The source of biodegraded bitumen seeps and tar sands in the Nigerian axis of the Gulf of Guinea province has been a contentious issue for decades. The most prevalent opinion is that the biodegraded bitumen seeps are migration oils that were degraded by bacterial. In the present study, outcrop source rocks (Lower Cretaceous), core samples (Upper Cretaceous) from a shallow well-x, and bitumen seeps and tar sands from the eastern axis of the Dahomey Basin of Nigeria were analyzed. Rock-Eval™ pyrolysis show that the outcrop rocks are classified as having excellent-very good source quality; in contrast, those from well-x are classified as having only poor-fair quality. The cross plot of hydrogen index (HI) against Tmax indicates that samples from the outcrops contain type II/III organic matter, whereas well samples contain type III organic matter and all source rocks are thermally immature, which is supported by vitrinite reflectance (Ro: 0.20–0.48 %), and biomarker maturity parameters (C32 (S/S + R), MPI-I). In the bitumen seeps and tar sands, isoprenoids, n-alkanes, steranes and hopanes have been degraded, and tricyclic and tetracyclic terpanes are still mostly intact. In addition, C30 hopane and homohopanes have been demethylated, and C25 norhopanes are present in abundance, suggesting that the bitumen seeps and tar sands experienced heavy biodegradation in the range of PM-6 or greater. The distribution of 4,9-DMD, 4,8-DMD and 3,4-DMD diamondoids and the δ13C of saturate and aromatic fractions indicate that the bitumen seeps and tar sands were generated from Types II and III source rocks. The ratio of demethylated Ts/Tm indicates that the samples are low maturity and were generated from immature source rocks. Cross plots of tricyclic terpane ratios (C25/C26TT vs C25TT/C24TeT, C23/C21TT vs (C19+20)/C23TT, and C24TeT/C24TeT + C26TT vs (C19+20)/C23TT) also reveal that the biodegraded bitumen seeps and tar sands are closely related to source rocks in outcrop groups 1 and 2. This conclusion is supported by the ternary plots of tricyclic terpanes, 4,9DMD, 4,8DMD and 3,4DMD diamondoids, and the cross plot of EAI against DMDI-1. The occurrence of exsudatinite in the outcrop source rocks in group 1, consistent with early hydrocarbon generation, and the low ratio of demethylated Ts/Tm (<1) in the bitumen samples confirms that the biodegraded bitumen seeps and tar sands in the Nigerian Dahomey Basin were generated by the Lower Cretaceous source rocks in group 1. The study advances on the previous propositions on the source of bitumen seeps and tar sands and contributes our knowledge in the Gulf of Guinea Basin.
{"title":"Geochemical evidences linking the Lower Cretaceous source rocks to the biodegraded bitumen seeps and tar sands in the Gulf of Guinea Basin","authors":"Abdulkareem Toyin , Ningning Zhong , Falilat Omotolani Idris , Olabisi Adekeye , Shengbao Shi","doi":"10.1016/j.orggeochem.2024.104866","DOIUrl":"10.1016/j.orggeochem.2024.104866","url":null,"abstract":"<div><div>The source of biodegraded bitumen seeps and tar sands in the Nigerian axis of the Gulf of Guinea province has been a contentious issue for decades. The most prevalent opinion is that the biodegraded bitumen seeps are migration oils that were degraded by bacterial. In the present study, outcrop source rocks (Lower Cretaceous), core samples (Upper Cretaceous) from a shallow well-x, and bitumen seeps and tar sands from the eastern axis of the Dahomey Basin of Nigeria were analyzed. Rock-Eval™ pyrolysis show that the outcrop rocks are classified as having excellent-very good source quality; in contrast, those from well-x are classified as having only poor-fair quality. The cross plot of hydrogen index (HI) against T<sub>max</sub> indicates that samples from the outcrops contain type II/III organic matter, whereas well samples contain type III organic matter and all source rocks are thermally immature, which is supported by vitrinite reflectance (R<sub>o</sub>: 0.20–0.48 %), and biomarker maturity