Micro-Scale Mapping of Soil Organic Carbon: The Potential of Soft X-Ray Spectromicroscopy

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However, the mechanisms governing SOC persistence and turnover are not fully understood, hindering effective carbon management strategies. Especially limiting are challenges to visualize and characterize spatial distribution patterns of SOC within the intact soil. This study presents a novel approach to map carbon content and composition in intact environmental samples using synchrotron X-ray spectromicroscopy at a 4-100 µm resolution. X-ray fluorescence (XRF) maps provided an overview of the total carbon distribution, enabling the identification of carbon-rich regions of interest. Near edge X-ray absorption fine structure (NEXAFS) spectromicroscopy was then employed to obtain spatially resolved carbon speciation data within these regions. This method enabled the analysis of relatively large intact samples (16,000 µm Ø and 15,000 µm height), preserving a variety of root and organic matter fragments as well as pores ranging in size from 35 to 850 mm. Spectral fitting using reference standards revealed distinct spatial patterns of aromatic, aliphatic, and carboxylic carbon compounds associated with different structural features. Aromatic carbon was enriched around root fragments and the soil matrix, while carboxylic compounds were concentrated at pore-matrix interfaces, suggesting a correlation between soil pore structure and carbon chemical composition. The proposed novel approach provides opportunities for future unprecedented insights into the interplay between pore architecture and organic molecular diversity, the two key factors governing mechanisms of SOC protection and persistence in the soil. Carbon Spectromicroscopy X-ray spectroscopic imaging NEXAFS Micro X-ray Fluorescence Soil Carbon Caron Sequestration Figures Figure 1 Figure 2 Figure 3 1. Introduction Long term preservation of soil carbon, the largest terrestrial carbon pool on earth, has implications for soil fertility, productivity, water flow, gas exchange, and global atmospheric greenhouse gas emissions(Friedlingstein et al. 2022 ). Soil pore structure serves as the scaffoldings for soil functioning – the framework in which most physical, biological and chemical processes take place, particularly such processes that contribute to decomposition or protection of soil organic carbon (SOC)(Tiedje et al. 2001 ; Carson et al. 2010 ; Kravchenko et al. 2019a ; Vogel et al. 2022 ). The soil functional complexity, derived to a great extent by the spatial heterogeneity of the pore structure, is leading to vast variability in SOC persistence and turnover rates(Schmidt et al. 2011 ; Lehmann et al. 2020 ). In addition, the effectiveness with which soil microorganisms decompose organic matter plays a role in determining how well carbon is sequestered in the soil(Baveye et al. 2018 ). Microbial decomposition is impacted by the microbial community composition, as well as by the physical and hydrological properties of the soil, which regulate the interactions between decomposers and carbon sources. Over the past decade, a growing body of research has recognized the relationship between pore sizes and their functionalities(Franklin et al. 2021 ). For example, pores in the size order of tens of microns are optimal as microbial habitats with prevalent decomposition of newly added C, while pores < 30 µm are regarded as sites for carbon storage and protection(Yao et al. 2011 ; Kravchenko et al. 2019a , b ; Franklin et al. 2021 ). Another aspect of carbon protection is the molecular composition of SOC. The molecular diversity of the organic compounds controls the decomposition process. Higher diversity can increase the decomposers' metabolic costs, leading to a greater proportion of persistent carbon compounds(Lane and Martin 2010 ; Lehmann et al. 2020 ). Thus, coupling these two aspects: pore structure spatial heterogeneity and organic molecular diversity is crucial for better understanding SOC protection and storage mechanisms. Currently, chemical characterization of SOC persistence (Schmidt et al. 2011 ; Lavallee et al. 2020 ; Lehmann et al. 2020 ; Weng et al. 2022a) and spatial heterogeneity of C composition at the mineral-SOC interface(Lehmann et al. 2008 ; Witzgall et al. 2021 ; Lippold et al. 2023 ) are explored either in disturbed bulk soils or at the nanometer scale. For example, nano-scale secondary ion mass spectrometry (NanoSIMS) was successfully used to map the soil organic-mineral complexes and the soil-root interfaces (Clode et al. 2009 ; Witzgall et al. 2021 ; Li et al. 2023 ). Moreover, techniques like Fourier-transform infrared (FTIR) spectromicroscopy(Lehmann et al. 2007 ; Shabtai et al. 2023 ) and scanning transmission X-ray spectromicroscopy (STXM)(Lehmann et al. 2008 ; Weng et al. 2022b ), both in transmission mode requiring thin sectioning, have also been reported to successfully mapping of organic compounds at the organic-soil interface to characterize mineral associated organic matter (MAOM). Considering the pervasiveness of soil heterogeneity at all spatial scales, it is crucial to analyze SOC within its natural context, i.e. intact samples. Moreover, modeling and predicting soil carbon processing requires addressing the influence of soil physical environment, as represented by the pore structure, at the scales relevant for SOC input from plant roots, its subsequent microbial processing, and protection. However, the lack of suitable measuring approaches currently limits the ability to quantify the effect of soil pore structure on SOC chemical composition. Recent advancements and accessibility of X-ray microtomography have enabled the well-established visualization and quantification of intact soil structures(Baveye et al. 2018 ; Kravchenko et al. 2019a ; Schlüter et al. 2020 ; Vogel et al. 2022 ). However, spatially resolving and co-localizing soil structural features with carbon content and speciation with hard x-rays remains elusive due to their low photon interaction cross section with light elements. We present here a new approach to map carbon chemistry for large, intact soil samples using synchrotron soft X-ray fluorescence (XRF) spectromicroscopy and microspectroscopy techniques. 