Soil & Water Res., 2024, 19(3):176-189 | DOI: 10.17221/47/2024-SWR

Computed tomographic visualisation and 2D/3D microscopic evaluation of soil macro- and micromorphologyOriginal Paper

Lubica Pospíšilová ORCID...1,3, Jana Plisková ORCID...1,6*, Victory Armida Janine Jaques ORCID...2, Tomáš Zikmund ORCID...2, Luboš Sedlák ORCID...3, Aleš Eichmeier ORCID...4, Aleš Klement ORCID...5, Radka Kodešová ORCID...5, Luboš Borůvka ORCID...5, Jozef Kaiser2, Ladislav Menšík6
1 Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
2 CEITEC – Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
3 Department of Pedology nad Geology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
4 Mendeleum Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czech Republic
5 Department of Soil Science and Soil Protection, Faculty of Agrobiology, Food and Natural Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
6 Division of Crop Management Systems, Crop Research Institute, Prague-Ruzyně, Czech Republic

Erratum in: Soil & Water Res., 20: 69. Doi: 10.17221/2/2025-SWR

Soil organic matter and pores distribution within aggregates were studied using X-ray computed tomography (XCT; Nikon XT H 225ST and GE Phoenix L240) and advanced 2D/3D measurements by the digital Keyence VHX-6000 microscope (Japan). A new methodological approach with computed tomography involvement for studying the spatial arrangement of pores, porosity, and soil morphology is presented. Changes in studied parameters are documented along the transect of intensively used Haplic Chernozem. Soil disturbance due to erosion and colluvial soil profile formation is reported. Moreover, soil organic matter quality and aggregate stability were evaluated. Obtained results showed statistically significant differences between the control and eroded sites and between eroded and accumulated sites. The correlation coefficients were the highest for soil organic carbon (SOC) and humic substances CHS (r = 0.805) and CHS and CHA/CFA (r = 0.764). The highest porosity, aggregates stability and coefficients stability were confirmed on the eroded site. The computed tomography measurements also document the high disturbance of Haplic Chernozem on the control site and the newly formed profile of Colluvisol. Despite excellent complementary technique further research is necessary to improve micro-XCT resolution and capacity for the soil micromorphological study.

Keywords: aggregate stability; porosity; soil organic matter; X-ray computed tomography

Received: May 13, 2024; Revised: August 28, 2024; Accepted: September 4, 2024; Prepublished online: September 24, 2024; Published: September 25, 2024  Show citation

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Pospíšilová L, Plisková J, Jaques VAJ, Zikmund T, Sedlák L, Eichmeier A, et al.. Computed tomographic visualisation and 2D/3D microscopic evaluation of soil macro- and micromorphology. Soil & Water Res. 2024;19(3):176-189. doi: 10.17221/47/2024-SWR.
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    References

