Insights from Mineralogical Diagenesis, SEM and FTIR Features of the Permian Mikambeni Shale of the Tuli Basin, Limpopo Province of South Africa

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Article Methanogenesis Potentials: Insights from Mineralogical Diagenesis, SEM and FTIR Features of the Permian Mikambeni Shale of the Tuli Basin, Limpopo Province of South Africa

George Oluwole Akintola 1,* , Francis Amponsah-Dacosta 1, Steven Rupprecht 2, Nithyadharseni Palaniyandy 3 , Sphiwe Emmanuel Mhlongo 1 , Wilson Mugera Gitari 4 and Joshua Nosa Edokpayi 5

1 Department of Mining and Environmental Geology, University of Venda, Thohoyandou 0950, South Africa; [email protected] (F.A.-D.); [email protected] (S.E.M.) 2 Department of Mining Engineering, University of Johannesburg, Johannesburg 2006, South Africa; [email protected] 3 Energy Centre, Council for Scientiﬁc and Industrial Research (CSIR), Pretoria 0184, South Africa; [email protected] 4 Department of Ecology Resource Management, University of Venda, Thohoyandou 0950, South Africa; [email protected] 5 Department of Hydrology and Water Resources, University of Venda, Thohoyandou 0950, South Africa; Citation: Akintola, G.O.; [email protected] Amponsah-Dacosta, F.; Rupprecht, S.; * Correspondence: [email protected] Palaniyandy, N.; Mhlongo, S.E.; Gitari, W.M.; Edokpayi, J.N. Abstract: Carbonaceous shale is more topical than ever before due to the associated unconventional Methanogenesis Potentials: Insights resources of methane. The use of FTIR, SEM-EDX, and mineralogical analyses has demonstrated from Mineralogical Diagenesis, SEM a promising approach to assess methanogenesis potentials in a more rapid and reliable manner and FTIR Features of the Permian for preliminary prospecting. Representative core samples from the borehole that penetrated the Mikambeni Shale of the Tuli Basin, carbonaceous Mikambeni shale Formations were investigated for methanogenesis potentials. The Limpopo Province of South Africa. absorption band stretches from 1650 cm−1 to 1220 cm−1 in wavenumber, corresponding to C- Minerals 2021, 11, 651. https:// doi.org/10.3390/min11060651 O stretching and OH deformation of acetic and phenolic groups in all studied samples, thereby suggesting biogenic methanogenesis. The CO2 was produced by decarboxylation of organic matter −1 −1 Academic Editor: around 2000 cm and 2300 cm and served as a source of the carboxylic acid that dissolved the + Leszek Marynowski feldspar. This dissolution process tended to release K ions, which facilitated the illitization of the smectite minerals. The SEM-EDX spectroscopy depicted a polyframboidal pyrite structure, which Received: 20 May 2021 indicated a sulfate reduction of pyrite minerals resulting from microbial activities in an anoxic milieu Accepted: 2 June 2021 and causes an increase in alkalinity medium that favors precipitation of dolomite in the presence of Published: 19 June 2021 Ca and Mg as burial depth increases. The contact diagenesis from the proximity of Sagole geothermal spring via Tshipise fault is suggested to have enhanced the transformation of smectite to chlorite Publisher’s Note: MDPI stays neutral via a mixed layer corrensite in a solid-state gradual replacement reaction pathway. The presence of with regard to jurisdictional claims in diagenetic chlorite mineral is characteristic of low-grade metamorphism or high diagenetic zone at a published maps and institutional afﬁl- temperature around 200 ◦C to 230 ◦C and corresponds to thermal breakdown of kerogen to methane iations. at strong absorption band around 2850 cm−1 and 3000 cm−1, indicating thermal methanogenesis.

Keywords: methanogenesis potentials; biogenic methanogenesis; thermal methanogenesis; carbonaceous shale; carboxylic; illitization; chloritization; framboidal pyrite Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and 1. Introduction conditions of the Creative Commons Attribution (CC BY) license (https:// Carbonaceous shale has been more topical than ever before due to the associated creativecommons.org/licenses/by/ unconventional resources for energy supply. Shale constitutes an essential component of 4.0/). unconventional gas generation due to the global clamor for an energy transition from heavy

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greenhouse domination to low-carbon natural gases [1–3]. With respect to climate change moderation, carbonaceous shale has been identified to promote a short-term accelerated action to achieve the 2015 Paris agreement climate targets of keeping the global temperature increases below 2 ◦C. In recent studies [4,5], shale gas exploration has been prioritized in the US from 2006 to 2020, cutting off well over 430 million tonnes of CO2 emission and accounting for over 30% of the financial fiscal year [6,7]. In contrast to conventional shale source rocks, carbonaceous shales tend to host natural gas under a low pressure and extremely low permeability but extractable using horizontal well-drilling and hydraulic fracturing technologies [8–11]. Despite many decades of research in carbonaceous shale, a reliable and rapid discriminative approach to identify a potential methane gas-bearing rock remains elusive. However, some studies have used petrographic and sedimentological properties [12,13], geophysical properties [14–16], and geochemical and mineralogical characteristics [17–20] to attribute most organic matter transformation to their burial. Furthermore, there is extensive recent literature [21–29] on the successful use of an organic geochemical method to determine petrophysical properties such as total organic carbon (TOC), thermal maturity, vitrinite content, and desorbed gas composition. Undoubtedly, these investigative approaches provide deterministic information rather than discrimination at the preliminary exploratory stage [30]. The discriminative approach identifies sweet-spot targets for further detailed and determinative investigations, which require huge cost implications. This research provides information on methane formation during the transformation of organic components of organic-rich sedimentary deposits. It applies evidence from mineralogical, structural, and functional-group features of the carbonaceous Mikambeni shale in the Tuli Basin. The Permian Tuli Basin is known as the Limpopo-area Karoo Basin, hosting coal resources used to power a coal-fired plant for electricity generation in the northeastern region of South Africa [31–34]. The potential for methanogenesis sources has not been given proper attention in the burial depth, having a thickness of 1 km or less.

Study Area The Tuli Basin is a trans-frontier depozone that straddles the triple junction of South Africa, Zimbabwe, and Botswana situated within latitudes 29◦36022.1900 E and 28◦25023.1500 E and longitudes 23◦11024.4500 S and 22◦43024.5400 S (Figure1). This basin is a back-bulge structural depression that resulted from crustal subsidence due to tectonic regimes adjacent to the Cape Fold Belt (CFB) orogenic belt. The subsidence controls the accommodation space that preserves the Carboniferous–Jurassic sedimentary sequence of the Tuli Basin in South Africa [35,36]. The succession of formations from oldest to youngest is the Tshidzi, Madzaringwe, Mikambeni, Fripp, Solitude, Klopperfontein, Bosbokpoort, and Clarens Formations [37] (Figure1). The Mikambeni Formation consists of the Permian black carbonaceous shale inter- calated with coal seams and alternating sandstone and siltstone [31]. The thickness of the Mikambeni Formation ranges from 60 to 100 m, corresponding to the proximal and distal points. The variation in shale thickness is interpreted to be caused by basin tecton- ics and differential subsidence trends as transporting river flowed from the northwest to deposit more sediments towards the southeast direction of the basin [34]. The coal seam associated with the Tuli Basin is dominated by collotellinite, suggesting organic matter input from cellulose and woody tissues of the higher terrestrial plant. Based on lithofacies description, the shale color and content suggest a reducing condition associated with oxygen deficiency causing decay of fauna and flora or plant organisms. Given the overall sedimentary sequence, the deposition represents a fluvial-to-aeolian milieu. This deposition reflects different paleo-climatic overprints of different ages spanning from the Permian to the Jurassic Period [38]. Besides the lignin, the cellulose and tannins of vascular plants dicroidium are partly responsible for the main coal seam associated with the carbonaceous shale of the Mikambeni Formation [31,39]. In contrast to lithofacies of Mkambeni, the Tshidzi Formation shows non-sorted to poorly sorted argillaceous or sandy Minerals 2021, 11, 651 3 of 17