parameters (C<sub>32</sub> (S/S + R), MPI-I). In the bitumen seeps and tar sands, isoprenoids, <em>n</em>-alkanes, steranes and hopanes have been degraded, and tricyclic and tetracyclic terpanes are still mostly intact. In addition, C<sub>30</sub> hopane and homohopanes have been demethylated, and C<sub>25</sub> norhopanes are present in abundance, suggesting that the bitumen seeps and tar sands experienced heavy biodegradation in the range of PM-6 or greater. The distribution of 4,9-DMD, 4,8-DMD and 3,4-DMD diamondoids and the δ<sup>13</sup>C of saturate and aromatic fractions indicate that the bitumen seeps and tar sands were generated from Types II and III source rocks. The ratio of demethylated Ts/Tm indicates that the samples are low maturity and were generated from immature source rocks. Cross plots of tricyclic terpane ratios (C<sub>25</sub>/C<sub>26</sub>TT vs C<sub>25</sub>TT/C<sub>24</sub>TeT, C<sub>23</sub>/C<sub>21</sub>TT vs (C<sub>19</sub>+<sub>20</sub>)/C<sub>23</sub>TT, and C<sub>24</sub>TeT/C<sub>24</sub>TeT + C<sub>26</sub>TT vs (C<sub>19</sub>+<sub>20</sub>)/C<sub>23</sub>TT) also reveal that the biodegraded bitumen seeps and tar sands are closely related to source rocks in outcrop groups 1 and 2. This conclusion is supported by the ternary plots of tricyclic terpanes, 4,9DMD, 4,8DMD and 3,4DMD diamondoids, and the cross plot of EAI against DMDI-1. The occurrence of exsudatinite in the outcrop source rocks in group 1, consistent with early hydrocarbon generation, and the low ratio of demethylated Ts/Tm (<1) in the bitumen samples confirms that the biodegraded bitumen seeps and tar sands in the Nigerian Dahomey Basin were generated by the Lower Cretaceous source rocks in group 1. The study advances on the previous propositions on the source of bitumen seeps and tar sands and contributes our knowledge in the Gulf of Guinea Basin.</div></div>","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"197 ","pages":"Article 104866"},"PeriodicalIF":2.6,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142417964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-26DOI: 10.1016/j.orggeochem.2024.104879
Zhaoxi Zuo , Jian Cao , Wenxuan Hu , Ruijie Zhang , Xiaolin Wang , Suping Yao , Bing Luo , Jingkun Zhang
Highly evolved pyrobitumen is an important and realistic object for maturity characterization of ancient and deeply buried organic matter, but measurement of its reflectance is challenging due to its strong optical anisotropy and nano-scale relief. Here we conducted a case study in the Sinian (Ediacaran) Dengying Formation of the Sichuan Basin, China. High-resolution, three-dimensional, morphological imaging by atomic force microscopy (AFM), laser Raman (LRM) spectroscopy, and reflectance studies were conducted on the reservoir pyrobitumen. Our results show that Young’s modulus and adhesion, which are mechanical maturity parameter, provides effective characterization of maturity. The increase in Young’s modulus of pyrobitumen lags that of the vitrinite, given that pyrobitumen is formed by oil cracking and is more hydrogen-rich than vitrinite. A quantitative relationship between Young’s modulus, adhesion and reflectance in bright and dark areas of pyrobitumen was established, which can be used for maturity characterization. The changes in Young’s modulus of the pyrobitumen is related to the condensation of organic matter and directional arrangement of microcrystals. Young’s modulus of organic matter is a robust mechanical maturity index at high organic matter maturity (Ro > 2.0 %), but it is important to pay attention to the influence of anisotropy. Compared to Young’s modulus, adhesion is less affected by anisotropy. The nano-mechanics such as Young’s modulus and adhesion will be new maturity indicator in addition to conventional optical and spectroscopic method. The nano-mechanical properties of organic matter are expected to be applied to maturity indicators and macerals classification in the field of organic petrology in the further research.
