# Impact of tectonics and fluid circulations on shale gas isotope geochemistry – A case study of the Rietheim Member at the Mont Terri anticline (Switzerland)

Catherine Lerouge, Michaela Blessing, Marie Bonitz, Ana-Maria Fernández, Christine Flehoc, Nicolas Maubec, Guillaume Wille, David Jaeggi, Michael Kühn

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## To cite this version:

Catherine Lerouge, Michaela Blessing, Marie Bonitz, Ana-Maria Fernández, Christine Flehoc, et al. Impact of tectonics and fluid circulations on shale gas isotope geochemistry – A case study of the Rietheim Member at the Mont Terri anticline (Switzerland). Applied Geochemistry, 2026, Applied Geochemistry vol 198, 198, pp.106696. 10.1016/j.apgeochem.2026.106696. hal-05459228

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Submitted on 27 Jan 2026

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# Impact of tectonics and fluid circulations on shale gas isotope geochemistry – A case study of the Rietheim Member at the Mont Terri anticline (Switzerland)

Catherine Lerouge<sup>a, *, †</sup>, Michaela Blessing<sup>a</sup>, Marie Bonitz<sup>c, e</sup>, Ana-Maria Fernández<sup>b</sup>, Christine Flehoc<sup>a</sup>, Nicolas Maubec<sup>a</sup>, Guillaume Wille<sup>a</sup>, David Jaeggi<sup>d</sup>, Michael Kühn<sup>c, e</sup>

## ARTICLE INFO

Editorial handling by Daniele L. Pinti

### Keywords:

- Black shales

- Thermogenic gases

- Carbon isotope reversals

- Diagenesis

- Mont terri anticline

## ABSTRACT

In the framework of the hydrological survey of the Mont Terri anticline (Mont Terri rock Laboratory in the Folded Jura, Switzerland), a 58 m-deep borehole (BHS-1) was drilled through the Jurassic low permeability shale sequence. Dedicated sampling was carried out to characterize gases within a 13 m-thick unit of organic matter-rich Early Jurassic Rietheim black shales and adjacent units, including the underlying Beggingen aquifer. A cone-in-cone calcite, observed at the bottom of the black shale, as identified as an indicator of oil-window conditions and records a maximal burial temperature of ~80–90 °C. Two fracture zones within the black shales, marked by calcite infillings, provide evidence for at least two episodes of water paleocirculations: (1) an early circulation between fractures at the top of black shales and the Main Fault, and (2) a later circulation between fracture zones within the black shales and the lower Beggingen aquifer. Gas migration was investigated within the complex geological context of regional uplift, Jura folding and thrusting, and associated water flows. Alkane data reveal a partial carbon isotope reversal of thermogenic gases within the black shales between the two fracture zones, strongly suggesting alkane migration linked to the second water paleocirculation episode.

## 1. Introduction

Over several decades, chemical and isotopic techniques have been developed to decipher the origin of natural gases in conventional oil and gas hydrocarbon reservoirs. Different plots based on molecular gas ratios and isotopic signatures of methane such as the Bernard-, Schoell-, or Whiticar-diagrams have been widely proposed to discriminate gas sources (microbial versus thermogenic) (Schoell, 1983). In natural thermogenic gases, carbon isotopic signatures decrease with the inverse carbon number of the gaseous molecules following kinetic Rayleigh models (Schoell, 1983; Chung et al., 1988). The carbon isotopic signatures of methane, ethane and propane generally become less negative in a predictable proportional manner, as the maturity of a thermogenic gas increases (Chung et al., 1988). However, as exploration has shifted to unconventional low-permeability hydrocarbon reservoirs, gas data

provide evidence of carbon isotope reversals, which consist of ethane/propane having more negative $\delta^{13}C$ values compared to methane that are not explained by current Rayleigh models (e.g. Burruss and Laughrey, 2010; Tilley et al., 2011; Zumberge et al., 2012; Faiz et al., 2018; Cesar, 2022; Gao et al., 2014; Nie et al., 2020). Among cases where normal thermogenic gas trend ($\delta^{13}C$ methane < $\delta^{13}C$ ethane < $\delta^{13}C$ propane) is not respected, gas data show $\delta^{13}C$ methane $\approx$ $\delta^{13}C$ ethane, others partial isotope reversals where $\delta^{13}C$ methane > $\delta^{13}C$ ethane < $\delta^{13}C$ propane, and others isotope reversals where $\delta^{13}C$ methane > $\delta^{13}C$ ethane > $\delta^{13}C$ propane (e.g. Tilley et al., 2011). The isotope geochemistry of unconventional compared to conventional reservoirs has demonstrated that the chemical and isotope distribution in these type of reservoir does not follow a simple rule, but results from different secondary processes including (1) partly reversible free radical reactions for the formation of isotopically light ethane, for methane

<footnote><sup>a</sup> BRGM, BP36009, Cedex 2, Orléans, 45060, France</footnote>

<footnote><sup>b</sup> CIEMAT, Departamento de Físión Nuclear, 28040, Madrid, Spain</footnote>

<footnote><sup>c</sup> GFZ German Research Centre for Geosciences, Fluid Systems Modelling, Telegrafenberg, 14473, Potsdam, Germany</footnote>

<footnote><sup>d</sup> Federal Office of Topography swisstopo, Seftigenstrasse 264, Wabern, 3084, Switzerland</footnote>

<footnote><sup>e</sup> University of Potsdam, Institute of Geosciences, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany</footnote>

<footnote>* Corresponding author.</footnote>

<footnote>E-mail address: c.lerouge@brgm.fr (C. Lerouge).</footnote>
cracking with subsequent generation of ethane and propane (Cheng et al., 2020) (2) gas migration due to diffusive fractionation during basin uplift (Cesar, 2022) or in tectonically fractured reservoir (Tilley et al., 2011), and (3) hydrocarbon mixing including gases issues from bacterial degradation, thermal degradation of kerogen and/or oil (Hao and Zou, 2013) or from methane oxidation (Cesar, 2022). Some of these processes require the presence of water to proceed under specific chemical reactions (Burruss and Laughrey, 2010; Zumberge et al., 2012; Gao et al., 2014). The complexity of these secondary processes demonstrates the shortcomings of diagrams used for gases in conventional reservoirs (Pytlak et al., 2016; Milkov and Etiope, 2018), and the needs of additional information such as geologic setting, thermal maturity of organic matter, gas geochemistry as function of depth through the reservoir, gas wetness, diagenetic sequence, inorganic geochemistry to provide robust assessments concerning hydrocarbon gas origins (Loomer et al., 2021).

