Palaeogeography, Palaeoclimatology, Palaeoecology 455 (2016) 1–15

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Palaeogeography, Palaeoclimatology, Palaeoecology

j ourna l homepage: www.e lsev ie r .com/ locate /pa laeo

A late Miocene methane-seep deposit bearing methane-trapping silicaminerals at Joetsu, central Japan

Yusuke Miyajima a,b,⁎, Yumiko Watanabe a, Yukio Yanagisawa c, Kazutaka Amano d,Takashi Hasegawa e, Norimasa Shimobayashi a

a Department of Geology and Mineralogy, Graduate School of Science, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japanb Research Fellow of the Japan Society for the Promotion of Science, Japanc Institute of Geology and Geoinformation, Geological Survey of Japan, AIST, Tsukuba City, Ibaraki 305-8567, Japand Department of Geoscience, Joetsu University of Education, 1 Yamayashiki, Joetsu City, Niigata 943-8512, Japane School of Natural System, College of Science and Engineering, Kanazawa University, Kanazawa City, Ishikawa 920-1192, Japan

⁎ Corresponding author at: Department of Geology andScience, Kyoto University, Oiwakecho, Kitashirakawa, Sak

E-mail address: yusukemiya@kueps.kyoto-u.ac.jp (Y. M

http://dx.doi.org/10.1016/j.palaeo.2016.05.0020031-0182/© 2016 Elsevier B.V. All rights reserved.

a b s t r a c t

a r t i c l e i n f o

Article history:Received 8 December 2015Received in revised form 20 April 2016Accepted 4 May 2016Available online 6 May 2016

The modern Japan Sea is characterized by active methane seeps associated with gas hydrates, but their ancientcounterparts are not fully understood. This study describes a newly discovered methane-seep carbonate block,the ‘Nakanomata Seep Deposit’, from the upper Miocene Nodani Formation in Joetsu City, central Japan. Theage of this deposit is constrained to 7.5–6.5 Ma based on its fossil diatom assemblage. The deposit contains mol-luscan fossils typical of methane seeps, including vesicomyid and bathymodiolin bivalves, and provannid gastro-pods, and it retains an almost entirely aragonitic mineralogy, despite its Miocene age. It is composed of clottedmicrocrystalline aragonite containing nodules and intraclasts, and is crosscut by vein-like networks of voidsand cavities rimmed with acicular aragonite. The δ13C values of the carbonate phases are as low as −41.1‰and the presence of lipid biomarkers (pentamethylicosane and crocetane) suggests that the deposit originatedfrom the anaerobic oxidation of methane. It is suggested that an initially diffuse methane seepage formed themicritic nodules, followedby amore rapid and intensemethane seepage that led to the development of abundantvoids in the sediment; finally, the sediment was cemented bymicrocrystalline aragonite and void-lining aciculararagonite. The seepdeposit also contains peculiar globular silicaminerals and authigenic quartz. During their pre-cipitation, these globular silica minerals may have trappedmethane gas bubbles, and the minerals may be pseu-domorphs after silica clathrate. Sufficient increase in pH and supersaturation of silica,which led to the dissolutionand subsequent precipitation of these silica minerals, could have resulted from the degassing of carbon dioxide,promoted by an effective supply of methane, and its supersaturation, thus forming gas bubbles.

© 2016 Elsevier B.V. All rights reserved.

Keywords:Late MioceneMethane seepAragoniteSilica

1. Introduction

Hydrocarbon seeps (or cold seeps) are known from both active andpassive continental margins of the world, such as the northeast, north-west, and southeast Pacific, the Gulf of Mexico, the Mediterranean Sea,the Black Sea, the East Atlantic, New Zealand, and the Japan Sea(e.g., Kennicutt et al., 1985; Kulm et al., 1986; Roberts and Aharon,1994; Sibuet and Olu, 1998; Peckmann et al., 2001; Han et al., 2004;Teichert et al., 2005; Sahling et al., 2008; Matsumoto et al., 2009;Campbell et al., 2010; Watanabe et al., 2010 and references therein).In the Japan Sea, bacterial mats and active methane seepages areknown from the Okushiri Ridge and off Joetsu (Takeuchi et al., 1992;Matsumoto et al., 2005).Methane seeps off Joetsu are of particular inter-est to scientists because they are characterized by a high methane flux,

Mineralogy, Graduate School ofyo-ku, Kyoto 606-8502, Japan.iyajima).

emanating gas bubbles (or methane plumes), and are associated withgas hydrate formation (Hiruta et al., 2009; Matsumoto et al., 2009). Ithas been suggested that the accumulation of organic-rich Neogene sed-iments, combined with high heat flow over the Japan Sea, producedthermogenic methane and that the faults that developed in these Neo-gene strata acted as migration pathways for the methane into the shal-low sediments where gas hydrates form (Matsumoto et al., 2009).

At methane seeps, methane-charged fluids seep out toward the sea-floor through conduits such as faults, andmethane is oxidized anaerobi-cally in the sediment. This reaction, known as the anaerobic oxidation ofmethane (AOM), occurs as follows:

CH4 þ SO42−→HS− þHCO3

− þH2O

and is performed by microbial consortia of anaerobic methanotrophicarchaea, ANME-1, -2, or -3 groups, and sulfate-reducing bacteria(e.g., Reeburgh, 1980; Masuzawa et al., 1992; Boetius et al., 2000;Orphan et al., 2001; Niemann and Elvert, 2008). Methane and sulfide

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ions are converted to energy and nutrients by chemosynthetic bacteria,and sustain unique biological communities (e.g., Sibuet and Olu, 1998;Levin, 2005; Campbell, 2006). Anaerobic oxidation of methane causesan increase in alkalinity and promotes the precipitation of carbonates,which inherit methane-derived carbon and its characteristic 13C-depleted isotopic composition (e.g., Ritger et al., 1987; Kulm andSuess, 1990; Sakai et al., 1992; Stakes et al., 1999). Methane-seep car-bonates derived from AOM are composed mainly of aragonite, calcite,and dolomite. They typically precipitate as microcrystalline concretionsor form unique, extensive mounds characterized by highly porous fab-rics and complex paragenetic sequences of cement and mineral phases(Campbell et al., 2002; Peckmann and Thiel, 2004; Reitner et al., 2005;Teichert et al., 2005). The δ13C values of AOM-derived carbonates areoften lower than −30‰ (relative to PDB); specific values depend onfluid composition and the degree of mixing with bicarbonate derivedfrom other sources, which is thought to be related to fluid flow intensity(Joye et al., 2004). In addition, these carbonates preserve lipid bio-markers of AOM consortia such as the isoprenoid hydrocarbons,pentamethylicosane (PMI), and crocetane, alongwith their unsaturatedderivatives, which originate from the cell membranes of ANMEs (Elvertet al., 1999; Blumenberg et al., 2004; Niemann and Elvert, 2008;Blumenberg, 2010).

These signatures of methane-seep carbonates (i.e., low δ13C valuesand lipid biomarkers of AOM-performing microorganisms) have beenrecognized in marine sedimentary strata dating back as far as the Car-boniferous (e.g., Beauchamp and Savard, 1992; Peckmann et al., 1999,2002; Peckmann and Thiel, 2004; Majima et al., 2005; Birgel et al.,2006, 2008; Campbell, 2006; Himmler et al., 2008; Jenkins et al., 2008;Tsuboi et al., 2010). Ancient methane-seep carbonates also contain fos-sils of invertebrates such as vesicomyid bivalves and bathymodiolinmussels (e.g., Peckmann et al., 2002; Campbell, 2006; Amano et al.,2010, 2013a; Kiel, 2010; Amano and Jenkins, 2013), whose extant coun-terparts include those living at hydrothermal vents and hydrocarbonseeps, and which host chemoautotrophic endosymbiotic bacteria(Fisher, 1990; Taylor and Glover, 2010). One can use the geochemicaland petrographic characteristics of ancient methane-seep deposits toinfer certain properties of ancient methane-seep environments, for ex-ample fluid flow intensity and composition (Peckmann and Thiel,2004; Peckmann et al., 2009).

