four replicates, and the average value was used for the porosity calculations. The standard deviation of the matrix volume was ±0.023 cm3, which is equivalent to ±1.5% and ±0.9% of the standard errors for the matrix volume and porosity, respectively. In this procedure, we may overestimate porosity, as drying samples at 105°C may result in the loss of some interlayer water in clay minerals.