Carbon mineralisation and pore size classes in undisturbed soil cores
Liesbeth Bouckaert A , Steven Sleutel A E , Denis Van Loo A B , Loes Brabant B C , Veerle Cnudde B D , Luc Van Hoorebeke B C and Stefaan De Neve A
+ Author Affiliations
- Author Affiliations
A Department of Soil Management, Coupure Links 653, Ghent University, Ghent 9000, Belgium.
B Centre for X-ray Tomography, Proeftuinstraat 86, Ghent University, Ghent 9000, Belgium.
C Department of Physics and Astronomy, Proeftuinstraat 86, Ghent University, Ghent 9000, Belgium.
D Department of Geology and Soil Science, Krijgslaan 281 (S8), Ghent University, Ghent 9000, Belgium.
E Corresponding author. Email: Steven.Sleutel@UGent.be
Soil Research 51(1) 14-22 https://doi.org/10.1071/SR12116
Submitted: 3 May 2012 Accepted: 13 January 2013 Published: 12 March 2013
Abstract
Soil pore network effects on organic matter turnover have, until now, been studied indirectly because of lack of data on the 3D structure of the pore network. Application of X-ray computed tomography (X-ray CT) to quantify the distribution of pore neck size and related pore sizes from undisturbed soil cores, with simultaneous assessment of carbon (C) mineralisation, could establish a relationship between soil organic matter (SOM) decomposition and soil pore volumes. Eighteen miniature soil cores (diameter 1.2 cm, height 1.2 cm) covering a range of bulk densities were incubated at 20°C for 35 days. Respiration was modelled with a parallel first- and zero-order kinetic model. The cores were scanned at 9.44 µm resolution using an X-ray CT scanner developed in-house. Correlation analysis between the slow pool C mineralisation rate, ks, and pore volume per pore neck class yielded significant (P < 0.05) positive correlations: r = 0.572, 0.598, and 0.516 for the 150–250, 250–350, and >350 µm pore neck classes, respectively. Because larger pores are most probably mainly air-filled, a positive relation with ks was ascribed to enhanced aeration of smaller pores surrounding large pores. The weak and insignificant relationship between the smallest pore neck class (<9.44 µm) and ks could be explained by obstructed microbial activity and mobility or diffusion of exo-enzymes and hydrolysis products as a result of limited oxygen availability. This study supports the hypothesis that the impact of soil structure on microbial processes occurs primarily via its determination of soil water distribution, which is possibly the main driver for the location of C mineralisation in the soil matrix.
Additional keywords: first- and zero-order kinetic C mineralisation model, image analysis, pore size distribution, SOM decomposition, 3D soil pore structure.
References
Abera G, Wolde-Meskel E, Bakken LR (2012) Carbon and nitrogen mineralization dynamics in different soils of the tropics amended with legume residues and contrasting soil moisture contents. Biology and Fertility of Soils 48, 51–66.| Carbon and nitrogen mineralization dynamics in different soils of the tropics amended with legume residues and contrasting soil moisture contents.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xkt1ersA%3D%3D&md5=3000a29b2a375183a9c045cc22b169b3CAS |
Anderson SH, Peyton RL, Gantzer CJ (1990) Evaluation of constructed and natural soil macropores using X-ray computed tomography. Geoderma 46, 13–29.
| Evaluation of constructed and natural soil macropores using X-ray computed tomography.Crossref | GoogleScholarGoogle Scholar |
Baveye PC, Laba M, Otten W, Bouckaert L, Dello Sterpaio P, Goswami RR, Grinev D, Houston A, Hu YP, Liu JL, Mooney S, Pajor R, Sleutel S, Tarquis A, Wang W, Wei Q, Sezgin M (2010) Observer-dependent variability of the thresholding step in the quantitative analysis of soil images and X-ray microtomography data. Geoderma 157, 51–63.
| Observer-dependent variability of the thresholding step in the quantitative analysis of soil images and X-ray microtomography data.Crossref | GoogleScholarGoogle Scholar |
Blake GR, Hartge KH (1986) Particle density. In ‘Methods of soil analysis. Part 1: Physical and mineralogical methods’. 2nd edn (American Society of Agronomy: Madison, WI)
Bouckaert L, Van Loo D, Ameloot N, Buchan D, Van Hoorebeke L, Sleutel S (2013) Compatibility of X-ray micro-computed tomography with soil biological experiments. Soil Biology & Biochemistry 56, 10–12.