However, ancient carbonates are commonly affected by late burialdiagenesis, resulting in a change inmineralogical composition and alter-ation of primary oxygen isotope signatures. For this reason, most an-cient seep carbonates are composed of calcite and dolomite, ratherthan aragonite (e.g., Beauchamp and Savard, 1992; Nyman et al.,2010). Furthermore, where Cenozoic (and a few Mesozoic) seep car-bonates do retain their aragonite mineralogy, the aragonite is oftenonly preserved as acicular or fibrous crystal aggregates or botryoids invoid spaces or cavities (Terzi et al., 1994; Savard et al., 1996;Peckmann et al., 1999, 2002; Campbell et al., 2008; Amano et al.,2010; Smrzka et al., 2015). Such diagenetic alteration of seep carbonateshampers accurate interpretation of the physical and chemical environ-ment of ancient hydrocarbon seeps.

Ancient seep carbonates are also often characterized by authigenicsilica phases that may be present as replacement minerals (e.g., formethane-derived carbonate phases, molluscan shells, worm tubes) oras cement in cavities (Peckmann et al., 2002; Himmler et al., 2008;Kuechler et al., 2012; Amano et al., 2013a; Smrzka et al., 2015 and refer-ences therein). The precipitation of these silica phases is considered topostdate early diagenetic AOM-derived carbonate phases. Based onthe results of numerical experiments, Smrzka et al. (2015) suggestedthat the dissolution and precipitation of silica phases are closely relatedto methane seepage and AOM processes.

Many vesicomyid fossils have been found in outcrops of Neogenestrata in the Japan Sea region, although their descendants do not appearto be present around Recent methane seeps in the Japan Sea (Kannoet al., 1989; Kanno et al., 1998; Amano et al., 2001, 2013b; Amano,

2003; Amano and Kanno, 2005; Majima et al., 2005; Amano et al.,2010; Amano and Jenkins, 2011). Based on faunal analysis, and isotopicand petrographic examinations, three of the vesicomyid fossil localitiesin the Japan Sea region have been confirmed as ancient methane-seepsites: the middle Miocene Bessho Formation in Nagano Prefecture(Tanaka, 1959; Sato et al., 1993; Kanno et al., 1998; Nobuhara, 2010);the uppermost middle Miocene Ogaya Formation in Niigata Prefecture(Ueda et al., 1995; Amano et al., 2010); and the upper Miocene MoraiFormation in Hokkaido (Amano, 2003; Ishimura et al., 2005). However,such geochemical studies, including lipid biomarker investigations,have not been carried out for many other fossil localities in this region.Furthermore, it is not known whether compositions of Neogene hydro-carbon seepage fluids in the Japan Sea region were mainly thermogenicin origin, like Recent methane seeps in this area.

This paper describes a newly discovered methane-seep carbonatefrom the upperMiocene Nodani Formation in Joetsu, Niigata Prefecture.Despite its Miocene age, this carbonate has retained its aragonitic min-eralogy in both its microcrystallinematrix and void-lining acicular crys-tals, and has relatively 18O-rich oxygen isotopic compositions. It alsocontains peculiar white to translucent, globular silica minerals thatprobably contain trapped hydrocarbon gases. The processes leading tothe formation of these seep carbonate and silica minerals are inferredbased on the paleontological, petrographical, mineralogical, isotopic,and biomarker properties of the rock. The discovery of hydrocarbon-trapping silica minerals directly hosted by a methane-seep carbonate,along with inferences about their processes of formation, provides evi-dence of a close relationship between methane seepage and silicaformation.

2. Geological setting

At the eastern margin of the Japan Sea, the Niigata–Shin'etsu sedi-mentary basin was formed by rapid subsidence caused by rifting duringthe opening of the Japan Sea in the early to middle Miocene (e.g., Iijimaand Tada, 1990; Jolivet and Tamaki, 1992; Takano, 2002). In the JapanSea, the stress field changed from tensional to compressional betweenthe late Miocene and Pliocene, causing basin inversion (Jolivet andTamaki, 1992; Sato, 1994; Okamura, 2000). The specific timing of thischange in the Niigata–Shin'etsu basin is estimated to be late Miocene(~7–6 Ma; Takeuchi, 1977; Okamura et al., 1995; Takano, 2002). Thicksequences of marine sediment were deposited in this basin throughoutthe Neogene, and these strata are well exposed in Nagano and Niigataprefectures (Fig. 1A). Many fossil vesicomyid bivalves have been re-ported from these units (Tanaka, 1959; Seki, 1983; Kanno et al., 1989,1998; Amano and Kanno, 2005), some of which are from methane-seep deposits (Amano et al., 2010; Nobuhara, 2010).

In the western area of Joetsu City in Niigata Prefecture, which repre-sents the northwestern part of the Niigata–Shin'etsu basin (Fig. 1B),middle Miocene to Pliocene strata are divided, in chronological order,into the Nambayama, Nodani, Kawazume, Nadachi, and Tanihama for-mations (Akahane and Kato, 1989). Northeast–southwest-trending an-ticline and syncline axes in this area were formed by E–Wcompressional tectonics in the late Miocene to Pliocene (Fig. 1B, Kanoet al., 1991; Sato, 1994). Fossil vesicomyids in this area have been re-ported from the middle Miocene Nambayama, upper Miocene Nodani,and Pliocene Kawazume and Nadachi formations (Kanno et al., 1989;Amano and Kanno, 1991, 2005). The Nodani Formation is composedmainly of alternating gray fine-grained sandstones and dark gray silt-stones that were deposited as submarine fan turbidites (Endo andTateishi, 1990). The depth of deposition of this formation is consideredto be lower sublittoral to upper bathyal based on molluscan fossil as-semblages (Amano, 2002). A tuff bed (the Kanaya Tuff) is intercalatedwith the middle part of the Nodani Formation and has been dated aslateMiocene (7.13±0.42Ma) in age usingfission track datingmethods(Muramatsu, 1989).

Fig. 1. Geological maps of the study area. (A) Generalized geological map of the Shin'etsu basin (based on https://gbank.gsj.jp/geonavi/geonavi.php). The geological map of the areaindicated by the square is shown in B. Previously reported ancient methane-seep sites in this area are shown by black circles with numbers, as follows: 1. Kuroiwa Limestone (Uedaet al., 1995; Amano et al., 2010); 2. Anazawa and Akanuda limestones (Tanaka, 1959; Sato et al., 1993; Kanno et al., 1998; Nobuhara, 2010). (B) Geological map of the western area ofJoetsu City (modified from Akahane and Kato, 1989; Takeuchi et al., 1994). A detailed regional geological map of the area indicated by the square is shown in C. (C) Detailed geologicalmap of the western area of Joetsu City showing the location of the Nakanomata Seep Deposit (based on the author's personal geological survey). The dashed line shows the rangecovered by the stratigraphic column shown in Fig. 2.

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3. Materials and methods

Severalfloat blocks of carbonates containing vesicomyid fossils werefound by the first author among riverbed gravels in Nakanomata River(Fig. 1C and 2). Three large blocks, which might have been derivedfrom a larger single carbonate body or fragments of carbonate boulderscontained in the host rock, were collected for analysis. One of these(Fig. 3), which is herein referred to as the ‘Nakanomata Seep Deposit’,is a 30-cm-diameter carbonate block bearing abundant vesicomyid fos-sils. The paleontological, petrographical, mineralogical, and geochemi-cal studies (including stable isotope and biomarker analysis)presented here were all conducted on this block. Other blocks have fun-damentally similar petrographic features to the Nakanomata Seep De-posit, but include sandy, non-carbonate-cemented soft parts, whichare not observed in the latter. The riverside cliffs near where theseblocks were found are composed of alternating sandstones and silt-stones of the upper Miocene Nodani Formation, but do not appear tocontain any concretionary beds from which the blocks could have orig-inated. Another hydrocarbon seep deposit was found near theNakanomata Seep Deposit in siltstone of the Nodani Formation. It con-tains vesicomyid fossils and small carbonate concretions, both ofwhich are, however, clearly different from those of the NakanomataSeep Deposit (Fig. 1C and 2).