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sedimentssuggests a with glacial particles or fluvioglacial size up to 2 environment m in diameter. resulting This argillaceous from a low diamictite energy suggests level of amudflow glacial or to fluvioglacial deposit well‐ environmentsorted sediments. resulting There from is a aprogressive low energy change level of from mudflow reducing to depositor anoxic well-sorted to the oxidizing sediments. environment There is a as progressive shale formations change frombecome reducing younger. or anoxic The Triassic to the oxidizingblack shale environment at the lower as unit shale of formations Solitude Formation become younger. has a dark The grey Triassic shale black and shale grey at shale the lowertowards unit overlying of Solitude Bosbokpoort Formation and has Clarens a dark grey Formations shale and [38]. grey This shale color towards variation overlying reflects Bosbokpoorta progressive and fall Clarens in water Formations level where [38]. This sediments color variation are deposited reflects aon progressive floodplains fall inof watermeandering level where rivers sediments under dry are depositedand oxidizing on floodplains conditions. of meanderingThe preponderance rivers under of dryred andcalcareous oxidizing concretions conditions. of The overlying preponderance the Bosbokpoort of red calcareous further concretions support of overlyingan oxidizing the Bosbokpoortenvironment furthertowards support the upper an oxidizing Tshipise Basin. environment towards the upper Tshipise Basin.

FigureFigure 1.1. Map and sedimentary sequencesequence ofof thethe TuliTuli BackbulgeBackbulge Basin. Basin.

2. Materials and Methods Mineralogical identification identification of of 16 16 core core samples samples from from the the borehole borehole that that penetrated penetrated the thecarbonaceous carbonaceous Mikambeni Mikambeni shale shale Formations Formations at different at different depths depths was was determined determined using using X‐ X-rayray diffraction diffraction (XRD) (XRD) at at Council Council for for Scientific Scientific and and Industrial Research (CSIR)(CSIR) PretoriaPretoria (Figure(Figure2 2).). Based onon thethe lithologicallithological facies,facies, 88 representativerepresentative shaleshale samplessamples correspondingcorresponding toto thethe formationsformations were selectedselected andand pulverizedpulverized inin anan agateagate mortar.mortar. TheThe clayclay fractionsfractions werewere dispersed in 0.70.7 mg/mLmg/mL of of distilled water and put in an ultrasonic water bath for 4040 ss toto preventprevent the the flocculation flocculation of of particles particles [40 [40].]. Afterward, Afterward, the the air-dried air‐dried samples samples were were treated treated with ethylenewith ethylene glycolation glycolation to identify to smectiteidentify mineralssmectite andminerals dimethyl and sulphoxide dimethyl tosulphoxide differentiate to kaolinitedifferentiate from kaolinite chlorite [ 41from]. Samples chlorite were [41]. tightly Samples mounted were on tightly oriented mounted sample on holder oriented with verysample little holder pressure with using very little black pressure loading using preparation black loading technique preparation using PANalytical technique X’Pert using Pro-powderPANalytical diffractometerX’Pert Pro‐powder equipped diffractometer with X’Celerator equipped detector with coupled X’Celerator with receiving detector slits,coupled variable with receiving divergence, slits, and variable Fe-filtered divergence, Cu-Kα andradiation Fe‐filtered at the Cu Energy‐Kα radiation Centre at CSIR the Pretoria.Energy Centre While CSIR the receiving Pretoria. slit While was positionedthe receiving at 0.040 slit ◦was, the positioned counting areaat 0.040°, was from the ◦ 2counting to 80 on area a 2 θwasscale from at 1.52 to s 80° [42 on]. Thea 2θ interstratifiedscale at 1.5 s [42]. I/S mineralsThe interstratified were measured I/S minerals on a lesswere than measured 2 µm fraction on a less of air-driedthan 2 μm samples fraction using of air Cu-K‐driedα radiation samples [using43]. Semi-quantitative Cu‐Kα radiation [43]. Semi‐quantitative mineral measurements were obtained using single line fitting of TOPAS software while the detection limits remained 1%.

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mineral measurements were obtained using single line ﬁtting of TOPAS software while the Minerals 2021, 11, x FOR PEER REVIEW detection limits remained 1%. 4 of 16

FigureFigure 2. Stratigraphic 2. Stratigraphic column column of the studied of the boreholestudied showingborehole lithologic showing description lithologic and description carbonaceous and shale samplingcarbonaceous depth. shale sampling depth.

The functional group information was provided by the Fourier Transform Infrared The functional(FTIR) group Alpha Brukerinformation spectrophotometer was provided at the Universityby the Fourier of Venda, Transform Limpopo. PulverizedInfrared (FTIR) Alpha Brukersamples spectrophotometer were placed in the measurement at the University position of of the Venda, spectrometer Limpopo. and scanned Pulverized between samples were aplaced minimum in andthe maximummeasurement wavelength position range of of 500the andspectrometer 4000 cm−1, respectively. and scanned The between a minimumabsorbance and spectrum maximum depicts wavelength the crystalline range phases of 500 which and reflect 4000 their cm functional−1, respectively. group. A Zeiss EVO MA15 scanning electron microscope (SEM) equipped with a tungsten The absorbance spectrum depicts the crystalline phases which reflect their functional filament and a Bruker energy-dispersive X-ray (EDX) spectrometer were used for the mor- group. phological analysis. The system was operated under a high system vacuum, approximately A Zeiss EVO7.03 MA15 e to 007 scanning mbar. The electron electron beam microscope was generated (SEM) with equipped an accelerating with voltage a tungsten of 20 kV filament and aand Bruker a probe energy current‐dispersive of approximately X‐ray 2nA. (EDX) The sample spectrometer was sprinkled were onto used a carbon for tapethe morphological substrateanalysis. and The carbon-coated system priorwas tooperated being loaded under into thea high SEM. Asystem secondary vacuum, electron detector was used to produce images at 300×, 600×, and 900× magnification. Some of approximately these7.03 e particles to 007 arembar. out The of focus, electron owing beam to the was three-dimensional generated with depth an loss accelerating of informa- voltage of 20 kV and a probe current of approximately 2nA. The sample was sprinkled onto a carbon tape substrate and carbon‐coated prior to being loaded into the SEM. A secondary electron detector was used to produce images at 300×, 600×, and 900× magnification. Some of these particles are out of focus, owing to the three‐dimensional depth loss of information; focusing one part results in the other being out of focus on some of these images, particularly at high magnifications.