| Compatibility of X-ray micro-computed tomography with soil biological experiments.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhslyntbzE&md5=79d26de32b9c212c2c8371ed6a4a2d3eCAS |
Brabant L, Vlassenbroeck J, De Witte Y, Cnudde V, Boone M, Dewanckele J, Van Hoorebeke L (2011) Three-dimensional analysis of high-resolution X-ray computed tomography data with Morpho+. Microscopy and Microanalysis 17, 252–263.
| Three-dimensional analysis of high-resolution X-ray computed tomography data with Morpho+.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXjsVyqtbY%3D&md5=b2aa3b1f5ceb089681978ed22c9a16dcCAS |
Chen X, Tang J, Jiang L, Li B, Chen J, Fang C (2010) Evaluating the impacts of incubation procedures on estimated Q10 values of soil respiration. Soil Biology & Biochemistry 42, 2282–2288.
| Evaluating the impacts of incubation procedures on estimated Q10 values of soil respiration.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhtlCjsLfE&md5=7ac87646b48263d0ccdfcd060d7d857bCAS |
Danielson RE, Sutherland PL (1986) Porosity. In ‘Methods of soil analysis. Part 1: Physical and mineralogical methods’. 2nd edn (American Society of Agronomy: Madison, WI)
De Gryze S, Jassogne L, Six J, Bossuyt H, Wevers M, Merck XR (2006) Pore structure changes during decomposition of fresh residue: X-ray tomography analyses. Geoderma 134, 82–96.
| Pore structure changes during decomposition of fresh residue: X-ray tomography analyses.Crossref | GoogleScholarGoogle Scholar |
De Neve S, Hofman G (2000) Influence of soil compaction on carbon and nitrogen mineralization of soil organic matter and crop residues. Biology and Fertility of Soils 30, 544–549.
| Influence of soil compaction on carbon and nitrogen mineralization of soil organic matter and crop residues.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3cXhtlCrtL8%3D&md5=b7f23db06c801898799c0c67cded7993CAS |
Dierick M, Van Loo D, Masschaele B, Boone M, Van Hoorebeke L (2010) A LabVIEW (R) based generic CT scanner control software platform. Journal of X-Ray Science and Technology 18, 451–461.
Ekschmitt K, Kandeler E, Poll C, Brune A, Buscot F, Friedrich M, Gleixner G, Hartmann A, Kastner M, Marhan S, Miltner A, Scheu S, Wolters V (2008) Soil-carbon preservation through habitat constraints and biological limitations on decomposer activity. Journal of Plant Nutrition and Soil Science – Zeitschrift Fur Pflanzenernahrung Und Bodenkunde 171, 27–35.
| Soil-carbon preservation through habitat constraints and biological limitations on decomposer activity.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXisFyhtbk%3D&md5=4779eb0b66f170dac478740d1156b6ffCAS |
Foster RC (1988) Microenvironments of soil microorganisms. Biology and Fertility of Soils 6, 189–203.
| Microenvironments of soil microorganisms.Crossref | GoogleScholarGoogle Scholar |
Gee GW, Bauder JW (1986) Particle-size analysis. In ‘Methods of soil analysis. Part 1: Physical and mineralogical methods’. 2nd edn (American Society of Agronomy: Madison, WI)
Kilbertus G (1980) Study of microhabitats in soil aggregates – relation to bacterial biomass and size of prokaryotes. Revue D Ecologie Et De Biologie Du Sol 17, 543–557.
Killham K, Amato M, Ladd JN (1993) Effect of substrate location in soil and pore-water regime on carbon turnover. Soil Biology & Biochemistry 25, 57–62.
| Effect of substrate location in soil and pore-water regime on carbon turnover.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK3sXht1emu7w%3D&md5=188d9dc56ee60b1c0e70136649049f23CAS |
McCarthy JF, Ilavsky J, Jastrow JD, Mayer LM, Perfect E, Zhuang J (2008) Protection of organic carbon in soil microaggregates via restructuring of aggregate porosity and filling of pores with accumulating organic matter. Geochimica et Cosmochimica Acta 72, 4725–4744.
| Protection of organic carbon in soil microaggregates via restructuring of aggregate porosity and filling of pores with accumulating organic matter.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhtFentLvF&md5=d0d331a23ad38ff6e30b300a40f02162CAS |
Nunan N, Wu KJ, Young IM, Crawford JW, Ritz K (2003) Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. FEMS Microbiology Ecology 44, 203–215.
| Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXjtFWrsro%3D&md5=2246289fa26cf9b4e14e41d12f6a0cfaCAS |
Nunan N, Ritz K, Rivers M, Feeney DS, Young IM (2006) Investigating microbial micro-habitat structure using X-ray computed tomography. Geoderma 133, 398–407.
