Comparison of nuclear magnetic resonance methods for the analysis of organic matter composition from soil density and particle fractions
Abstract
Environmental context The association of specific organic matter (OM) compounds with clay mineral surfaces is believed to protect these compounds from degradation and thus result in long-term protection in soil. The molecular-level composition of soil OM associated with soil fractions was measured and compared using solid-state 13C nuclear magnetic resonance (NMR) and solution-state 1H NMR methods. Combining these methods allowed more detailed characterisation of OM associated with different soil fractions and will improve the understanding of OM dynamics in soil. Abstract Organic matter (OM) associated with fine soil fractions is hypothesised to be protected from complete biodegradation by soil microbes. It is therefore important to understand the structure and stage of decomposition of OM associated with various soil fractions. Solid-state 13C nuclear magnetic resonance (NMR) spectroscopy has been used extensively to investigate the OM composition of soils and soil fractions. Solution-state 1H NMR spectroscopy has not been used as much but is an emerging tool for analysing soil OM because 1H NMR spectra are often better resolved and provide information that complements the structural information obtained from solid-state 13C NMR experiments. This study compares one-dimensional solution-state 1H NMR and solid-state 13C NMR methods for assessing the degradation and composition of OM in three different soils, and their light and clay-size fractions. The alkyl/O-alkyl degradation parameter was consistent across all NMR methods and showed that OM associated with clay-size fractions were at more advanced stages of degradation as compared to that in light density soil fractions. Solution-state 1H and diffusion edited (DE) 1H NMR results showed the presence of high concentrations of microbial-derived peptidoglycan and peptide side-chains in clay-sized fractions. Lignin was also identified in clay-sized fractions using solid-state 13C and solution-state 1H NMR techniques. The combination of solid-state 13C and solution-state 1H NMR methods provides a more detailed analysis of OM composition and thereby facilitates a better understanding of the fate and preservation of OM in soil.
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Other methods to characterize quality and quantity of total soil organic matter, such as thermal and spectroscopic methods, are rapidly developing.
“Other methods to characterize (quality and quantity) of total soil organic matter such as thermal and spectroscopic methods are rapidly developing”
From Soil quality – A critical review (2018) · cites this paper as Clemente et al., 2012
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Soil quality – A critical review
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“D 1H NMR spectra (Simpson et al., 2002b, 2003; Deshmukh et al., 2005; Feng et al., 2005, 2008; Clemente et al., 2011, 2012).”
BackgroundMethodInfluentialSelf-citationSoil warming and nitrogen deposition alter soil organic matter composition at the molecular-level
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“Chemical shift assignments are based on previously published data (Clemente et al. 2012; Deshmukh et al. 2003, 2007; Kelleher and Simpson 2006; Pautler et al. 2013; Simpson et al. 2001, 2004, 2007; Woods et al. 2011) and confirmed by 2-”
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“…(2.9–4.1 ppm); the 1H on an a-C from peptides (4.1–4.8 ppm); the 1H in anomeric structures of carbohydrates (4.8–5.2 ppm); aromatic structures attributed to lignin and peptide side chains (6.2–7.8 ppm); amide structures from peptides (7.8–8.4 ppm; Clemente et al. 2012; Simpson et al. 2007).”
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“The solution-state (1)H NMR and DE (1)H NMR spectra were integrated into seven regions (Clemente et al., 2012): alkyl proton (0.”
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“Since the solution-state NMR data showed slight sorption of protein-derived DOM to gibbsite (Supplementary Materials Figure S9c), the aromatic signals observed using HR-MAS NMR likely originated from aromatic amino acids such as phenylalanine and tyrosine [43,45].”
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“This trend is consistent with the results of several studies which show that microbially-derived compounds dominate in fine size fractions (Clemente et al., 2011, 2012; Dümig et al., 2012).”
BackgroundResultSelf-citationLinking organic matter composition in acid sulfate soils to pH recovery after re-submerging
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“This trend may be attributed to the following: 1) preservation of the lignin compounds (depleted in C) in LF (Natelhoffer and Fry, 1988; Golchin et al., 1994; Clemente et al., 2012); and 2) a microbial fractionation effect of crop residue decomposition (Deléens et al.”
Márquez, C. O., García, V. J., Schultz, R. C., & Isenhart, T. M. (2017) · European Journal of Soil Science · doi:10.1111/ejss.12422 · Cited by 15 · see citing works
“, 2017) and lignin with minor contributions from proteins (Clemente et al., 2012).”