The age of the Nakanomata Seep Deposit was determined based onits fossil diatom content. Diatom fossils were extracted from small(b0.5 cm) chips of the material by reaction with dilute hydrochloricacid. Molluscan fossils in the deposit were cleaned and extracted usingan air scribe and needles.

Selected cut slabs of the deposit were polished using carborundumabrasives and scanned. Thin sections (48 × 28 mm or 76 × 52 mm,

30 μm thickness) were then prepared and examined using a polarizingmicroscope under plane- and cross-polarized light.

Uncovered thin sections were coated with carbon and examinedusing a scanning electron microscope (HITACHI S-3000H SEM)equipped with an energy dispersive X-ray spectrometer (EDS) at theDepartment of Geology and Mineralogy, Kyoto University, Japan, to de-termine themineralogical and chemical composition of certain textures.Operating conditions included a 20 kV accelerating voltage, 0.30 nAbeam current, and 15 mmworking distance.

Powdered samples were collected from selected slabs using ahand-held rotary microsaw (5 mm diameter, 1 mm width). X-raydiffraction analysis (XRD) was then carried out on the powdersusing a diffractometer with Cu-Kα radiation (Rigaku SmartLab) atthe Department of Geology and Mineralogy, Kyoto University, to de-termine the mineralogy of the carbonates. Powdered bivalve shellsamples were prepared by grinding shell fragments that had beenscraped away from the deposit using an air scribe. Scans were runat 40 kV and 40 mA over a scanning range of 5.0 to 70° 2θ, at a rateof 10°/min and with a step size of 0.04° 2θ. The magnesium concen-tration of the calcite phases was inferred from the positions of the (10 4) peaks, in accordance with Griffin (1971). Calcite containingb5 mol% MgCO3 is referred to as low-Mg calcite, and that containing5–20 mol% MgCO3 is referred to as high-Mg calcite, after Burton andWalter (1987).

Powdered samples for carbon and oxygen stable isotopic analysiswere extracted from the counterparts of the thin sections or other cutslabs using a high-precision micromill (Geomill 326, Izumo-Web)equipped with a computer-controlled microdrill (b10 μm diameter).Some samples were collected from ground shell fragments and a moldof an articulated bivalve. Samples were taken from each carbonate

Fig. 2. Stratigraphic column for the Nakanomata River region showing the stratigraphicposition of the site where the Nakanomata Seep Deposit was found. Note that thedashed arrow does not indicate the horizon in which the float block was originallycontained.

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phase recognized in thin section. Each sample (30–95 μg)was reacted ina glass vial with 100% orthophosphoric acid under vacuum at 90 °C for1000 s. TheCO2 thatwas producedwas analyzed in amass spectrometer(IsoPrime 100) at the Department of Geology and Mineralogy, Kyoto

Fig. 3.Overview and selectedmacroscopic features of the Nakanomata Seep Deposit. (A) Photofacies; V, void spaces and cavities. Scale bar= 5 cm. (B) Authigenic euhedral quartz crystals (blbar = 5 mm. (C) Acicular aragonite crystal aggregates (ac) in the inside cavity of an articulate

University. All isotope values are reported in delta notation as per mildeviation from the Pee Dee Belemnite (PDB) standard ([δ = Rsample/Rstandard − 1] × 1000, where R is the ratio of minor to major isotopes).The reproducibility of the standard materials (shown as one standarddeviation) is less than 0.10‰ for δ18O and less than 0.22‰ for δ13C.

To prepare samples for biomarker analysis, selected fragments of thecarbonate were cut into small pieces using a diamond saw to removeweathered parts and then washed in distilled water, followed byultrasonication in methanol (MeOH) and then dichloromethane(DCM). The samples were then crushed using a hammer and groundinto powder using a tungsten pestle and mortar. Lipids were extractedfrom 20 g of the powdered samples by ultrasonication in DCM:MeOH(7:3, v:v) for 15 min. The extracts were removed and centrifuged for20 min (3000 rpm) and the supernatants were decanted. Lipids wereextracted from the residual powders in the same way two more times.Reduced copperwas added to the combined supernatants to remove el-emental sulfur. Lipids in the combined supernatants were separatedusing silica gel column chromatography into hydrocarbon (n-hexane),aromatic (n-hexane:DCM, 3:1, v:v), ketone (DCM), and polar fractions(DCM:MeOH, 4:1, v:v). The hydrocarbon fractions were then driedunder a N2 gas flow, dissolved in 200 μl n-hexane, and then injectedinto a gas chromatograph-mass spectrometer (GC‐MS) (SHIMADZUGC-2010 coupled with GCMS-QP2010) equipped with a HP-5MS capil-lary column (30m× 0.25mm i.d., 0.25 μm film thickness, Agilent Tech-nologies), at the Laboratory of evolution of earth environment,Kanazawa University, Japan. Helium was used as the carrier gas andthe ionization voltage was 70 V. The GC oven temperature was pro-grammed as follows: sample injection at 50 °C (splitless); temperatureincrease from 50 to 120 °C at 30 °C/min; temperature increase from 120to 310 °C at 3.0 °C/min; then 15 min isothermal. Identification of indi-vidual compounds was based mainly on their retention times andmass spectra with references to published data (e.g., for PMI: Elvertet al., 1999; for crocetane and phytane: Ogihara et al., 2003).

One of the white globular minerals (see Results) was removed fromthe carbonate deposit, mounted in resin on a glass slide, and polished. Athin section of the globular mineral was prepared by adhering anotherglass slide onto the polished surface of the mounted sample and thenpolishing it to remove the slide on which the sample was mounted.The thin sectionwas coatedwith carbon and the elemental compositionof the globular mineral was determined using a field emission scanningelectronmicroscope (JEOL JSM-7001F FESEM) equippedwith an energydispersive X-ray spectrometer (EDS) at Kyoto University. Operatingconditions included a 250 pA beam current, 10 mm working distance,

graph of the Nakanomata Seep Deposit. DGM, dark gray-colored matrix; LCF, light-coloredack arrow) developed on the surface of the light-colored facies (LCF) in a large cavity. Scaled bivalve found in the dark gray-colored matrix (DGM). Scale bar = 1 cm.

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and 5.0 kV accelerating voltage to reduce the excited area of the spotanalysis to about 400 nm in diameter.

After removing the carbon coating from the thin section, the chem-ical composition of the volatile components in the globular mineralwas determined using a Raman spectrometer (JASCO NRS-3100) atKyoto University. The excitation wavelength was the 532 nm line of aDPSS laser (Cobolt Samba) with a laser power of 2.9 mWon the samplesurface; the acquisition time was 30 s.

4. Results

4.1. Age of the carbonate deposit

Diatom fossils have been reported from the Pliocene strata exposedin the study area, but not from the Miocene strata (Yanagisawa andAmano, 2003). The Nakanomata Seep Deposit contains abundant dia-tom fossils. Although the fossils are partially dissolved and poorly pre-served, it was possible to determine that the assemblage ischaracterized by the absence of the genera Denticulopsis andNeodenticula, an abundance of Thalassionema nitzschioides, and the ab-sence of T. schraderi. It can therefore be placed within the Rouxiacalifornica zone (NPD7A) of Yanagisawa and Akiba (1998), which corre-sponds to the lateMiocene (7.7–6.5Ma). This age is consistent with theresults of the fission track dating of the Kanaya Tuff (7.13 ± 0.42 Ma:Muramatsu, 1989), which has a stratigraphic position about 130 mabove the Nakanomata Seep Deposit (Fig. 2). It is therefore concludedthat the carbonate deposits from this study, including the NakanomataSeep Deposit, are late Miocene in age (at least 7.7–6.5 Ma) and aremost likely derived from a nearby outcrop of the upperMiocene NodaniFormation.

