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Site C0020 site summary

Expedition 337 was the first expedition dedicated to subseafloor microbiology using riser drilling technology. Hole C0020A is the deepest hole in the history of scientific ocean drilling. On 9 September 2012, we terminated drilling at a total drilling depth of 2466 mbsf. Site C0020 is the extension of JAMSTEC Hole C9001D drilled during the Chikyu shakedown cruise in 2006 (Aoike, 2007), when drilling pilot holes by both riserless and riser systems was terminated at 647 mbsf and 36 and 20 inch casings were installed to 511 mbsf. During Expedition 337, we drilled from 647 mbsf to the final depth of 2466 mbsf (Table T1).

The use of riser drilling technology in very deep sediments created both unique opportunities and new challenges for the science party. Our experiences and results will be of great strategic value to future missions of deep scientific ocean drilling. Our scientific objectives focusing on the deeply buried coalbed strictly required the use of riser drilling technology. This technology enabled implementation of several operations of direct relevance to the Expedition 337 scientific objectives. For example, the use of a newly installed mud-gas monitoring laboratory provided the opportunity to monitor a range of biogeochemically relevant gases, including real-time measurements of isotopic compositions of methane. For the first time in scientific ocean drilling, we conducted downhole fluid analysis and sampling. Logging operations yielded data of unprecedented quality. At the same time, the riser drilling technology, in particular the use of drilling mud, created substantial obstacles that posed considerable threats to the scientific success of Expedition 337. Riser drilling mud is saline, alkaline, contains a multitude of organic compounds, and, most importantly, high microbe concentrations. Our strategies to detect, quantify, and minimize contamination, as well as to deal with residual levels thereof, have consequently played an important role for the shipboard scientific program and will undoubtedly require careful interpretation of all future data. A substantial portion of this chapter will therefore be dedicated to quality assurance/quality control (QA/QC) of the sampled materials and data. Nevertheless, at the very least from an operational point of view, this expedition was successful: we carried out nearly all intended operations, we drilled and sampled several coalbed layers, and we were able to drill 266 m deeper than our initial target depth. The recovered samples hold the potential to extend the currently accepted evidence of deepest life below the seafloor (Roussel et al., 2008) by >800 m and provide the opportunities to address all major objectives related to the relationship of deep coalbeds and microbial life. In the following sections, we will provide principal results according to discipline followed by a synthesis of currently available information as pertaining to our scientific objectives.

Lithostratigraphy and biostratigraphic age constraints

Riser drilling during Expedition 337 provided an unprecedented record of dynamically changing depositional environments during the late Oligocene and Miocene in the former forearc basin off the Shimokita Peninsula. This record is composed of a rich diversity of lithologic facies reflecting environments ranging from warm-temperate coastal backswamps to cool-water continental shelf. Four distinct lithologic units were identified in Hole C0020A on the basis of combined analyses of cuttings and cores and assisted by inspection of X-ray computed tomography (CT) scan images and wireline logging data (Figs. F3, F4, F5).

Shipboard micropaleontology included identifications of diatoms, calcareous nannofossils, organic-walled dinoflagellate cysts (dinocysts), pollen, and spores. Through micropaleontological analyses, we were able to constrain an age of early Pliocene at the top of Hole C0020A at 647 mbsf and a probable age of late Oligocene–early Miocene at the base of the hole at 2466 mbsf (Fig. F3). Diatoms were recovered from the upper parts of Hole C0020A but were absent, or very poorly preserved, throughout most of lithologic Units II, III, and IV (defined below). The samples could be loosely dated, and to 1076.5 mbsf, all samples were consistent with Pliocene age. Diatoms were identifiable until the base of Unit I, where they appear to be Miocene in age; however, marker species were not identified and the boundary between the early Pliocene–late Miocene was not observed. Calcareous nannofossils were rare and poorly preserved. Hence, calcareous nannofossils did not inform the age model presented here:

  • Unit I (647–1256.5 m mud depth below seafloor [MSF]) consists primarily of diatom-bearing silty clay. This unit resulted from sedimentation in an offshore marine environment. Diatoms were best and most abundantly preserved in Unit I, along with predominantly heterotrophic dinocysts. Diatom floras in Unit I are consistent with a Pliocene cool-water continental shelf succession. Heterotrophic dinocyst communities feeding off diatom blooms are suggestive of elevated marine productivity.