2. Experimental 2.1 Sample preparation The studied soil was a silty loam Ultisol from a permanent pasture located at the USDA-ARS Farming Systems Project long-term field trial in Beltsville Maryland. The soil texture was 23.8% sand, 59.6% silt, and 16.7% clay, with 1.3% SOC. Intact soil cores (5 cm Ø) were collected from 5–10 cm depth. The cores were then sub-sampled into polycarbonate cylinders (16,000 µm Ø and 15,000 µm height), hereafter, cores (Fig. 1a). The spectromicroscopy measurements are best performed on flat surfaces to avoid artifacts stemming from the short penetration depth of soft x-rays. Therefore, the cores were fixed with sodium silicate (30%) (Radnor, PA, USA) and subsequently polished to create smooth surfaces. Sodium silicate was chosen for fixation due to its low viscosity, which facilitates sample infiltration, and to avoid introducing additional carbon to the soil. It is used as a soil stabilizer(Koohestani et al. 2021 ) as well as a binder for sand foundry(Owusu 1982 ) due to its ability to solidify mainly through dehydration or reaction with atmospheric carbon dioxide to form silica-gel. The cores were initially embedded in sodium silicate using a two-step process. First, saturation was achieved from the bottom until the core surface appeared wet (~ 15 min). Then, the cores were completely submerged and placed under a vacuum of -40 kPa overnight. This step removed air from the soil pores. Once ambient pressure was restored, the sodium silicate penetrated the pores and subsequently cured for 5 days at 40°C. As water evaporates from the sodium silicate solution, it becomes more concentrated and eventually solidifies into a glassy substance(Owusu 1982 ). Finally, the cores were polished with a series of polishing papers. 2.2 Spectromicroscopy and near edge X-ray adsorption fine structure (NEXAFS)spectroscopy X-ray maps and spectroscopy data acquisition was carried at the spherical grating monochromator (SGM) beamline at the Canadian Light Source (Saskatoon, SK). A silicon drift detector (Amptek Fast SDD), positioned at 90 o to the incident beam in the plane of polarization to minimize scattering, was used to collect the C partial fluorescence yield (PFY) of the sample with an energy resolution of around 100 eV. A measurement of the B PFY for pure Boron Nitride was used to correct for changes in the incident beam intensity by dividing the raw C PFY by the boron PFY. Energy calibration was confirmed using a the C1s (C = O) to π* transition at 288.7 eV of a citric acid standard(Solomon et al. 2009 ). A map of the soil carbon content of the soil core surface was assessed by a X-ray fluorescence (XRF) map made with an excitation energy of 320 eV (above the C K-edge) with 35 µm resolution (Fig. 1b). The XRF carbon map coupled with light microscopy image of the surface was used to find a region of interest that will include a C ‘hotspot’. Next, a XRF stack of 60 individual maps acquired with incident photon between 282–294 eV (0.2 eV step size) was collected, capturing the C K-edge spectral data for every pixel (Fig. 1c). In Addition, NEXAFS spectra from pressed pellets of organic compounds references were collected. 15 individual 60 s slew scans were collected at different positions on each sample and combined to create the NEXAFS measurement for that reference compound. The references represented aromatic, aliphatic and carboxylic acid compounds of plant and microorganisms’ origin prevalent in soils(Solomon et al. 2005 , 2009 ) and included tanic acid, starch, and malic acid. Linear combination fitting using these three reference pen_spark spectra was calculated for each pixel in the spectromicroscopy stacks. All data visualization and analysis was performed in Python (ver. 3.9) using numpy(Harris et al. 2020 ), scipy(Virtanen et al. 2020 ), and scikit-learn(Pedregosa et al. 2011 ) libraries. 3. Results and Discussion The workflow for micro-scale mapping of soil organic carbon at 35 µm resolution is presented in Fig. 1. The carbon-free fixation agent, sodium silicate, are able to successfully preserve the structure of the soil core. This allowed polishing the surface to minimize roughness, a common issue with soil samples that can lead to shadowing and edge effect artifacts during soft X-ray analysis. Moreover, the developed sample preparation method enabled us to work with a relatively large intact soil core (16,000 µm Ø and 15,000 µm height) (Fig. 1a), where a variety of root and particulate organic matter fragments as well as a variety of pores ranging in size from 35 to 850 µm were present on the exposed measured surface (Fig. 1a). To our knowledge, intact imaging of soil cores of this size range was previously achievable only with carbon-based resins(Lippold et al. 2023 ), while only much smaller samples (< 500 µm Ø) could be non-destructively imaged through thin sectioning techniques (Weng et al. 2022b ; Shabtai et al. 2023 ). The total carbon content XRF map acquired at 320 eV (Fig. 1b) demonstrated good contrast and clearly delineated carbon rich features in the image (e.g. roots). Due to the relatively short acquisition