3. Results The mineralogical identification of the carbonaceous shale samples obtained from different depths of two boreholes analyzed using X‐ray diffraction (XRD) values and patterns is presented in Table 1 and Figure 3a,b. The results show the presence of clay minerals composed of montmorillonite, mixed illite/smectite (I/S), illite, chlorite, and non‐ clay minerals such as dolomite, albite, microcline, pyrite, and quartz. The average quartz

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content was 29.42%, ranging from 25.10% to 35.60%. However, quartz with higher values was found at a depth of 470 m. The relatively high quartz content may be attributed to the Minerals 2021, 11, 651 preserved detrital silica input from associated siltstone facies, since it has high resistance5 of 17 to mechanical alteration, although diagenetic quartz can precipitate from the dissolution of feldspar [38,44].

Table 1. Mineraltion; focusing composition one of part the carbonaceous results in the shale other samples being from out different of focus depths. on some of these images, particularly at high magniﬁcations. Mineral Composition (%) Sample ID Formation Depth (m) 3. Results Qtz Micr Alb Chl Ill I/S Mont Dol Cal Pyr SBH1 The mineralogical370 25.95 identiﬁcation 13.05 8.40 of the2.15 carbonaceous 15.20 8.25 shale21.35 samples ‐ obtained5.30 ‐ from SBH2 different depths380 of two25.10 boreholes 12.85 7.25 analyzed 2.70 using16.80 X-ray 9.80 diffraction 21.90 ‐ (XRD)4.40 values ‐ and SBH3 patterns is390 presented 29.55 in Table 8.801 and 6.05 Figure 3.453a,b. 14.85 The results9.70 show20.50 ‐ the presence6.45 of1.50 clay SBH4 minerals composed410 of25.75 montmorillonite, 10.45 4.90 mixed3.55 illite/smectite15.90 9.05 (I/S),18.05 illite, ‐ chlorite,8.80 and3.02 non- Mikambeni SBH5 clay minerals430 such as25.60 dolomite, 9.15 albite, 5.05 microcline, 2.05 18.50 pyrite, 10.40 and 18.25 quartz. 10.35 The ‐ average1.20 quartz SBH6 content was440 29.42%, ranging33.02 9.50 from 25.10%4.45 3.73 to 35.60%. 19.26 However,11.98 9.85 quartz 7.30 with ‐ higher1.00 values SBH7 was found450 at a depth34.80 of 470 m.8.80 The 3.05 relatively 3.15 high19.70 quartz 12.20 content 7.80 may 11.05 be attributed ‐ ‐ to the SBH8 preserved470 detrital silica35.60 input 9.75 from ‐ associated4.05 siltstone20.50 facies,13.20 since5.40 it has10.65 high ‐ resistance1.50 to Note: Qtz‐Quartz, Micr‐Microcline,mechanical Alb‐ alteration,Albite, Chl‐Chlorite, although Ill diagenetic‐Illite, I/S‐Mixed quartz Iliite/Smectite, can precipitate Mont from‐ Montmorillonite, the dissolution of Dol‐Dolomite, Calcite‐Cal, Pyrfeldspar‐ Pyrite. [38 ,44].

Figure 3. Cont.

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FigureFigure 3. X 3.‐rayX-ray diffractogram diffractogram patterns patterns of of the the studied studied carbonaceous shale shale from from depth depth (a) 370(a) 370 m to m 410 to m410 (b m) 430 (b) m 430 to 470m to m 470 m (note:(note: ch ch-chlorite,‐chlorite, Q Q—Quartz,‐Quartz, M M—Microcline,‐Microcline, Al Al—Albite,‐Albite, I‐ I—Illite,Illite, Mt Mt—Montmorillinite,‐Montmorillinite, I/S—mixed I/S—mixed layer layer Illite Illite-Smectite,‐Smectite, C‐ C—Calcite, D—Dolomite, P—Pyrite). Calcite, D‐Dolomite, P‐Pyrite).

Table 1. MineralIn composition contrast to of the the quartz carbonaceous content, shale the samples average from amount different of microcline depths. and albite was 10.17% and 5.45%. However, there is no albite mineral present at a depth of 470 m. Feldspars are susceptible to dissolution Mineralreaction Composition as burial depth (%) increases, as the albite Sample ID Formation Depth (m) minerals progressivelyQtz Micrreduce Albuntil the Chl 470 m Ill [45,46]. I/S As burial Mont depth Dol increases, Cal Pyrthe SBH1 montmorillonite370 25.95 content 13.05 progressively 8.40 2.15 decreases 15.20 from 8.25 21.35% 21.35 to 5.40%, - while, 5.30 on the - SBH2other 380hand, the 25.10illite and 12.85 mixed 7.25 I/S contents 2.70 increased 16.80 9.80from 15.20% 21.90 to 20.50% - 4.40and 8.25 -to SBH313.20%. 390 This observation 29.55 8.80 is ascribed 6.05 to the 3.45 illitization 14.85 reaction 9.70 at 20.50 burial depth - temperature 6.45 1.50 SBH4 410 25.75 10.45 4.90 3.55 15.90 9.05 18.05 - 8.80 3.02 Mikambeni less than 200 °C in which precursor minerals of K‐feldspar or smectite transform to illite SBH5or mixed 430 Smectite/illite 25.60 9.15(S/I) in 5.05the presence 2.05 of 18.50 sufficient 10.40 K+ [47–49]. 18.25 The 10.35 chlorite - content 1.20 SBH6has an 440 average value 33.02 of 9.503.42% and 4.45 ranges 3.73 from 19.26 2.20% to 11.98 5.65% 9.85 in a dispersed 7.30 sequence - 1.00 in SBH7 450 34.80 8.80 3.05 3.15 19.70 12.20 7.80 11.05 - - SBH8all samples. 470 The 35.60 presence 9.75 of - chlorite 4.05 mineral 20.50 13.20suggests 5.40 a by 10.65‐product - of 1.50the montmorillonite‐illitization‐chloritization transformation. This transformation process Note: Qtz—Quartz, Micr—Microcline, Alb—Albite, Chl—Chlorite, Ill—Illite, I/S—Mixed Iliite/Smectite, Mont—Montmorillonite, Dol—Dolomite, Calcite—Cal, Pyr—Pyrite.occurs in a closed system having a low ratio of fluid to shale rock [50]. The distribution of dolomite showed a progressive increment in concentration from 5.30 to 11.05 with burial depth.In Since contrast the toorganic the quartz‐rich shale content, has the a low average fluid amount‐to‐rock ofratio, microcline the idea and of dolomite albite was 2+ 10.17%replacing and calcite 5.45%. with However, the saturated there fluid is noof Mg albitemay mineral not be present feasible. at The a depth explanation of 470 is m. theFeldspars precipitation are susceptible of primary to dissolutiondolomite and reaction stepwise as burial recrystallization depth increases, due to as bacterial the albite mediationminerals progressively [51]. It is worth reduce noting until that a the high 470 fluid–rock m [45,46 ratio]. As is burialnecessary depth for a increases, steady and the 2+ saturatedmontmorillonite supply content of Mg progressively for dolomitization decreases fromreplacement 21.35% toof 5.40%, calcite, while, which on thefavors other permeablehand, the illite sandstone and mixed over I/S impermeable contents increased buried from shales. 15.20% High to 20.50% burial and temperature 8.25 to 13.20%. is insufficientThis observation to destroy is ascribed the evidence to the of illitization pyrite grain reaction history at or burial origin. depth Hence, temperature its presence less suggestedthan 200 ◦ detritalC in which grain precursor devoid of minerals oxidizing of setting K-feldspar but associated or smectite with transform anoxic, aridity, to illite or or fluvial settings [52,53].