  • Unit II (1256.5–1826.5 m MSF) consists mostly of silty shale with some interspersed intervals of sandstone and siltstone. Cuttings samples show a lower amount of sand and an increase of silt at the Unit I/II boundary. The abundance of biogenic siliceous material, glauconite, and plant remains also differentiate Unit II from the overlying unit. Unit II was divided into two different subunits: sandstone and siltstone associated with marine fossiliferous material (Subunit IIa; 1256.5–1500 m MSF) and organic-rich shale and sandstone associated with plant remains (Subunit IIb; 1500–1826.5 m MSF). The upper part of Unit II represents an offshore environment, possibly with a paleoposition close to the shelf margin; with increasing depth the paleoenvironment gradually changes into a shallow-marine setting. The bottom part of Unit II is situated in the intertidal zone. This shift is consistent with microfossil assemblages that exhibit few identifiable diatoms and poor dinocysts; reworked dinocysts in Unit II, as in deeper units, have Paleogene ages that broadly fall in the range of early middle Eocene–late Oligocene. Pollen and spores are moderately well represented but are abundant near the base of Unit II, which is consistent with increasing terrestrial influence in shallow-marine sediment.

  • Unit III (1826.5–2046.5 m MSF) is dominated by several coal horizons, which we divided into coaly shale, siltstone, and sandstone. Almost all coal horizons consist of fine-detritic to xylodetritic coal with some layers of xylitic coal. Water content, color, and vitrinite reflectance measurements of the coal suggest that the coal has low maturity (see Fig. F6). Bioturbation and sedimentary features like flaser bedding, lenticular bedding, or cross-bedding suggest a nearshore depositional environment with tidal flats and tidal channels. The presence of siderite bands at the bottom of this unit suggests a back-barrier marine environment in combination with wetlands (e.g., salt marsh or swamp). Small terrestrial influence might occur within sand bodies that overlie coal horizons. This could be due to channels from deltaic environments. Unit III contains excellent pollen and spore assemblages in the coal and associated terrestrial to coastal shallow-marine sediment. However, dinocysts are scarce and contain few useful biostratigraphic markers. The pollen floras tentatively suggest an age of early middle Miocene for Unit III.

  • Unit IV (2046.5–2466 m MSF) is dominated by silty shales in the upper part, sandstone intercalated with siltstone and shale associated with sand in the middle part, and sandstone intercalated with silt and a thin coal layer in the lower part. Wireline logs and cuttings samples suggest a thick homogeneous shale layer between the Unit III boundary and Core 337-C0020A-27R (2200 m core depth below seafloor, Method B [CSF-B]). The depositional environment of Unit IV resembles that of Unit III, except that the former contains only one thin coalbed. Like Unit III, Unit IV experienced high-frequency fluctuations of the depositional environment. Within a few meters, there are sediments related to tidal flats and tidal channels, which are overlain by organic-rich material of a marsh that resulted in formation of peat. The pollen floras place a maximum age of late Oligocene for the base of Unit IV.

Physical properties

A series of physical properties measurements were performed on core and cuttings samples from Hole C0020A. Gamma ray attenuation density, magnetic susceptibility, natural gamma radiation, P-wave velocity, and noncontact electrical resistivity were measured with the multisensor core logger. Measurements of thermal conductivity were made mostly on working-half cores. Discrete samples taken from working-half cores and some whole-round core samples were applied to moisture and density (MAD) analyses to calculate porosity, bulk density, grain density, and water content. P-wave velocity analysis and electrical impedance analysis were made on cubic discrete samples. Cuttings samples were also applied to MAD analysis. Cuttings samples were separated into four categories: original bulk and sieved size categories of >4.0, 1.0–4.0, and 0.25–1.0 mm. Large-size fraction of the cuttings samples were cut off cubic samples and applied to the P-wave velocity analysis and the electrical impedance analysis. Anelastic strain recovery analysis was made on some whole-round cores. Vitrinite reflectance analysis was performed on some coaly samples, indicating generally low maturity of coal (Ro = 0.2–0.4) in Hole C0020A. Porosity of siltstone, sandstone, and shale gradually decreased with increasing depth (Fig. F7). Porosity corresponds to lithologic variation, with carbonate-cemented sandstone and siltstone having much lower values than noncemented sandstone and siltstone. The porosity of coal does not deviate from the major trend of the other lithologies, although we cannot exclude that the coal may have expanded after recovery. The cuttings also show a gradual decrease in porosity but have generally higher values than core samples. Discrete core samples are likely more representative of in situ porosity than cuttings.