time (~ 60 min), these maps are ideal for identifying regions of interest for further investigation using techniques requiring longer times, such as high-resolution carbon maps (achievable up to ~ 4 µm in our current setup) and/or spectromicroscopy. In Fig. 2 we present the results of the XRF spectromicroscopy stack acquired for an area (~ 3.3×10 6 µm 2 ) surrounding a carbon-rich root fragment which not only produced a good contrast between different soil components (pores, root, soil matrix), but also depicted variations in spectral information within different regions of interests (Fig. 2 ). As expected, low intensity C signal was found in soil pores, or in carbon-deficient areas. The spectra measured for the root area shows peaks at 285.3, 287, and 288.4 eV associated with aromatic, aliphatic and carboxylic carbon moieties(Solomon et al. 2005 ; Lutfalla et al. 2019 ). Interestingly, the soil matrix in the vicinity of the pores exhibited higher overall carbon content, despite showing a relatively similar spectral composition to other soil matrix regions. Additionally, a peak at 290.1 eV associated with carbonate moiety(Lutfalla et al. 2019 ) was present in the soil matrix regions. The demonstrated ability to visualize the spatial distribution of these species and compounds is particularly intriguing since they play a significant role in carbon protection and persistence(Kravchenko et al. 2019a ; Lehmann et al. 2020 ). In Fig. 3, we demonstrate a procedure for fitting reference organic compounds to the spectromicroscopy stack using linear combinations to obtain compositional maps. By fitting NEXAFS spectra references to the spectromicroscopy stack data, we observed internal contrast within the map, revealing regions with distinct chemical composition (Fig. 3). Analysis of the different compositional maps (Fig. 3c) reveals a high concentration of aromatic carbon around the root and soil matrix, particularly in the vicinity of the pores. Additionally, a high concentration of aliphatic compounds is observed mainly in the root area, while the pore-matrix interface exhibits a higher concentration of carboxylic compounds. This spatial distribution suggests a correlation between the soil structure and the distribution of carbon compounds. The root acts as a primary carbon source. Pores facilitate microbial decomposition(Kravchenko et al. 2019a ), which explains the high concentration of carboxylic compounds around the pore interface. Finally, the soil matrix serves as a carbon sink, containing more complex, aromatic carbon compounds. By preserving soil structure and enabling the visualization of carbon distribution in relation to key soil features such as pores, roots, and the soil matrix, this approach provides unique insights into the spatial relationships between soil structure and SOC composition. The observed patterns of carbon compounds associated with different soil structural features suggest a complex interplay between carbon sources, microbial activity, and soil physical properties. Future applications of this technique, combined with complementary imaging methods, could significantly enhance our understanding of soil carbon cycling and Fig. 3. Mapping carbon composition of an intact soil sample surface. (a) reference standard NEXAFS spectra of aromatic, aliphatic and carboxylic compounds. (b) composite image of aromatic (red), aliphatic (blue), and carboxylic (green) carbon following a linear combination fit, and the separate compositional maps channels (c). storage. 4. Conclusions This study introduces a novel approach to mapping carbon contents and compositions on surfaces of landscape relevant, intact samples at micron-scale resolution using synchrotron X-ray spectromicroscopy. The ability to analyze relatively large samples without compromising their structural integrity is a significant advancement that can be extended to other environmental or engineered samples where spatially resolved chemical carbon information is required. This approach opens new possibilities for investigating the mechanisms of carbon protection and persistence in soils, bridging the gap between micro-scale processes and landscape-level carbon dynamics. By integrating spatially resolved structural and chemical information from intact samples, this work paves the way for a more comprehensive and quantitative understanding of carbon sequestration and storage mechanisms, with potential implications for soil carbon management and climate change mitigation strategies. Declarations Competing Interests The authors have no relevant financial or non-financial interests to disclose. Funding This work was supported by the United Stated Department of Agriculture (Grant number 2023-67019-39840) References Baveye PC, Otten W, Kravchenko A et al (2018) Emergent properties of microbial activity in heterogeneous soil microenvironments: Different research approaches are slowly converging, yet major challenges remain. 