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mixed Smectite/illite (S/I) in the presence of sufficient K+ [47–49]. The chlorite content has an average value of 3.42% and ranges from 2.20% to 5.65% in a dispersed sequence in all samples. The presence of chlorite mineral suggests a by-product of the montmorillonite- illitization-chloritization transformation. This transformation process occurs in a closed system having a low ratio of fluid to shale rock [50]. The distribution of dolomite showed a progressive increment in concentration from 5.30 to 11.05 with burial depth. Since the organic-rich shale has a low fluid-to-rock ratio, the idea of dolomite replacing calcite with the saturated fluid of Mg2+ may not be feasible. The explanation is the precipitation of primary dolomite and stepwise recrystallization due to bacterial mediation [51]. It is worth noting that a high fluid–rock ratio is necessary for a steady and saturated supply of Mg2+ for dolomitization replacement of calcite, which favors permeable sandstone over impermeable buried shales. High burial temperature is insufficient to destroy the evidence of pyrite grain history or origin. Hence, its presence suggested detrital grain devoid of oxidizing setting but associated with anoxic, aridity, or fluvial settings [52,53]. The Fourier Transform Infrared (FTIR) spectra of the studied carbonaceous shale depict different absorbance bands of organic and mineral content at the various diagnostic wavelength of the infrared spectrum (Figure4). Each absorbance band indicates the functional group representing the whole molecular structure of a material [30]. Most of the studied samples exhibit a strong characteristic absorbance peak around 650–900 cm−1, corresponding to the aromatic phenolic group, C=C-OH. However, the peak reduces as temperature increases with depth due to bond deformation [54]. The aromatic C=C absorption group suggests a wavelength band that is typical of terrigenous plants that have lignin-derivative materials [55]. The peak stretching from around 1000 cm−1 to 1220 cm−1 indicates the C-O stretching and OH deformation of the carboxylic, COOH groups, suggesting decarboxylation of organic matter [56]. The deformation of the carboxylic group releases the −1 CO2, reflecting a characteristic strong absorption around 2000–2300 cm [30]. However, the aliphatic hydrocarbon is considered to contain more carboxylic- and phenolic-OH functional groups with a micelle-like structure that has a relative macromolecular weight ranging from 3500 to 100,000 Da compared with aromatic hydrocarbon [57]. In aromatic hydrocarbon, the voids among the carbon chain serve to act as trapping and binding sites for organic lipids and inorganic materials such as hydrous oxides and clay minerals [57]. −1 The hydrocarbon gas, CH4, shows infrared absorbance peaks between 2850 and 3000 cm due to aliphatic C-H stretching of methyl and methylene vibration [54,58]. The low absorption peak around 3500 cm−1 corresponds to water desorption wavelength [59]. The spectra showed inconspicuous peaks of the carboxylic group at greater burial depths around 450 m, suggesting over-maturation of organic matter beyond the methanogenesis window. Representative SEM images of the studied carbonaceous shales are presented in Figure5a–d. The image depicts a mixture of pore structures, organic matter, and mineral contents. The image (Figure5a) revealed conspicuous intragranular pores among grains of quartz, feldspars, chlorite, illite, carbonate, and pyrite minerals as shown by the XRD, forming an interconnected pore. The interconnected pores provide migration pathways for gaseous hydrocarbon during organic matter (OM) maturation [60]. The carbonate compound of calcite and dolomite was found to dominate the shale, with carbon elemental content ranging from 65% to 73% (Figure6c). Furthermore, the organic matters were also hosted in the intragranular pores of mineral grain, which suggests dissolution cavity of carbonate minerals since intrapore of clay minerals such as feldspar is difficult to observe [61]. Non-spherical, closely packed polyframboidal pyrite was observed, which is affirmed by the multiple occurrences of Fe-elemental contents on the EDX result. The presence of the polyframboidal pyrites suggests an anaerobic condition that favors organic matter degradation and thermal maturation as burial depth increases [62]. The thermal maturity of the organic matter is further supported by the presence of fibrous chlorite and illite minerals (Figure6d), which are index minerals for high-diagenetic temperature zone and quality hydrocarbon reservoirs [63]. Minerals 2021, 11, x FOR PEER REVIEW 7 of 16

The Fourier Transform Infrared (FTIR) spectra of the studied carbonaceous shale depict different absorbance bands of organic and mineral content at the various diagnostic wavelength of the infrared spectrum (Figure 4). Each absorbance band indicates the functional group representing the whole molecular structure of a material [30]. Most of the studied samples exhibit a strong characteristic absorbance peak around 650–900 cm−1, corresponding to the aromatic phenolic group, C=C‐OH. However, the peak reduces as temperature increases with depth due to bond deformation [54]. The aromatic C=C absorption group suggests a wavelength band that is typical of terrigenous plants that have lignin‐derivative materials [55]. The peak stretching from around 1000 cm−1 to 1220 cm−1 indicates the C‐O stretching and OH deformation of the carboxylic, COOH groups, suggesting decarboxylation of organic matter [56]. The deformation of the carboxylic group releases the CO2, reflecting a characteristic strong absorption around 2000–2300 cm−1 [30]. However, the aliphatic hydrocarbon is considered to contain more carboxylic‐ and phenolic‐OH functional groups with a micelle‐like structure that has a relative macromolecular weight ranging from 3500 to 100,000 Da compared with aromatic hydrocarbon [57]. In aromatic hydrocarbon, the voids among the carbon chain serve to act as trapping and binding sites for organic lipids and inorganic materials such as hydrous oxides and clay minerals [57]. The hydrocarbon gas, CH4, shows infrared absorbance peaks between 2850 and 3000 cm−1 due to aliphatic C‐H stretching of methyl and methylene vibration [54,58]. The low absorption peak around 3500 cm−1 corresponds to water desorption wavelength [59]. The spectra showed inconspicuous peaks of the Minerals 2021, 11, 651 8 of 17 carboxylic group at greater burial depths around 450 m, suggesting over‐maturation of organic matter beyond the methanogenesis window.

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thermal maturity of the organic matter is further supported by the presence of fibrous Figure 4. FTIR spectra of the studied carbonaceous shale showing functional groups representing molecules (R-OH-phenolic, Figure 4. FTIR spectra of thechlorite studied and carbonaceous illite minerals shale (Figure showing 6d), functional which are groups index representing minerals for molecules high‐diagenetic (R‐OH‐ C-C-OH-acetic, carboxylic, carbon (IV), COOH-carboxylic, CO2-carbon (IV) oxide, CH4-methane, H2O-water). phenolic, C‐C‐OH‐acetic, carboxylic,temperature carbon zone (IV), and COOH quality‐carboxylic, hydrocarbon CO2‐carbon reservoirs (IV) [63].oxide, CH4‐methane, H2O‐water).