The Lower Jurassic black shales of the Rietheim Member at the Mont Terri rock laboratory, northwestern Switzerland, are a marine clay unit of the Staffelegg Formation, rich in organic matter attributed to the Toarcian Oceanic Anoxic Event (T-OAE) (Suan et al., 2015). Otherwise known as Posidonia Shale, they are well known for their hydrocarbon contents (Montero-Serrano et al., 2015). Previous works provided evidence of traces thermogenic alkanes in the overlying Middle Jurassic Opalinus clay Formation (Lerouge et al., 2015; Vinsot et al., 2018). By their location in the Mont Terri anticline, the Staffelegg and Opalinus Formations underwent deep burial and important deformation during the folding and thrusting of the Jura Mountains. A large fault, also called Main Fault is observed near the Staffelegg-Opalinus transition (Nussbaum et al., 2018). In 2021, a 58 m-deep borehole (BHS-1) was drilled to study the hydrogeochemical system through the bottom of the Opalinus Clay and the entire underlying Staffelegg Formation (Jaeggi et al., 2021), providing evidence of two water-bearing fracture zones, in the Rietheim Member and in limestones of the Beggingen Member at the bottom of the Staffelegg Formation (Bonitz et al., 2025). During the drilling campaign, a sampling was dedicated to the characterization of gases in black shales of the Rietheim Member and adjacent members of the Staffelegg Formation, including the two water-bearing fracture zones. The objective of this work was to characterize gases in black shales and adjacent members, determine their origin(s) and have a better understanding of alkane formation and migration in such complex geological setting of an anticline and water flows. The sampling was regular through the black shales to establish a complete profile of gases. Gases were extracted by core degassing at ambient temperature for a duration defined by the time necessary for reaching a steady state of the gas pressure (Lerouge et al., 2015). This technique has demonstrated its efficiency to limit the isotopic fractionation during the experiment (Hendry et al., 2017; Blessing et al., 2025). Additional petrological and isotopic data of carbonates in black shales and fractures from the two water-bearing fracture zones in the Staffelegg Formation allowed estimating the maximum burial temperature and discuss the possible origins and the relative timing of fluids from which precipitated carbonate fills in fractures.

## 2. Geological setting

The Mont Terri rock laboratory located at Saint Ursanne (north-western Switzerland) (Fig. 1a) is an international research laboratory dedicated to the hydrogeological, geochemical and geotechnical characterisation of the Opalinus Clay targeted as repository host rocks for nuclear waste deep disposal (Bossart et al., 2017). The laboratory corresponds to the safety gallery of a motorway tunnel which traverses the southern limb of the Mont Terri anticline; this anticline is the most external one in the Folded Jura (Fig. 1b) (Bossart et al., 2017).

The investigated sediments of the Staffelegg and Opalinus formations were deposited from the Early (~200 Ma) to Middle Jurassic (~171 Ma) in a shallow-marine epicontinental sea, which was delimited from the Tethys by the Alemannic Islands (Lauper et al., 2021; Wetzel et al.,

2003). The beginning of this period is marked by the deposition of organic-rich lithologies under a global marine oxygen deficiency during a very short-lived warming event, also termed the Toarcian Oceanic Anoxic Event (T-OAE) (Branski, 2012; Suan et al., 2015). The Opalinus Clay is overlain by Dogger mudstone, sandy marl, limestone and iron ooliths of the Passwang Formation (Hostettler et al., 2017). The marine conditions prevailed until Late Cretaceous, when the basin was inverted. At the end of Cretaceous, the maximum burial depth of Opalinus Clay was estimated at ~1350 m beneath seafloor (mbsf) resulting in a maximum temperature of 85 °C (Mazurek et al., 2006). A regional uplift and erosion in the early Tertiary followed. The lithological pile was strongly deformed and folded in the thin-skinned fold belt of the Jura Mountains in the period 10.5–3 Ma, followed by partial erosion of the anticline (Elie and Mazurek, 2008). The Mont Terri anticline was sheared off and thrust over the Tabular Jura of the Ajoie (Schaeren et al., 1989). Currently, the Opalinus Clay dips to the southeast In the Mont Terri anticline. Triassic and Jurassic rocks of the asymmetrical fold outcrop on the surface of Mont Terri. The present overburden at the rock laboratory site is 250 m–320 m. The rocks of the anticline were penetrated by three sets of fractures (Bossart and Thury, 2008; Nussbaum et al., 2011). Two sets of fractures (SSE dipping faults parallel to bedding and SW-dipping sub-horizontal faults) are related to the folding and thrusting of the Jura Mountains, and the third one (N- to NNE-striking normal faults) to the Oligocene Rhine-Bresse graben system (Nussbaum et al., 2011). The largest fault also called the “Main Fault” is a 1-3 m-thick and SSE-dipping fault subparallel to the bedding, observed near the Staffelegg-Opalinus transition at greater depth and in the center of the Opalinus Clay at shallower depth (Fig. 1b) (Nussbaum et al., 2018).

The shales of the Staffelegg and Opalinus Formations are low to very low permeability rocks, forming a confined sequence. Shales are considered to have water saturated pore spaces with practically no water migration. The overlying Malm formation represents a regional karstic aquifer (i.e. Hauptrogenstein), while Liassic marl and limestones of the Staffelegg Formation are only weakly karstified with local water inflow. The Main Fault acts as a sealed fault with no occurrence of water flow. In 2013, a 247.5 m-deep borehole (BDB-1) was realized to study the hydrogeological system associated to the Opalinus Clay aquitard in the context of the Mont Terri anticline; the borehole was drilled through the overlying Passwang Formation, the entire Opalinus Clay, and then was quickly stopped after crossing the uppermost 10 m of the underlying Staffelegg Formation at a water-bearing fracture within the Rietheim Member (Hostettler et al., 2017). In 2021, a second 58 m-deep borehole (BHS-1) was drilled through the bottom of the Opalinus Clay and the entire underlying Staffelegg Formation (Jaeggi et al., 2021), providing evidence of two water-bearing fracture zones, in black shales of the Rietheim Member and in strongly fractured and karstified limestones of the Beggingen Member at the bottom of the Staffelegg Formation (Bonitz et al., 2025). No water flow occurred during drilling, but the groundwater influence is identified by fractures and calcite veins in the two water-bearing fracture zones (Bonitz et al., 2025). In black shales, isolated sealed fractures perpendicular to bedding are present at 12.60 m (Z1), ~1 m below the upper boundary, and at 23.80–24.25 m in the limestone marker bed “Unterer Stein” (Z2), ~0.6–1 m above the lower boundary. The presence of the redox-sensitive trace element enrichment at the top of the Rietheim Member suggests that groundwater only has a limited influence, and the overlying Gross Wolf Member acts as a caprock (Bonitz et al., 2025).