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Accessed 20 May 2024 Supplementary Files graphicalAbs.tif Cite Share Download PDF Status: Published Journal Publication published 02 Jan, 2025 Read the published version in Environmental Chemistry Letters → Version 1 posted Reviewers agreed at journal 23 Jul, 2024 Reviewers invited by journal 17 Jul, 2024 Editor assigned by journal 11 Jul, 2024 First submitted to journal 08 Jul, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4707647","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":328380552,"identity":"bb05be79-53da-4195-b9bf-8b86f202b96f","order_by":0,"name":"Maoz Dor","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAArElEQVRIiWNgGAWjYDCCAxBKDkKxkaDFmHQtiQ1Ea+E73vt0w4+KuvS1/WcMGD6UHSasRfLMcbObPWfYcrfdyDFgnHGOCC0GN9LYbvC28QC18Bgw87YRqeXm3zaJdLPzZwyY/xKr5TZvm0GC2YEcA2ZGYrRInjnGdlvmTILhthtpBQd7zqUT1sJ3vI3t5puKOnmz84c3PvhRZk1YCwo4QKL6UTAKRsEoGAW4AAC7vz5Zl9XKTAAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0001-9037-3799","institution":"Michigan State University","correspondingAuthor":true,"prefix":"","firstName":"Maoz","middleName":"","lastName":"Dor","suffix":""},{"id":328380553,"identity":"97864a56-8c0a-4c89-86d2-127a862c5d25","order_by":1,"name":"Tom Regier","email":"","orcid":"","institution":"Canadian Light Source Inc","correspondingAuthor":false,"prefix":"","firstName":"Tom","middleName":"","lastName":"Regier","suffix":""},{"id":328380554,"identity":"b67975d2-2f14-40ff-a7de-e34b70f23c31","order_by":2,"name":"Zachary Arthur","email":"","orcid":"","institution":"Canadian Light Source Inc","correspondingAuthor":false,"prefix":"","firstName":"Zachary","middleName":"","lastName":"Arthur","suffix":""},{"id":328380555,"identity":"225c0bb3-1f21-4e04-aa7e-d8bedf8de626","order_by":3,"name":"Andrey Guber","email":"","orcid":"","institution":"Michigan State University","correspondingAuthor":false,"prefix":"","firstName":"Andrey","middleName":"","lastName":"Guber","suffix":""},{"id":328380556,"identity":"99af1f9e-b6a7-4394-a70a-24bcc2a20f94","order_by":4,"name":"Alexandra Kravchenko","email":"","orcid":"","institution":"Michigan State University","correspondingAuthor":false,"prefix":"","firstName":"Alexandra","middleName":"","lastName":"Kravchenko","suffix":""}],"badges":[],"createdAt":"2024-07-08 19:38:41","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4707647/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4707647/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s10311-024-01817-0","type":"published","date":"2025-01-02T15:57:41+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":62655398,"identity":"6dc607cf-73dc-45b4-b190-1fd8f81969df","added_by":"auto","created_at":"2024-08-17 01:34:31","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":1116822,"visible":true,"origin":"","legend":"\u003cp\u003eWorkflow for carbon mapping and spectromicroscopy in soil samples. (a) soil core. (b) XRF map acquired at 320 eV above the C K-edge to map total carbon in the sample and identify regions of interest (marked with red dashed rectangle) for spectromicroscopy stack acquisition. (c) Spectromicroscopy stack of 60 XRF maps acquired across the C K-edge (282-294 eV) with 0.2 eV step size. (d) Spectral data representing the sum of partial fluorescence yield from all partial fluorescence measurements of the stack, used for carbon compound speciation.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-4707647/v1/46f7071e7ff15b292f3a5a4b.png"},{"id":62655397,"identity":"98cc5ba9-4e6a-4dbf-b1e9-ab4b94d6f347","added_by":"auto","created_at":"2024-08-17 01:34:31","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":390803,"visible":true,"origin":"","legend":"\u003cp\u003eSelected regions of interests of different soil phases, marked with rectangles (1-2 pores, 3 root fragment, 4-5 soil matrix), on a carbon content map (a) comprising different levels of carbon content, and their respective spectral data (b) which allows to spatially resolve C spectral information. Dash lines marks (from left to right) energies associated with aromatic (285.3 eV), aliphatic (287.3 eV), carboxylic (288.4 eV), and carbonate (290.1 eV) carbon moieties.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-4707647/v1/94ad33766570fd6aa7399565.png"},{"id":62655667,"identity":"f66b709d-bf4a-44a8-ad37-dafb802aa088","added_by":"auto","created_at":"2024-08-17 01:42:32","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1419005,"visible":true,"origin":"","legend":"\u003cp\u003eMapping carbon composition of an intact soil sample surface. (a) reference standard NEXAFS spectra of aromatic, aliphatic and carboxylic compounds. (b) composite image of aromatic (red), aliphatic (blue), and carboxylic (green) carbon following a linear combination fit, and the separate compositional maps channels (c).\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-4707647/v1/6038b7853ff65dbe9c6acf4c.png"},{"id":73093399,"identity":"1d1949a2-21b0-49e7-9c25-8ab7488ee477","added_by":"auto","created_at":"2025-01-06 16:17:02","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3003965,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4707647/v1/4d084f05-268e-45ee-a152-fedc38cedda0.pdf"},{"id":62655399,"identity":"b59072b8-759b-4801-beca-3ec5cc56d5bc","added_by":"auto","created_at":"2024-08-17 01:34:32","extension":"tif","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":2047706,"visible":true,"origin":"","legend":"","description":"","filename":"graphicalAbs.tif","url":"https://assets-eu.researchsquare.com/files/rs-4707647/v1/693735df2dba2a5c767398fc.tif"}],"financialInterests":"","formattedTitle":"Micro-Scale Mapping of Soil Organic Carbon: The Potential of Soft X-Ray Spectromicroscopy","fulltext":[{"header":"1. Introduction","content":"\u003cp\u003eLong term preservation of soil carbon, the largest terrestrial carbon pool on earth, has implications for soil fertility, productivity, water flow, gas exchange, and global atmospheric greenhouse gas emissions(Friedlingstein et al. \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). Soil pore structure serves as the scaffoldings for soil functioning \u0026ndash; the framework in which most physical, biological and chemical processes take place, particularly such processes that contribute to decomposition or protection of soil organic carbon (SOC)(Tiedje et al. \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2001\u003c/span\u003e; Carson et