Bridging Pedology and Data Science: Machine Learning Applications for Soil Organic Matter and Carbon Analysis
Source abstract
Abstract
Accurate quantification of soil organic matter (SOM) and carbon content is critical for understanding climate change, evaluating soil health, supporting agricultural sustainability, and implementing carbon sequestration policies. For decades, classical analytical and statistical approaches have underpinned soil carbon assessment, but the emergence of machine learning (ML) techniques offers new opportunities to improve prediction accuracy, scalability, and efficiency. This review summarises the current knowledge on classical and ML-based approaches for analysing SOM and carbon content. We examine the strengths, limitations, and practical applications of conventional methods, including wet chemistry, dry combustion analysis, and geostatistical techniques, alongside modern ML approaches such as random forests (RFs), gradient boosting machines, neural networks, deep learning, and hybrid ML-geostatistical frameworks. Special emphasis is placed on comparative analysis across dimensions, including prediction accuracy, computational requirements, data availability needs, interpretability, uncertainty quantification, and scalability. Soil carbon stocks and dynamics are tightly regulated by indigenous soil microbial communities and their management-driven alterations, creating substantial biologically driven variation that remains difficult to capture with current modelling approaches. We therefore explore hybrid approaches that integrate classical pedological knowledge with ML capabilities. Finally, we discuss emerging challenges, future research directions, and the complementary role these approaches play in advancing soil carbon science. This review concludes that neither classical nor ML approaches alone are sufficient for accurate carbon assessment across diverse scales and environments. Instead, their strategic integration, combining classical mechanistic grounding alongside machine learning’s scalability, represents the most promising path toward realistic soil carbon evaluation for climate change mitigation and agricultural sustainability.
Source: crossref · Quality: baseline
Research context
OpenAlex topics: Soil Geostatistics and Mapping · Soil Carbon and Nitrogen Dynamics · Iron oxide chemistry and applications
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
Affiliations
UWA School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia
UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
References (100+)
Show source-provided references
1. Global stocks and capacity of mineral-associated soil organic carbon10.1038/s41467-022-31540-9 ↗
2. Soil Carbon Sequestration Impacts on Global Climate Change and Food Security10.1126/science.1097396 ↗
3. Global change pressures on soils from land use and management10.1111/gcb.13068 ↗
4. Total carbon and nitrogen in the soils of the world10.1111/j.1365-2389.1996.tb01386.x ↗
5. Soil carbon sequestration and land-use change: Processes and potential10.1046/j.1365-2486.2000.00308.x ↗
6. A global meta-analysis of soil organic carbon in the Anthropocene10.1038/s41467-023-39338-z ↗
7. Temporal adjustment approach for high-resolution continental scale modeling of soil organic carbon10.1038/s41598-025-89503-1 ↗
8. Attribution of crop yield responses to application of organic amendments: A critical review10.1016/j.still.2018.10.002 ↗
9. Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales10.1128/AEM.00324-19 ↗
10. Țopa, D.C., Căpșună, S., Calistru, A.E., and Ailincăi, C. (2025). Sustainable Practices for Enhancing Soil Health and Crop Quality in Modern Agriculture: A Review. Agriculture, 15.10.3390/agriculture15090998 ↗
11. Methods assessment for organic and inorganic carbon quantification in calcareous soils of the Mediterranean region10.1016/j.geodrs.2017.12.001 ↗
12. Prediction of soil organic and inorganic carbon concentrations in Tunisian samples by mid-infrared reflectance spectroscopy using a French national library10.1016/j.geoderma.2020.114469 ↗
13. A partitioned conditioned Latin hypercube sampling method considering spatial heterogeneity in digital soil mapping10.1038/s41598-025-95631-5 ↗
14. Evaluating sampling efforts of standard laboratory analysis and mid-infrared spectroscopy for cost effective digital soil mapping at field scale10.1016/j.geoderma.2019.113925 ↗
15. Artificial intelligence in soil science10.1111/ejss.70080 ↗
16. Bouslihim, Y., Rochdi, A., Aboutayeb, R., El Amrani-Paaza, N., Miftah, A., and Hssaini, L. (2021). Soil Aggregate Stability Mapping Using Remote Sensing and GIS-Based Machine Learning Technique. Front. Earth Sci., 9.10.3389/feart.2021.748859 ↗
17. Challenges and opportunities in remote sensing-based crop monitoring: A review10.1093/nsr/nwac290 ↗
18. Environmental variables improve the accuracy of remote sensing estimation of soil organic carbon content10.1038/s41598-024-68424-5 ↗