## 3. Material and analytical techniques

### 3.1. Borehole BHS-1 and sampling

The ~58 m-deep BHS-1 borehole drilled through the bottom of the Opalinus Clay and underlying Staffelegg Formation crosscut organic matter rich-black shales of the Rietheim Member between 11.37 and
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<figure><img src="image_4.png" /><figcaption>**Fig. 1.** (a) Location of the Mont Terri laboratory; (b) Geological cross-section of the Mont Terri anticline and location of the BHS-1 borehole; (c) Lithological column of the BHS-1 borehole; (d) Photogragh of calcite-filled fracture at the top of the Rietheim Member (12.6 m); (e) Photograph of an open fracture crosscutting the limestone marker at 24.2 m; (f) a cm-thick layer of cone-in-cone calcite in the lower part of the Rietheim Member; (g) An open fracture crosscutting the Beggingen Member; (h) Detail of a calcite coating on the open fracture in the Beggingen Member.</figcaption></figure>
24.87 m (Jaeggi et al., 2021). The lithostratigraphy of the borehole is described in Fig. 1c and presented in detail in Hostettler et al. (2022). The main mineralogical, geochemical and petrophysical data of the Staffelegg Formation are presented in Bonitz et al. (2025). Black shales of the Rietheim Member contain between 3 and 8 wt % of organic matter and consist of variable amounts clay minerals (illite-mica, illite-smectite mixed layers, minor kaolinite, chlorite and glauconite) (29–47 %) associated with a detrital quartz-feldspar silty fraction (7–24 wt%) and carbonates (21–51 wt%) including 5–50 % calcite and 1–6 wt% dolomite, with minor pyrite (2–8 wt%) (Bonitz et al., 2024, 2025). Seventeen core samples, including eight black shales and one limestone from the Rietheim Member, two marls from the overlying Gross Wolf Member, four samples of marls from the underlying Mont Terri Member and two limestones from the Beggingen Member, were collected during the drilling campaign of the BHS-1 borehole (Fig. 1c). In the Rietheim Member, two samples containing isolated fractures were taken: the first one in black shales at 12.6 m just below the upper boundary (also called fracture zone Z1) and the second one in limestone at 24.2 m just above the lower boundary (also called fracture zone Z2). All the samples selected for carbonate study were conditioned in aluminium foil under vacuum. Among them, fourteen samples of marl were selected for the long-term rock degassing (CO₂, O₂, N₂ alkanes); they were conditioned in glass jars and Schott flasks in the Mont Terri Laboratory.

## 3.2. Sample characterization

The samples analysed for dissolved gases and few samples crosscut by fractures were observed under optical microscope and in cathodoluminescence to describe mineralogical and textural relationships and define diagenetic mineral sequence in the Rietheim Member. Complementary analyses of major elements were carried out in the different generations of diagenetic carbonates.

Cathodoluminescence (CL) observations were carried out with a cold cathode Cathodyne from NEWTEC. The electron beam has adjustable energies up to 2–4 kV and currents up to 200 µA. The Cathodyne is mounted on a Nikon microscope allowing magnification up to 10. The system is equipped with a tri-CCD digital camera.

Chemical analyses of major elements (Ca, Fe, Mg, Mn) in carbonates were performed using a Camebax SX five electron microprobe with a 15 kV acceleration voltage, a current beam of 12 nA and a 1–2 µm beam width. Counting time for each element is 10s. Standards used included both well-characterized natural minerals and synthetic oxides. Matrix corrections were made with a ZAF computing program.

## 3.3. Carbon and oxygen isotopic geochemistry of carbonates

The (C. O) isotopic compositions of calcite, dolomite/ankerite from the matrix were determined by successive extractions with 100 % phosphoric acid on about 400 mg of bulk rock powder. Calcite is extracted after a first reaction at 25.2 °C during 4 h, then dolomite and ankerite are extracted after a second reaction at 100 °C during 2 h, according to Rosenbaum and Sheppard (1986). Additional calcite separates (~80 µg) were analysed using an isoFLOW headspace analyzer coupled with an Isoprime PrecisION IRMS (Elementar).

## 3.4. Core degassing and isotopic geochemistry of dissolved gases

Dissolved gases were obtained by core degassing in glass jars and Schott flasks under He pressure of 600–800 mbars, according to the method described in Lerouge et al. (2020). Total gas pressure ($P_{total}$ expressed in bar) and concentrations of the gas species ($X_{gas species}$ given in volume percent) including CO₂, alkanes, O₂ and N₂, were measured on a Varian star 3400 CX gas chromatograph over several months (at least 2 months) until observing a steady state. The uncertainty on the concentrations of gas species was 3 %. The detection limits for gas concentrations were 0.001 % for CO₂, O₂ and N₂, and 0.0002 % for

alkanes. The uncertainty on the total pressure measured in the chromatograph was 3 .10⁻³ bar. The concentrations of gas species ([Gas species]) were recalculated in mmol per kilogram of rock according to equation (1) given in (Lerouge et al., 2020):

$$ [Gas species] = \frac{X_{gas species}}{100} \times P_{total} \times \left\{ \left( \frac{V_G}{R \times T} \right) / \left( \frac{M}{1000} \right) + \frac{1}{K_{H(gas species)}} \right\} \quad (\text{eq 1}) $$

Where M is the sample mass in grams, V_G the gas volume in the glass jar in L, R is the gas constant: 0.08314 L·bar/(mol·K), T the temperature in Kelvin, [Gas species] in mmol/L, X_{gas species} in bars, P_{total} in bars. K_H is the Henry's Law Constant in M/bar.

At the final stage of core degassing, an aliquot of gas was transferred into He-flushed Labco®-vials to analyse the carbon isotopic composition of CO₂ (δ¹³C₅CO₂) and the carbon (δ¹³C₅C₁-C₄) and hydrogen (δD₅C₁) isotopic compositions of alkanes. The δ¹³C₅CO₂ was analysed with a continuous flow Thermo Finnigan Delta plus XP isotope ratio mass spectrometer equipped with a GasBench II (Thermo Finnigan). The δ¹³C₅C₁-C₄ and δD₅C₁ were measured by GC/IRMS using a Trace GC Ultra gas chromatograph interfaced to a Delta plus XP (Thermo Finnigan), according to the method described in Blessing et al. (2015).

All the isotopic compositions are reported in δ units relative to international standards defined by: δ = (R_{Sample}/R_{Standard} - 1) x 1000 ‰, where R is the measured isotopic ratio in the sample and in the standard: Vienna Pee Dee Belemnite (V-PDB) for carbon, Vienna Standard Mean Ocean Water (V-SMOW) for oxygen and hydrogen. Standard deviations are better than ±0.5 ‰ for carbon, 0.2 ‰ for oxygen and ±5 ‰ for hydrogen.

# 4. Results

## 4.1. Petrology

### 4.1.1. Black shales from the Rietheim Member

Black shales consist of a clay fraction associated with a detrital quartz-feldspar silty fraction and a carbonate fraction of dominant diagenetic origin (Fig. 2a). Diagenetic carbonates include early micrite (calcite 1 - dark red in CL) and rare <20 µm-sized euhedral carbonates (calcite 2 - red in CL and dolomite 1 - orange-yellow in CL) associated with framboids of pyrite (pyrite 1) disseminated in the clay matrix (Fig. 2b and c). Calcites 1 and 2 are almost pure and differ by their Fe/ (Fe + Mg) atomic ratio, respectively 0.04–0.08 and up to 0.28–0.35 (SD1). In the lower part of the black shales below the “Unterer Stein” marker bed, a third generation of calcite which is quite pure and marked by a bright orange in CL (calcite 3) occurs as late cement of silty quartz-feldspar laminates (Fig. 2d and e), as anastomosed networks associated to euhedral pyrite (pyrite 2), and as cm-thick layers of cone-in-cone calcite (BHS-1-24.44 m) (Fig. 2f). The “Unterer Stein” marker bed at 23.8–24.2 m depth is a bedded marly limestone (Fig. 2g) formed of an anastomosed network of bright orange to yellow calcite associated with euhedral pyrite (Py 2) (Fig. 2h) parallel to the bedding. The CL color of calcite (Fig. 2i) is broadly similar to the calcite type 3 observed in the lower part of the black shales.