al. \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2010\u003c/span\u003e; Kravchenko et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2019a\u003c/span\u003e; Vogel et al. \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). The soil functional complexity, derived to a great extent by the spatial heterogeneity of the pore structure, is leading to vast variability in SOC persistence and turnover rates(Schmidt et al. \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2011\u003c/span\u003e; Lehmann et al. \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). In addition, the effectiveness with which soil microorganisms decompose organic matter plays a role in determining how well carbon is sequestered in the soil(Baveye et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). Microbial decomposition is impacted by the microbial community composition, as well as by the physical and hydrological properties of the soil, which regulate the interactions between decomposers and carbon sources. Over the past decade, a growing body of research has recognized the relationship between pore sizes and their functionalities(Franklin et al. \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). For example, pores in the size order of tens of microns are optimal as microbial habitats with prevalent decomposition of newly added C, while pores\u0026thinsp;\u0026lt;\u0026thinsp;30 \u0026micro;m are regarded as sites for carbon storage and protection(Yao et al. \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e2011\u003c/span\u003e; Kravchenko et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2019a\u003c/span\u003e, \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003eb\u003c/span\u003e; Franklin et al. \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). Another aspect of carbon protection is the molecular composition of SOC. The molecular diversity of the organic compounds controls the decomposition process. Higher diversity can increase the decomposers' metabolic costs, leading to a greater proportion of persistent carbon compounds(Lane and Martin \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2010\u003c/span\u003e; Lehmann et al. \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Thus, coupling these two aspects: pore structure spatial heterogeneity and organic molecular diversity is crucial for better understanding SOC protection and storage mechanisms.\u003c/p\u003e \u003cp\u003eCurrently, chemical characterization of SOC persistence (Schmidt et al. \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2011\u003c/span\u003e; Lavallee et al. \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Lehmann et al. \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Weng et al. 2022a) and spatial heterogeneity of C composition at the mineral-SOC interface(Lehmann et al. \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e2008\u003c/span\u003e; Witzgall et al. \u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Lippold et al. \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2023\u003c/span\u003e) are explored either in disturbed bulk soils or at the nanometer scale. For example, nano-scale secondary ion mass spectrometry (NanoSIMS) was successfully used to map the soil organic-mineral complexes and the soil-root interfaces (Clode et al. \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e2009\u003c/span\u003e; Witzgall et al. \u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Li et al. \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). Moreover, techniques like Fourier-transform infrared (FTIR) spectromicroscopy(Lehmann et al. \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2007\u003c/span\u003e; Shabtai et al. \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e2023\u003c/span\u003e) and scanning transmission X-ray spectromicroscopy (STXM)(Lehmann et al. \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e2008\u003c/span\u003e; Weng et al. \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2022b\u003c/span\u003e), both in transmission mode requiring thin sectioning, have also been reported to successfully mapping of organic compounds at the organic-soil interface to characterize mineral associated organic matter (MAOM). Considering the pervasiveness of soil heterogeneity at all spatial scales, it is crucial to analyze SOC within its natural context, i.e. intact samples. Moreover, modeling and predicting soil carbon processing requires addressing the influence of soil physical environment, as represented by the pore structure, at the scales relevant for SOC input from plant roots, its subsequent microbial processing, and protection. However, the lack of suitable measuring approaches currently limits the ability to quantify the effect of soil pore structure on SOC chemical composition. Recent advancements and accessibility of X-ray microtomography have enabled the well-established visualization and quantification of intact soil structures(Baveye et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2018\u003c/span\u003e; Kravchenko et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2019a\u003c/span\u003e; Schl\u0026uuml;ter et al. \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Vogel et al. \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). However, spatially resolving and co-localizing soil structural features with carbon content and speciation with hard x-rays remains elusive due to their low photon interaction cross section with light elements. We present here a new approach to map carbon chemistry for large, intact soil samples using synchrotron soft X-ray fluorescence (XRF) spectromicroscopy and microspectroscopy techniques.