19. Soil organic carbon estimation using remote sensing data-driven machine learning10.7717/peerj.17836 ↗
20. John, K., Abraham Isong, I., Michael Kebonye, N., Okon Ayito, E., Chapman Agyeman, P., and Marcus Afu, S. (2020). Using Machine Learning Algorithms to Estimate Soil Organic Carbon Variability with Environmental Variables and Soil Nutrient Indicators in an Alluvial Soil. Land, 9.10.3390/land9120487 ↗
21. Miao, T., Ji, W., Li, B., Zhu, X., Yin, J., Yang, J., Huang, Y., Cao, Y., Yao, D., and Kong, X. (2024). Advanced Soil Organic Matter Prediction with a Regional Soil NIR Spectral Library Using Long ShortTerm Memory–Convolutional Neural Networks: A Case Study. Remote Sens., 16.10.3390/rs16071256 ↗
22. Knowledge-guided machine learning can improve carbon cycle quantification in agroecosystems10.1038/s41467-023-43860-5 ↗
23. Machine learning-based estimation of soil organic carbon in Thailand’s cash crops using multispectral and SAR data fusion combined with environmental variables10.1080/10095020.2024.2440608 ↗
24. Abrar, M.M., Waqas, M.A., Mehmood, K., Fan, R., Memon, M.S., Khan, M.A., Siddique, N., Xu, M., and Du, J. (2025). Organic carbon sequestration in global croplands: Evidenced through a bibliometric approach. Front. Environ. Sci., 13.10.3389/fenvs.2025.1495991 ↗
25. Estimation of soil organic carbon as a function of soil pretreatment and spectral features of radiometers within the visible and near-infrared spectra10.1080/00224561.2025.2528348 ↗
26. Temperature and soil organic matter decomposition rates—Synthesis of current knowledge and a way forward10.1111/j.1365-2486.2011.02496.x ↗
27. Reverse microdialysis: A window into root exudation hotspots10.1016/j.soilbio.2022.108829 ↗
28. Global turnover of soil mineral-associated and particulate organic carbon10.1038/s41467-024-49743-7 ↗
29. Climate and parent material controls on organic matter storage in surface soils: A three-pool, density-separation approach10.1016/j.geoderma.2008.07.010 ↗
30. Topographic controls of soil organic carbon on soil-mantled landscapes10.1038/s41598-019-42556-5 ↗
31. Wang, X., Chi, Y., and Song, S. (2024). Important soil microbiota’s effects on plants and soils: A comprehensive 30-year systematic literature review. Front. Microbiol., 15.10.3389/fmicb.2024.1347745 ↗
32. Tillage and land use management effects on soil organic matter and soil microbial biomass in a field network of practical farms in France, Romania, and Sweden10.1016/j.apsoil.2024.105584 ↗
33. Influence of Vegetation Coverage and Climate Environment on Soil Organic Carbon in the Qilian Mountains10.1038/s41598-019-53837-4 ↗
34. Temperature effects on carbon storage are controlled by soil stabilisation capacities10.1038/s41467-021-27101-1 ↗
35. Climate controls the global distribution of soil organic and inorganic carbon10.1016/j.ecolind.2025.113514 ↗
36. Clay amount and distribution influence organic carbon content in sand with subsoil clay addition10.1016/j.still.2018.08.001 ↗
37. Topography and land use impact erosion and soil organic carbon burial over decadal timescales10.1016/j.catena.2022.106578 ↗
38. Zhang, P., and Shao, M. (2014). Spatial Variability and Stocks of Soil Organic Carbon in the Gobi Desert of Northwestern China. PLoS ONE, 9.10.1371/journal.pone.0093584 ↗
39. Soil organic carbon depth profiles and centennial and millennial decay rates in tidal marsh, mangrove and seagrass blue carbon ecosystems10.1038/s43247-025-02390-2 ↗
40. Davis, M., Alves, B., Karlen, D., Kline, K., Galdos, M., and Abulebdeh, D. (2018). Review of Soil Organic Carbon Measurement Protocols: A US and Brazil Comparison and Recommendation. Sustainability, 10.10.3390/su10010053 ↗
41. Bravo-García, J., Camarillo-Naranjo, J.M., Blanco-Velázquez, F.J., and Anaya-Romero, M. (2025). Soil Organic Carbon Mapping Through Remote Sensing and In Situ Data with Random Forest by Using Google Earth Engine: A Case Study in Southern Africa. Land, 14.10.3390/land14071436 ↗
42. Advances in Molecular and Microscale Characterization of Soil Organic Matter: Current Limitations and Future Prospects10.1021/acs.est.2c00421 ↗
43. An Examination of The Degtjareff Method for Determining Soil Organic Matter, and A Proposed Modification of The Chromic Acid Titration Method10.1097/00010694-193401000-00003 ↗
44. Is the Walkley–Black Method Suitable for Organic Carbon Determination in Chilean Volcanic Soils?10.1080/00103620902896746 ↗
45. Comparison of methods for determining organic carbon content of urban soils in Central Ohio10.1016/j.geodrs.2023.e00680 ↗
46. Soil carbon determination by thermogravimetrics10.7717/peerj.6 ↗
47. Estimating soil organic carbon through loss on ignition: Effects of ignition conditions and structural water loss10.1111/ejss.12224 ↗
48. Refining Soil Organic Matter Determination by Loss-on-Ignition10.1016/S1002-0160(11)60149-5 ↗
49. Schulte, E.E., and Hopkins, B.G. (2015). Estimation of Soil Organic Matter by Weight Loss-On-Ignition. Soil Organic Matter: Analysis and Interpretation, Soil Science Society of America, Inc.