{"title":"Maturity characterization and formation mechanisms of nano-scale anisotropic pyrobitumen based on atomic force microscopy (AFM)","authors":"Zhaoxi Zuo , Jian Cao , Wenxuan Hu , Ruijie Zhang , Xiaolin Wang , Suping Yao , Bing Luo , Jingkun Zhang","doi":"10.1016/j.orggeochem.2024.104879","DOIUrl":"10.1016/j.orggeochem.2024.104879","url":null,"abstract":"<div><div>Highly evolved pyrobitumen is an important and realistic object for maturity characterization of ancient and deeply buried organic matter, but measurement of its reflectance is challenging due to its strong optical anisotropy and nano-scale relief. Here we conducted a case study in the Sinian (Ediacaran) Dengying Formation of the Sichuan Basin, China. High-resolution, three-dimensional, morphological imaging by atomic force microscopy (AFM), laser Raman (LRM) spectroscopy, and reflectance studies were conducted on the reservoir pyrobitumen. Our results show that Young’s modulus and adhesion, which are mechanical maturity parameter, provides effective characterization of maturity. The increase in Young’s modulus of pyrobitumen lags that of the vitrinite, given that pyrobitumen is formed by oil cracking and is more hydrogen-rich than vitrinite. A quantitative relationship between Young’s modulus, adhesion and reflectance in bright and dark areas of pyrobitumen was established, which can be used for maturity characterization. The changes in Young’s modulus of the pyrobitumen is related to the condensation of organic matter and directional arrangement of microcrystals. Young’s modulus of organic matter is a robust mechanical maturity index at high organic matter maturity (<em>R</em><sub>o</sub> > 2.0 %), but it is important to pay attention to the influence of anisotropy. Compared to Young’s modulus, adhesion is less affected by anisotropy. The nano-mechanics such as Young’s modulus and adhesion will be new maturity indicator in addition to conventional optical and spectroscopic method. The nano-mechanical properties of organic matter are expected to be applied to maturity indicators and macerals classification in the field of organic petrology in the further research.</div></div>","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"197 ","pages":"Article 104879"},"PeriodicalIF":2.6,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142322796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-25DOI: 10.1016/j.orggeochem.2024.104880
Nicole R. Coffey , Christian Dewey , Kieran Manning , Yuri Corilo , William Kew , Lydia Babcock-Adams , Amy M. McKenna , Rhona K. Stuart , Rene M. Boiteau
Increased accessibility of liquid chromatography mass spectrometry (LC-MS) metabolomics instrumentation and software have expanded their use in studies of dissolved organic matter (DOM) and exometabolites released by microbes. Current strategies to annotate metabolomes generally rely on matching tandem MS/MS spectra to databases of authentic standards. However, spectral matching approaches typically have low annotation rates for DOM. An alternative approach is to annotate molecular formula based on accurate mass and isotopic fine structure measurements that can be obtained from state-of-the-art ultrahigh resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICR MS), but instrument accessibility for large metabolomic studies is generally limited. Here, we describe a strategy to annotate exometabolomes obtained from lower resolution LC-MS systems by matching metabolomic features to a molecular formula library generated for a representative sample analyzed by LC 21T- FT-ICR MS. The molecular formula library approach successfully annotated 53% of exometabolome features of the marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 6% annotation rate achieved using a conventional MS/MS approach. There was 94% agreement between assigned formula that were annotated with both approaches, and mass error analysis of the discrepancies suggested that the FT-ICR MS formula assignments were more reliable. Differences in the exometabolome of P. tricornutum grown under iron replete and iron limited conditions revealed 668 significant metabolites, including a suite of peptide-like molecules released by P. tricornutum in response to iron deficiency. These findings demonstrate the utility of FT-ICR MS formula libraries for extending the accuracy and comprehensiveness of metabolome annotations.
液相色谱质谱(LC-MS)代谢组学仪器和软件的普及扩大了其在溶解有机物(DOM)和微生物释放的外代谢物研究中的应用。目前注释代谢组的策略一般依赖于将串联 MS/MS 图谱与真实标准数据库进行匹配。然而,光谱匹配法对 DOM 的注释率通常较低。另一种方法是根据最先进的超高分辨率傅立叶变换离子回旋共振质谱(FT-ICR MS)获得的精确质量和同位素精细结构测量结果来注释分子式,但大型代谢组学研究的仪器可及性通常有限。在此,我们介绍了一种通过将代谢组学特征与 LC 21T- FT-ICR MS 分析的代表性样品生成的分子式库进行匹配来注释从低分辨率 LC-MS 系统获得的外代谢组的策略。分子式库方法成功地注释了海洋硅藻 Phaeodactylum tricornutum 53% 的外代谢组特征,比传统 MS/MS 方法的 6% 注释率提高了近 10 倍。两种方法注释的分配公式之间的一致性达到 94%,对差异进行的质量误差分析表明,FT-ICR MS 公式分配更可靠。在缺铁和缺铁条件下生长的三疣梭子蟹外代谢组的差异揭示了 668 种重要的代谢物,其中包括三疣梭子蟹在缺铁时释放的一系列肽类分子。这些发现证明了 FT-ICR MS 配方库在提高代谢组注释的准确性和全面性方面的实用性。