\u003c/p\u003e"},{"header":"2. Experimental","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003e2.1 Sample preparation\u003c/h2\u003e \u003cp\u003eThe studied soil was a silty loam Ultisol from a permanent pasture located at the USDA-ARS Farming Systems Project long-term field trial in Beltsville Maryland. The soil texture was 23.8% sand, 59.6% silt, and 16.7% clay, with 1.3% SOC. Intact soil cores (5 cm \u0026Oslash;) were collected from 5\u0026ndash;10 cm depth. The cores were then sub-sampled into polycarbonate cylinders (16,000 \u0026micro;m \u0026Oslash; and 15,000 \u0026micro;m height), hereafter, cores (Fig.\u0026nbsp;1a).\u003c/p\u003e \u003cp\u003eThe spectromicroscopy measurements are best performed on flat surfaces to avoid artifacts stemming from the short penetration depth of soft x-rays. Therefore, the cores were fixed with sodium silicate (30%) (Radnor, PA, USA) and subsequently polished to create smooth surfaces. Sodium silicate was chosen for fixation due to its low viscosity, which facilitates sample infiltration, and to avoid introducing additional carbon to the soil. It is used as a soil stabilizer(Koohestani et al. \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2021\u003c/span\u003e) as well as a binder for sand foundry(Owusu \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e1982\u003c/span\u003e) due to its ability to solidify mainly through dehydration or reaction with atmospheric carbon dioxide to form silica-gel. The cores were initially embedded in sodium silicate using a two-step process. First, saturation was achieved from the bottom until the core surface appeared wet (~\u0026thinsp;15 min). Then, the cores were completely submerged and placed under a vacuum of -40 kPa overnight. This step removed air from the soil pores. Once ambient pressure was restored, the sodium silicate penetrated the pores and subsequently cured for 5 days at 40\u0026deg;C. As water evaporates from the sodium silicate solution, it becomes more concentrated and eventually solidifies into a glassy substance(Owusu \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e1982\u003c/span\u003e). Finally, the cores were polished with a series of polishing papers.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003e2.2 Spectromicroscopy and near edge X-ray adsorption fine structure (NEXAFS)spectroscopy\u003c/h2\u003e \u003cp\u003eX-ray maps and spectroscopy data acquisition was carried at the spherical grating monochromator (SGM) beamline at the Canadian Light Source (Saskatoon, SK). A silicon drift detector (Amptek Fast SDD), positioned at 90\u003csup\u003eo\u003c/sup\u003e to the incident beam in the plane of polarization to minimize scattering, was used to collect the C partial fluorescence yield (PFY) of the sample with an energy resolution of around 100 eV. A measurement of the B PFY for pure Boron Nitride was used to correct for changes in the incident beam intensity by dividing the raw C PFY by the boron PFY. Energy calibration was confirmed using a the C1s (C\u0026thinsp;=\u0026thinsp;O) to π* transition at 288.7 eV of a citric acid standard(Solomon et al. \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2009\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eA map of the soil carbon content of the soil core surface was assessed by a X-ray fluorescence (XRF) map made with an excitation energy of 320 eV (above the C K-edge) with 35 \u0026micro;m resolution (Fig.\u0026nbsp;1b). The XRF carbon map coupled with light microscopy image of the surface was used to find a region of interest that will include a C \u0026lsquo;hotspot\u0026rsquo;. Next, a XRF stack of 60 individual maps acquired with incident photon between 282\u0026ndash;294 eV (0.2 eV step size) was collected, capturing the C K-edge spectral data for every pixel (Fig.\u0026nbsp;1c). In Addition, NEXAFS spectra from pressed pellets of organic compounds references were collected. 15 individual 60 s slew scans were collected at different positions on each sample and combined to create the NEXAFS measurement for that reference compound. The references represented aromatic, aliphatic and carboxylic acid compounds of plant and microorganisms\u0026rsquo; origin prevalent in soils(Solomon et al. \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e2005\u003c/span\u003e, \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2009\u003c/span\u003e) and included tanic acid, starch, and malic acid. Linear combination fitting using these three reference pen_spark\u003c/p\u003e \u003cp\u003espectra was calculated for each pixel in the spectromicroscopy stacks. All data visualization and analysis was performed in Python (ver. 3.9) using numpy(Harris et al. \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2020\u003c/span\u003e), scipy(Virtanen et al. \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e2020\u003c/span\u003e), and scikit-learn(Pedregosa et al. \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e2011\u003c/span\u003e) libraries.\u003c/p\u003e \u003c/div\u003e"},{"header":"3. Results and Discussion","content":"\u003cp\u003eThe workflow for micro-scale mapping of soil organic carbon at 35 \u0026micro;m resolution is presented in Fig.\u0026nbsp;1. The carbon-free fixation agent, sodium silicate, are able to successfully preserve the structure of the soil core. This allowed polishing the surface to minimize roughness, a common issue with soil samples that can lead to shadowing and edge effect artifacts during soft X-ray analysis. Moreover, the developed sample preparation method enabled us to work with a relatively large intact soil core (16,000 \u0026micro;m \u0026Oslash; and 15,000 \u0026micro;m height) (Fig.