Organic Geochemistry最新文献

{"title":"Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library","authors":"Nicole R. Coffey ,&nbsp;Christian Dewey ,&nbsp;Kieran Manning ,&nbsp;Yuri Corilo ,&nbsp;William Kew ,&nbsp;Lydia Babcock-Adams ,&nbsp;Amy M. McKenna ,&nbsp;Rhona K. Stuart ,&nbsp;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}

{"title":"Abiotic chlorination of organic matter in the soil environment: A simulation study","authors":"Fanfan Ju ,&nbsp;Liuzhu Chen ,&nbsp;Yaoyao Kong ,&nbsp;Teng Ma ,&nbsp;Chi Zhang ,&nbsp;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(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 &gt; humus &gt; 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.</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}

{"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 ,&nbsp;Yun Li ,&nbsp;Wenmin Jiang ,&nbsp;Yongqiang Xiong ,&nbsp;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 &gt;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}

{"title":"Geochemistry Articles – July 2024","authors":"","doi":"10.1016/j.orggeochem.2024.104853","DOIUrl":"10.1016/j.orggeochem.2024.104853","url":null,"abstract":"","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"196 ","pages":"Article 104853"},"PeriodicalIF":2.6,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142228824","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}

{"title":"Hydroxylated GDGTs-0 in marine methane seep environments: A putative indicator for archaeal methanogenesis","authors":"Hongxiang Guan ,&nbsp;Lei Liu ,&nbsp;Daniel Birgel ,&nbsp;Jörn Peckmann ,&nbsp;Dong Feng ,&nbsp;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 δ¹³C_{lipid-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.</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}

{"title":"Geochemistry Articles – June 2024","authors":"","doi":"10.1016/j.orggeochem.2024.104849","DOIUrl":"10.1016/j.orggeochem.2024.104849","url":null,"abstract":"","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"196 ","pages":"Article 104849"},"PeriodicalIF":2.6,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142228732","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}

{"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 ,&nbsp;Jago Jonathan Birk ,&nbsp;Stefanie Klassen ,&nbsp;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, 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 &gt; ASE &gt; MAE, as well as for concentrations &lt;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.</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}

{"title":"Interaction between peptide and solid lignin suggest mechanisms of abiotic covalent bond formation","authors":"João Vitor dos Santos ,&nbsp;Amanda Koenig ,&nbsp;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 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.</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}

{"title":"Modified rapid small-scale fractionation method for quantitatively separating pyrrolic nitrogen compounds, phenols-ketones and carboxylic acids fractions from petroleum","authors":"Krzysztof J. Jurek","doi":"10.1016/j.orggeochem.2024.104850","DOIUrl":"10.1016/j.orggeochem.2024.104850","url":null,"abstract":"<div><p>This research outlines a fast and efficient technique for separating the pyrrolic, phenolic-ketonic, and carboxylic acid fractions from oils in a small-scale setting. This approach enables the separation and analysis of neutral nitrogen fractions that contain indoles, carbazoles, and benzocarbazoles, as well as ketonic-phenolic fractions that contain phenols and ketones. The study showcases the potential for accurately measuring petroleum composition. The reliability of the fractions’ concentration results is determined by the mass of the separated fraction, with completely reliable results achievable for masses exceeding 1.4 mg. The fraction’s mass can also be used to evaluate the relative expanded uncertainty of a single separation procedure. As the mass and concentration of the fraction increase, the relative expanded uncertainty of the concentration decreases, and this can be modelled using a power function.</p></div>","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"196 ","pages":"Article 104850"},"PeriodicalIF":2.6,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0146638024001153/pdfft?md5=bb75b2d1640851c10960117df10e01ad&pid=1-s2.0-S0146638024001153-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142040987","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}

{"title":"From swamp to sea: Quantifying terrestrial dissolved organic carbon in a tropical shelf sea using hydrogen isotope ratios","authors":"A’an Johan Wahyudi ,&nbsp;Nikita Kaushal ,&nbsp;Cristian Gudasz ,&nbsp;Patrick Martin","doi":"10.1016/j.orggeochem.2024.104851","DOIUrl":"10.1016/j.orggeochem.2024.104851","url":null,"abstract":"<div><p>Dissolved organic carbon (DOC) is a key component of coastal biogeochemical cycles, but its composition and reactivity depend on the relative contribution of autochthonous aquatic versus allochthonous terrigenous DOC (tDOC). In complex coastal waters, tDOC is commonly quantified using the bulk DOC stable carbon isotope ratio (<em>δ</em>¹³C_DOC). However, several limitations can hamper the use of <em>δ</em>¹³C_DOC in marine ecosystems, such as (1) the narrow and often overlapping separation of the autochthonous and allochthonous endmembers, and (2) mineralization of tDOC to dissolved inorganic carbon creates a reservoir effect such that autochthonous DOC can acquire a terrigenous-like <em>δ</em>¹³C_DOC. The stable isotope ratio of non-exchangeable hydrogen in the DOC (<em>δ</em>²H_n) has emerged as a new tool that can potentially overcome these limitations: (1) <em>δ</em>²H_n has a large separation between aquatic and terrigenous endmembers (&gt;50‰) and (2) it is not subject to reservoir effects caused by tDOC mineralization. Here, we evaluate the potential of <em>δ</em>²H_n obtained from solid phase-extracted dissolved organic matter (SPE-DOM), by comparing it to <em>δ</em>¹³C_DOC and chromophoric DOM (CDOM) optical properties. We collected samples at a site in Southeast Asia’s Sunda Shelf that experiences substantial seasonal variation in tDOC input, driven primarily by the monsoon-induced physical advection of peatland-derived tDOC. Over a 1-year monthly time series, the terrigenous fraction of DOC (<em>f</em>_terr) determined using <em>δ</em>²H_n of SPE-DOM and <em>δ</em>¹³C_DOC of bulk DOC was well correlated (r² = 0.42), and there was no significant difference in <em>f</em>_terr between the two isotope systems. In fact, <em>δ</em>²H_n displayed slightly stronger correlations with salinity and CDOM optical properties compared to <em>δ</em>¹³C_DOC. Our results indicate that <em>δ</em>²H_n of SPE-DOM is effective for quantifying tDOC across coastal gradients, potentially offering greater sensitivity than <em>δ</em>¹³C_DOC, and is a viable alternative in settings where <em>δ</em>¹³C_DOC is inadequate.</p></div>","PeriodicalId":400,"journal":{"name":"Organic Geochemistry","volume":"196 ","pages":"Article 104851"},"PeriodicalIF":2.6,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142040988","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}