ISSN 0137-0944
eISSN 2949-6144
En Ru
ISSN 0137-0944
eISSN 2949-6144
Focused ion beam scanning electron microscopy in soil science: new approaches to soil structure analysis

Focused ion beam scanning electron microscopy in soil science: new approaches to soil structure analysis

Abstract

This paper examines the use of focused ion beam imaging combined with scanning electron microscopy (FIB-SEM) to study the submicron structure of soil aggregates. The study focused on migratory-micellar chernozem soil from the Central Chernozem Reserve. A comparative analysis was conducted between images obtained using FIB-SEM and X-ray computed tomography. The primary objective of the study was to determine whether FIB-SEM studies could complement those using computed tomography alone. FIB-SEM demonstrated the ability to detect pores with a radius of less than 1 μm, which are inaccessible to tomography, and to identify organic inclusions and specific pore morphotypes (crack-like, elongated, and jagged), reflecting physicochemical processes at the nanoscale. However, the limited field of view and the high complexity of segmentation reduce the representativeness of the method. The obtained results confirm the applicability of FIB-SEM as a supplement to traditional tomography in the study of soil nanostructure, opening up prospects for the analysis of the spatial organization of organic matter and clarification of the mechanisms of structure formation at the submicron level.

References

1.    Абросимов К.Н. и др. Томография в почвоведении: от первых опытов к современным методам (обзор) // Почвоведение. 2021. Т. 55, № 9. С. 1097–1112. https://doi.org/10.31857/S0032180X21090021
2.    Герке К.М., Скворцова Е.Б., Корост Д.В. Томографический метод исследования порового пространства почв: состояние проблемы и изучение некоторых почв России // Почвоведение. 2012. № 7. С. 781–781.
3.    Иванов А.Л., Шеин Е.В., Скворцова Е.Б. Томография порового пространства почв: от морфологической характеристики к структурно-функциональным оценкам // Почвоведение. 2019. № 1. С. 61–69. https://doi.org/10.1134/S0032180X19010064
4.    Полевой определитель почв. М., 2008. 182 с.
5.    Романенко К.А., Абросимов К.Н., Курчатова А.Н. и др. Опыт применения рентгеновской компьютерной томографии в исследовании микростроения мерзлых пород и почв // Криосфера Земли. 2017. Т. 21, № 4. С. 75–81. https://doi.org/10.21782/KZ1560-7496-2017-4(75-81)
6.    Скворцова Е.Б. и др. Влияние многократного замораживания-оттаивания на микроструктуру агрегатов дерново-подзолистой почвы (микротомографический анализ) // Почвоведение. 2018. № 2. С. 187–196. https://doi.org/10.7868/S0032180X18020065
7.    Скворцова Е.Б. и др. Микротомографический метод изучения и оценки почвенной структуры // В сб.: Новые методы и результаты исследований ландшафтов в Европе, Центральной Азии и Сибири. 2018. С. 84–89. https://doi.org/10.25680/1044.2018.79.91.114
8.    Скворцова Е.Б. Строение порового пространства естественных и антропогенноизмененных почв: Дис. … д-ра с.-х. наук. М., 1999. 397 с.
9.    Толстыгин К.Д., Фомин Д.С., Юдина А.В. и др. Анализ гидрофизических свойств почв с использованием поросетевых моделей // Бюлл. Почвенного института им. В.В. Докучаева. 2025. Т. 123. С. 30–64. https://doi.org/10.19047/0136-1694-2025-123-30-64
10.    Фомин Д.С., Валдес-Коровкин И.А., Голуб А.П. и др. Оптимизация анализа агрегатного состава почв методом автоматического рассева // Бюлл. Почвенного института им. В.В. Докучаева. 2019. № 96. С. 149–177. https://doi.org/10.19047/0136-1694-2019-96-149-177
11.    Шеин Е.В. Курс физики почв: Учебник. М., 2005. 432 с.
12.    Abràmoff M.D., Magalhães P.J., Ram S.J. Image processing with ImageJ // Biophotonics International. 2004. Vol. 11, № 7. P. 36–42.
13.    Andrew M. A quantified study of segmentation techniques on synthetic geological XRM and FIB-SEM images // Computational Geosciences. 2018. Vol. 22, № 6. P. 1503–1512. https://doi.org/10.1007/s10596-018-9768-y