Downhole logging

Because of the very good borehole condition and relatively simple lithology, logging data of excellent quality was obtained from Hole C0020A. The relatively simple lithology consists of sandstone, siltstone, shale, coal, and conglomerates, most of which show typical log response and are intercalated by a number of marker layers (i.e., coal and cemented sandstone). This resulted in straightforward interpretation of logging data with respect to lithology, compensated for our lack of cored materials in the majority of the drilled section, and ultimately led to the establishment of a database that fully reconstructs the sedimentation history at Site C0020 (Fig. F5).

Log characteristics suggest that Unit I lithology is similar to that of Unit II, which consists of alternation of relatively thick layers of massive sandstones and siltstones. Unit III is characterized by frequent coal layers in a few meters thickness of sandstone and siltstone alternation sequence. Based on correlations of log data and visual core descriptions, 7 coal layers, including the thickest 2, were acquired by coring from a total of 13 identified layers with thicknesses >30 cm. Unit IV consists of thick (~200 m) massive shale in the upper half; the lower half exhibits alternations of sandstone and shale of a few meters thickness each. One thin coal layer was observed in Core 337-C0020A-30R; log data suggest that this coal represents a single depositional event in Unit IV.

Resistivity borehole images suggest that the sandstones in Unit II are massive and include conglomerates, whereas those in Units III and IV consist of thin sandstones of centimeter thickness or lamina of this scale, suggesting a change in the sedimentary environment at the Unit II/III boundary. By combining the logging data and core descriptions, sandstones that may be of high permeability were identified in Units II and III.

By using a formation-testing tool, fluid samples were acquired from six permeable sandstone layers. The 31 “pretest” measurements prior to fluid sampling indicate that formation pore pressure is hydrostatic or elevated by only a few percent of the hydrostatic value to depths of at least 2425 m wireline log matched depth below seafloor (WMSF) (the depth of the deepest reliable measurement).

Borehole temperature was measured with two types of logging tools. The maximum temperature at the bottom of Hole C0020A was estimated by examining the temperature build-up pattern during the logging operation. The estimated temperature gradient was 24.0°C/km or slightly lower (Fig. F8).

Preliminary log-seismic integration was carried out based on the time-depth curve derived from vertical seismic profile operation and synthetic seismogram calculation. The time-migrated seismic profile for seismic survey Line ODSR03-BS (Taira and Curewitz, 2005) was converted with the time-depth relationship and compared with logging data. Strong reflectors are well correlated with the abrupt change on the logging curves.


Expedition 337 investigated the role of the Shimokita coalbed as a potential energy and carbon source for the deep subseafloor biosphere. In this context, geochemical studies are aimed at elucidating the cycling of carbon and nutrients, the conversion and transport of hydrocarbons, the flux of both thermogenically and biologically produced organic compounds, their utilization by the deep subseafloor biosphere, and the impact of deep hydrocarbon sources on the carbon budget of the shallower surface. To this end, geochemists investigated solid phase, gas, and fluid samples at Site C0020.

Organic matter quantity and origin

Shipboard analysis of solid phase samples showed a strong lithologic control of the TOC contents in sediment: lignite layers had the highest average TOC contents (40.9 ± 9.9 wt%), followed by clayey (1.4 ± 1.0 wt%), silty (0.43 ± 0.29 wt%), and sandy (0.26 ± 0.18 wt%) materials (Fig. F9). The coal layers in Unit III were evident not only in the high TOC contents of visually identified coal layers in sediment cores but also in the elevated TOC contents of randomly sampled cuttings. In general, TOC contents in cuttings were slightly higher than in the corresponding cores, possibly because of mixing effects with the drilling mud. Since land plants contain less nitrogen than protein-rich marine plankton, the atomic ratio of TOC and total nitrogen (TN) is a useful first indicator for the origins of organic matter. Throughout cores taken form Hole C0020A, TOC/TN ratios ranged from 3 to 58, with higher values indicating a stronger contribution of higher land plant-derived organic matter to TOC. Like TOC contents, TOC/TN ratios were controlled by lithology. The highest TOC/TN ratios of ~58 were observed in coal. In general, clayey sediment had TOC/TN ratios of ~22, which are still indicative of terrigenous organic matter, whereas sandy and silty lithologies showed lower TOC/TN ratios of ~13. However, the clastic sediment had a large within-group variation in the TOC/TN ratio (1σ = 7–10), making it difficult to link the origins of organic matter (i.e., terrestrial or marine) to lithologic compositions. The total sulfur (TS) values were generally low (from below detection to 1.4 wt%) and showed no clear associations with lithology or specific trends with depth. The cluster of samples with low TS contents in Unit III contained samples of different lithology, including lignite coal. Rock-Eval pyrolysis (e.g., Tissot and Welte, 1984) provided some initial information on the type and maturity of organic matter. In Units II–IV, most of the core samples yielded maximum temperature (Tmax) values in the range of 400°–440°C, indicating organic matter in a thermally immature to early mature state. The average values of parameters S2, S3, and hydrogen index (HI) decreased in the order of coal > clayey materials > silty or sandy materials, suggesting higher contents of hydrogen-rich organic matter in fine-grain sediment and coal (Fig. F9).