Fig. 4.Molluscan fossils from theNakanomata SeepDeposit. All specimens are stored at theDep(B) Right valve hinge; (C) Left valve hinge; (D) Left valve; (E)Modeof fossil occurrence showingvalve; (G) SEM-image of the left valve of a juvenile specimen (platinum-coated). (H) Provanna hB–C and I; 1 mm for G.

Amano and Kanno (2001, 2005) described a 20-cm-thick calcareousmudstone containing vesicomyid fossils from within the middle Mio-cene Nambayama Formation, cropping out about 1 km upstream fromthe study site in this paper and present in the float of the NakanomataRiver. Although this calcareous mudstone could not be found in thefield, specimens thought to have come from the Nambayama Formationare held at the Department of Geosciences, Joetsu University of Educa-tion, Japan, and have clearly different petrographical features to the car-bonate deposits in this study. For example, they contain completelyrecrystallized shells, whereas the carbonates in this study contain shellsthat have retained their original shell mineralogy.

4.2. Paleontology

The Nakanomata Seep Deposit contains abundant vesicomyid fossilsof a single species. This species has a relatively large, thick, and elongateshell, two cardinal teeth in its right valve, and three cardinal teeth in itsleft valve (Fig. 4A–E). The shell surfaces of relatively large specimenscontain concentric ridges. It closely resembles Adulomya kuroiwaensis,which was described by Amano and Kiel (2011) from the uppermostmiddle Miocene Ogaya Formation, in terms of shell size, but has thickervalves than A. kuroiwaensis. Because the inner features of thevesicomyid species from the studied deposit could not be established,it is tentatively named Adulomya sp. Most of the vesicomyid fossils inthe Nakanomata Seep Deposit are fragmented and disarticulated valves(articulation rate 22%, n = 139), showing no evidence of abrasion(Figs. 4E and 6D) and retaining their original shell mineralogy (mostlyaragonite). Juveniles are frequently found as articulated valves.

In addition to the vesicomyids, the Nakanomata Seep Deposit con-tains fossils of the bathymodiolin mussel, Bathymodiolus akanudaensis(Fig. 4F–G). Only eight specimens were found, five of which are

artment of Geology andMineralogy, Kyoto University. (A–E)Adulomya sp.: (A) Right valve;disarticulated and fragmented valves (arrows). (F–G)Bathymodiolus akanudaensis: (F) Leftirokoae. (I) Provanna sp. (J)Neilonella sp. A. Scale bar= 1 cm for A, D–F, H, and J; 5 mm for

Fig. 5. Photographs (A–D) and XRD pattern (E) of selected slabs from the NakanomataSeep Deposit. (A) Polished slab section of the carbonate deposit close to a large cavity(V). DGM, dark gray-colored matrix; LCF, light-colored facies. White squares showwhere the microphotographs in Fig. 6 were taken. (B) Polished slab section showing thelight-colored facies forming networks of veins that crosscut the dark gray-coloredmatrix. nd, nodule. (C) Polished slab section showing a pebble-sized nodule (nd) andyellowish spot (white arrow) in the dark gray-colored matrix. (D) Polished slab sectionshowing an intraclast (ic) rimmed with the light-colored facies. White squares showwhere the microphotographs in Fig. 6 were taken. All scale bars = 1 cm. (E) XRDpattern of the microcrystalline dark gray-colored matrix. Vertical lines below the XRDpattern indicate the major peak positions of aragonite (pink) and calcite (blue).

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disarticulated valves. Unlike the vesicomyid fossils, there are no signs offragmentation. This species has also been reported from the Anazawaand Akanuda limestones of the middle Miocene Bessho Formation inNagano Prefecture (Tanaka, 1959; Nobuhara, 2010), and the KuroiwaLimestone of the uppermost middle Miocene Ogaya Formation, whichcrops out in the northeastern area of Joetsu City (Amano et al., 2010).These carbonates are both considered to be ancient methane-seepdeposits.

The most abundant fossils in the Nakanomata Seep Deposit after thevesicomyids are of the provannid gastropod, Provanna hirokoae (Fig. 4H;Table 1). This species has also been reported from the Kuroiwa Lime-stone (Amano et al., 2010; Amano and Little, 2014). The NakanomataSeep Deposit contains fossils of another provannid, Provanna sp.(Fig. 4I). This species has axial ribs on its bodywhorls and a less roundedshoulder than P. hirokoae. Most provannid fossils occur in the light-colored facies of the deposit (described in Section 4.3). Recent Provannaspecies are known to grazemainly on bacteria and detritus in hydrocar-bon seeps and hydrothermal vent areas (e.g., Sasaki et al., 2010). Fossilsof this genus frequently co-occur with those of Bathymodiolus in Ceno-zoic methane-seep deposits (Amano and Jenkins, 2013).

Other fossils from the Nakanomata Seep Deposit include Neilonellasp. A (Fig. 4J), N. sp. B, one small specimen of Vesicomyidae? gen. etsp. indet., and two unidentified bivalve specimens (Table 1). The faunalassociation found in theNakanomata SeepDeposit is very similar to thatof the Kuroiwa Limestone (Fig. 1; Amano et al., 2010).

4.3. Carbonate petrography and mineralogy

The Nakanomata Seep Deposit contains a dark gray-colored matrixand a creamy, light-colored facies (DGM and LCF, respectively) (Figs. 3and 5A–D). The light-colored facies crosscuts the dark-colored matrixin vein-like networks (Fig. 5B). There are many variably sized voidspaces and cavities in the dark-colored matrix that are rimmed withthe light-colored facies and authigenic euhedral quartz crystals. Peculiarwhite or translucent globularminerals (described in detail below) occurin the voids (Figs. 3B and 9A–C). The dark-coloredmatrix contains darkbrown pebble- to cobble-sized nodules (nd) and brownish to yellowishspots (Fig. 5C). The dark-colored matrix is also locally present as partlyisolated intraclasts (ic) separated by the light-colored facies (Fig. 5D).Nodules and intraclasts can be distinguished by differences in theircolor, as well as their mineralogy. In addition, nodules have well-defined sharp boundaries and can be easily removed from the matrix,while intraclasts have more irregular-shaped boundaries. The light-colored facies is rare in the nodules and intraclasts.

The dark-coloredmatrix is composedmainly ofmicrocrystalline ara-gonitewithminor amounts of calcite (Fig. 5E). Themicrocrystalline ara-gonite shows clotted and peloidal fabrics, and contains abundantdetrital quartz, pyrite crystals and framboids, shell fragments, and dia-toms (Fig. 6A). Nodules in the dark-colored matrix are composed ofmicrite or microsparite, and like the intraclasts are rimmed with pyrite(Fig. 6B and G). Results from the EDS analysis of the microcrystallinematrix show an absence of Mg and minor amounts of Sr. In contrast,the micrite of the nodules is composed of high-Mg calcite with minor

Table 1Molluscan species in the Nakanomata Seep Deposit and number of specimens of each.