50. A global spectral library to characterize the world’s soil10.1016/j.earscirev.2016.01.012 ↗
51. Mid-infrared spectroscopy for accurate measurement of an extensive set of soil properties for assessing soil functions10.1016/j.soisec.2022.100043 ↗
52. Fourier-transform infrared spectroscopy for soil organic matter analysis10.1002/saj2.20583 ↗
53. FT-MIR Spectroscopic Analysis of the Organic Carbon Fractions in Australian Mineral Soils10.1111/ejss.70084 ↗
54. Development of Reflectance Spectral Libraries for Characterization of Soil Properties10.2136/sssaj2002.9880 ↗
55. Using combustion analysis to simultaneously measure soil organic and inorganic carbon10.1016/j.geoderma.2024.117066 ↗
56. Virk, S., Tucker, M., Harris, G., Smith, A., Levi, M., and Lessl, J. (2025). Efficacy and Economics of Different Soil Sampling Grid Sizes for Site-Specific Nutrient Management in Southeastern USA. Agronomy, 15.10.3390/agronomy15040903 ↗
57. Grid-based soil sampling for Northeast Region phosphorus index assessment10.1002/saj2.70156 ↗
58. Sampling for validation of digital soil maps10.1111/j.1365-2389.2011.01364.x ↗
59. Using targeted sampling to process multivariate soil sensing data10.1016/j.geoderma.2011.04.004 ↗
60. Effects of sampling density on interpolation accuracy for farmland soil organic matter concentration in a large region of complex topography10.1016/j.ecolind.2018.05.044 ↗
61. Radočaj, D., Jug, I., Vukadinović, V., Jurišić, M., and Gašparović, M. (2021). The Effect of Soil Sampling Density and Spatial Autocorrelation on Interpolation Accuracy of Chemical Soil Properties in Arable Cropland. Agronomy, 11.10.3390/agronomy11122430 ↗
62. Spatial prediction models for landslide hazards: Review, comparison and evaluation10.5194/nhess-5-853-2005 ↗
63. Geostatistics in soil science: State-of-the-art and perspectives10.1016/S0016-7061(98)00078-0 ↗
64. Fongaro, C.T., Demattê, J.A.M., Rizzo, R., Lucas Safanelli, J., Mendes, W.D.S., Dotto, A.C., Vicente, L.E., Franceschini, M.H.D., and Ustin, S.L. (2018). Improvement of Clay and Sand Quantification Based on a Novel Approach with a Focus on Multispectral Satellite Images. Remote Sens., 10.10.3390/rs10101555 ↗
65. Digital mapping of soil organic carbon in a plain area based on time-series features10.1016/j.ecolind.2025.113215 ↗
66. Dhawale, N.M., Adamchuk, V.I., Prasher, S.O., and Viscarra Rossel, R.A. (2021). Evaluating the Precision and Accuracy of Proximal Soil vis–NIR Sensors for Estimating Soil Organic Matter and Texture. Soil Syst., 5.10.3390/soilsystems5030048 ↗
67. Microbial trait multifunctionality drives soil organic matter formation potential10.1038/s41467-024-53947-2 ↗
68. PLS-regression: A basic tool of chemometrics10.1016/S0169-7439(01)00155-1 ↗
69. Large scale mapping of soil organic carbon concentration with 3D machine learning and satellite observations10.1016/j.geoderma.2021.115402 ↗
70. van Wesemael, B., Chabrillat, S., Dias, A.S., Berger, M., and Szantoi, Z. (2023). Remote Sensing for Soil Organic Carbon Mapping and Monitoring. Remote Sens., 15.10.3390/rs15143464 ↗
71. The knowns, known unknowns and unknowns of sequestration of soil organic carbon10.1016/j.agee.2012.10.001 ↗
72. Comparing Four Methods of Measuring Soil Organic Matter in North Carolina Soils10.2136/sssaj2018.03.0105 ↗
73. Optimal interpolation and isarithmic mapping of soil properties: I The semi-variogram and punctual kriging10.1111/ejss.12784 ↗
74. Smart farming revolution: Leveraging machine learning for sustainable agriculture10.1016/j.jclepro.2025.146434 ↗
75. Xing, Y., Xie, Y., and Wang, X. (2025). Enhancing soil health through balanced fertilization: A pathway to sustainable agriculture and food security. Front. Microbiol., 16.10.3389/fmicb.2025.1536524 ↗
76. Yang, M., Xu, D., Chen, S., Li, H., and Shi, Z. (2019). Evaluation of Machine Learning Approaches to Predict Soil Organic Matter and pH Using vis-NIR Spectra. Sensors, 19.10.3390/s19020263 ↗