### 4.1.2. Calcite fractures in the Rietheim and Beggingen Members

The fracture zone Z1 at 12.6 m consists of a small network of ~1 cm-thick and calcite-filled fractures that crosscut the bedding of black shales (Fig. 2j). The micro-textures of fills suggest crack-seal veins filled by blocky calcite, which precipitated first as greyish medium crystals (calcite type 4) followed by limpid coarse grains (calcite type 5) (Fig. 2k). Both types are marked by high Fe (Fe/(Fe + Mg) atomic ratios (up to ~0.54) and dark red to red colour zoning in CL. The cathodoluminescence also provides evidence of a ~0.5–1 mm thick vein filled by late bright orange to locally yellow calcite (calcite type 6) along the main fracture filled by calcite type 4/5 (Fig. 2k). This calcite is quite
<figure><img src="image_5.png" /><figcaption>**Fig. 2.** Microscopic observations of the Rietheim Member (a) BHS-1-14.3 m micrograph showing the general aspect of the marl matrix (natural light); (b) BHS-1-14.3 m CL image showing the distribution of calcite 1 and calcite 2 in marl; (c) CL image showing the detail of carbonates in the clay matrix; (d) BHS-1-24.44 m photograph of the thin section; (e) BHS-1-24.44 m CL image showing calcite 3 cementing silty layer; (f) BHS-1-22.44 m CL image of cone-in-cone calcite layer subparallel to the bedding; (g) BHS-1-22.42 m micrograph showing the general aspect of the “Unterer Stein” marker bed (natural light); (h) BHS-1-24.42 m diagenetic calcite associated with euhedral pyrite (pyrite 2); (i) BHS-1-24.42 m CL image of the general aspect of the “Unterer Stein” marker bed; (j) BHS-1-24.44 m general aspect of the black shale crosscut by a calcite fill in fracture; (k) BHS-1-24.44 m CL image of the calcite fracture; (l) BHS-1-47 m Beggingen limestone; (m) Micrograph of the calcite fill fracture.</figcaption></figure>

pure and poor in Fe.

The fracture zone Z2 at 24.2 m is marked by an open fracture across the limestone marker bed “Unterer Stein”, which has a coating of limpid and pure calcite.

Limestones from the Beggingen Member are microfractured and crosscut by open fractures (Fig. 2l). A generation of sparite associated with pyrite fills matrix porosity and microfractures. Another generation of limpid and microcrystalline calcite covers sparite fills in still open fractures (Fig. 2m).

## 4.2. Carbon and oxygen isotopes of carbonates

The $\delta^{13}\text{C}$ and $\delta^{18}\text{O}$ were analysed in calcite and dolomite of the bulk matrix in black shales, marls and limestones of all the members from the Staffelegg Formation, and in calcite from veins in the Rietheim Member and limestone from the Beggingen Member (Table 1).

The $\delta^{13}\text{C}$ of calcite and dolomite in bulk matrix of black shales, marls and limestones of the Staffelegg Formation are in the range -3.3 to +0.8 ‰ V-PDB of marine carbonates. The most negative $\delta^{13}\text{C}$ values are measured in the Rietheim Member enriched in organic matter and in some calcite fills in fractures. In marls and limestones of the other

members, the $\delta^{13}\text{C}$ values are positive or close to 0 ‰ V-PDB. The $\delta^{18}\text{O}$ of calcite and dolomite in bulk matrix of black shales, marls and limestones of the Staffelegg Formation are in the range 18.9 to +28.3 ‰ V-SMOW. The highest values of 27.1–28.3 ‰ V-SMOW, measured in the underlying marls of the Mont Terri Member and limestones of the Beggingen Member, are representative of marine carbonates. The lower values measured in the Rietheim and Gross Wolf members are comparable to diagenetic carbonates in marine environment. The dolomite $\delta^{18}\text{O}$ is systematically lower than that of calcite.

The blocky calcite type 4/5 filling fracture that crosscut the black shales at the top of the Rietheim Member (fracture zone Z1) has similar $\delta^{13}\text{C}$ (0.0 ‰) to calcite in the marl matrix, but a significantly lower $\delta^{18}\text{O}$ (20.2 ‰). The late calcite type 6 reworking the calcite type 4/5 has significant different isotopic signature with $\delta^{13}\text{C}$ of -2.9 ‰ and $\delta^{18}\text{O}$ of 23.6 ‰. The limpid calcite in vein crosscutting the limestone at 24.2 m (fracture zone Z2) has a $\delta^{13}\text{C}$ of -1.6 ‰ and $\delta^{18}\text{O}$ of 22.6 ‰.

The two generations of calcite filling fractures in limestones of the Beggingen Member have significantly lower isotopic signatures than that of the limestone itself. The first generation of calcite fill shows low $\delta^{13}\text{C}$ of -5.9 ‰ and a $\delta^{18}\text{O}$ (24.4 ‰). The second generation has a less negative $\delta^{13}\text{C}$ of -1.9 ‰ and a $\delta^{18}\text{O}$ of 21.4/21.8 ‰.
<caption>**Table 1**</caption>

Carbon and oxygen isotopic compositions of calcite and dolomite in the bulk matrix and carbon and oxygen isotopic compositions of selected calcite separates in veins.

<table><thead><tr><th rowspan="3">Sample</th><th colspan="2">calcite bulk matrix</th><th colspan="2">dolomite bulk matrix</th><th colspan="3">Calcite veins</th></tr><tr><th>δ<sup>13</sup>C</th><th>δ<sup>18</sup>O</th><th>δ<sup>13</sup>C</th><th>δ<sup>18</sup>O</th><th rowspan="2">comments</th><th>δ<sup>13</sup>C</th><th>δ<sup>18</sup>O</th></tr><tr><th>‰ V-PDB</th><th>‰ V-SMOW</th><th>‰ V-PDB</th><th>‰ V-SMOW</th><th>‰ V-PDB</th><th>‰ V-SMOW</th></tr></thead><tbody><tr><td>Gross Wolf</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>BHS-1- 5.5 m</td><td>0.4</td><td>25.3</td><td>-0.4</td><td>25.2</td><td></td><td></td><td></td></tr><tr><td>Rietheim</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>BHS-1 - 12.6 m</td><td>-0.4</td><td>25.2</td><td>-0.9</td><td>22.0</td><td>Blocky Cc</td><td>0.00</td><td>20.2</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td>veinlet</td><td>0.3</td><td>21.3</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td>veinlet</td><td>-2.9</td><td>23.6</td></tr><tr><td>BHS-1 - 14.5 m</td><td>0.7</td><td>24.4</td><td>0.3</td><td>21.0</td><td></td><td></td><td></td></tr><tr><td>BHS-1 - 19 m</td><td>0.4</td><td>24.1</td><td>0.2</td><td>21.6</td><td></td><td></td><td></td></tr><tr><td>BHS-1 - 21.3 m</td><td>-3.3</td><td>25.7</td><td>-3.3</td><td>25.0</td><td></td><td></td><td></td></tr><tr><td>BHS-1 - 24.2 m</td><td>-1.9</td><td>25.9</td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>BHS-1 - 24.4 m</td><td>-1.8</td><td>23.8</td><td>-2.3</td><td>18.9</td><td>Cc open fracture</td><td>-2.9</td><td>22.7</td></tr><tr><td>Mont Terri</td><td></td><td></td><td></td><td></td><td>Cone-in-cone Cc</td><td>-1.6</td><td>22.6</td></tr><tr><td>BHS-1 - 28.3 m</td><td>1</td><td>28.3</td><td>0.8</td><td>26.7</td><td></td><td></td><td></td></tr><tr><td>BHS-1 - 34.6 m</td><td>0.3</td><td>27.1</td><td>-0.2</td><td>26.3</td><td></td><td></td><td></td></tr><tr><td>Beggingen</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>BHS-1 - 45.2 m</td><td>0.2</td><td>27.3</td><td></td><td></td><td>Cc open fracture</td><td>-1.9</td><td>21.8</td></tr><tr><td>BHS-1 - 47.1 m</td><td>0.3</td><td>28.3</td><td></td><td></td><td>Cc microfracture</td><td>-5.6</td><td>24.4</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td>Cc open fracture</td><td>-1.9</td><td>21.4</td></tr></tbody></table>