Species Number of individuals

Neilonella sp. A 5Neilonella sp. B 1Bathymodiolus akanudaensis 8Adulomya sp. 139Vesicomyidae? gen. et sp. indet. 1Unidentified bivalve A 1Unidentified bivalve B 1Provanna hirokoae 21Provanna sp. 3

amounts of dolomite. The brownish to yellowish spots are composedof microsparite. Void spaces and cavities in the microcrystalline matrixare rimmedwith acicular to fibrous crystal aggregates (ac), correspond-ing to the light-colored facies, which are composed of aragonite withminor calcite (Figs. 3 and 6C). These acicular to fibrous aragonite aggre-gates also form botryoids and isopachous layers. In large cavities, theyform aggregations of globular botryoids (gbt) that truncate the tips ofthe acicular crystals lining the cavities (Fig. 6E). Some of the globularbotryoids have cracks that have been infilled with fine-grained carbon-ates (Fig. 6F). The pyrite-rimmed intraclast is also rimmed with light-coloredmicrocrystalline aragonite (lm) that contains almost no detritalquartz and pyrite (Fig. 6G). This light-coloredmicrocrystalline aragoniteis itself rimmedwith acicular to fibrous aragonite that forms isopachouslayers (is) (Fig. 6G–H). The bivalve shells consist of aragonite withminor calcite, and their original microstructure is either well preservedor somewhat recrystallized (Fig. 6D). The internal molds of bivalveshells are composed mainly of calcite.

4.4. Carbon and oxygen stable isotopes

The carbon and oxygen isotope compositions of the carbonates inthe Nakanomata Seep Deposit are shown in Fig. 7 and listed in

Fig. 6.Microphotographs showing typical petrographic features of the Nakanomata Seep Deposit. (A) Clotted fabric of the microcrystalline aragonite. Plane-polarized light. (B) Micriticnodule (nd) rimmed with pyrite (black arrow). Plane-polarized light. (C) Void space in the microcrystalline aragonite rimmed with acicular aragonite crystal aggregates (ac). Plane-polarized light. (D) Fragmented aragonitic bivalve shell. Original shell microstructure is preserved. Plane-polarized light. (E) Globular botryoidal aragonites (gbt) filling a large cavity inthe microcrystalline aragonite (m) that is rimmed with acicular aragonite crystals (ac). These botryoids cut the outer tips of the acicular crystals (black arrows). Crossed-polarizedlight. (F) Globular botryoids (gbt) with cracks containing fine-grained carbonates in their centers. Plane-polarized light. (G) Intraclast (ic) rimmed with light-colored microcrystallinearagonite (lm) and isopachous aragonite layers (is). Crossed-polarized light. (H) Light-colored microcrystalline aragonite (lm) rimmed with acicular to fibrous aragonite crystalaggregates that form isopachous layers (is). Plane-polarized light. All scale bars = 1 mm.

7Y. Miyajima et al. / Palaeogeography, Palaeoclimatology, Palaeoecology 455 (2016) 1–15

Table 2. The δ13C values of the microcrystalline aragonites in the dark-colored matrix and intraclasts range from −35.5‰ to −23.4‰, andthose of the micrite in the nodules range from −37.0‰ to−19.0‰. The microsparites from the matrix have similar δ13C valuesto the microcrystalline aragonites (−32.0‰ to −19.9‰). The acicu-lar to fibrous aragonites, including those forming globular botryoidsand isopachous layers, give slightly lower δ13C values (−41.1‰ to−28.0‰). The two δ13C values from the light-colored microcrystal-line aragonite that lines the intraclasts are also low (−23.8‰ and−22.1‰). Bivalve shells mostly yield δ13C values typical of marine

carbonate (−1.9‰ to −0.2‰), with the exception of one sample(−12.1‰), which could have been contaminated by the surroundingmatrix during sample preparation (Table 2). One sample from themicritic internal mold of an articulated bivalve gave a relativelyhigh δ13C value (−4.1‰).

δ18O values are moderately high and fall into a narrow range be-tween +2.0‰ and +3.4‰, with the exception of four samples (micro-crystalline aragonite, microsparite, acicular to fibrous aragonite, andshell). One sample from the inner mold of a bivalve gave a highly nega-tive δ18O value (−8.6‰).

Fig. 7. Cross plot of carbon and oxygen stable isotope compositions for various carbonatephases from the Nakanomata Seep Deposit. Standard deviations are ≤0.1‰ for δ18O andb0.22‰ for δ13C.

8 Y. Miyajima et al. / Palaeogeography, Palaeoclimatology, Palaeoecology 455 (2016) 1–15

4.5. Biomarkers

The hydrocarbon fraction extracted from the Nakanomata Seep De-posit is characterized by high abundances of phytane (2,6,10,14-tetramethylhexadecane) and crocetane (2,6,11,15-tetramethylhexadecane) (Fig. 8). Because crocetane has the same mo-lecular weight as, and a similar structure to, phytane, these two com-pounds appear at similar retention times in the chromatogram. Thepeaks for pristane (2,6,10,14-tetramethylpentadecane) and PMI(2,6,10,15,19-pentamethylicosane) are also prominent. N-alkanes arenot abundant and only n-C23 is identified. There are also moderatelyhigh amounts of C27 to C29 steroids and C29 and C30 hopanoids. The frag-ments of Nakanomata Seep Deposit from which these hydrocarbonswere extracted were dominated by the dark-colored matrix withsmaller amounts of the light-colored facies.

4.6. Globular silica minerals

The Nakanomata Seep Deposit contains white or translucent globu-larminerals (gs) in void spaces that are rimmedwith acicular to fibrousaragonite (ac) (Fig. 9A–C). These minerals occur as ~1-mm-diameter

single spheres or aggregations of smaller ~100-μm-diameter spheres(Fig. 9A–C). The single spheres are entirely coveredwith small euhedralquartz crystals, and the spheres themselves are composed of microcrys-talline silica or chalcedony that shows undulose extinction undercrossed-polarized light (Fig. 9D). The globular silica minerals presum-ably formed after the acicular aragonite and before the euhedral quartzcrystals that cover them. A backscattered electron image of one sphereshows a clear contrast between the dark inside of the sphere and thebright quartz crystals surrounding it (Fig. 10A). In contrast to the quartzcrystals, the sphere is highly porous with abundant pore spaces of~100 nm in size (Fig. 10B). Energy dispersive X-ray spectrometry anal-ysis was performed on flat surfaces of the globular mineral whereN400 nm in diameter. The analyses show that the globular silicamineralhas a total mass of less than 100% (92.4–94.8%; Table 3). This could be aresult of the mineral's high porosity or because it contains a componentof something other than Si andO, including a gas or liquid phase. Aswellas the sharp quartz peaks at ~460 cm−1, the Raman spectra of the glob-ular silica mineral show weak and broad peaks or humps betweenaround 2900 and 2930 cm−1 and at ~3060 cm−1 (Fig. 11). Thesepeaks roughly coincide with the reported Raman bands for methane(a sharp peak at 2917 and a weak peak at 3020 or 3058 cm−1) and eth-ane (2954 cm−1) (Kortus et al., 2000; Frezzotti et al., 2012).