Representative SEM images of the studied carbonaceous shales are presented in Figure 5a–d. The image depicts a mixture of pore structures, organic matter, and mineral contents. The image (Figure 5a) revealed conspicuous intragranular pores among grains of quartz, feldspars, chlorite, illite, carbonate, and pyrite minerals as shown by the XRD, forming an interconnected pore. The interconnected pores provide migration pathways for gaseous hydrocarbon during organic matter (OM) maturation [60]. The carbonate compound of calcite and dolomite was found to dominate the shale, with carbon elemental content ranging from 65% to 73% (Figure 6c). Furthermore, the organic matters were also hosted in the intragranular pores of mineral grain, which suggests dissolution cavity of carbonate minerals since intrapore of clay minerals such as feldspar is difficult to observe [61]. Non‐spherical, closely packed polyframboidal pyrite was observed, which is affirmed by the multiple occurrences of Fe‐elemental contents on the EDX result. The presence of the polyframboidal pyrites suggests an anaerobic condition that favors organic matter degradation and thermal maturation as burial depth increases [62]. The

Figure 5. SEM images of the studied carbonaceous shale showing (a) intergranular pores hosting OM, (b) intragranular Figure 5. SEM images of the studied carbonaceous shale showing (a) intergranular pores hosting OM, (b) intragranular pores hosting OM, (c) SEM images of Chlorite‐chl, Quartz‐Q, Illite‐I minerals, and (d) veinlet of Illite minerals. pores hosting OM, (c) SEM images of Chlorite-chl, Quartz-Q, Illite-I minerals, and (d) veinlet of Illite minerals.

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FigureFigure 6. (a) 6. vertical,(a) vertical, cylindrical cylindrical pipes pipes with with open apices,apices, (b ()b simple,) simple, mostly mostly vertical vertical shaft-like shaft trace‐like fossils, trace (fossils,c) close ( upc) ofclose the up of the wallwall of of the the digit digit-like‐like structure structure showing showing the the extensively extensively branching branching burrow burrow system system with random with random orientation( orientation(d) Large-scaled) Large‐ scale tracetrace fossils fossils showing showing lateral lateral bifurcations bifurcations on a on sub-horizontal a sub‐horizontal surface surface (modiﬁed (modified from [37 ]).from [37]).

4. Discussion4. Discussion 4.1.4.1. Diagenetic Diagenetic Alteration Alteration Pathways Pathways TheThe mechanical mechanical compactioncompaction of detritalof detrital sediments sediments and terrestrial and terrestrial plant materials plant follow- materials ing sedimentation of the 40 m thick Fripp Formation over Mikambeni Formation initiate following sedimentation of the 40 m thick Fripp Formation over Mikambeni Formation their diagenetic changes. At this initial stage, the brackish interstitial fluid or pore water initiateand bacterial their diagenetic activities are changes. pronounced At this due initial to the stage, degradation the brackish of plant interstitial material to producefluid or pore waterhumic and material. bacterial Humic activities substances are pronounced are composed due of weak to the acidic degradation electrolytes of with plant aliphatic material to produceand aromatic humic hydrocarbon,material. Humic which substances may incorporate are composed atomic radicals of weak N, acidic O, or electrolytes S [57]. The with aliphatichumic acidand gainsaromatic significance hydrocarbon, at a wavenumber which may absorption incorporate peak atomic around radicals 650–900 cmN,− O,1, or S [57].corresponding The humic acid to the gains acetic significance and phenolic at a group. wavenumber The compaction absorption process peak leads around to de-650–900 cmhydroxylation−1, corresponding in which to the the acetic pore fluid and isphenolic released, group. as indicated The compaction by the water process absorbance leads to −1 dehydroxylationband around 1300–1900 in which cm the .pore More fluid evidence is released, of the early-stage as indicated organic by the degradation water absorbance in the Tuli Basin was marked the by bioturbation of burrowing organisms (Figure6). In the band around 1300–1900 cm−1. More evidence of the early‐stage organic degradation in the studied basin, soft sediment burrowing organisms such as beetles and ants have produced Tuliun-bifurcated Basin was ichnofossilsmarked the which by bioturbation are tentatively of recognizedburrowing as organismsSkolithosi sp. (Figure and other 6). In the studiedbifurcated basin, trace soft fossils sediment [36]. burrowing organisms such as beetles and ants have produced un‐bifurcatedWith an ichnofossils increase in burial which pressure are tentatively and depth ofrecognized about 360 as m thick,Skolithosi which sp results and other bifurcatedfrom successive trace fossils overlying [36]. sediments of the Solitude, Klopperfontein, Bosbokpoort, and ClarensWith formations, an increase the in elevated burial temperaturepressure and causes depth further of about geochemical 360 m and thick, mineralogical which results fromchanges. successive The gradual overlying decrease sediments in montmorillonite of the Solitude, and a Klopperfontein, parallel progressive Bosbokpoort, increase of and Clarensillite minerals formations, were observed, the elevated while mixed-layered temperature montmorillonite-illite causes further (M-I)geochemical mark the and extent of progress along with series of reactions between burial depths of about 370 m mineralogical changes. The gradual decrease in montmorillonite and a parallel to 470 m. In Mikambeni shale, the first series of the illitization reaction progress is made progressivepossible due increase to the presence of ofillite microcline minerals and montmorillonitewere observed, minerals while as expressed mixed‐ inlayered montmorilloniteEquation (1) [64‐].illite Alternatively, (M‐I) mark diagenetic the extent illite of may progress have crystallized along with from series geochemical of reactions betweeninteraction burial between depths kaolinite of about and 370 microcline m to 470 orm. potassiumIn Mikambeni ion (K shale,+), but the the first absence series of of the illitization reaction progress is made possible due to the presence of microcline and montmorillonite minerals as expressed in Equation (1) [64]. Alternatively, diagenetic illite may have crystallized from geochemical interaction between kaolinite and microcline or potassium ion (K+), but the absence of kaolinite inhibits that reaction’s progress pathway. Retrospective studies [44,65] have reported the kaolinite illitization via reactions with k‐ feldspar, K+, or H+ as burial depth increases; however, this reaction mechanism is hindered due to the absence of kaolinite minerals in Mikambeni shale. Kaolinites may have precipitated due to increasing quartz concentrations, but it is likely to be consumed