    1. Abramoff M., Magalhães P., Ram S.J. (2003): Image processing with ImageJ. Biophotonics International, 11: 36-42.
    2. Compostella C., Trombino L., Caccianiga M. (2013): Late Holocene soil evolution and treeline fluctuation in the Northern Apennines. Quaternary International, 298: 46-59. Go to original source...
    3. Dal Ferro N., Charrier P., Morari F. (2013): Dual-scale micro-CT assessment of soil structure in a long-term fertilization experiment. Geoderma, 204-205: 84-93. Go to original source...
    4. Diel J., Vogel H.J., Schlüter S. (2019): Impact of wetting and drying cycles on soil structure dynamics. Geoderma, 345: 63-71. Go to original source...
    5. Fan W., Wu J., Ahmed S., Hu J., Chen X., Li X., Zhu W., Opoku-Kwanowaa Y. (2020): Short-term effects of different straw returning methods on the soil physicochemical properties and quality index in dryland farming in China. Sustainability (Switzerland), 12: 1-12. Go to original source...
    6. Ferreira T.R., Pires F.L., Klus R. (2022): 4D X-ray computed tomography in soil science: An overview and future perspectives at mogno/sirius. Brazilian Journal of Physics, 52: 33. Go to original source...
    7. Ferreira T.R., Archilha N.L., Cássaro F.A.M., Pires L.F. (2023): How can pore characteristics of soil aggregates from contrasting tillage systems affect their intrinsic permeability and hydraulic conductivity? Soil and Tillage Research, 230: 105704. Go to original source...
    8. Fomin D.S., Yudina A.V., Romanenko V., Abrosimov K., Karsanina M.V., Gerke K. (2023): Soil pore structure dynamics under steady-state wetting-drying cycle. Geoderma, 432: 116401. Go to original source...
    9. Gerke K.M., Korostilev E.V., Romanenko K.A., Karsanina M.V. (2021): Going submicron in the precise analysis of soil structure: A FIB-SEM imaging study at nanoscale. Geoderma, 383: 114739. Go to original source...
    10. Guenat C., Schomburg A., Fischer F., Luiset A., Le Bayon C., Turberg P. (2019): Extraction of monoliths in unconsolidated soils. In: 8th Int. Symp. Interactions of Soil Minerals with Organic Components and Microorganisms (ISMOM2019), Seville, June 23-28, 2019: 86-87.
    11. Helliwell J.R., Sturrock C.J., Mairhofer S., Craigon J., Ashton R.W., Miller A.J., Whalley W.R., Mooney S.J. (2017): The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface. Scientific Reports, 7: 14875. Go to original source... Go to PubMed...
    12. Holz M., Agustin J. (2021): Erosion effect on soil carbon and nitrogen dynamics on cultivated slopes: A meta-analysis. Geoderma, 397: 115045. Go to original source...
    13. IUSS Working Group WRB (2022): World Reference Base for Soil Resources. International Soil Classification System for Naming Soils and Creating Legends for Soil Maps. 4th Ed. Vienna, IUSS, Austria.
    14. Kandeler E. (1996): Aggregate stability. In: Schinner F., Öhlinger R., Kandeler E., Margesin R. (eds.): Methods in Soil Biology. Berlin, Springer-Verlag: 390-395.
    15. Karsanina M.V., Gerke K.M., Skvortsova E.B., Ivanov A.L., Mallants D. (2018): Enhancing image resolution of soils by stochastic multiscale image fusion. Geoderma, 314: 138-145. Go to original source...
    16. Koestel J. (2018): Soil: An image plugin for the semiautomatic processing of three-dimensional X-ray images of soils. Vadose Zone Journal, 17: 1-7. Go to original source...
    17. Kononova M.M., Belčikova N.P. (1963): Short fractionation method of humic substances determination in mineral soils. In: Kononova M.M. (ed): Soil Organic Matter. Moscow, Moscow State University: 228-234. (in Russian)
    18. Lavallee J.M., Soong J.L., Cotrufo M.F. (2020): Conceptualizing soil organic matter into particulate and mineral-associated forms to address global change in the 21st century. Global Change Biology, 26: 261-273. Go to original source... Go to PubMed...
    19. Lavrukhin E.V., Konstantin A.N., Marina K.V., Kirill G., Romanenko K.A., Romaanenko K., Abrosimov K. (2021): 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, 209: 104942. Go to original source...
    20. Le Bissonnais Y. (1996): Aggregate stability and assessment of soil crustability and erodibility: 1. Theory and methodology. European Journal of Soil Science, 47: 425-437. Go to original source...
    21. Mairhofer S., Zappala S., Tracy S., Sturrock C., Bennett M.J., Mooney S.J., Pridmore T.P. (2013): Recovering complete plant root system architectures from soil via X-ray μ-computed tomography. Plant Methods, 9: 1-7. Go to original source... Go to PubMed...
    22. Marshall T.J., Holmes J.W. (1988): Soil Physics. 2nd Ed. Cambridge, New York, Port Chester, Melbourne, Sydney: Cambridge University Press.
    23. Nelson D.W., Sommers L.E. (1996): Total carbon, organic carbon and organic matter. In: Sparks D.L., Page A.L., Helmke P.A., Loeppert R.H., Soltanpour P.N., Tabatabai M.A., Johnston C.T., Sumner M.E. (eds.): Methods of Soil Analysis. Part 3. Chemical Methods. Madison, Soil Science Society of America: 961-1110. Go to original source...
    24. Němeček J., Muhlhanselová M., Macků J., Vokoun J., Vavříček D., Novák P. (2011): Taxonomic Soil Classification System of the Czech Republic. 2nd Ed. Prague, Czech University of Agriculture. (in Czech)