5. Discussion

5.1. Formation of the methane-seep deposit

The Nakanomata Seep Deposit is composed of clotted microcrystal-line aragonite that contains micrite nodules and intraclasts, and hasabundant void spaces and cavities. These spaces are rimmed with acic-ular to fibrous aragonite that forms botryoids and isopachous layers.These petrographical features, especially the clotted microcrystallinefabric and the acicular to fibrous aragonite, are frequently observed inmethane-seep carbonates (e.g., Terzi et al., 1994; Savard et al., 1996;Peckmann et al., 1999, 2001, 2002; Peckmann and Thiel, 2004;Teichert et al., 2005; Campbell et al., 2008; Amano et al., 2010). Boththe microcrystalline matrix, including the nodules and intraclasts, andthe acicular to fibrous aragonite have strongly negative δ13C values(−37.0‰ to −19.0‰ and −41.1 to −28.0‰, respectively; Fig. 7;Table 2). This suggests the incorporation of bicarbonate produced bythe anaerobic oxidation of methane (AOM)with smaller amounts of bi-carbonate derived from the sulfate reduction of sedimentary organicmatter and that dissolved in seawater. The lowest δ13C value of the car-bonates (−41.1‰) is suggestive of biogenically derived methane,which has values ranging from −110‰ to −50‰ (Whiticar, 1999).However, the higher δ13C values (e.g., up to −19.0‰) suggest thatsome carbon from thermogenicmethane,whichhas δ13C values rangingfrom −50‰ to −20‰, was also incorporated into the carbonates. Themostly positive δ18O values of the carbonate phases of the NakanomataSeepDeposit fall within a narrow range, suggesting that this deposit hasnot been strongly affected by diagenesis; this inference is supported bythe aragonitic mineralogy and the lack of late diagenetic void-filling ce-ments such as blocky calcite spar (cf. Campbell et al., 2002). The carbon-ate deposit, including the acicular to fibrous crystals, contains both PMIand crocetane (Fig. 8). Both of these hydrocarbons are typical bio-markers for AOM-performing anaerobic methanotrophic archaea(ANME) and methanogenic archaea. The presence of crocetane mayalso indicate that the AOM-performingmicrobial community was dom-inated by ANME-2 archaea (Blumenberg et al., 2004). However, to con-firm this it would be necessary to determine the compound-specificcarbon isotopic compositions of these biomarkers as well as other frac-tions, such as alcohols. The studied deposit contains n-tricosane (n-C23),which is also suggested to be a biomarker of an AOM-related microor-ganism (Thiel et al., 2001). However, there were no prominentmethylsteroids, which are potential biomarkers of aerobicmethanotrophic bacteria (Birgel and Peckmann, 2008).

Table 2Oxygen and carbon isotope ratios (expressed in delta notation as permil,‰, deviation from the Pee Dee Belemnite (PDB) standard)measured in carbonate samples from theNakanomataSeep Deposit. Sampling methods are shown for all samples. Ag, aragonite; b, bulk prepared by grinding bivalve shell fragments; Cc, calcite; Dm, dolomite; md, microdrill; ms, microsaw.

Sample Texture Mineralogy δ18O δ13C Sampling method

nk1301 Acicular aragonite Ag 2.9 −33.4 mdnk1302 Microcrystalline aragonite Ag, Cc 2.8 −31.9 mdnk1303 Microsparite Cc 2.9 −20.6 mdnk1304 Bivalve shell Ag 2.7 −0.2 mdnk1305 Globular botryoids Ag 3.0 −34.1 mdnk1306 Microcrystalline aragonite Ag, Cc 2.7 −35.5 mdnk1307 Microcrystalline aragonite Ag, Cc 0.7 −27.9 mdnk1309 Acicular aragonite Ag 2.7 −38.8 mdnk1310 Microcrystalline aragonite Ag, Cc 2.7 −35.3 mdnk1311 Nodule microsparite Cc 2.8 −19.0 mdnk1312 Nodule micrite Cc, Dm 2.7 −20.6 mdnk1313 Fibrous aragonite Ag 3.1 −35.0 mdnk1314 Microsparite Cc, Ag 2.8 −32.0 mdnk1315 Microcrystalline aragonite Ag, Cc 2.7 −34.8 mdnk1318 Microcrystalline aragonite Ag, Cc 2.7 −33.6 mdnk1319 Nodule microsparite Cc 2.6 −37.0 mdnk1320 Bivalve shell Ag −0.3 −2.0 mdnk1321 Acicular aragonite Ag 3.2 −32.1 mdnk1322 Microcrystalline aragonite Ag, Cc 3.2 −23.4 mdnk1323 Microsparite Cc 1.5 −23.1 mdnk1324 Microcrystalline aragonite Ag, Cc 2.7 −31.6 mdnk1325 Fibrous aragonite Ag −0.7 −38.5 mdnk1326 Microsparite Cc 2.7 −29.6 mdnk1327 Fibrous aragonite Ag 2.9 −41.1 mdnk1328 Globular botryoids Ag 3.3 −38.6 mdnk1329 Globular botryoids Ag 2.7 −37.9 mdnk1330 Bivalve shell Ag 2.4 −0.4 mdnk1331 Microsparite Cc 3.1 −19.9 mdnk1332 Bivalve shell Ag 2.0 −12.1 bnk1333 Bivalve mold Cc −8.6 −4.1 msnk1334 Acicular aragonite Ag 3.4 −28.2 mdnk1335 Intraclast Ag, Cc 3.0 −29.6 mdnk1336 Light-colored microcrystalline aragonite Ag, Cc 2.7 −22.1 mdnk1337 Isopachous layers Ag 3.1 −28.0 mdnk1339 Intraclast Ag, Cc 3.0 −24.9 mdnk1340 Light-colored microcrystalline aragonite Ag, Cc 2.8 −23.8 mdnk1341 Isopachous layers Ag 2.6 −31.3 mdnk1342 Isopachous layers Ag 2.9 −30.8 md

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The micritic nodules in the microcrystalline matrix of theNakanomata Seep Deposit are believed to have formed before the ce-mentation of the matrix, as suggested by their different mineralogy(the nodules are made of calcite; the matrix is made of aragonite) andthe scarcity of voids rimmed with acicular to fibrous aragonites. Thesenodules could have formed by weak and diffusive seepage (cf. Nesbittet al., 2013). In contrast, the void spaces such as veins and cavities, aswell as the intraclasts in the microcrystalline matrix, possibly formedlater as a result of more rapid and intense fluid flow through the sedi-ments. This may also explain the fact that the δ13C values in the acicularto fibrous crystals lining the voids and cavities are slightly lower thanthose in the microcrystalline matrix. That is, rapid flow and precipita-tion could have resulted in less bicarbonate derived from sulfate reduc-tion or seawater (i.e., bicarbonate that was not derived from methane

Fig. 8. Total ion chromatogram of the hydrocarbon fraction extracted from theNakanomata Seep Deposit. Some fragments of the deposit, which are dominated by thedark-colored matrix, were selected for the extraction of hydrocarbons. Black circles, n-alkanes; black squares, steroids; PMI, pentamethylicosane; white squares, hopanoids.Numbers above symbols indicate carbon numbers.

oxidation) being incorporated into the carbonate (cf. Terzi et al., 1994;Joye et al., 2004; Peckmann et al., 2009). In addition, aragonite isknown to form as a result of intense fluid flow close to the seafloor(Luff andWallmann, 2003). The cracks seen in some globular botryoids(Fig. 6F)may relate to an increase in cavity pressure during intense fluidflow and subsequent hydrofracturing. Such an increase in pressurecould have been caused by the precipitation of botryoids that filledand plugged the cavities through which the seepage fluids flowed(Peckmann et al., 2001; Nyman et al., 2010; Hryniewicz et al., 2012).In addition, the presence of the bathymodiolin mussel,B. akanudaensis, may also be linked to intense fluid flow, as extantbathymodiolin mussels, some species of which harbor methanotrophicsymbionts (Fisher, 1990), are known to live in hydrocarbon seeps withrising gas bubbles and relatively high fluid flux (MacDonald et al., 1989;Olu et al., 1996; Wagner et al., 2013). The presence of crocetane is alsoconsistent with this view, as it suggests that the AOM-performing com-munity was dominated by ANME-2 archaea, which are associated withhigher methane partial pressures than the ANME-1 archaea(Blumenberg et al., 2004).