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immediately after crystallization as expressed in Equation (2) due to high temperature. Minerals 2021, 11, 651 Studies [66–68] have unequivocally demonstrated that the kaolinite dissolution in shale10 of 17 rock can take place at a lower temperature than 60 °C. AlSiO[OH].nHO+KAlSiO ⇾ KAlSi[OH] +SiO +nHO (1) ( ) ( ) kaoliniteAl inhibits+SiO +2.5H that reaction’sO⇾0.5Al progressSiO OH pathway. kaolinite Retrospective+3H studies [44(2),65 ] have Furthermore,reported the kaolinitethe organic illitization and inorganic via reactions interaction with k-feldspar, promotes Kthe+, or illitization H+ as burial by depth + initiatingincreases; the release however, of the this H ion reaction from mechanismthe carboxylic is hinderedacid functional due to group the absence as expressed of kaolinite in Equationminerals (3). inThe Mikambeni carboxylic shale. C=O band Kaolinites can remain may have approximately precipitated at due a wavenumber to increasing of quartz 1000 toconcentrations, 1225 cm−1 stretching but it is likely regardless to be consumed of the source immediately material. after The crystallization CO2 produced as expressed by decarboxylationin Equation of (2) organic due to highmatter temperature. is commonly Studies suggested [66–68 ]as have a source unequivocally of the acid demonstrated that dissolvesthat the the microcline kaolinite dissolution feldspar [69]. in shale This rock carbon can takedioxide, place CO at a2, lower is recognized temperature fromthan its 60 ◦C. characteristic strong absorptions around 2000 and 2300 cm−1. AlCH2SiO4O (10carboxylic[OH]2·nH 2groupO + KAlSi) +H3OO⇾CO8 KAl3+4HSi3[OH ]2 + SiO2 + nH2O(3) (1) The presence of a carboxyl group increases solubility properties. As such, the labile 3+ + microcline mineralAl interacts+ SiO 2with+ 2.5H the2 Opore0.5Al water2Si 2concentratedO5(OH)4(kaolinite with )carboxylic+ 3H and (2) phenolic acidsFurthermore, to produce the silica organic and and potass inorganicium cation, interaction which promotes enhances the illitization illitization of by ini- montmorillonitetiating the releasemineral ofas the represented H+ ion from in Equation the carboxylic (4). This acid resulting functional authigenic group as silica expressed likely incontributes Equation to (3). the The increasing carboxylic quartz C=O co bandntent can with remain burial approximately diagenesis, although at a wavenumber the presence of preserved detrital−1 quartz inputs cannot be discounted. With the siltstone of 1000 to 1225 cm stretching regardless of the source material. The CO2 produced by facies interbeddeddecarboxylation with ofthe organic carbonaceous matter shale, is commonly the input suggested of detritalas silica a source is possible of the since acid that quartz is largely stable at high temperatures. Nonetheless, the increasing quartz contents dissolves the microcline feldspar [69]. This carbon dioxide, CO2, is recognized from its tend tocharacteristic significantly strong improve absorptions the shale around reservoir 2000 quality and 2300 because cm− 1it. imparts a brittleness property and enhances the fracability of shale [70]. CH O (carboxylic group) + H O CO + 4H+ (3) 2 1 2 2 KAlSiO (microcline) +H ⇾ 2 SiO + K (4) The presence of a carboxyl group increases solubility properties. As such, the labile As the reaction continues, more K+ ions are concentrated via replacement K-feldspar microcline mineral interacts with the pore water concentrated with carboxylic and phenolic (microcline) by the albite at a higher temperature between 120 °C and 180 °C as acids to produce silica and potassium cation, which enhances illitization of montmorillonite represented in Equation (5) [66,71]. The absence of kaolinite minerals with a parallel mineral as represented in Equation (4). This resulting authigenic silica likely contributes to increase in chlorite suggests complete dissolution of kaolinite at such a high temperature. the increasing quartz content with burial diagenesis, although the presence of preserved detrital quartzKAlSi inputsO (microcline cannot be) discounted.+ Na ⇾NaAlSi With theO siltstone(Albite) facies+ K interbedded(5) with the carbonaceous shale, the input of detrital silica is possible since quartz is largely stable + Withat high further temperatures. burial diagenes Nonetheless,is, the presence the increasing of a high quartz concentration contents of tend potassium to significantly K fluid promotesimprove the the shale illitization reservoir processes quality becauseof montmorillonite it imparts a brittleness minerals. propertyHowever, and other enhances factorsthe such fracability as time, offluid/rock shale [70 ].ratio, nature of starting material, and kinetic mechanism have been considered as important for illitization. It is worth noting that the direct conversion of smectite to illite as expressed in Equation (6) [72]1 does not suggest a solid- KAlSi O (microcline) + H+ SiO + K+ (4) state reaction but rather shows 3the8 quantitative and compositional2 2 changes in shale mineralogy that takes place during burial diagenesis. Importantly, this conversion of As the reaction continues, more K+ ions are concentrated via replacement K-feldspar smectite to illite reaction has been indicated to take place at similar temperature intervals (microcline) by the albite at a higher temperature between 120 ◦C and 180 ◦C as represented as the maturation index for organic matter and the release of interstitial water during I-M in Equation (5) [66,71]. The absence of kaolinite minerals with a parallel increase in chlorite diagenesis to enhance hydrocarbon migration [69]. By implication, the range for the suggests complete dissolution of kaolinite at such a high temperature. change in I/S ordering from random to regular during smectite illitization in shales coincides with the temperature range of organic+ matter maturity and the onset+ of oil KAlSi3O8 (microcline) + Na NaAlSi3O8 (Albite) + K (5) generation in young sedimentary basins. 2NaWith( furtherAl Mg burialFe diagenesis,)Si O the(OH presence) (Smectite of a) high+0.85 concentrationK + 1.07H of potassium K+ fluid. promotes. the. illitization. processes of montmorillonite minerals. However, other ⇾ 1.065K (Al Mg )(Si Al )O (OH) (illite) +4.6SiO (6) factors such as. time,. fluid/rock. ratio,. nature. of starting material, and kinetic mechanism +0.36Fe(OH) +0.56Mg +0.8Na +0.9H O have been considered as important for illitization. It is worth noting that the direct con- Althoughversion of present smectite in to illitelow asquantities expressed (Table in Equation 1), chlorite (6) [72 ]minera does notl is suggest increasingly a solid-state crystallizedreaction as buta discrete rather showsphase therather quantitative than evolutionary and compositional trend phases changes of inkaolinite shale mineralogy and carbonate.that takesThe evolutionary place during burialphase diagenesis.involves the Importantly, chloritization this phase conversion of kaolinite of smectite in the to illite presencereaction of iron- has and been magnesium-supplied indicated to take place smecti atte similar illitization temperature processes intervals at a temperature as the matura- betweention 165 index and for 200 organic °C [73], matter but reaction and the releaseprogress of is interstitial inhibited waterdue to during the absence I-M diagenesis of kaolinite.to enhance At a lower hydrocarbon temperature migration of about [69 ].120 By °C implication, and in the the presence range for of the carbonate change in I/S minerals,ordering another from chloritization random to regularreaction during via kaolinite smectite and illitization iron oxide in could shales occur coincides [12,74]. with the