{"title":"Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library","authors":"Nicole R. Coffey , Christian Dewey , Kieran Manning , Yuri Corilo , William Kew , Lydia Babcock-Adams , Amy M. McKenna , Rhona K. Stuart , Rene M. Boiteau","doi":"10.1016/j.orggeochem.2024.104880","DOIUrl":"10.1016/j.orggeochem.2024.104880","url":null,"abstract":"<div><div>Increased accessibility of liquid chromatography mass spectrometry (LC-MS) metabolomics instrumentation and software have expanded their use in studies of dissolved organic matter (DOM) and exometabolites released by microbes. Current strategies to annotate metabolomes generally rely on matching tandem MS/MS spectra to databases of authentic standards. However, spectral matching approaches typically have low annotation rates for DOM. An alternative approach is to annotate molecular formula based on accurate mass and isotopic fine structure measurements that can be obtained from state-of-the-art ultrahigh resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICR MS), but instrument accessibility for large metabolomic studies is generally limited. Here, we describe a strategy to annotate exometabolomes obtained from lower resolution LC-MS systems by matching metabolomic features to a molecular formula library generated for a representative sample analyzed by LC 21T- FT-ICR MS. The molecular formula library approach successfully annotated 53% of exometabolome features of the marine diatom <em>Phaeodactylum tricornutum</em> – a nearly ten-fold increase over the 6% annotation rate achieved using a conventional MS/MS approach. There was 94% agreement between assigned formula that were annotated with both approaches, and mass error analysis of the discrepancies suggested that the FT-ICR MS formula assignments were more reliable. Differences in the exometabolome of <em>P. tricornutum</em> grown under iron replete and iron limited conditions revealed 668 significant metabolites, including a suite of peptide-like molecules released by <em>P. tricornutum</em> in response to iron deficiency. These findings demonstrate the utility of FT-ICR MS formula libraries for extending the accuracy and comprehensiveness of metabolome annotations.</div></div>","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"197 ","pages":"Article 104880"},"PeriodicalIF":2.6,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142417967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-19DOI: 10.1016/j.orggeochem.2024.104877
Fanfan Ju , Liuzhu Chen , Yaoyao Kong , Teng Ma , Chi Zhang , Zhanqiang Chen
Chlorination of organic matter occurs naturally and is an important part of the chlorine cycle. To investigate the likelihood that inorganic oxidants, (Fe(NO3)3, H2O2, and hydroxyl radicals (·OH), frequently present in soil environments, could promote the synthesis of chlorinated organic matter in the soil environment, litterfall, humus, and soil (0–20 cm) were collected and used in laboratory based simulation experiments. Results indicate that these inorganic oxidants might promote the synthesis of chlorinated organic matter, but their impact varied due to varying suitable reaction circumstances. Litterfall was the most sensitive to chlorination, likely caused by the presence of abundant amounts of labile organic matter, and the chlorination process was limited by its Cl− level. Hydroxyl radicals showed a dual effect (producing or degrading chlorinated organic matter) on the three materials assessed, which was controlled by both ·OH concentration and the stability of organic matter, and the dual effect was evident in order of litterfall > humus > soil. The Fe(NO3)3-mediated chlorination of organic matter was only significant in litterfall due to its labile organic matter composition, while the peroxidative reaction caused by H2O2 in the producing chlorinated organic matter was only obvious in soil, most likely due to the presence of metals, facilitating the process. Combined this study sheds light on the chlorine cycle by verifying that inorganic oxidants might mediate abiotic chlorination of organic matter in a natural soil environment.
{"title":"Abiotic chlorination of organic matter in the soil environment: A simulation study","authors":"Fanfan Ju , Liuzhu Chen , Yaoyao Kong , Teng Ma , Chi Zhang , Zhanqiang Chen","doi":"10.1016/j.orggeochem.2024.104877","DOIUrl":"10.1016/j.orggeochem.2024.104877","url":null,"abstract":"<div><div>Chlorination of organic matter occurs naturally and is an important part of the chlorine cycle. To investigate the likelihood that inorganic oxidants, (Fe(NO<sub>3</sub>)<sub>3</sub>, H<sub>2</sub>O<sub>2</sub>, and hydroxyl radicals (·OH), frequently present in soil environments, could promote the synthesis of chlorinated organic matter in the soil environment, litterfall, humus, and soil (0–20 cm) were collected and used in laboratory based simulation experiments. Results indicate that these inorganic oxidants might promote the synthesis of chlorinated organic matter, but their impact varied due to varying suitable reaction circumstances. Litterfall was the most sensitive to chlorination, likely caused by the presence of abundant amounts of labile organic matter, and the chlorination process was limited by its Cl<sup>−</sup> level. Hydroxyl radicals showed a dual effect (producing or degrading chlorinated organic matter) on the three materials assessed, which was controlled by both ·OH concentration and the stability of organic matter, and the dual effect was evident in order of litterfall > humus > soil. The Fe(NO<sub>3</sub>)<sub>3</sub>-mediated chlorination of organic matter was only significant in litterfall due to its labile organic matter composition, while the peroxidative reaction caused by H<sub>2</sub>O<sub>2</sub> in the producing chlorinated organic matter was only obvious in soil, most likely due to the presence of metals, facilitating the process. Combined this study sheds light on the chlorine cycle by verifying that inorganic oxidants might mediate abiotic chlorination of organic matter in a natural soil environment.</div></div>","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"198 ","pages":"Article 104877"},"PeriodicalIF":2.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142652444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-05DOI: 10.1016/j.orggeochem.2024.104864