Although the vesicomyid fossils from the Nakanomata Seep Depositare mostly disarticulated and fragmented, they are not significantlyabraded (Fig. 4E). It is not possible to rule out the idea that they weretransported from their original habitat, but the presence of juvenilessuggests that they are autochthonous and may have been fragmentedin situ by vigorous, probably explosive, fluid flow or by predators suchas crustaceans. Bathymodiolin fossils are not significantly fragmentedand are rare relative to vesicomyids. The reasons for these differentmodes of fossil occurrence are unclear at this stage. However, in viewof the known habitats of the extant bathymodiolin mussels, it is

Fig. 9. Photographs andmicrophotographs of globular silicaminerals in theNakanomata SeepDeposit. (A)White globular silicamineral (gs) in a void rimmedwith acicular aragonite (ac).m, microcrystalline aragonite. (B) Translucent globular silica mineral (gs) and euhedral quartz crystals (q) in a void. (C) Aggregation of small globular silica minerals (gs) and euhedralquartz crystals (q) in a void. (D) Microphotograph of the thin section of a globular silica mineral composed of radial fibrous microcrystalline crystal aggregates and rimmed witheuhedral quartz crystals. Colored circles with numbers indicate the points from which the corresponding Raman spectra shown in Fig. 11 were obtained. Crossed-polarized light. Scalebars = 1 mm for A–C and 100 μm for D.

10 Y. Miyajima et al. / Palaeogeography, Palaeoclimatology, Palaeoecology 455 (2016) 1–15

plausible that the bathymodiolins colonized this seep site after the rapidand vigorous fluid flow had started.

Based on the above, the studied methane-seep deposit is proposedto have formed in three stages (Fig. 12). In Stage 1, AOM-derivedmicritenodules formed by diffuse methane seepage in sediment that was alsobeing colonized by vesicomyid bivalves. In Stage 2, rapid and intense(probably explosive) fluid flow led to the formation of intraclasts aswell as abundant void spaces and cavities in the sediment. These net-works of voids and cavities enabled methane seepage to become morefocused. Vesicomyid shells may have become fragmented under this in-tense fluid flow, and bathymodiolin mussels probably colonized thesediment during this stage. In Stage 3, with a continuous supply ofmethane-charged fluid, both the sediment close to the seafloor andthe intraclasts were cemented by AOM-derived microcrystalline arago-nite to form the dark-colored matrix. Later, void spaces and cavitieswere rimmed with acicular to fibrous aragonite, corresponding to thelight-colored facies. In large cavities, these aragonite crystal aggregatesformed botryoids. Intraclasts were rimmed with light-colored micro-crystalline aragonite (depleted in 13C) and later with the isopachouslayers. Although the origin of this light-colored microcrystalline arago-nite is unknown, Peckmann et al. (2003) reported similar pure, highlyhomogeneous, bright-gray authigenicmicrite,which also lacked detritalgrains, lining cavities in the late Eocene ‘Whiskey Creek’methane-seepdeposit. They referred to it as “seam-micrite” and reported that it ex-hibits intense autofluorescence under a fluorescence microscope, sug-gesting that organic matter was involved in its formation.

Reitner et al. (2005) reported black microbial mats composed ofconsortia of ANME-2 methanotrophic archaea and Desulfosarcinales/Desulfobacterium (DSS) sulfate-reducing bacteria from Black Seamethane-seep carbonate precipitates. They showed that early calcifica-tion within the mats starts within intracellular aggregates of iron sul-fides in the DSS bacteria. This is followed by the formation of high-Mgcalcite seams around themicrobial consortia, then isopachous aragonitecements, and later, micrite (Fig. 4D of Reitner et al., 2005). This

paragenetic sequence is consistent with observations made on the mi-crocrystalline intraclasts of the Nakanomata Seep Deposit in that theseintraclasts are rimmed with pyrite, then light-colored microcrystallinearagonite, and finally isopachous aragonite layers (Fig. 6G). This sug-gests that ANME-2 consortia colonized the surfaces of the intraclastsand promoted the precipitation of void-lining carbonate cements.

The middle Miocene Nambayama and upper Miocene Nodani for-mations in the study area are considered to be submarine fan turbidites(Endo and Tateishi, 1990), and corresponding marine sedimentarystrata of Niigata Prefecture are known source and reservoir rocks(Okui et al., 2008). Rapid clastic sedimentation in the basin (includingthe study area) during theMiocene could have promoted the accumula-tion of organic matter and the generation of thermogenic gas in thedeep subsurface and/or biogenic methane in shallower sediments.These could represent the origins of the methane-charged fluids thatled to the formation of the Nakanomata Seep Deposit. Although the mi-gration pathway of the fluid is unknown, subsurface faults or permeablesandstone layers in the Nodani Formation might have acted as effectivefluid conduits, supplying methane to the seep site.

5.2. Precipitation of authigenic silica and its implications

The increase in pH that accompanies AOM is thought to promote thedissolution of silica phases; this dissolved silica could then re-precipitate when AOM ceases and pH decreases once more (Kuechleret al., 2012). The Nakanomata Seep Deposit contains partially dissolveddiatom fossils as well as authigenic euhedral quartz crystals and globu-lar silicaminerals in cavities. Therefore, it is possible that the dissolutionof diatom frustules was caused by the increase in pH associated withAOM, and that this dissolved silica was subsequently precipitated inthe form of authigenic quartz and globular silicaminerals in the cavitiesafter both methane seepage and AOM ceased and the pH dropped.

Based on the results of numerical experiments, Smrzka et al. (2015)suggest that degassing of carbon dioxide by active seepage and the

Fig. 10. SEM images of a globular silica mineral. (A) Backscatter image of a globular silicamineral. Yellow circles with numbers indicate areas where EDS analyses listed in Table 3were performed. The square indicates the area shown in B. Scale bar = 100 μm.(B) Enlarged SEM image of the silica mineral shown in A. The flat area in the left part ofthe image is a euhedral quartz crystal (q) that surrounds the globular mineral. Scalebar = 1 μm.

Table3

Resu

ltsof

theED

San

alyses

ofeu

hedral

quartz

(Area1)

andaglob

ular

silic

amineral

(Areas

2–4).E

lemen

talcom

position

swerede

term

ined

from

5or

6sp

ots(n

=nu

mbe

rof

spots)

ineach

oftheareassh

ownin

Fig.10

A.R

esults

aregive

nas

mass

percen

tan

don

estan

dard

deviation(Std.d

ev.).T

heco

unting

error(σ

)of

each

spot

analysisisless

than

0.35

forOan

dless

than

0.43

forSi.

Area

nO

SiTo

tal

1(Q

uartz)

a5

53.3

46.7

100.0

Std.

dev.

0.14

0.22

0.27

25

50.8

43.1

93.9

Std.

dev.

0.99

0.23

1.08

36

51.3

43.5

94.8

Std.

dev.

0.74

0.33

0.97

46

49.9

42.5

92.4

Std.

dev.

1.50

0.50

1.83

aRe

sultswereob

tained

usingaqu

artz

crystalsurroun

ding

theglob

ular

mineral

asOKα

andSi

Kα

stan

dards.

11Y. Miyajima et al. / Palaeogeography, Palaeoclimatology, Palaeoecology 455 (2016) 1–15

formation of gas bubbles consumes protons and results in a higher pHthan if there were no degassing, as follows:

Hþ þ HCO3−↔H2CO3↔CO2 gð Þ þ H2O:

Indeed, they suggested that a solution may only become supersatu-rated with amorphous silica if carbon dioxide degassing is involved.They concluded that silica mobilization could only occur in seepswhere not all of the methane is oxidized, allowing for supersaturationof methane and the formation of gas bubbles, whichwould also removecarbon dioxide. Thus, the presence of authigenic silica phases in theNakanomata Seep Deposit may indicate that the methane seepagethat formed the seep deposit was associated with supersaturation ofmethane and gas bubble formation. During precipitation, the globularsilica minerals could have trapped gas bubbles of any methane andprobably ethane that remained in cavities (Figs. 11 and 13). Gas bubblesor inclusionswere not observed by optical microscopy or SEM analyses,but trace amounts of gas might be present within the crystal lattices ofminerals.