77. Predicting soil organic carbon with ensemble learning techniques by using satellite images for precision farming10.1038/s41598-025-09804-3 ↗
78. Towards Explainable AI: Interpreting Soil Organic Carbon Prediction Models Using a Learning-Based Explanation Method10.1111/ejss.70071 ↗
79. Enhanced VNIR and MIR proximal sensing of soil organic matter and PLFA-derived soil microbial properties through machine learning ensembles and external parameter orthogonalization10.1016/j.geoderma.2024.117037 ↗
80. Ben Ghorbal, A., Grine, A., Eid, M.M., and El-kenawy, E.S.M. (2025). Sustainable soil organic carbon prediction using machine learning and the ninja optimization algorithm. Front. Environ. Sci., 13.10.3389/fenvs.2025.1630762 ↗
81. Improving spatial prediction of soil organic matter in central Vietnam using Bayesian-enhanced machine learning and environmental covariates10.1080/03650340.2024.2448623 ↗
82. Narváez-Ortiz, W.A., Reyes-Valdés, M.H., Cabrera-De la Fuente, M., and Benavides-Mendoza, A. (2022). Multiple Linear and Polynomial Models for Studying the Dynamics of the Soil Solution. Soil Syst., 6.10.3390/soilsystems6020042 ↗
83. A detailed mapping of soil organic matter content in arable land based on the multitemporal soil line coefficients and neural network filtering of big remote sensing data10.1016/j.geoderma.2024.116941 ↗
84. Practical Bayesian support vector regression for financial time series prediction and market condition change detection10.1080/14697688.2016.1267868 ↗
85. Elhallaoui Oueldkaddour, F.Z., Wariaghli, F., Brirhet, H., Yahyaoui, A., and Jaziri, H. (2025). Comparison of Machine Learning Models for Real-Time Flow Forecasting in the Semi-Arid Bouregreg Basin. Limnol. Rev., 25.10.3390/limnolrev25010006 ↗
86. A comparative assessment of support vector regression, artificial neural networks, and random forests for predicting and mapping soil organic carbon stocks across an Afromontane landscape10.1016/j.ecolind.2014.12.028 ↗
87. On the optimization of the support vector machine regression hyperparameters setting for gas sensors array applications10.1016/j.chemolab.2018.11.011 ↗
88. Quantifying the ability of environmental parameters to predict soil texture fractions using regression-tree model with GIS and LIDAR data: The case study of Denmark10.1016/j.ecolind.2011.10.006 ↗
89. Modelling and prediction of major soil chemical properties with Random Forest: Machine learning as tool to understand soil-environment relationships in Antarctica10.1016/j.catena.2023.107677 ↗
90. Modelling species presence-only data with random forests10.1111/ecog.05615 ↗
91. Random forest regression kriging modeling for soil organic carbon density estimation using multi-source environmental data in central Vietnamese forests10.1007/s40808-024-02158-1 ↗
92. Random forest algorithm for classification of multiwavelength data10.1088/1674-4527/9/2/011 ↗
93. Random forest missing data algorithms10.1002/sam.11348 ↗
94. Hyperparameters and tuning strategies for random forest10.1002/widm.1301 ↗
95. Spatial prediction of soil organic carbon: Combining machine learning with residual kriging in an agricultural lowland area (Lombardy region, Italy)10.1016/j.geoderma.2024.116953 ↗
96. An ensemble estimate of Australian soil organic carbon using machine learning and process-based modelling10.5194/soil-10-619-2024 ↗
97. Applicability of machine learning models for predicting soil organic carbon content and bulk density under different soil conditions10.37501/soilsa/165879 ↗
98. Li, Y., Yao, G., Li, S., and Dong, X. (2025). Predicting and Mapping of Soil Organic Matter with Machine Learning in the Black Soil Region of the Southern Northeast Plain of China. Agronomy, 15.10.3390/agronomy15030533 ↗
99. Natekin, A., and Knoll, A. (2013). Gradient boosting machines, a tutorial. Front. Neurorobot., 7.10.3389/fnbot.2013.00021 ↗
100. XGBoost: A Scalable Tree Boosting System