### 4.3. Extracted gases – concentrations and isotopic compositions

Gases (O₂, N₂, CO₂ and alkanes) extracted by degassing were analysed in fourteen core samples; all the data are available in (Bonitz et al., 2024). Oxygen concentrations are generally lower than the detection

limit and N₂ concentrations lower than 2 %, except in the upper part of the borehole (Fig. 3a). Nitrogen is the main component measured in the gas phase, followed by CO₂ and alkanes. In the following, CO₂ and alkanes data were expressed as partial pressure for CO₂, and as concentrations of gas species given in µmol per kilogram of rock for alkanes.

<figure><img src="image_6.png" /><figcaption>**Fig. 3.** (a) Profiles of oxygen (in %), nitrogen (in %), pCO₂ (in mbar) δ¹³C of CO₂ (in ‰ V-PDB), alkane (C1 to C6) concentrations (in mmol/kg of rock) and alkane (C1-Cn) δ¹³C (in ‰ V-PDB) with depth; (b) Profiles of alkane (C1 to C6) concentrations (in mmol/kg of rock) and alkane (C1-Cn) δ¹³C (in ‰ PDB) with depth. The lithological column, fracture zones in the black shales and the beggingen aquifer are indicated in blue for information. Z1 corresponds to the sealed fracture zone at the top of black shales close to the Main Fault and Z2 corresponds to the zone of open fractures in the limestone marker bed. The two red points correspond to core degassing where we have detected a gas leak, grey points where we have suspected a slight gas leak. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)</figcaption></figure>
Partial pressure of CO₂ (pCO₂) through the BHS-1 borehole ranges between 2.3 and 12.10⁻³ bar (Fig. 3a). The highest values are measured in the black shales. The carbon isotopic compositions of CO₂ (δ¹³C CO₂) are almost homogeneous: from -7 to -10 ‰ in the Gross Wolf Member, from -14.6 to -9 ‰ in the Rietheim Member, and from -10 to -11 ‰ in the Mont Terri Member (Fig. 3a).

The concentrations of total degassed alkanes through the BHS-1 borehole increase from 0 in the Beggingen and the bottom of the Mont Terri members to 170 µmol/kg of rock in the upper part of the Rietheim Member to decrease rapidly to 45 µmol/kg of rock at the top of the Rietheim and 27 µmol/kg of rock in the Gross Wolf Member (Fig. 3a). The C3 and C4 are the dominant alkane species followed by C1–C2, in the Gross Wolf, Rietheim and Mont Terri members except at the top of the Rietheim Member (Fig. 3b). The C1, C2 and C3 concentrations progressively increase as the total alkane concentrations increase toward the upper part of the Rietheim Member. At the top of the black shales which contain calcite fractures (fracture zone Z1 at 12.6 m), C1 becomes the major alkane and C3 is depleted compared to others. The δ¹³C of total alkanes is -35/-36 ‰ in the Gross Wolf, the Mont Terri and lower part of the Rietheim members; it decreases to -39 ‰ towards the upper part and finally increases to -33 ‰ at the top of the Rietheim Member (Fig. 3b).

The C1 to C5 alkanes in the Gross Wolf and the Mont Terri members, respectively overlying and underlying the Rietheim Member, have almost similar δ¹³C features: δ¹³C C1 -46/-44 ‰, δ¹³C C2 -42/-40 ‰, δ¹³C C3 -37/-36 ‰, δ¹³C C4 ~ -33/-32 ‰, δ¹³C C5 ~ -29/-28 ‰. The δ¹³C of the n-alkanes (C1 to C5) increases with the carbon number. The δ¹³C of the alkanes C1 to C5 in the Rietheim Member are more heterogeneous (Fig. 3b). The δ¹³C C1 decreases from -39 to -44 ‰ with depth, while the δ¹³C C2 (-27/-31 ‰) is high at the top of the formation in contact with the Gross Wolf Member then increases from -47 to -41 ‰ with depth. The δ¹³C C3, δ¹³C C4 and δ¹³C C5 are quite homogeneous through the entire profile, except the δ¹³C C3 at the top of the formation in contact with the Gross Wolf Member which is high and close to the δ¹³C C2 (-31 ‰). The alkane data of Rietheim Member show partial isotope reversals: δ¹³C C1< δ¹³C C2> δ¹³C C3 < δ¹³C C4< δ¹³C C5, at the top of the formation in contact with overlying Gross Wolf Member, δ¹³C C1> δ¹³C C2< δ¹³C C3< δ¹³C C4< δ¹³C C5 in the upper part of the member, while the δ¹³C of the n-alkanes (C1 to C5) normally increases with the carbon number in the ~60 cm at the bottom of the formation, like in the Gross Wolf and Mont

Terri Members.

## 5. Discussion

### 5.1. Diagenetic evolution of the Rietheim Member

The mineral sequence relative to the burial curve of the Rietheim Member was determined using petrographic observations and δ¹⁸O of the different generations of diagenetic carbonates (Fig. 4). Since oxygen isotopes fractionate with temperature during mineral precipitation, formation temperatures of calcite and dolomite present in the marl and limestone matrix were estimated from their δ¹⁸O, using the calcite–water oxygen isotopic fractionation data of Kim and O’Neil (1997) and the dolomite–water oxygen isotopic fractionation data of Chacko and Deines (2008) and assuming that they precipitated from marine-derived waters (δ¹⁸O values ≈ 0 ‰ V-SMOW). Origins of fluids from which calcite fills precipitated in fractures were discussed using their δ¹⁸O and our knowledge of the geological and hydrological setting.

#### 5.1.1. Early diagenesis and burial

The framboidal pyrite associated with early calcite cementation (calcite 1) is characteristic of pyrite formed by bacterial sulfate reduction (BSR) associated with OM degradation in marine clay sediment near the water/sediment interface, resulting in anoxic conditions (Lerouge et al., 2011, 2014; Turchyn et al., 2021). The low impurity content and the low Fe/(Fe + Mg) ratios of calcite and dolomite 1 are largely due to the consumption of iron to form pyrite (Raiswell, 1982). In clay formation, the BSR may cease for several reasons: lack of sulfates, lack of iron and/or decrease of pore size (size of bacteria 0.7–3 µm; (Brock et al., 1994). Some rare euhedral crystals of calcite 2 and dolomite 2 in the clay matrix have rims with Fe/(Fe + Mg) ratios up to 0.28. The formation of diagenetic carbonates richer in iron and of glauconite rather suggests that iron was still available in marl pore waters once BSR ceased during compaction.