14.    Arachchige P.S.P., Hettiarachchi G.M., Rice C.W. et al. Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates // Scientific Reports. 2018. Vol. 8, № 1. P. 16810. https://doi.org/10.1038/s41598-018-34981-9
15.    FitzPatrick E.A. Soil Microscopy and Micromorphology. Chichester, 1993. Т. 158. Vol. 16.
16.    Fomin D.S., Yudina A.V., Romanenko K.A. et al. Soil pore structure dynamics under steady-state wetting-drying cycle // Geoderma. 2023. Vol. 432. P. 116401. https://doi.org/10.1016/j.geoderma.2023.116401
17.    Gao W., Schlüter S., Blaser S.R. et al. A shape-based method for automatic and rapid segmentation of roots in soil from X-ray computed tomography images: Rootine // Plant and Soil. 2019. Vol. 441. P. 643–655. https://doi.org/10.1007/s11104-019-04053-6
18.    Gerke K.M., Korostilev E.V., Romanenko K.A. et al. Going submicron in the precise analysis of soil structure: A FIB-SEM imaging study at nanoscale // Geoderma. 2021. Vol. 383. P. 114739. https://doi.org/10.1016/j.geoderma.2020.114739
19.    Gerke K.M., Vasilyev R.V., Korost D.V. et al. D Determining physical properties of unconventional reservoir rocks: from laboratory methods to pore-scale modeling // SPE Asia Pacific Unconventional Resources Conference and Exhibition. SPE, 2013. Paper SPE-167058-MS. https://doi.org/10.2118/167058-MS
20.    Groeber M.A., Haley B.K., Uchic M.D. et al. 3D reconstruction and characterization of polycrystalline microstructures using a FIB–SEM system // Materials Characterization. 2006. Vol. 57, № 4–5. P. 259–273.
21.    Gui-Yuan L.I., Hao-Ming F.A.N. Effect of freeze-thaw on water stability of aggregates in a black soil of Northeast China // Pedosphere. 2014. Vol. 24, № 2. P. 285–290. https://doi.org/10.1016/S1002-0160(14)60015-1
22.    Hashemi M.A., Khaddour G., François B. et al. A tomographic imagery segmentation methodology for three-phase geomaterials based on simultaneous region growing // Acta Geotechnica. 2014. 9. P. 831–846. https://doi.org/10.1007/s11440-013-0289-5
23.    Karsanina M.V., Gerke K.M., Skvortsova E.B. et al. Universal spatial correlation functions for describing and reconstructing soil microstructure // PLoS One. 2015. Vol. 10, № 5. Paper e0126515. https://doi.org/10.1371/journal.pone.0126515
24.    Kelly S., El-Sobky H., Torres-Verdín C. et al. Assessing the utility of FIB-SEM images for shale digital rock physics // Advances in Water Resources. 2016. Vol. 95. P. 302–316. https://doi.org/10.1016/j.advwatres.2015.06.010
25.    Kizilyaprak C. et al. FIB-SEM tomography in biology // Electron microscopy: methods and protocols. Totowa, NJ, 2013. P. 541–558. https://doi.org/10.1007/978-1-62703-776-1_24
26.    Kravchenko A.N., Guber A.K. Soil pores and their contributions to soil carbon processes // Geoderma. 2017. Vol. 287. P. 31–39. https://doi.org/10.1016/j.geoderma.2016.06.027
27.    Lastoskie C., Gubbins K.E., Quirke N. Pore size distribution analysis of microporous carbons: a density functional theory approach // The Journal of Physical Chemistry. 1993. Vol. 97, № 18. P. 4786–4796. https://doi.org/10.1021/j100120a035
28.    Lavrukhin E.V., Gerke K.M., Romanenko K.A. et al. Assessing the fidelity of neural network-based segmentation of soil XCT images based on pore-scale modelling of saturated flow properties // Soil and Tillage Research. 2021. Vol. 209. Paper 104942. https://doi.org/10.1016/j.still.2021.104942
29.    Li L., Wen K., Li C. et al. FIB/SEM imaging of microbial induced calcite precipitation in sandy soil // Microscopy and Microanalysis. 2017. Vol. 23, № S1. P. 310–311.
30.    Li Y., Dick W.A., Tuovinen O.H. Fluorescence microscopy for visualization of soil microorganisms—a review // Biology and fertility of soils. 2004. Vol. 39. P. 301–311. https://doi.org/10.1007/s00374-004-0722-x