Jun Shi , Yun Li , Wenmin Jiang , Yongqiang Xiong , Hua Wang
An oil with an initial equivalent maturity of 0.74 %Ro, was pyrolyzed in a closed gold tube pyrolysis system with added silica sand and no added water under simulated conditions spanning 0.7 %–2.1 % EasyRo. The internal fluid pressure, ranging from 0 to >150 MPa at individual maturities states of 1.0 %, 1.5 % and 2.1 % EasyRo, was controlled by increasing sample mass and setting external confining pressure (50, 100 and 150 MPa). Results indicate that the increasing fluid pressure initially promoted and then gradually retarded crude oil cracking. The free-radical reaction mechanism (hydrogen radical supply), free space of vessels, and characteristics of pressure medium control the influence of fluid pressure on the chemical reaction process. The decreasing free space of volume-constant vessels and the difference of hydrogen radicals supplied in various thermal maturity stages together gradually reduce the reaction rate of crude oil cracking. Thus, the yields of methane, wet gas, and light and heavy hydrocarbons increase at low fluid pressure ranges and then decrease at high-pressure conditions. Moreover, the physical controls of fluid phase behaviors include the evolution of fluid phase states influencing the increased rates of fluid pressure and fluid pressure influencing the production of multi-phase hydrocarbons. The increase in fluid pressure is faster in the saturated gas–liquid phase than in the unsaturated phase; thus, the phase behaviors induce the yields of product change. The increasing fluid pressure induces the occurrence of multi-phase hydrocarbons and accumulation of light oil and condensate. This study introduces a novel approach to investigate the influence of fluid pressure on reservoir oil cracking, emphasising phase behavior analysis, and shedding light on the evolution of organic matter in deep and ultra-deep strata.
{"title":"Effects of fluid pressure on the occurrence of multi-phase oil and accumulation of light oil and condensate from crude oil cracking: Insights from modified gold tube pyrolysis experiments","authors":"Jun Shi , Yun Li , Wenmin Jiang , Yongqiang Xiong , Hua Wang","doi":"10.1016/j.orggeochem.2024.104864","DOIUrl":"10.1016/j.orggeochem.2024.104864","url":null,"abstract":"<div><p>An oil with an initial equivalent maturity of 0.74 %<em>R</em>o, was pyrolyzed in a closed gold tube pyrolysis system with added silica sand and no added water under simulated conditions spanning 0.7 %–2.1 % EasyRo. The internal fluid pressure, ranging from 0 to >150 MPa at individual maturities states of 1.0 %, 1.5 % and 2.1 % EasyRo, was controlled by increasing sample mass and setting external confining pressure (50, 100 and 150 MPa). Results indicate that the increasing fluid pressure initially promoted and then gradually retarded crude oil cracking. The free-radical reaction mechanism (hydrogen radical supply), free space of vessels, and characteristics of pressure medium control the influence of fluid pressure on the chemical reaction process. The decreasing free space of volume-constant vessels and the difference of hydrogen radicals supplied in various thermal maturity stages together gradually reduce the reaction rate of crude oil cracking. Thus, the yields of methane, wet gas, and light and heavy hydrocarbons increase at low fluid pressure ranges and then decrease at high-pressure conditions. Moreover, the physical controls of fluid phase behaviors include the evolution of fluid phase states influencing the increased rates of fluid pressure and fluid pressure influencing the production of multi-phase hydrocarbons. The increase in fluid pressure is faster in the saturated gas–liquid phase than in the unsaturated phase; thus, the phase behaviors induce the yields of product change. The increasing fluid pressure induces the occurrence of multi-phase hydrocarbons and accumulation of light oil and condensate. This study introduces a novel approach to investigate the influence of fluid pressure on reservoir oil cracking, emphasising phase behavior analysis, and shedding light on the evolution of organic matter in deep and ultra-deep strata.</p></div>","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"196 ","pages":"Article 104864"},"PeriodicalIF":2.6,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142151851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-28DOI: 10.1016/j.orggeochem.2024.104862
Hongxiang Guan , Lei Liu , Daniel Birgel , Jörn Peckmann , Dong Feng , Sanzhong Li