Due to the impossibility to separate the generations of calcite (calcite 1 and 2) in a marl, the δ¹⁸O of carbonates were analysed in the bulk marl matrix. Consequently, the estimated temperatures correspond to an average formation temperature of a mixing of carbonate generations formed during early diagenesis and burial. Nevertheless, these data inform on the carbonate cementation duration/timing. Calcite and

<figure><img src="image_7.png" /><figcaption>Fig. 4. Burial curve of the Staffelegg formation and diagenetic mineral sequence.</figcaption></figure>
dolomite in the black shale matrix precipitated from marine-derived fluids at ~55–65 and ~70–80 °C, respectively.

The cone-in-cone calcite type 3 which is essentially observed in the lower part of the Rietheim Member fills opening structures sub-parallel to the bedding and is often associated to formation of euhedral pyrite (pyrite 2). This calcite is pure with a low Fe/(Fe + Mg) ratio probably due to the consumption of iron by the formation of pyrite 2. Its δ¹³C is similar to that of the marl matrix, and consistent with unmodified seawater origin. Its formation temperature deduced from its δ¹⁸O is ~80 ± 10 °C, and slightly higher than that estimated from carbonates in the clay matrix, and broadly comparable to that estimated in the overlying Opalinus Clay (85°C; Elie and Mazurek, 2008). The textures and temperatures of cone-in cone calcite in the Rietheim Member are comparable to that of cone-in-cone calcite commonly formed in marine organic-rich shale in which oil or gas migrate in a temperature range of 70–120 °C (Cobbold et al., 2013).

### 5.1.2. Late diagenesis associated with tectonics at the Mont Terri anticline – carbonate fills in fractures

The calcite filling fractures in the two fracture zones (Z1 and Z2) in black shales are the record of fluid paleocirculations through the complex fracture network at the scale of the Mont Terri anticline. The origins of these fluids are difficult to determine, due to mixing of marine-derived waters with external components such as present-day pore waters at Mont Terri and Mont Russelin (Pearson et al., 2003) and ground waters of the Beggingen Member aquifer in the Staffelegg Formation at Mont Terri and at Mont Russelin (Mazurek and de Haller, 2017). The δ¹³C (−1.9 ‰) and δ¹⁸O (+21.4/21.8 ‰) values of latest microcrystalline calcite in open fracture of the Beggingen Member of the BHS-1 borehole allow characterizing local meteoric-derived ground waters in the karstified limestone aquifer.

According to the location of the BHS-1 borehole in the Mont Terri laboratory, the fracture zone Z1 at 12.6 m might be related to the “Main Fault” that affected Opalinus Clay during the Jura thrusting in the period 10.5–3 Ma (Nussbaum et al., 2011). This fault crosscut the Mont Terri anticline and is closed to the transition between the Staffelegg Formation and the Opalinus Clay. The generation of coarse blocky calcite (calcites 4 and 5) sealing the <1 cm-thick fractures show oscillatory zoning and dark red luminescence which are not observed in the clay matrix of the fracture walls, suggesting that fluids were not penetrative in the clay matrix. This calcite type 4/5 is characterized by the highest values of Fe/(Fe + Mg) ratio (~0.50–0.55), that are not observed elsewhere in the Staffelegg Formation, but comparable to that of late diagenetic calcite and ankerite in overlying Opalinus Clay (Lerouge et al., 2014, 2015). Its δ¹⁸O (+20.2 ‰) is in the range of values of calcite in veins associated to the Main Fault in Opalinus Clay at Mont Terri (19.32–21.07 ‰; Mazurek and de Haller, 2017). The fractionation between bulk matrix calcite and calcite filling fracture is 5.03 ‰ V-SMOW, suggesting that calcite precipitated either from marine-derived waters in fractures at ~90 °C, a temperature higher than that estimated from the matrix, or from fluids with negative δ¹⁸O values. Ninety degrees is a value significantly higher than the burial temperature of ~55 °C estimated at Miocene, the age of the Main Fault (Mazurek et al., 2006). If we consider that calcite precipitated at 55 °C, the fluids from which calcite precipitated in fractures associated to the Main Fault and the Jura thrusting had a negative δ¹⁸O value of ~ −6/-4 ‰, consistent with a dominant meteoric/ground water component. The calcite type 6 precipitated later than calcite type 4/5 has a lower δ¹³C (−2.9 ‰) and higher δ¹⁸O (+23.6 ‰), rather suggesting it also precipitated from meteoric/ground waters at lower temperatures. The limestone sample collected at 24.2 m in the fracture zone Z2 consists of isolated open fracture showing a coating of limpid calcite. The δ¹³C (−2.9 ‰) and a δ¹⁸O (+22.7 ‰) of the limpid calcite might be compared to calcite 6 filling micro-fracture at the top of the member and be formed from similar meteoric/ground water at low temperatures. The calcite 6 filling micro-fracture at 12.6 m and at 24.2 m in black shales are very similar to

latest microcrystalline calcite in open fracture of the Beggingen Member of the BHS-1 borehole representative of local meteoric-derived ground waters in the karstified limestone aquifer.

The study of calcite in fractures and the fluids from which they precipitated gives evidence at least of two fluid paleocirculations through the fractures affecting black shales:

1) a first paleocirculation of meteoric-derived waters in the fracture zone Z1 at the top of the black shales connected to the Main Fault at the Opalinus – Staffelegg transition;

2) A second paleocirculation of meteoric-derived ground waters of the Beggingen aquifer toward the black shales through connected fracture zones Z1 and Z2, in favour of a shortening fault structure that have created a link between the Beggingen aquifer and the Rietheim Member (Bonitz et al., 2025).

### 5.2. Gas concentrations and origins in organic-rich black shales

Gas extracted from organic-rich black shales of the Rietheim Member contains nitrogen, carbon dioxide and light hydrocarbons (alkanes C1–C6), gas species that are common in black shales (Nie et al., 2020). Gas is in the form of free/dissolved gas and gas adsorbed on the surface of clay minerals and organic matter (Milkov et al., 2020; Nie et al., 2020). According to the canister degassing technique of core sample immersed in water for several days used to recover adsorbed gas in unconventional shale gas reservoirs (Tao et al., 2021), the degassing of shale at ambient temperature is dominated by free/dissolved gas, the adsorbed gas being extracted only at reservoir temperature or high temperature. Here we have made the choice to use the core degassing technique by equilibrium with a gas phase at ambient temperature for long duration to have a good recovery of dissolved gas and possibly of part of adsorbed gas by displacement in term of concentration and isotopic signatures (Prinzhofer et al., 2009; Lerouge et al., 2015; Hendry et al., 2017; Vinsot et al., 2018; Blessing et al., 2025).

Nitrogen in black shales and marls of the adjacent members is the major component of the gas (43–91 ‰). The nitrogen content expressed in mmol/L of pore waters ranges between 0.3 and 1.4 mmol/L, what is slightly lower than the value of 2.2 ± 0.6 mmol/L measured in overlying Opalinus Clay during the in-situ gas experiment conducted at the Mont Terri Laboratory (Vinsot et al., 2018). Two high values of 4.6 and 5.1 are measured in the core of the black shales where the organic matter content is the highest one (Bonitz et al., 2024), probably due to the extraction of natural adsorbed nitrogen. The origin of nitrogen remains unknown (Vinsot et al., 2018).