Biomarker evidence for origin and thermal maturity of organic matter

Further insights into the origin and thermal maturity of organic matter come from the analysis of lipid biomarkers. A large proportion of n-alkanes with an odd-over-even carbon number predominance in the C29 range and n-alkanoic acids with an even-over-odd predominance in the C26 range, as well as the general predominance of C29 sterenes derived from C29 sterols abundant in higher plants (Fig. F10), suggest that terrestrially derived organic matter substantially contributes to TOC (Huang and Meinschein, 1979). The extent of this contribution appears to reach a maximum close to the transition from Unit I to Unit II (~1200 m MSF), with another maximum near the coal-bearing horizons.

In addition, the degree of thermal alteration of sediment can be gauged from the conversion of sterenes to steranes and using biomarker data previously calibrated against temperature in the Hokkaido region (Amo et al., 2007). A critical temperature threshold for this process in the subsurface is the range of 40°–60°C (Amo et al., 2007). The extent of sterene-to-sterane conversion for Site C0020 is consistent with previous work and the estimated geothermal gradient of 24°C/km, as well as the bottom-hole temperatures measured during Expedition 337 (Fig. F11).


For the composition of gases above, in, and below the Shimokita coalbed, about 1 million discrete data points could be recorded by mud-gas monitoring (i.e., the continuous extraction and online analysis of gases that are brought up from the formation to the Chikyu with the recycling of drilling mud during riser drilling). Mud-gas monitoring was supplemented by gas analysis in >100 samples from cuttings and cores. Analysis focused on the content and carbon isotopic composition of methane but also included higher hydrocarbon gases, N2, O2, Ar, H2, and CO. Although the determination of absolute in situ concentrations is not possible, the relative ratio of gas species in the mud gas is very informative, particularly the C1/C2 ratio. Because the thermogenic generation of hydrocarbons is associated with production of higher hydrocarbon gases, low C1/C2 ratios indicate thermogenic methane formation. The downhole profile with its rather high C1/C2 ratios at Site C0020 points unambiguously to the predominance of biogenic methane sources (Fig. F12). Interestingly, the ratios found in mud gas of coal-bearing sediment horizons at ~2000 m MSF showed a strong positive inflection, suggestive of an active source of biologically produced methane.

O2/Ar, N2/Ar, and H2/Ar ratios were used to monitor corrosive processes during drilling. O2/Ar and N2/Ar ratios resembled atmospheric values throughout the drilling process, and the lack of oxygen consumption suggests that only little corrosion occurred. Nevertheless, H2 contents were distinctly elevated above atmospheric levels in mud gas and core samples, and the extent to which H2 concentrations are impacted by drilling activities is not fully resolved at this point.

In summary, shipboard solid phase and gas analyses suggest that organic matter from predominantly terrigenous sources is available for the deep biosphere not only in coal but also in TOC-rich clay. Moreover, organic matter is apparently thermally relatively immature to 2466 mbsf and rich in hydrogen, which might be released as molecular H2 over the course of diagenesis. Finally, C1/C2 ratios suggest that methane is predominantly formed by biogenic processes.


Expedition 337 is the second riser drilling IODP expedition, and Hole C0020A is only the second hole from which interstitial water has been retrieved from riser drilled cores (following IODP Expedition 319 Hole C0009A; Expedition 319 Scientists, 2010). We recovered interstitial water from 2405 m CSF-B, extending the world record for deepest interstitial water recovered by 820 m (Expedition 319 Scientists, 2010). In addition, this is the first cruise to obtain large-volume formation water samples from specific lithologic intervals in the borehole using Schlumberger’s Quicksilver device. A total of six formation water samples were sampled downhole, from 1279 to 1978 m WMSF.