    25. Pansu M., Gautheyrou J. (2006): Handbook of Soil Analysis. Mineralogical, Organic and Inorganic Methods. Springer. Go to original source...
    26. Picha F.J., Stráník Z., Krejčí O. (2006): Geology and hydrocarbon resources of the Outer Western Carpathians and their foreland, Czech Republic. In: Golonka J., Picha F.J. (eds.): The Carpathians and Their Foreland: Geology and Hydrocarbon Resources. AAPG Memoir, 84: 49-175. Go to original source...
    27. Pires L.F., Ferreira T.R., Cássaro F.A.M., Cooper H.V., Mooney S.J. (2022): A comparison of the differences in soil structure under long-term conservation agriculture relative to a secondary forest. Agriculture, 12: 1783. Go to original source...
    28. Possinger A.R., Zachman M.J., Enders A., Levin B.D.A., Muller D.A., Kourkoutis L.F., Lehmann J. (2020): Organo-organic and organo-mineral interfaces in soil at the nanometer scale. Nature Communication, 11: 6103. Go to original source... Go to PubMed...
    29. Pospíšilová L., Vlček V., Lukas V., Šarapatka B., Netopil P., Bednář M., Černohorský J., Badalíková B., Vašinka M. (2019): Pedogeochemical characterization of localities Bošovice, Hrušky, and Zástřizly. Brno. Folia Universitatis Agriculturae et Silviculturae Mendelianae Brunensis: XII: 69. (in Czech)
    30. Quitt E. (1971): Climatic Regions of Czechoslovakia. Studia Geographica 16. Brno, ČSAV-GU. (in Czech)
    31. Rooney E.C., Bailey V.L., Patel K.F., Dragila M., Battu A.K., Buchko A.C., Gallo A.C., Hatten J., Passinger A.R., Qafoku O., Reno L.R., SanClements M., Varga T., Lybrand R.A. (2022): Soil pore network response to freeze-thaw cycles in permafrost aggregates. Geoderma, 411: 115674. Go to original source...
    32. Schneider C.A., Rasband W.S., Eliceiri K.W. (2012): NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9: 671-675. Go to original source... Go to PubMed...
    33. Six J. (1998): Aggregation and soil organic matter accumulation in cultivated and native grassland soils. Soil Science Society of America Journal, 62: 1042-1049. Go to original source...
    34. Six J., Paustian K. (2014): Aggregate-associated soil organic matter as an ecosystem property and a measurement tool. Soil Biology and Biochemistry, 68: A4-A9. Go to original source...
    35. Six J., Elliott, E.T., Paustian K. (2000a): Soil structure and soil organic matter II. A normalized stability index and the effect of mineralogy. Soil Science Society of America Journal, 64: 1042-1049. Go to original source...
    36. Six J., Elliott E.T., Paustian K. (2000b): Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under no-tillage agriculture. Soil Biology and Biochemistry, 32: 2099-2103. Go to original source...
    37. Six J., Bossuyt H., Degryze S., Denef K. (2004): A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics. Soil and Tillage Research, 79: 7-31. Go to original source...
    38. Sodhi N.S., Posa M.R.C., Lee T.M., Bickford D., Koh L.P., Brook B.W. (2009): The state and conservation of Southeast Asian biodiversity. Journal of Biodiversity and Conservation, 19: 317-328. Go to original source...
    39. Thai S., Davídek T., Pavlů L. (2022): Causes clarification of the soil aggregates stability on mulched soil. Soil and Water Research, 17: 91-99. Go to original source...
    40. Tobiašová E. (2011): The effect of organic matter on the structure of soils of different land use. Soil and Tillage Research, 114: 183-192. Go to original source...
    41. Tobiašová E., Barančíková G., Gömöryová E., Dębska B., Banach-Szott M. (2018): Humus substances and soil aggregates in the soils 644 with a different texture. Soil and Water Research, 13: 44-50. Go to original source...
    42. Van Veelen, A., Koebernick, N., Scotson C.S., McKay-Fletcher D., Huthwelker T., Mosselmans T.F.W., Roose T. (2020): Root-induced soil deformation influences Fe, S and P: rhizosphere chemistry investigated using synchr tron XRF and XANES. New Phytologist, 225: 1476-1490. Go to original source... Go to PubMed...
    43. Vrána M., Kubát J.F., Kavka P., Zumr D. (2024): A laser diffractometry technique for determining the soil water stable aggregates index. Geoderma, 441: 116756. Go to original source...
    44. Wang N., Zhang T. (2024): Soil pore structure and its research methods: A review. Soil and Water Research, 19: 1-24. Go to original source...
    45. Weng Z.H., Johannes Lehmann J., Van Zwieten L., Joseph S., Archanjo B.S., Cowie B., Thomsen L., Tobin M.J., Vongsvivut J., Klein A., Doolette C.L., Hou H., Mueller C.W., Enzo Lombi E., Kopittke P.M. (2022): Probing the nature of soil organic matter. Critical Reviews in Environmental Science and Technology, 52: 4072-4093. Go to original source...
    46. Yang X., Varga T., Lie Ch., Scheibe T.D. (2017): What can we learn from in-soil imaging of a live plant: X-ray computed tomography and 3D numerical simulation of root-soil system. Rhizosphere, 3: 259-262. Go to original source...
    47. Zádorová T., Penížek V., Koubová M., Lisá L., Pavlů L., Tejnecký V., Žížala D., Drábek O., Němeček K., Vaněk A., Kodešová R. (2023): Formation of Colluvisols in different soil regions and slope positions (Czechia): Post-sedimentary pedogenesis in colluvial material. Catena, 229: 107233. Go to original source...

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