Marine methane seeps are environments with a high microbial diversity, but are known for one biogeochemical key process, the sulfate-driven anaerobic oxidation of methane (SD-AOM) performed by anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). SD-AOM is also the dominant process at methane seeps in the South China Sea based on the lipid biomarker inventory of authigenic seep carbonates characterized by crocetane, a high sn2-hydroxyarchaeol over archaeol ratio, low contents of glycerol dibiphytanyl glycerol tetraethers (GDGTs), and δ13Clipid-methane offsets of −52 ± 4‰. Combined with the dominance of aragonite over other carbonate minerals, such pattern suggests high seepage intensity with a predominance of ANME-2/SRB consortia. Interestingly, the studied seep carbonates also yielded some uncommon biomarkers for these consortia, which may derive from methanogenic archaea. Methylotrophic methanogenesis has been shown to be the dominant mode of methanogenesis in seep environments where non-competitive substrates like methanol or trimethylamine are abundant. The presence of methylotrophic methanogens is possibly indicated by high contents (more than 50% of all GDGTs) of hydroxylated GDGTs-0 (OH-GDGT-0 and 2OH-GDGT-0) with extreme 13C-depletion (−128‰ to −116‰); this unique pattern is recognized in only some of the studied seep carbonates, while other carbonates are dominated by typical distributions of ANME-2 lipids, also comprising GDGTs with 0 to 4 rings, but lacking high contents of OH-GDGTs. The overall lack of crenarchaeol, the specific biomarker of planktonic Thaumarchaeota, agrees with the tentative assignment of the highly abundant OH-GDGTs-0 to methanogenic archaea. Such interpretation is necessarily circumstantial considering that the compound and carbon isotope composition of the membranes of ANME and methanogenic archaea is similar. Although production of OH-GDGTs has been previously reported for both planktonic Thaumarchaeota and ANME, OH-GDGT-0 as sole and highly abundant OH-GDGT has only been recognized in one culture of methanogenic archaea. Therefore, the high abundance of 13C-depleted hydroxylated GDGTs-0 compared to only minor contents of regular, ANME-derived GDGTs 1–4 with similar 13C-depletions can possibly be used as an indicator for methylotrophic methanogenesis in seep environments. Future experimental work is needed and should test if 13C-depleted hydroxylated GDGTs-0 are indeed biomarkers of methylotrophic methanogenesis at seeps.
{"title":"Hydroxylated GDGTs-0 in marine methane seep environments: A putative indicator for archaeal methanogenesis","authors":"Hongxiang Guan , Lei Liu , Daniel Birgel , Jörn Peckmann , Dong Feng , Sanzhong Li","doi":"10.1016/j.orggeochem.2024.104862","DOIUrl":"10.1016/j.orggeochem.2024.104862","url":null,"abstract":"<div><div>Marine methane seeps are environments with a high microbial diversity, but are known for one biogeochemical key process, the sulfate-driven anaerobic oxidation of methane (SD-AOM) performed by anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). SD-AOM is also the dominant process at methane seeps in the South China Sea based on the lipid biomarker inventory of authigenic seep carbonates characterized by crocetane, a high <em>sn</em>2-hydroxyarchaeol over archaeol ratio, low contents of glycerol dibiphytanyl glycerol tetraethers (GDGTs), and δ<sup>13</sup>C<sub>lipid-methane</sub> offsets of −52 ± 4‰. Combined with the dominance of aragonite over other carbonate minerals, such pattern suggests high seepage intensity with a predominance of ANME-2/SRB consortia. Interestingly, the studied seep carbonates also yielded some uncommon biomarkers for these consortia, which may derive from methanogenic archaea. Methylotrophic methanogenesis has been shown to be the dominant mode of methanogenesis in seep environments where non-competitive substrates like methanol or trimethylamine are abundant. The presence of methylotrophic methanogens is possibly indicated by high contents (more than 50% of all GDGTs) of hydroxylated GDGTs-0 (OH-GDGT-0 and 2OH-GDGT-0) with extreme <sup>13</sup>C-depletion (−128‰ to −116‰); this unique pattern is recognized in only some of the studied seep carbonates, while other carbonates are dominated by typical distributions of ANME-2 lipids, also comprising GDGTs with 0 to 4 rings, but lacking high contents of OH-GDGTs. The overall lack of crenarchaeol, the specific biomarker of planktonic Thaumarchaeota, agrees with the tentative assignment of the highly abundant OH-GDGTs-0 to methanogenic archaea. Such interpretation is necessarily circumstantial considering that the compound and carbon isotope composition of the membranes of ANME and methanogenic archaea is similar. Although production of OH-GDGTs has been previously reported for both planktonic Thaumarchaeota and ANME, OH-GDGT-0 as sole and highly abundant OH-GDGT has only been recognized in one culture of methanogenic archaea. Therefore, the high abundance of <sup>13</sup>C-depleted hydroxylated GDGTs-0 compared to only minor contents of regular, ANME-derived GDGTs 1–4 with similar <sup>13</sup>C-depletions can possibly be used as an indicator for methylotrophic methanogenesis in seep environments. Future experimental work is needed and should test if <sup>13</sup>C-depleted hydroxylated GDGTs-0 are indeed biomarkers of methylotrophic methanogenesis at seeps.