BackgroundKölbl, A., Bucka, F. B., Marschner, P., Mosley, L. M., Fitzpatrick, R. W., Schulz, S., Lueders, T., & Kögel‐Knabner, I. (2019) · Geoderma · doi:10.1016/j.geoderma.2019.04.006 · Cited by 14 · see citing works
Lin, Y., Lin, Y.-Z., & Lin, Y. (2022) · Scientific Reports · doi:10.1038/s41598-022-19714-3 · Cited by 12 · see citing works
Pautler, B. G., Sanborn, P. T., Simpson, A. J., & Simpson, M. J. (2013) · Organic Geochemistry · doi:10.1016/j.orggeochem.2013.08.009 · Cited by 12 · see citing works
Self-citationMyers‐Pigg, A., Grieger, S., Roebuck, A., Barnes, M., Bladon, K. D., Bailey, J. D., Barton, R., Chu, R., Graham, E. B., Homolka, K., et al. (2024) · Environmental Science & Technology · doi:10.1021/acs.est.3c10826 · Cited by 13 · see citing works
Kang, H., Gao, H., & Yu, W. (2017) · Spectroscopy Letters · doi:10.1080/00387010.2017.1297956 · Cited by 10 · see citing works
“The spectra were integrated into the following chemical shift regions: alkyl carbon (0–50 ppm), O-alkyl carbon (50–110 ppm), aromatic carbon (110–160 ppm), and carbonyl carbon (160–200 ppm).([16])”
BackgroundCourtier‐Murias, D., Farooq, H., Longstaffe, J. G., Kelleher, B. P., Hart, K. M., Simpson, M. J., & Simpson, A. J. (2014) · Geoderma · doi:10.1016/j.geoderma.2014.03.006 · Cited by 10 · see citing works
Self-citationMan, M., Gregorich, E., Beare, M., Ellert, B., & Simpson, M. J. (2023) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2023.10.008 · Cited by 8 · see citing works
Self-citationTong, H., Behazin, M., & Simpson, M. J. (2022) · Applied Clay Science · doi:10.1016/j.clay.2022.106808 · Cited by 9 · see citing works
Self-citationStoica, I., Anaraki, M. T., Muratore, T., Knorr, M. A., Frey, S. D., & Simpson, M. J. (2023) · ACS Earth and Space Chemistry · doi:10.1021/acsearthspacechem.2c00380 · Cited by 7 · see citing works
Self-citationEnvironmental NMR: Diffusion Ordered Spectroscopy Methods
Zheng, G. F., & Price, W. S. (1996) · doi:10.1002/9780470034590.emrstm1336 · Cited by 7 · see citing works
Nie, X., Jiao, P., Yang, L., & Li, Z. (2025) · Geoderma · doi:10.1016/j.geoderma.2025.117348 · Cited by 6 · see citing works
Liu, Q., Cao, Y., Huang, Y., Zhang, Y., Lin, J., Lin, J. M., & Xu, L. (2013) · Contemporary Problems of Ecology · doi:10.1134/s1995425513050077 · Cited by 6 · see citing works
Surface soil organic carbon in temperate and subtropical oriental oak stands of East China
Yu, W., Fahey, T. J., Kang, H., & Zhou, P. (2016) · Canadian Journal of Forest Research · doi:10.1139/cjfr-2015-0324 · Cited by 6 · see citing works
Liu, Y., Chen, X., Leng, Y., Wang, S., Liu, H., Zhang, W., Li, N., Li, N., Ning, Z., Gao, W., et al. (2024) · Environmental Research · doi:10.1016/j.envres.2024.119903 · Cited by 5 · see citing works
Solid-State 13 C Nuclear Magnetic Resonance (NMR) Analysis of Soil Organic Matter
Simpson, M. J., Simpson, A. J., & Kingery, W. L. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-409548-9.10275-1 · Cited by 5 · see citing works
Self-citationnmrrr: A Reproducible Workflow for Binning and Visualizing NMR Spectra From Environmental Samples
Patel, K., Myers‐Pigg, A., Bond‐Lamberty, B., & Barnes, M. (2023) · Journal of Geophysical Research Biogeosciences · doi:10.1029/2023jg007768 · Cited by 4 · see citing works
“The interpretation of these peaks and groups may vary by sample/matrix type and ecological context; users are referred to reviews by Clemente et al. (2012), Mitschke et al. (2023), Simpson et al. (2018), and Cade-Menun (2005, 2015) for more details on the different functional groups identified…”
BackgroundMethodInfluentialAplicaciones de técnicas espectroscópicas para el análisis de suelos
Rodríguez, W., R., P. A. G., & Alberto Fajardo, O. (2016) · Revista Facultad de Ciencias Básicas · doi:10.18359/rfcb.2030 · Cited by 4 · see citing works
Tong, H., Behazin, M., & Simpson, M. J. (2023) · Applied Geochemistry · doi:10.1016/j.apgeochem.2023.105746 · Cited by 3 · see citing works