Minerals 2021, 11, x FOR PEER REVIEW 10 of 16 immediately after crystallization as expressed in Equation (2) due to high temperature. Studies [66–68] have unequivocally demonstrated that the kaolinite dissolution in shale rock can take place at a lower temperature than 60 °C. AlSiO[OH].nHO+KAlSiO ⇾ KAlSi[OH] +SiO +nHO (1) Al +SiO +2.5HO⇾0.5AlSiO(OH)(kaolinite) +3H (2) Furthermore,Minerals 2021the , organic11, 651 and inorganic interaction promotes the illitization by 11 of 17 initiating the release of the H+ ion from the carboxylic acid functional group as expressed in Equation (3). The carboxylic C=O band can remain approximately at a wavenumber of 1000 to 1225 cm−1 stretching regardless oftemperature the source range material. of organic The CO matter2 produced maturity by and the onset of oil generation in young decarboxylation of organic matter is commonlysedimentary suggested basins. as a source of the acid that dissolves the microcline feldspar [69]. This carbon dioxide, CO2, is recognized from its −1 + + characteristic strong absorptions around 2000 and 23002Na 0.4cmAl. 1.47 Mg0.29Fe0.18 Si4O10(OH)2(Smectite) + 0.85K + 1.07H CHO (carboxylic group) +HO⇾CO1.065K +4H0.80 Al 1.98Mg0.02 (Si3.22(3)Al 0.78)O10(OH)2(illite) + 4.6SiO2 (6) 2+ + The presence of a carboxyl group increases solubility+0.36Fe properties.(OH)3 + 0.56Mg As such,+ the0.8Na labile + 0.9H2O microcline mineral interacts with the pore water concentrated with carboxylic and phenolic acids to produce silica and potassiumAlthough cation, present which inenhanc low quantitieses illitization (Table of1 ), chlorite mineral is increasingly crystal- montmorillonite mineral as represented inlized Equation as a discrete (4). This phase resulting rather authigenic than evolutionary silica trend phases of kaolinite and carbonate. likely contributes to the increasing quartzThe content evolutionary with burial phase diagenesis, involves thealthough chloritization the phase of kaolinite in the presence of presence of preserved detrital quartz inpuiron-ts cannot and magnesium-supplied be discounted. With smectite the siltstone illitization processes at a temperature between 165 and 200 ◦C[73], but reaction progress is inhibited due to the absence of kaolinite. At a facies interbedded with the carbonaceous shale, the input of detrital silica is◦ possible since quartz is largely stable at high temperatureslower. Nonetheless, temperature the of increasing about 120 quartzC and contents in the presence of carbonate minerals, another chlo- tend to significantly improve the shale reservoirritization quality reaction because via kaolinite it imparts and irona brittleness oxide could occur [12,74]. The possible explanation for hydrothermal chloritization cannot be discounted in the Mikambeni carbonaceous property and enhances the fracability of shale [70]. shale owing to the presence of Sagole thermal spring via the Tshipise fault [75,76]. This 1 KAlSiO (microclineinterpretation) +H ⇾ is2 consistentSiO + K with the chloritization(4) processes reported at the geothermal area of Iceland in which iron-rich smectite (saponite) is transformed into mixed-layer smectite- As the reaction continues, more K+ ionschlorite are concentrated (S-C) at about via 200replacement to 230 ◦C[ K-feldspar50]. In support of the S-C mixed layer, corrensite is (microcline) by the albite at a higher temperaturea resulting mineral between composed 120 °C ofand 50% 180 of °C each as chlorite and smectite mineral [77]. With a represented in Equation (5) [66,71]. The furtherabsence increase of kaolinite in temperature minerals with due toa burialparallel depth, chlorite crystallizes at temperatures increase in chlorite suggests complete dissolutiongreater thanof kaolinite 240 ◦C dueat such to a a gradual high temperature. replacement of iron-rich smectite with daughter chlorite mineral in close zonation contact [78]. This reaction mechanism suggests a solid-state KAlSiO (microcline) + Na ⇾NaAlSiO (Albite) + K (5) gradual replacement; however, the reaction pathway may be a continuous series transition With further burial diagenesis, the presenceinstead of of a a high stepwise concentration progression of [potassium79] since shale K+ has a low pore fluid to rock ratio due to fluid promotes the illitization processes poorof montmorillonite interconnectivity minerals. of pores. However, Stepwise transitionother is noted to predominate in the system factors such as time, fluid/rock ratio, naturewith of highstarting pore-fluid-to-rock material, and kinetic ratio such mechanism as sandstone; hence, chloritization in the studied have been considered as important for shaleillitization. may beIt ais by-productworth noting of smectitethat the illitization. direct Although the rise in temperature of conversion of smectite to illite as expresseddiagenetic in Equation chlorite (6) [72] could does be not promoted suggest bya solid- contact diagenesis associated with the Sagole state reaction but rather shows the quantitativegeothermal and area, compositional the pore fluid changes of Mikambeni in shale shale is unaffected by the thermal spring mineralogy that takes place during burialdue di toagenesis. extremely Importantly, highly impermeable this conversion shale. of Carbonate minerals commonly revert to smectite to illite reaction has been indicatedthe to thermodynamically take place at similar stable temperature mineral intervals as dolomite replaces limestones in the deep-burial as the maturation index for organic matterdiagenetic and the release realm, ofas interstitial represented water in during Equation I-M (7) [79]. Calcite dissolution increases with diagenesis to enhance hydrocarbon migratioburialn dolomitization[69]. By implication, in the presencethe range of for an organic-richthe and interstitial fluid via stepwise change in I/S ordering from random to precipitationregular during of dolomite. smectite illitization in shales coincides with the temperature range of organic matter maturity and the onset of oil 2+ 2+ 2+ generation in young sedimentary basins. CaCO3 + Fe + Mg 2CaMg(CO3)2 + 2Ca (7) 2Na.(Al. Mg.Fe.)SiO(OHThe)( disappearanceSmectite) +0.85 ofK calcite+ 1.07H at relatively greater burial depths suggests a low pH ⇾ 1.065K. (Al.Mg.)(Si.medium,Al.) whileO(OH its) replacement(illite) +4.6SiO by dolomite (6) indicates an alkaline setting corresponding ◦ +0.36Fe(OH) +0.56Mg +0.8Nato oil window+0.9H andO organic matter maturation at a temperate range of 80–120 C[80–82]. Promoted by sulfate reduction of pyrite mineral resulting from microbial activities, an Although present in low quantities (Table 1), chlorite mineral is increasingly increase in alkalinity medium favors precipitation of dolomite in the presence of Ca and Mg crystallized as a discrete phase rather than evolutionary trend phases of kaolinite and as burial depth increases [83]. The reduction process of Fe3+ to Fe2+ in the form of pyrite carbonate. The evolutionary phase involves the chloritization phase of kaolinite in the is evident from the framboidal structure revealed by SEM microscopy, thus suggesting a presence of iron- and magnesium-suppliedreducing smectite orillitization anoxic environment. processes at a Framboidal temperature pyrites having bioclast structures that result between 165 and 200 °C [73], but reactionfrom progress the reduction is inhibited of organic due to matter the absence in an organic-rich of shale. kaolinite. At a lower temperature of about 120 °C and in the presence of carbonate minerals, another chloritization reaction via4.2. kaolinite Methanogenesis and iron Potentials oxide could of the occur Carbonaceous [12,74]. Shale The biogenic methanogenesis from diagenetic carbonaceous shale may be attributed both to microbial degradation of organic matters and their thermal maturation as burial depth −1 increases (Figure7). The carboxyl C=O stretching absorption peak, around 1000–1220 cm , is stronger in spectra. The presence carboxyl group increases solubility properties. The post-depositional activities of microbial degradation on organic matter of shale deposit tend Minerals 2021, 11, 651 12 of 17

to produce biogenic methane, sulﬁde gases, and organic acids ﬂuid capable of dissolving Minerals 2021, 11, x FOR PEER REVIEW some reactive mineral phases. 12 of 16

FigureFigure 7. 7.MethanogenesisMethanogenesis potential potential ofof the the studied studied carbonaceous carbonaceous shale. shale.