</div></div>","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"198 ","pages":"Article 104862"},"PeriodicalIF":2.6,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142652443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The performance of Soxhlet (SOX), microwave-assisted (MAE) and accelerated-solvent extraction (ASE) in the analysis of faecal lipid biomarkers (FLB, Δ5-sterols, stanols, stanones) from archaeological soils was investigated to assess effectiveness and reproducibility of the extraction methods. Results from two Anthrosols that were analysed in six replicates show that SOX achieves significantly higher extraction yields for individual substances and steroid sums than MAE, while ASE produces the lowest lipid yields. Regarding the FLB ratios, which are used for sourcing of faeces, the three extraction methods show comparable values with three out of five ratios differing significantly between different soil samples. The reproducibility of extraction yields decreases with SOX > ASE > MAE, as well as for concentrations <100 ng g−1 sediment. Analyses of six different soils indicate a weak influence of soil properties (pH, texture, total organic carbon and cation exchange capacity) on the effectiveness of extraction methods. From our study we conclude that the classical SOX is still the preferred extraction approach when reliably higher FLB yields are of foremost interest or low concentrations are expected, as it is most effective and reproducible. However, considering the drawbacks of SOX (high extraction times and high solvent consumption), MAE and ASE appear to be comparably attractive for extracting FLBs in archaeological contexts. In addition to comparable FLB ratios, MAE and ASE are economically more efficient, as they reach a higher sample throughput and waste lower amounts of extractant.
{"title":"A matter of extraction – Extraction yields and ratios of faecal lipid biomarker from archaeological soils using Soxhlet, microwave-assisted and accelerated-solvent extraction","authors":"Sascha Scherer , Jago Jonathan Birk , Stefanie Klassen , Sabine Fiedler","doi":"10.1016/j.orggeochem.2024.104863","DOIUrl":"10.1016/j.orggeochem.2024.104863","url":null,"abstract":"<div><div>The performance of Soxhlet (SOX), microwave-assisted (MAE) and accelerated-solvent extraction (ASE) in the analysis of faecal lipid biomarkers (FLB, Δ<sup>5</sup>-sterols, stanols, stanones) from archaeological soils was investigated to assess effectiveness and reproducibility of the extraction methods. Results from two Anthrosols that were analysed in six replicates show that SOX achieves significantly higher extraction yields for individual substances and steroid sums than MAE, while ASE produces the lowest lipid yields. Regarding the FLB ratios, which are used for sourcing of faeces, the three extraction methods show comparable values with three out of five ratios differing significantly between different soil samples. The reproducibility of extraction yields decreases with SOX > ASE > MAE, as well as for concentrations <100 <!--> <!-->ng<!--> <!-->g<sup>−1</sup> sediment. Analyses of six different soils indicate a weak influence of soil properties (pH, texture, total organic carbon and cation exchange capacity) on the effectiveness of extraction methods. From our study we conclude that the classical SOX is still the preferred extraction approach when reliably higher FLB yields are of foremost interest or low concentrations are expected, as it is most effective and reproducible. However, considering the drawbacks of SOX (high extraction times and high solvent consumption), MAE and ASE appear to be comparably attractive for extracting FLBs in archaeological contexts. In addition to comparable FLB ratios, MAE and ASE are economically more efficient, as they reach a higher sample throughput and waste lower amounts of extractant.</div></div>","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"197 ","pages":"Article 104863"},"PeriodicalIF":2.6,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142417966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-23DOI: 10.1016/j.orggeochem.2024.104861
João Vitor dos Santos , Amanda Koenig , Patrick G. Hatcher
The mechanisms behind the formation of soil organic matter (SOM) and associated nitrogen immobilization remain partially elusive, while ongoing research continues to shed light on carbon and nitrogen sequestration in the environment. Studies show that quinone-like structures within alkali-soluble humic extracts of SOM can bond covalently with nitrogen-containing molecules derived from proteinaceous organic matter. However, direct molecular evidence for this chemical bonding with lignin in the solid form and non-solvent-extracted SOM is lacking. Using gel-state 1H-15N heteronuclear single quantum coherence (HSQC) high-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) spectroscopy, we demonstrate that a 15N-labeled peptide (glycine-glycine-glycine-arginine, GGGR), can covalently bind to solid, untreated, brown rotted wood as well as 1,2-naphthoquinone, a quinone-model molecule typically found in degraded lignin. The new peaks in both reactions represent a change in the environment surrounding the N-functional groups. Interaction of the 15N-labeled peptide with the model quinone produced NMR cross peaks that are similar to those of the solid lignin. This suggests that the quinone-like structures are the most likely functional groups to form covalent bonds with peptides in the degraded lignin. Both Michael addition and Schiff base formation is proposed when the peptide GGGR interacts with white oak lignin and 1,2-naphthoquinone. These processes are of considerable importance to N incorporation into SOM and offer insights into how proteinaceous molecules could potentially be preserved and sequestered through covalent bond formation.