Self-citationDia, M., Farjon, J., Raveleau, C., Simpson, A. J., Peyneau, P., Bechet, B., & Courtier‐Murias, D. (2024) · Magnetic Resonance in Chemistry · doi:10.1002/mrc.5487 · Cited by 3 · see citing works
Self-citationIMPACTS OF CLIMATE CHANGE ON SOIL MICROORGANISMS IN NORTHERN HARDWOOD FORESTS
Kratz, C. (2014) · doi:10.37099/mtu.dc.etds/755 · Cited by 3 · see citing works
Mitchell, P. J., Simpson, A. J., & Simpson, M. J. (1996) · Encyclopedia of Magnetic Resonance · doi:10.1002/9780470034590.emrstm1348 · Cited by 3 · see citing works
Self-citationBongiorno, G. (2020) · doi:10.18174/509232 · Cited by 2 · see citing works
Water-mediated NOE: a promising tool for interrogating interfacial clay–xenobiotic interactions
Soong, R., Botana, A., Wang, J., Farooq, H., Courtier‐Murias, D., & Simpson, A. J. (2017) · Chemical and Biological Technologies in Agriculture · doi:10.1186/s40538-016-0084-2 · Cited by 2 · see citing works
Self-citationnmrrr: Binning and Visualizing NMR Spectra in Environmental Samples
Patel, K., & Myers‐Pigg, A. (2023) · doi:10.32614/cran.package.nmrrr · Cited by 2 · see citing works
Characterization of Natural Organic Matter in Bentonite Clays and Clay-rich Sediments
Marshall, H. M. M. (2014) · TSpace (University of Toronto)
Huang, L., Huang, Y., Nie, J., Geng, M., Lu, Y., Liao, Y., & Xue, B. (2022) · Research Square · doi:10.21203/rs.3.rs-1695905/v1
Lu, Y. Q., Zhang, T. Z., Yang, P., Li, L., Zhong, M., Zhang, Y., & Shi, X. W. (2026) · European Journal of Environmental and Civil engineering · doi:10.1080/19648189.2026.2628999
Román, A. X. S., Frey, S. D., Knorr, M. A., Tong, H., Melillo, J. M., & Simpson, M. J. (2026) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2026.181777
Self-citationEscobar, A. B., O’Donnell, A. J., Nealon, G. L., & Grierson, P. F. (2026) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2026.181938
Román, A. X. S., Chen, G., Ronda, K., Muratore, T., Knorr, M. A., Frey, S. D., Wang, J., Simpson, A. J., & Simpson, M. J. (2026) · Environmental Science & Technology · doi:10.1021/acs.est.6c04800
Self-citationField portable soil spectroscopy: What’s beyond Vis-NIR?
Huang, Y., Ng, W., O’Donoghue, T., Minasny, B., & McBratney, A. B. (2026) · Computers and Electronics in Agriculture · doi:10.1016/j.compag.2026.112321
Norris, C. E., Young, E. H., Adesanya, T., Beauregard, J., Carodenuto, S., Diochon, A., Jones, M. D., Karst, J., Laganière, J., McIntosh, A. C. S., et al. (2026) · Canadian Journal of Soil Science · doi:10.1139/cjss-2026-0052
Self-citationRomán, A. X. S., Weng, Y., Dunfield, K. E., Wagner‐Riddle, C., & Simpson, M. J. (2026) · Agriculture Ecosystems & Environment · doi:10.1016/j.agee.2026.110800
Self-citation
- Authors
- Clemente, J. S., Gregorich, E. G., Simpson, A. J., Kumar, R., Courtier-Murias, D., & Simpson, M. J.
- Affiliations
- University of Toronto (CA)
- Agriculture and Agri-Food Canada (CA)
- Bruker (Canada) (CA)
- ADepartment of Chemistry, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.
- Corresponding author
- Simpson, Myrna J.
- Venue
- Environmental Chemistry
- Publisher
- CSIRO Publishing
- Published
- 2012-02-23
- Volume
- 9
- Issue
- 1
- Pages
- 97-107
- ISSN
- 1448-2517 (ISSN-L)
- 1449-8979
- OpenAlex
- W2112619788
- Cited by
- 67
- References
- 62
- Citations by year
- 2026: 7 · 2025: 1 · 2024: 5 · 2023: 5 · 2022: 4 · 2021: 2 · 2020: 3 · 2019: 3 · 2018: 3 · 2017: 9 · 2016: 7 · 2015: 2 · 2014: 8 · 2013: 3 · 2012: 3
- FWCI
- 7.81
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Environmental Chemistry (publishedVersion)
- Funders
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
- Physical Sciences › Environmental Science › Environmental Engineering › Soil Geostatistics and Mapping
- Keywords
- soil organic matter, organic matter composition, clay content, organic matter decomposition, peptidoglycan, peptide side chains, lignin, solid-state 13C NMR, soil organic matter protection, soil organic matter dynamics
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