Recovering fluids from such deep sediment is not without its challenges, however. Pressure changes during core recovery provoke phase changes in dissolved gases and lead to expansion of cores along fracture planes. Sediment cores have low porosity (see Fig. F7), are prone to fracturing along laminations, and thus are easily contaminated by drilling mud. Thus, among the objectives of shipboard inorganic chemists was assessing contamination of interstitial water and sampled formation water by the drilling process (see below). Because of low porosity and permeability, only 24 of the processed 48 whole-round cores yielded interstitial fluid through squeezing, with volumes of 0.2–33.5 mL despite squeezing up to 70 cm long whole-round cores. Of the cores that yielded pore water, 15 were from Unit II, 7 from Unit III, and 2 from Unit IV; the relationship between interstitial water yields and lithology is illustrated in Figure F13.

In addition to analyses on interstitial and formation fluids, for the first time the inorganic chemistry of both drilling mud and drilling cuttings data were analyzed in the context of sample contamination. Because there was no coring through Unit I (i.e., 647–1256.5 m MSF), the only geochemical information from this depth interval was from the drilling cuttings and mud-gas logging. Whereas the cuttings did not provide reliable information about the pore water from the depths at which they were obtained, they did provide information on interactions between drilling mud and sediment samples.


Expedition 337 was the first riser ocean drilling expedition to incorporate extensive shipboard microbiological and molecular biological analyses. These were performed with state-of-the-art equipment in the designated microbiology laboratory aboard the Chikyu. Because the target sedimentary habitat is strictly anaerobic, all the cored materials were immediately transferred to anaerobic conditions where they were processed for shipboard and shore-based microbiological analyses.

Previous studies in continental margin sediment have shown that microbial populations and activity generally decrease with increasing sediment depth (e.g., Parkes et al., 2000). However, the various geophysical and geochemical factors that constrain the extent of the deep biosphere remain unknown. Therefore, one of the key objectives of the Expedition 337 microbiology program was the quantification of microbial cells and detection of molecular signatures of “indigenous” deep subseafloor life from sediment cored by riser drilling. In deeply buried horizons, microbial cell densities approach the detection limits of most established cell counting protocols (Expedition 329 Scientists, 2011), necessitating whole-cell extractions and cell concentration procedures and complementary use of different cell counting methods (e.g., manual and image-based microscopy and high performance flow cytometry). Results obtained by different methods can then be compared to evaluate method-inherent biases. To implement these ultra-sensitive assays for the detection of deep subseafloor life, QA/QC is extremely important. The high cell concentrations of >100 million cells/cm3 in riser drilling mud required careful monitoring of core contamination by adding chemical tracers to drilling mud, DNA fingerprinting of contaminant microbes, and checking pore fluid for ionic species that had been added to drilling mud.

Critical steps such as microbiological sample processing, cell counts, cultivation, and molecular studies were performed aseptically in the microbiology laboratory on the Chikyu. Preliminary cell detections and enumerations showed extremely small cells to be present at very low concentrations in samples from as deep as 2457 m CSF-B (Fig. F14). These cells represent the deepest subseafloor life that has ever been studied through scientific ocean drilling. Complementary to gas compositional profiles suggesting biological activity in the deep coalbed, functional genes indicative of anaerobic microbial carbon cycling were consistently detected in strata near the coalbed. However, preliminary community-fingerprinting analysis based on polymerase chain reaction–amplified 16S rRNA genes showed that even very carefully collected samples are not free of signals from contaminant microbes; careful examination of all available lines of evidence is thus required for obtaining a comprehensive view of the potentially deepest subseafloor ecosystem ever studied.

To more fully address some of the primary scientific objectives, various types of microbiological and biogeochemical samples were prepared for shore-based studies. These include more than 1700 samples, which will be used for stable isotope probing combined with NanoSIMS and lipid-based experiments, quantitative functional gene surveys, whole-shot gun metagenomics and single cell genomics, batch-type and bioreactor cultivation experiments, and geobiological application of CO2 capture and sequestration (see Fig. F15). In addition, biomineralogical studies are planned for some minerals that likely precipitated in the course of modern and/or past geomicrobial processes such as pyrite and siderite, which were found in the deeply buried coalbeds.

In conclusion, the goals of the shipboard microbiology program were successfully accomplished. Extensive research using samples and data collected during Expedition 337 will significantly expand our knowledge of the deep subseafloor biosphere and contribute to a better understanding of the biogeochemical carbon cycle.