AtAmong greater the depth, evidence the oforganic methanogenesis functional processes group arecomprising the imprints mainly of burrowing phenolic and carboxylic,organisms, which which were suggest observed a connection alongside with mineralogical bioturbation processes components capable of illite of expelling and chlorite biogenic gases from carbonaceous matter in shales [84]. The micro-FTIR revealed several was associated with thermal methanogenesis. At depths greater than 2500 m, recent linking bonds such as aromatic C=C stretching and amide group N=H bending in the studiesacetic [87] and propionichave established functional the group, presence thus consistent of diagenetic with the illite organic and maceralschlorite richminerals in to characterizedprotein, carbohydrate, geochemical lipids, zones and lignin in which [85]. Atthe this temperature stage, dewatering is above of pores 180 first°C and occurs the low metamorphicat 10–50 ◦C, zone. followed Although by biogenic the Mikambeni methane from shale residual is shallower, lignin at 50–70the proximity◦C (Figure of7 )Sagole andand Siloam characterized geothermal by carbonate fields may minerals play a and role acetic in the organic elevated group. temperature The water absorption that caused the diageneticspectra stretch and thermal between 3500maturation and 4000 of cm organic−1 wavenumber matter. The band. alteration This observation in I‐M alludesordering to from 13 randomthe carbon to δregularC isotopic during analysis, montmorillonite which reported anillitization aceticlastic and decomposition chloritization of aliphatic in shales coincidesto aromatic with components the temperature with the range generation of organic of early matter methane maturity gas [86]. and the onset of the oil At greater depth, the organic functional group comprising mainly phenolic and and gas window in the Mikambeni shale. Depending on the nature of the organic matter, carboxylic, which were observed alongside mineralogical components of illite and chlorite marinewas associated diatoms and with fora thermal‐minifera methanogenesis. undergo a Atcatagenesis depths greater at the than oil 2500window, m, recent while the terrestrialstudies [87higher] have plant established materials the exceed presence catagenesis of diagenetic to illitemethanogenesis and chlorite mineralsat about to200 °C, as characterizedindicated by geochemicalthe organic carboxylic zones in which group the [87,88]. temperature The methane is above 180is indicated◦C and the by low a strong absorptionmetamorphic band zone. around Although 3015 cm the− Mikambeni1 and a band shale around is shallower, 1305 cm the−1. proximity of Sagole andThe Siloam formation geothermal of solid fields carbon may play components a role in the involves elevated a temperature multi‐stage that process caused of the kerogen degradation,diagenetic and initiated thermal by maturation deposition of organic of organic matter. matters The alteration [89]. Sources in I-M orderingof organic from matter couldrandom be either to regular derived during from montmorillonite the ocean, illitizationconsisting and of chloritizationphytoplanktonic in shales remains, coincides or land, with the temperature range of organic matter maturity and the onset of the oil and gas which consists mainly of vascular plant remains. However, accumulation of both marine window in the Mikambeni shale. Depending on the nature of the organic matter, marine anddiatoms land‐derived and fora-minifera organic matter undergo is common a catagenesis at deltas at the or oil floodplains window, while of meandering the terrestrial rivers [90,91].higher Under plant materials this oxic exceed condition catagenesis in the water to methanogenesis column, the at aerobic about 200 degradation◦C, as indicated of organic matterby the continued organic carboxylic until the group dissolved [87,88]. Theoxygen methane was is less indicated than by 0.2 a strongmL/L absorptionH2O [92]. The deficiencyband around in 3015oxygen cm− 1mayand abe band due around to climatic 1305 cm −overprint,1. sea‐level changes, tectonic activities,The and formation hydrographic of solid carbon factors, components resulting involves in an a insufficient multi-stage process supply of of kerogen oxygen to oxidizedegradation, the organic initiated materials by deposition [93,94]. of organic In mattersaddition, [89 ].the Sources faster of organicrate of matter organic could matter accumulationbe either derived in sediments from the ocean, more consisting than the ofaerobic phytoplanktonic degradation remains, and orbacterial land, which oxidation consists mainly of vascular plant remains. However, accumulation of both marine and land- processes may contribute to the enrichment of organic carbon beyond its decomposition derived organic matter is common at deltas or floodplains of meandering rivers [90,91]. [95].Under Below this 0.2 oxic mL/L condition H2O oxygen in the water concentration, column, the anaerobic aerobic degradation conditions of organicand degradation matter of organic matter begin, giving rise to the solid carbon‐containing components in shale sediments [95]. This anoxic setting is established as all the oxidants in the shale sediments deplete due to further reduction processes caused by increasing burial depth, promoting the activities of sulfide‐reducing bacteria [96]. Studies [97–100] have highlighted minerals and compounds such as pyrite, sphalerite, hydrogen sulphide, and iron sulfide as evidence of the reduction process that ensued from sulfide‐driven bacteria. With further increase in burial depth below the sediment–water interface, the methanogens begin to degrade the organic carbon to generate biogenic methane. This is consistent with the

Minerals 2021, 11, 651 13 of 17

continued until the dissolved oxygen was less than 0.2 mL/L H2O[92]. The deficiency in oxygen may be due to climatic overprint, sea-level changes, tectonic activities, and hydrographic factors, resulting in an insufficient supply of oxygen to oxidize the organic materials [93,94]. In addition, the faster rate of organic matter accumulation in sediments more than the aerobic degradation and bacterial oxidation processes may contribute to the enrichment of organic carbon beyond its decomposition [95]. Below 0.2 mL/L H2O oxygen concentration, anaerobic conditions and degradation of organic matter begin, giving rise to the solid carbon-containing components in shale sediments [95]. This anoxic setting is established as all the oxidants in the shale sediments deplete due to further reduction processes caused by increasing burial depth, promoting the activities of sulfide- reducing bacteria [96]. Studies [97–100] have highlighted minerals and compounds such as pyrite, sphalerite, hydrogen sulphide, and iron sulfide as evidence of the reduction process that ensued from sulfide-driven bacteria. With further increase in burial depth below the sediment–water interface, the methanogens begin to degrade the organic carbon to generate biogenic methane. This is consistent with the previous work of Tourtelot (1979), which argued that methane is unlikely to form unless all sulphates are depleted while vanadium and nickel are concentrated.

5. Conclusions The combination of FTIR, SEM-EDX, and mineralogical analyses demonstrated a promising approach to assess methanogenesis potentials in carbonaceous shale rock. In shale rock that is dominated by terrigenous higher plants, the biogenic methanogenesis is found to correspond to the absorption spectrum stretching from 1650–1220 cm−1 frequen- cies. This spectrum reﬂects the C-O stretching and OH deformation of acetic and phenolic groups in all studied samples. Given the strong absorptions around 2000–2300 cm−1, CO2 is produced by decarboxylation of organic matter. The gas becomes acidiﬁed and dissolves feldspar to release K+ ions, which promoted the illitization of smectite. The SEM microscopy depicted a framboidal structure, which indicated a sulfate reduction of pyrite mineral. The reduction process results from microbial activities in an anoxic milieu and causes an increase in alkalinity medium that favors precipitation of dolomite in the presence of Ca and Mg as burial depth increases. The contact diagenesis from the proximity of Sagole geothermal spring via Tshipise fault is suggested to have enhanced the transformation of smectite to chlorite via a mixed-layer corrensite in a solid-state gradual replacement reaction pathway. The presence of diagenetic chlorite mineral is characteristic of low-grade metamorphism or high diagenetic zone at a temperature around 200–230 ◦C and corresponds to thermal breakdown of kerogen to methane at a a strong absorption band around 2850–3000 cm−1.

Author Contributions: The conceptualization and writing of the original manuscript were con- ducted by G.O.A.; project administration and supervision by F.A.-D. and S.R.; formal analysis and methodology by N.P. and W.M.G.; resources, data curation, and software by S.E.M. and J.N.E. All authors have read and agreed to the published version of the manuscript. Funding: This research received no external funding. Acknowledgments: The authors are grateful for the assistance provided by Ally Mahlaule during the data collections. Conﬂicts of Interest: The authors declare no conﬂict of interest.

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