Carbon dioxide in black shales and adjacent marls accounts for 5–53 ‰ of the total extracted gas. The carbon dioxide data allow determining its origin and possible contribution of oxidation of organic matter and/or alkanes in the gas balance. The pCO₂, ranging between 2.3·10⁻³ and 12.10⁻³ bar, are consistent with pCO₂ of marine reduced formations (Gaucher et al., 2010; Lerouge et al., 2015, 2020; Tremosa et al., 2012; Wersin et al., 2016). The pCO₂ values in the black shales are comparable to that of organic matter-rich Toarcian black shales in southeastern France (Lerouge et al., 2015; Tremosa et al., 2012). The range of δ¹³C–CO₂ values in marls and black shales of the Staffelegg formation is consistent with the δ¹³C–CO₂ of the CO₂ component internally controlled by calcite in the clays estimated to about −11 to −9 ‰ based on δ¹³C-calcite and carbon isotopic fractionation between calcite and CO₂(g) of +10.2 ‰ at 20 °C (Deines et al., 1974; Mook et al., 1974). Some lower δ¹³C–CO₂, from −14.6 to −12.6 ‰, are measured in the fracture zone Z1 at the top of the Rietheim where the CO₂ component is higher, strongly suggesting a slight oxidation of organic matter (−30 to −25 ‰ V-PDB; Lerouge et al., 2020) or of alkane (Blessing et al., 2025).

Light hydrocarbons account for a small portion (2–18 ‰) of the total extracted gas. The highest alkane concentrations (170 µmol/kg of rock) are measured in the black shales of the Rietheim Member and are related to their high organic carbon content given in Bonitz et al. (2024). The
alkane concentrations are significantly lower in overlying marls of the Gross Wolf Member (27 µmol/kg) and underlying marls of the Mont Terri Member (10–25 µmol/kg), indicating that black shales are the source of alkanes. The presence of C2+ alkanes, the δ¹³C and δD of methane plotted in the δ¹³C~C₁~ - δD~C₁~ diagram of Milkov et al. (2020) (Fig. 5a), the range of temperatures recorded by the cone-in-cone calcite (80 ± 10 °C), the maximum burial of ~1350 m attained by black shales correspond to the formation of thermogenic gases at the beginning of the gas window in Mesozoic source rocks that initiates at ~60 °C and ~1–2 km depth (Hunt, 1996; Cobbold et al., 2013; do Couto et al., 2021), what is in agreement with the geochemical characterization of organic matter in Rietheim black shales at Mont Terri and in northern Switzerland (Elie and Mazurek, 2008).

However, in comparison with the few data available on organic matter-rich shales that have undergone comparable burial temperatures, alkane concentrations analysed in the Rietheim Member from the BHS-1 borehole are significantly lower than values measured with the same technique of core degassing in the “Schistes Carton” of Tournemire (southeastern France) (110–120 °C; 6600–7200 µmol/kg) or Toarcian OM-rich shales (85–120 °C; 1400–1800 µmol/kg) (Lerouge et al., 2015), but are in the same range as near-surface Callovian-Oxfordian OM-rich black shales (150 °C; 20–290 µmol/kg) close to the Rochasson methane micro-seep, French Alps (Blessing et al., 2025). The δ¹³C of the C1–C5 alkanes reported in a Chung diagram show complex partial isotope reversals in some Rietheim black shales at Mont Terri (Fig. 5b) that do not occur in overlying Opalinus clay at Mont Terri and Posidonia Shales elsewhere in Europe (Schistes Carton at Tournemire; Lerouge et al., 2015; Posidonia Shales in Hils syncline in NW Germany: Stahl, 1993) (Fig. 5c). The unusual low concentrations and the partial isotope reversals in the black shales of the Rietheim Member at Mont Terri give

evidence of secondary processes that are discussed below.

### 5.3. Origins of partial isotope reversals in the Rietheim black shales from the Mont Terri anticline

The stable isotope classification systems used to determine the origin and thermal maturity of natural gases are primarily based on empirical observations made in conventional reservoirs. These diagrams may not be readily applicable to unconventional shale gas reservoirs where isotope reversals is commonly encountered (Tilley et al., 2011; Zumberge et al., 2012; Tilley and Muehlenbachs, 2013; Cao et al., 2015; Faiz et al., 2018; Milkov and Etiope, 2018; Milkov et al., 2020).

As seen above, the concentrations and isotopic signatures of alkanes in the Rietheim black shales and adjacent members at Mont Terri testify to complex molecular and isotopic fractionation processes that result in partial isotope reversals. This part of the discussion proposes to reconstruct evolution of thermogenic gases (concentrations and isotope) in black shales and their migration during the different successive geological stages including burial diagenesis, regional uplift, folding and thrusting of the Jura Mountains, the Main Fault and water flows. Gas transport in low permeability clay rocks is complex and involve different mechanisms: (1) advective and diffusive transport of dissolved gas, (2) two-phase flow, (3) microscopic fracturing controlled by the gas production rate and (4) macroscopic gas- and hydro-fracturing. Complex tectonic and hydrogeological setting, ductile/deformation, fracturing and water circulations play an important role on these mechanisms. The present-day shales of the Staffelegg Formation have low gas content and are water-saturated with a low water flow; for this reason, we consider in a first approach that the advective and diffusive transport of dissolved gas prevails; it is mainly governed by three laws: (1) the Darcy's Law,

<figure><img src="image_8.png" /><figcaption>**Fig. 5.** (a) Binary diagrams of empirical genetic gas fields of Milkov et al. (2020); (b) Chung diagram (1988) illustrating δ¹³C~Cn~ of the different alkanes in function of the reciprocal carbon number (1/Cn); (c) Chung diagram showing alkane data in different black shales (Schistes Carton at Tournemire and Pliensbachian at Bure in France; Lerouge et al., 2015; Posidonia Shales in Hils syncline in NW Germany: Stahl, 1993).</figcaption></figure>
which describes the advective water flow, (2) the Fick's Law, which describes the diffusion of dissolved gas due to concentration gradients, and (3) the Henry Law, which describes the solubility of gas in pore waters.

Thermogenic gases in Rietheim black shales were generated by low to moderate maturation of organic matter that begun at ~50–65 °C up to maximum burial temperature of ~80 ± 10 °C. During this period, black shales acted as the main source and the main reservoir of thermogenic gases. The slight δ¹³C enrichment of methane does not indicate a contribution of microbial methane or mixing of various sources of organic matter. The low amounts of thermogenic gas with “normal” kinetic trend of C1–C5 alkanes (δ¹³CC₁ < δ¹³CC₂ < δ¹³CC₃ < δ¹³CC₄ < δ¹³CC₅) in the overlying and underlying members of black shales of the BHS1 borehole and in overlying Opalinus clay in another borehole at Mont Terri (Lerouge et al., 2015; Vinsot et al., 2018) suggest a weak migration of dissolved gas by diffusion from black shales towards adjacent members. The abnormal low C1 component and the slight deviation from a straight line due to higher δ¹³CC₁ might result from the significant higher diffusion rate of methane at burial temperature (Pokharel et al., 2018).

The regional uplift and erosion during Tertiary induced a decrease of temperature (down to ~50–60 °C), which probably stopped the organic matter maturation, and a decrease of pressure that resulted in a lower solubility of gas in water and might create a gas phase (two-phases). Since that time, black shales have only served as a reservoir.