\u0026nbsp;1a), where a variety of root and particulate organic matter fragments as well as a variety of pores ranging in size from 35 to 850 \u0026micro;m were present on the exposed measured surface (Fig.\u0026nbsp;1a). To our knowledge, intact imaging of soil cores of this size range was previously achievable only with carbon-based resins(Lippold et al. \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2023\u003c/span\u003e), while only much smaller samples (\u0026lt;\u0026thinsp;500 \u0026micro;m \u0026Oslash;) could be non-destructively imaged through thin sectioning techniques (Weng et al. \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2022b\u003c/span\u003e; Shabtai et al. \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e2023\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe total carbon content XRF map acquired at 320 eV (Fig.\u0026nbsp;1b) demonstrated good contrast and clearly delineated carbon rich features in the image (e.g. roots). Due to the relatively short acquisition time (~\u0026thinsp;60 min), these maps are ideal for identifying regions of interest for further investigation using techniques requiring longer times, such as high-resolution carbon maps (achievable up to ~\u0026thinsp;4 \u0026micro;m in our current setup) and/or spectromicroscopy.\u003c/p\u003e \u003cp\u003eIn Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e2\u003c/span\u003e we present the results of the XRF spectromicroscopy stack acquired for an area (~\u0026thinsp;3.3\u0026times;10\u003csup\u003e6\u003c/sup\u003e \u0026micro;m\u003csup\u003e2\u003c/sup\u003e) surrounding a carbon-rich root fragment which not only produced a good contrast between different soil components (pores, root, soil matrix), but also depicted variations in spectral information within different regions of interests (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e2\u003c/span\u003e). As expected, low intensity C signal was found in soil pores, or in carbon-deficient areas. The spectra measured for the root area shows peaks at 285.3, 287, and 288.4 eV associated with aromatic, aliphatic and carboxylic carbon moieties(Solomon et al. \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e2005\u003c/span\u003e; Lutfalla et al. \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). Interestingly, the soil matrix in the vicinity of the pores exhibited higher overall carbon content, despite showing a relatively similar spectral composition to other soil matrix regions. Additionally, a peak at 290.1 eV associated with carbonate moiety(Lutfalla et al. \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e2019\u003c/span\u003e) was present in the soil matrix regions. The demonstrated ability to visualize the spatial distribution of these species and compounds is particularly intriguing since they play a significant role in carbon protection and persistence(Kravchenko et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2019a\u003c/span\u003e; Lehmann et al. \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2020\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eIn Fig.\u0026nbsp;3, we demonstrate a procedure for fitting reference organic compounds to the spectromicroscopy stack using linear combinations to obtain compositional maps. By fitting NEXAFS spectra references to the spectromicroscopy stack data, we observed internal contrast within the map, revealing regions with distinct chemical composition (Fig.\u0026nbsp;3).\u003c/p\u003e \u003cp\u003eAnalysis of the different compositional maps (Fig.\u0026nbsp;3c) reveals a high concentration of aromatic carbon around the root and soil matrix, particularly in the vicinity of the pores. Additionally, a high concentration of aliphatic compounds is observed mainly in the root area, while the pore-matrix interface exhibits a higher concentration of carboxylic compounds. This spatial distribution suggests a correlation between the soil structure and the distribution of carbon compounds. The root acts as a primary carbon source. Pores facilitate microbial decomposition(Kravchenko et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2019a\u003c/span\u003e), which explains the high concentration of carboxylic compounds around the pore interface. Finally, the soil matrix serves as a carbon sink, containing more complex, aromatic carbon compounds.\u003c/p\u003e \u003cp\u003eBy preserving soil structure and enabling the visualization of carbon distribution in relation to key soil features such as pores, roots, and the soil matrix, this approach provides unique insights into the spatial relationships between soil structure and SOC composition. The observed patterns of carbon compounds associated with different soil structural features suggest a complex interplay between carbon sources, microbial activity, and soil physical properties. Future applications of this technique, combined with complementary imaging methods, could significantly enhance our understanding of soil carbon cycling and \u003cb\u003eFig.\u0026nbsp;3.\u003c/b\u003e Mapping carbon composition of an intact soil sample surface. (a) reference standard NEXAFS spectra of aromatic, aliphatic and carboxylic compounds. (b) composite image of aromatic (red), aliphatic (blue), and carboxylic (green) carbon following a linear combination fit, and the separate compositional maps channels (c).\u003c/p\u003e \u003cp\u003estorage.