It is possible that the globular silica mineral is a pseudomorph aftersilica clathrate. As with gas hydrates, silica clathrates, also calledclathrasils, are known to contain molecules of various gases, such asmethane, carbon dioxide, nitrogen, and hydrogen sulfide, in the cage-like pores of the SiO2 framework (Tribaudino et al., 2008; Mommaet al., 2011). Three silica clathrates (melanophlogite, chibaite, and an-other that is as yet unnamed) have been reported and they have differ-ent framework structures. They are isostructural with cubic structure Ihydrate, cubic structure II hydrate, and hexagonal structure H hydrate,

Fig. 11. Raman spectra of a globular silicamineral. Spectra 1 (green), 2 (blue), and 3 (red)were obtained from points 1, 2, and 3 in Fig. 9D, respectively. Reported bands for methaneand ethane trapped in silica clathrates (Köhler et al., 1999; Tribaudino et al., 2008;Momma et al., 2011) are indicated by solid and dashed lines, respectively.

Fig. 12. Schematic diagrams showing the proposed formation process of the NakanomataSeep Deposit. In Stage 1, AOM-derived micritic nodules were formed by diffuse methaneseepage in the sediments and vesicomyids colonized. In Stage 2, rapid and intensemethane seepage formed networks of abundant voids and cavities, and also intraclastsin the sediments. Vesicomyid shells were probably fragmented by vigorous fluid flowand the sediment was colonized by bathymodiolins. Finally, in Stage 3 the sedimentswere cemented by AOM-derived microcrystalline aragonite and voids were rimmedwith acicular to fibrous aragonite. In large cavities, acicular aragonite formed globularbotryoids. Intraclasts were rimmed with light-colored microcrystalline aragonite andisopachous layers.

12 Y. Miyajima et al. / Palaeogeography, Palaeoclimatology, Palaeoecology 455 (2016) 1–15

respectively (Momma et al., 2011). Although they originally form cubicor tetragonal crystals,white or transparent globular opal is known in as-sociation with melanophlogite in the Northern Apennines of Italy(Adorni and Tateo, 2007). The positions of Raman bands for methanetrapped in the cages of silica clathrates are lower than those for freemethane due to interaction between the cages andmethanemolecules;at least two sharp peaks for methane have been observed correspond-ing to two cage types in the silica clathrate framework (Köhler et al.,1999; Kortus et al., 2000; Tribaudino et al., 2008; Momma et al.,2011). The broad peaks observed in the Raman spectra of the globularsilica mineral cover the bands for methane and ethane trapped incages of melanophlogite and chibaite reported in those studies (meth-ane: 2905 and 2914 cm−1, 2906 and 2917 cm−1, 2901 and2910 cm−1, or 2902.9 and 2910.7 cm−1; ethane: 2885.0 and2938.8 cm−1). Therefore, the globular silica minerals of theNakanomata Seep Deposit may have originally been silica clathratescontaining gas molecules of methane and ethane, and were later re-placed by chalcedony. Köhler et al. (1999) and Kortus et al. (2000) sug-gested that the intensities of the Raman bands representing thevibrations of methane enclosed in cages of melanophlogite depend onboth the cage structure andwhether all cages are occupied bymethane.It is unclear why the Raman spectra of the globular silica mineral showbroad peaks or humps around 2900 to 3060 cm−1. However, if the glob-ular silica minerals truly are pseudomorphs after silica clathrates, theseweakhumpsmight representmethane or ethanemolecules that incom-pletely occupied the original cages or alteration of the original cagestructure. Although melanophlogite has been reported as a thin cruston a carbonate precipitate from a cold seep environment in the Cascadiamargin, offshore Oregon (Köhler et al., 1999), there are no records of sil-ica clathrates in ancient seep carbonates.

The presence of the peculiar globular silica mineral in theNakanomata Seep Deposit suggests venting of gas bubbles in the seepenvironment. If these globular silica minerals truly have retained gasfrom the seepage fluid, it may be possible to determine the origin ofthe fluid by measuring the molecular composition and stable carbonisotope ratio of the trapped gas. This would help us to understand theorigins of Neogene hydrocarbon seeps in the Japan Sea region.

6. Conclusion

Newly discovered vesicomyid-bearing aragonitic blocks, includingthe Nakanomata Seep Deposit, from Joetsu City, Niigata Prefecture, areconfirmed as late Miocene in age (7.7–6.5 Ma). The Nakanomata SeepDeposit contains molluscan fossils typical of methane seeps, includingvesicomyids, bathymodiolins, and provannids. Observed carbonate tex-tures, highly negative δ13C values, and the presence of lipid biomarkers(PMI and crocetane) suggest that the Nakanomata Seep Deposit is de-rived from the anaerobic oxidation of methane (AOM). It is believedto have formed first by diffuse seepage, and then by intense and morefocused fluid flow through the sediments. An increase in pH associatedwith AOM could have promoted the dissolution of diatom frustules, andauthigenic quartz and globular silicaminerals could have precipitated inthe cavities of the deposit once AOM and methane seepage ceased andpH dropped. The globular silica minerals may have resulted from silicaprecipitation that trapped gas bubbles of methane and ethane, and itis possible that they are pseudomorphs after silica clathrate. Therecould have been a sufficient supply ofmethane to causemethane super-saturation and venting of gas bubbles. This methane-seep carbonatefrom the Japan Sea borderland shows that biogenic and/or thermogenicmethane was produced during the late Miocene in underlying organic-

Fig. 13. Schematic diagrams showing the precipitation of authigenic quartz and globular silicaminerals, as proposed in the text. Duringmethane seepage, an increase in pHassociatedwithAOMpromoted the dissolution of diatom frustules. A sufficient supply ofmethane could have causedmethane supersaturation in the porewaters, leading to gas bubble formation and alsopromoting carbon dioxide degassing. This could have resulted in supersaturation of dissolved silica. After seepage and AOM had ceased, the concomitant decrease in pH could havepromoted the precipitation of dissolved silica as euhedral quartz and globular silica minerals, probably trapping gases remaining in voids.

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richmarine sediments, the lower part of the upperMioceneNodani For-mation, or the underlying strata, including the middle MioceneNambayama Formation. This methane then migrated through subsur-face faults or permeable sandstone layers to cause high-flux methaneseepage, similar to that seen in Recent methane seeps in the Japan Sea.

Acknowledgments

We are grateful to Takao Ubukata, Hajime Naruse, and HiroshigeMatsuoka (Kyoto University, Japan) for their valuable comments anddiscussions as well as helpful encouragement. We are very thankful toHisao Tsutsumi and Masaki Takaya (Kyoto University) for preparingthin sections, and also to Ryohei Takahashi and Junya Matsuno (KyotoUniversity) for performing the XRD and FESEM analyses. Masaki Takayaalso helpedwith the EDS analysis. Kenta Yoshida (Osaka City University,Japan) is acknowledged for kindly performing the Raman spectroscopyanalysis. We are also grateful to Yusuke Seto (Kobe University, Japan)for suggestions regarding the globular silica mineral. Kazumi Zenitani(Kyoto University) is thanked for help in searching the literature. Wesincerely thankRobert G. Jenkins andAkikoGoto (KanazawaUniversity,Japan) for their very kind help and thoughtfulness in biomarker analysisand also valuable discussions. We wish to express our sincere apprecia-tion to Hakuichi Koike (Shinshushinmachi Fossil Museum, Japan) forhelp and encouragement in the field. We sincerely appreciate the com-ments and valuable suggestions on the early version of the manuscriptby Steffen Kiel (Swedish Museum of Natural History, Stockholm). Wealso thank an anonymous reviewer, Jörn Peckmann (University of Ham-burg, Germany), and the journal editor Thierry Corrège (University ofBordeaux, France) for careful reviews and constructive comments thatgreatly improved the manuscript. We acknowledge the staff at StallardScientific Editing for improving the English in the manuscript.

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