土壤有机物质(SOM)的形成和相关的氮固定机制仍有部分令人难以捉摸,而正在进行的研究则继续揭示环境中的碳和氮固存问题。研究表明,SOM 的碱溶性腐殖质萃取物中的类醌结构可与蛋白质有机物中的含氮分子共价结合。然而,这种化学键与固态木质素和非溶剂萃取的 SOM 的直接分子证据还很缺乏。利用凝胶态 1H-15N 异核单量子相干(HSQC)高分辨率魔角旋转(HRMAS)核磁共振(NMR)光谱、我们证明,15N 标记的多肽(甘氨酸-甘氨酸-甘氨酸-精氨酸,GGGR)能与未经处理的棕色固体腐木以及 1,2-萘醌(降解木质素中常见的醌类分子)共价结合。这两种反应中出现的新峰值代表了 N-官能团周围环境的变化。15N 标记的肽与模型醌相互作用产生的 NMR 交叉峰与固体木质素的交叉峰相似。这表明类醌结构是最有可能与降解木质素中的肽形成共价键的官能团。当肽 GGGR 与白橡木木质素和 1,2-萘醌相互作用时,可能会形成迈克尔加成和希夫碱。这些过程对于将氮掺入 SOM 中具有相当重要的意义,并有助于深入了解如何通过共价键的形成来保存和封存蛋白质分子。
{"title":"Interaction between peptide and solid lignin suggest mechanisms of abiotic covalent bond formation","authors":"João Vitor dos Santos , Amanda Koenig , Patrick G. Hatcher","doi":"10.1016/j.orggeochem.2024.104861","DOIUrl":"10.1016/j.orggeochem.2024.104861","url":null,"abstract":"<div><div>The mechanisms behind the formation of soil organic matter (SOM) and associated nitrogen immobilization remain partially elusive, while ongoing research continues to shed light on carbon and nitrogen sequestration in the environment. Studies show that quinone-like structures within alkali-soluble humic extracts of SOM can bond covalently with nitrogen-containing molecules derived from proteinaceous organic matter. However, direct molecular evidence for this chemical bonding with lignin in the solid form and non-solvent-extracted SOM is lacking. Using gel-state <sup>1</sup>H-<sup>15</sup>N heteronuclear single quantum coherence (HSQC) high-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) spectroscopy, we demonstrate that a <sup>15</sup>N-labeled peptide (glycine-glycine-glycine-arginine, GGGR), can covalently bind to solid, untreated, brown rotted wood as well as 1,2-naphthoquinone, a quinone-model molecule typically found in degraded lignin. The new peaks in both reactions represent a change in the environment surrounding the N-functional groups. Interaction of the <sup>15</sup>N-labeled peptide with the model quinone produced NMR cross peaks that are similar to those of the solid lignin. This suggests that the quinone-like structures are the most likely functional groups to form covalent bonds with peptides in the degraded lignin. Both Michael addition and Schiff base formation is proposed when the peptide GGGR interacts with white oak lignin and 1,2-naphthoquinone. These processes are of considerable importance to N incorporation into SOM and offer insights into how proteinaceous molecules could potentially be preserved and sequestered through covalent bond formation.</div></div>","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"197 ","pages":"Article 104861"},"PeriodicalIF":2.6,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142533628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}