Between 10.5 and 3 Ma, the sedimentary pile was folded to form the Mont Terri anticline, during the folding and thrusting of the Jura Mountains. The Mont Terri, faulted during this period, began being eroded at the same time. In this structure, the sedimentary pile currently dips to the southeast and is fractured. Black shales are at the footwall of the Main Fault and partially outcrop at the top of the anticline. According to the study of calcite in the fractures, the small fracture zone Z1 at the top of black shales is (was) connected to the Main Fault above, and to the fracture zone Z2 at the bottom of black shales and to the Beggingen aquifer. In this context, the decrease of pressure initiated during Tertiary and the gas migration have been enhanced by the tilting of the units, the fracturing and possibly the exposure of black shales. This latter might favour local desaturation of black shales, two-phase flow and short hydrocarbon leakage.

The heterogeneous C1–C6 concentrations and complex partial isotope reversals in black shales between the two fracture zones Z1 and Z2 (Fig. 3b and Fig. 5b) strongly suggest that the secondary processes affecting thermogenic gases and their migration are related to the fracture zones and water flows. The broadly flat depth profiles of the C4+ concentrations and δ¹³CC₄+ through the black shales strongly suggest a little influence of secondary processes on C4+ thermogenic alkanes, while the depth profiles of shorter C1–C3 alkane concentrations are marked by a decrease from the highest values in the upper part of the black shales to the lowest values toward the fracture zone Z2, a drop of values in the fracture zone Z1 and slightly different δ¹³CC₂-₃ marked by ¹³C-enriched values in the fracture zone Z1. With regards to C1–C3 isotopic signatures, the C1–C2 isotope reversals are regular in black shales above the fracture zone Z2, except in the fracture zone Z1 where methane is abnormally ¹³C-enriched. According to these data, the thermogenic C1–C6 alkanes in the black shales between the two fracture zones Z1 and Z2 show different migration behaviour which introduces a significant variability in the molecular compositions of gases through the member, and fractionation effects, where different rates of isotope fractionation between hydrocarbon molecules during gas flow cause a change of the shape of compound-specific-isotope curves within the Chung-diagram from a normal linear trend to either more convex or concave shapes. They give evidence that the shorter C1–C2 alkanes diffuse faster and desorb more ¹²C than larger alkane molecules (C3–C6) over time. Residual gases within black shales show molecular fractionation and a partial isotope reversal: more C3 and C4 alkanes present compared with C1–C2 and a reversed Chung-trend where CH₄ and C₂H₆

are isotopically heavier compared with the longer chain hydrocarbons. The shapes of the depth profiles of the short C1–C3 concentrations in the two fracture zones at the boundaries of the black shales inform on the roles of the fracture network and possibly of water flows. At the upper boundary of the black shales, groundwater only has a limited influence, and the overlying Gross Wolf Member seems to act as a caprock (Bonitz et al., 2025). The drop of short-chain alkane concentrations and abnormal ¹³C-enrichment of methane limited to the fracture zone Z1 suggest a significant but time-limited gas migration of C1–C3. The abnormally high ¹³C-enriched value of methane might be related to the migration of free methane during the thrusting and the formation of the Main Fault rather than diffusion of dissolved methane. Currently the Main Fault is considered as sealed by calcite and celestite veins and µm-shear zones (Nussbaum et al., 2018). At lower boundary of the black shales, the decrease in short-chain alkane concentrations is more regular toward the fracture zone Z2 that is connected to the Beggingen aquifer, suggesting instead migration by advection (and diffusion) of dissolved gas associated with restricted water flows.

## 6. Conclusion

In the Mont Terri underground rock laboratory, a 58 m long borehole was drilled to investigate the entire Early Jurassic Staffelegg Formation. The examined section contains the Rietheim Member, otherwise known as Posidonia Shales, that consists of ~13.5 m-thick organic matter-rich (3–8 wt%) black shales. Rock samples were analysed first to better constrain diagenetic evolution of the Rietheim Member and second to characterize light hydrocarbons in black shales, determine their origins and define the impact of tectonics and groundwater circulations on shale gas isotope geochemistry at the scale of the Mont Terri anticline.

Petrological and geochemical data of cone-in-cone calcite and calcite in fractures provide information of fluid origins circulating through the fracture network:

* Cone-in-cone calcite observed in the Lower part of the Rietheim Member is formed at the maximum burial temperature of ~80 ± 10 °C from marine-derived waters; its texture and temperature formation are in good agreement with the beginning of the oil window (low to moderate maturity of organic matter) in Mesozoic source rocks.

* A first generation of blocky calcite in fracture (Z1) at the top of the Rietheim Member precipitated at temperatures lower than 55 °C from meteoric-derived waters that circulated in a fracture network connected to the Main Fault during the Jura thrusting.

* A second generation of calcite in fractures (Z2) at the top of the Rietheim Member and in limestone marker bed "Unterer Stein" in the lower part of the Rietheim Member precipitated at low temperatures from meteoric-derived ground waters that circulated in fractures connected to the Beggingen aquifer.

The analyses of gases obtained by core degassing through the Rietheim Member inform on the nature of gases in the black shales, their concentrations, their origin, and allow discussing mechanisms of gas migration:

* Nitrogen is the main component measured in the gas phase, followed by CO₂ and alkanes.

* The pCO₂ and δ¹³C CO₂ indicate that the CO₂ is at equilibrium with calcite in the clays. Some rare lower δ¹³C CO₂ are measured at the top of the Rietheim Member that could be due to slight contribution of OM degradation or alkane oxidation.

* The alkane concentrations in the black shales of the Rietheim at Mont Terri are very low compared to other black shales having similar contents and maturity of organic matter, probably due to low diffusive migration of the short alkanes. The alkane δ¹³CCn are consistent with a thermogenic origin of the gases.
* Partial isotopic reversals is observed between the two fracture zones Z1 and Z2, suggesting complex secondary (post-genetic) fractionation due to migration of the lighter alkanes (C1–C3) related to water flows (adveptive transport) in fracture network connected with the Beggingen aquifer.

### CRediT authorship contribution statement

**Catherine Lerouge:** Writing – original draft, Visualization, Validation, Supervision, Project administration, Methodology, Investigation, Funding acquisition, Data curation, Conceptualization. **Michaela Blessing:** Writing – original draft, Methodology, Investigation. **Marie Bonitz:** Writing – review & editing, Data curation. **Ana-Maria Fernández:** Writing – review & editing, Investigation, Formal analysis. **Christine Flehoc:** Writing – review & editing, Formal analysis. **Nicolas Maubec:** Writing – review & editing, Formal analysis. **Guillaume Wille:** Writing – review & editing, Formal analysis. **David Jaeggi:** Writing – review & editing, Supervision, Resources, Investigation. **Michael Kühn:** Supervision, Project administration, Investigation, Conceptualization.

### Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

### Acknowledgments

This research has been financially supported by the partners of the Mont Terri Consortium participating in the HS-A Experiment (BGR, Helmholtz, NWS, swisstopo) and by the BRGM Research. We thank Benoit Henry from BRGM for the gas analyses. We thank Editor in chief, Dr Zimeng Wang, Associated Editor, Dr Daniele Pinti and the two references for their constructive comments and significant improvements to the manuscript.

### Data availability

Data are available on https://doi.org/10.5880/GFZ.3.4.2024.001

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