31.    Liu S., Qi X., Han C. et al. Novel nano-submicron mineral-based soil conditioner for sustainable agricultural development // Journal of Cleaner Production. 2017. Vol. 149. P. 896–903. https://doi.org/10.1016/j.jclepro.2017.02.155
32.    Milani M., Drobne D., Tatti F. How to study biological samples by FIB/SEM // Modern Research and Educational Topics in Microscopy. 2007. Vol. 2. P. 787–794.
33.    Miranda-Velez J.F., Leuther F., Koehne J.M. et al. Effects of freeze-thaw cycles on soil structure under different tillage and plant cover management practices // Soil and Tillage Research. 2023. Vol. 225. Paper 105540. https://doi.org/10.1016/j.still.2022.105540
34.    Mitchell R.L., Davies P., Kenrick P. et al. Correlative Microscopy: a tool for understanding soil weathering in modern analogues of early terrestrial biospheres // Scientific Reports. 2021. Vol. 11, № 1. Paper 12736. https://doi.org/10.1038/s41598-021-92184-1
35.    Nan N., Wang J. FIB‐SEM three‐dimensional tomography for characterization of carbon‐based materials // Advances in Materials Science and Engineering. 2019. Т. 2019, № 1. P. 8680715. https://doi.org/10.1155/2019/8680715
36.    Sleutel S., Cnudde V., Masschaele B. et al. Comparison of different nano-and micro-focus X-ray computed tomography set-ups for the visualization of the soil microstructure and soil organic matter // Computers & Geosciences. 2008. Vol. 34, № 8. P. 931–938. https://doi.org/10.1016/j.cageo.2007.10.006
37.    Vogel C., Mueller C.W., Höschen C. et al. Submicron structures provide preferential spots for carbon and nitrogen sequestration in soils // Nature Communications. 2014. Vol. 5, № 1. P. 2947.
38.    Vogel H.J., Balseiro‐Romero M., Kravchenko A. et al. A holistic perspective on soil architecture is needed as a key to soil functions // European Journal of Soil Science. 2022. Vol. 73, № 1. P. e13152. https://doi.org/10.1038/ncomms3947
39.    Voltolini M., Taş N., Wang S. et al. Quantitative characterization of soil micro-aggregates: New opportunities from sub-micron resolution synchrotron X-ray microtomography // Geoderma. 2017. Vol. 305. P. 382–393. https://doi.org/10.1016/j.geoderma.2017.06.005
40.    Wang W., Kravchenko A.N., Smucker A.J.M. et al. Comparison of image segmentation methods in simulated 2D and 3D microtomographic images of soil aggregates // Geoderma. 2011. Vol. 162, № 3–4. P. 231–241. https://doi.org/10.1016/j.geoderma.2011.01.006
41.    Watteau F., Villemin G. Soil microstructures examined through transmission electron microscopy reveal soil-microorganisms interactions // Frontiers in Environmental Science. 2018. Vol. 6. P. 106. https://doi.org/10.3389/fenvs.2018.00106
42.    Wen K., Li L., Zhang R. et al. Micro-scale analysis of microbial-induced calcite precipitation in sandy soil through SEM/FIB imaging // Microscopy Today. 2019. Vol. 27, № 1. Р. 24–29. https://doi.org/10.1017/S1551929518001293
43.    Xu C.S., Hayworth K.J., Lu Z. et al. Enhanced FIB-SEM systems for large-volume 3D imaging // LIFE. 2017. Vol. 6. Paper e25916. https://doi.org/10.7554/eLife.25916
44.    Yudina A., Kuzyakov Y. Dual nature of soil structure: The unity of aggregates and pores // Geoderma. 2023. Vol. 434. Paper 116478. https://doi.org/10.1016/j.geoderma.2023.116478
45.    Zheng J., Hryciw R.D. Segmentation of contacting soil particles in images by modified watershed analysis // Computers and Geotechnics. 2016. Vol. 73. P. 142–152. https://doi.org/10.1016/j.compgeo.2015.11.025
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Received: 09/20/2025

Accepted: 11/30/2025

Accepted date: 02/13/2026

Keywords: nanostructure; focused ion beam; Euler characteristic; tomography; pore classification

DOI: 10.55959/MSU0137-0944-17-2026-81-1-139-149

Available in the on-line version with: 12.02.2026

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