\u003c/p\u003e"},{"header":"4. Conclusions","content":"\u003cp\u003eThis study introduces a novel approach to mapping carbon contents and compositions on surfaces of landscape relevant, intact samples at micron-scale resolution using synchrotron X-ray spectromicroscopy. The ability to analyze relatively large samples without compromising their structural integrity is a significant advancement that can be extended to other environmental or engineered samples where spatially resolved chemical carbon information is required. This approach opens new possibilities for investigating the mechanisms of carbon protection and persistence in soils, bridging the gap between micro-scale processes and landscape-level carbon dynamics. By integrating spatially resolved structural and chemical information from intact samples, this work paves the way for a more comprehensive and quantitative understanding of carbon sequestration and storage mechanisms, with potential implications for soil carbon management and climate change mitigation strategies.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e \u003ch2\u003eCompeting Interests\u003c/h2\u003e \u003cp\u003eThe authors have no relevant financial or non-financial interests to disclose.\u003c/p\u003e \u003c/p\u003e\u003ch2\u003eFunding\u003c/h2\u003e \u003cp\u003eThis work was supported by the United Stated Department of Agriculture (Grant number 2023-67019-39840)\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eBaveye PC, Otten W, Kravchenko A et al (2018) Emergent properties of microbial activity in heterogeneous soil microenvironments: Different research approaches are slowly converging, yet major challenges remain. 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Accessed 20 May 2024\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"environmental-chemistry-letters","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"ecle","sideBox":"Learn more about [Environmental Chemistry Letters](https://www.springer.com/journal/10311)","snPcode":"10311","submissionUrl":"https://submission.nature.com/new-submission/10311/3","title":"Environmental Chemistry Letters","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Carbon Spectromicroscopy, X-ray spectroscopic imaging, NEXAFS, Micro X-ray Fluorescence, Soil Carbon, Caron Sequestration","lastPublishedDoi":"10.21203/rs.3.rs-4707647/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4707647/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eSoil organic carbon (SOC) plays a crucial role in soil fertility, productivity, and global carbon cycling. However, the mechanisms governing SOC persistence and turnover are not fully understood, hindering effective carbon management strategies. Especially limiting are challenges to visualize and characterize spatial distribution patterns of SOC within the intact soil. This study presents a novel approach to map carbon content and composition in intact environmental samples using synchrotron X-ray spectromicroscopy at a 4-100 \u0026micro;m resolution. X-ray fluorescence (XRF) maps provided an overview of the total carbon distribution, enabling the identification of carbon-rich regions of interest. Near edge X-ray absorption fine structure (NEXAFS) spectromicroscopy was then employed to obtain spatially resolved carbon speciation data within these regions. This method enabled the analysis of relatively large intact samples (16,000 \u0026micro;m \u0026Oslash; and 15,000 \u0026micro;m height), preserving a variety of root and organic matter fragments as well as pores ranging in size from 35 to 850 mm. Spectral fitting using reference standards revealed distinct spatial patterns of aromatic, aliphatic, and carboxylic carbon compounds associated with different structural features. Aromatic carbon was enriched around root fragments and the soil matrix, while carboxylic compounds were concentrated at pore-matrix interfaces, suggesting a correlation between soil pore structure and carbon chemical composition. The proposed novel approach provides opportunities for future unprecedented insights into the interplay between pore architecture and organic molecular diversity, the two key factors governing mechanisms of SOC protection and persistence in the soil.\u003c/p\u003e","manuscriptTitle":"Micro-Scale Mapping of Soil Organic Carbon: The Potential of Soft X-Ray Spectromicroscopy","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-08-17 01:34:27","doi":"10.21203/rs.3.rs-4707647/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"reviewerAgreed","content":"","date":"2024-07-23T08:53:56+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-07-17T19:02:19+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-07-11T08:38:48+00:00","index":"","fulltext":""},{"type":"submitted","content":"Environmental Chemistry Letters","date":"2024-07-08T15:38:29+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"environmental-chemistry-letters","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"ecle","sideBox":"Learn more about [Environmental Chemistry Letters](https://www.springer.com/journal/10311)","snPcode":"10311","submissionUrl":"https://submission.nature.com/new-submission/10311/3","title":"Environmental Chemistry Letters","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"091cf901-5b7f-445e-8a91-294aa7ffc83d","owner":[],"postedDate":"August 17th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-01-06T16:03:26+00:00","versionOfRecord":{"articleIdentity":"rs-4707647","link":"https://doi.org/10.1007/s10311-024-01817-0","journal":{"identity":"environmental-chemistry-letters","isVorOnly":false,"title":"Environmental Chemistry Letters"},"publishedOn":"2025-01-02 15:57:41","publishedOnDateReadable":"January 2nd, 2025"},"versionCreatedAt":"2024-08-17 01:34:27","video":"","vorDoi":"10.1007/s10311-024-01817-0","vorDoiUrl":"https://doi.org/10.1007/s10311-024-01817-0","workflowStages":[]},"version":"v1","identity":"rs-4707647","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4707647","identity":"rs-4707647","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}