| Investigating microbial micro-habitat structure using X-ray computed tomography.Crossref | GoogleScholarGoogle Scholar |
O’Donnell AG, Young IM, Rushton SP, Shirley MD, Crawford JW (2007) Visualization, modelling and prediction in soil microbiology. Nature Reviews. Microbiology 5, 689–699.
| Visualization, modelling and prediction in soil microbiology.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXptFyku7w%3D&md5=9e91235d8ee9e112b96bb744607f219aCAS |
Or D, Smets BF, Wraith JM, Dechesne A, Friedman SP (2007) Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review. Advances in Water Resources 30, 1505–1527.
| Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review.Crossref | GoogleScholarGoogle Scholar |
Ruamps LS, Nunan N, Chenu C (2011) Microbial biogeography at the soil pore scale. Soil Biology & Biochemistry 43, 280–286.
| Microbial biogeography at the soil pore scale.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhtlGnsA%3D%3D&md5=d75a81138a1ab7fcacbbe2a2935fa163CAS |
Six J, Bossuyt H, De Gryze S, Denef K (2004) A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics. Soil & Tillage Research 79, 7–31.
| A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics.Crossref | GoogleScholarGoogle Scholar |
Sleutel S, De Neve S, Roibas MRP, Hofman G (2005) The influence of model type and incubation time on the estimation of stable organic carbon in organic materials. European Journal of Soil Science 56, 505–514.
| The influence of model type and incubation time on the estimation of stable organic carbon in organic materials.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXps1CntbY%3D&md5=f6cbb9c80db5f8ae32f4897c5051fa4aCAS |
Sleutel S, Cnudde V, Masschaele B, Vlassenbroek J, Dierick M, Van Hoorebeke L, Jacobs P, De Neve S (2008) 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 34, 931–938.
| Comparison of different nano- and micro-focus X-ray computed tomography set-ups for the visualization of the soil microstructure and soil organic matter.Crossref | GoogleScholarGoogle Scholar |
Sleutel S, Bouckaert L, Buchan D, Van Loo D, Cornelis WM, Sanga HG (2012) Manipulation of the soil pore and microbial community structure in soil mesocosm incubation studies. Soil Biology & Biochemistry 45, 40–48.
| Manipulation of the soil pore and microbial community structure in soil mesocosm incubation studies.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhs1CrtLjI&md5=6e8df0e6444852124d9a376a3b9f7dc0CAS |
Strong DT, De Wever H, Merckx R, Recous S (2004) Spatial location of carbon decomposition in the soil pore system. European Journal of Soil Science 55, 739–750.
| Spatial location of carbon decomposition in the soil pore system.Crossref | GoogleScholarGoogle Scholar |
Thomsen IK, Schjonning P, Jensen B, Kristensen K, Christensen BT (1999) Turnover of organic matter in differently textured soils: II. Microbial activity as influenced by soil water regimes. Geoderma 89, 199–218.
| Turnover of organic matter in differently textured soils: II. Microbial activity as influenced by soil water regimes.Crossref | GoogleScholarGoogle Scholar |
Tomasi C, Manduchi R (1998) Bilateral filtering for gray and color images. In ‘Sixth International Conference on Computer Vision’. 4–7 January 1998, Bombay, India. pp. 839–846. (Narosa Publishing House: New Delhi, India)
Tuller M, Or D, Dudley LM (1999) Adsorption and capillary condensation in porous media: liquid retention and interfacial configurations in angular pores. Water Resources Research 35, 1949–1964.
| Adsorption and capillary condensation in porous media: liquid retention and interfacial configurations in angular pores.Crossref | GoogleScholarGoogle Scholar |
van der Linden AMA, Jeurissen LJJ, Van Veen JA, Schippers B (1989) Turnover of the soil microbial biomass as influenced by soil compaction. In ‘Nitrogen in organic wastes applied to soils’. (Academic Press: London)
Van Veen JA, Kuikman PJ (1990) Soil structural aspects of decomposition of organic-matter by microorganisms. Biogeochemistry 11, 213–233.
| Soil structural aspects of decomposition of organic-matter by microorganisms.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK3MXkt1yisb4%3D&md5=cb2b4f43500ad0a69dd444146f67f9e6CAS |
Vlassenbroeck J, Dierick M, Masschaele B, Cnudde V, Hoorebeke L, Jacobs P (2007) Software tools for quantification of X-ray microtomography at the UGCT. Nuclear Instruments & Methods in Physics Research Section A – Accelerators Spectrometers Detectors and Associated Equipment 580, 442–445.
| Software tools for quantification of X-ray microtomography at the UGCT.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXpvVertLw%3D&md5=ce9fa4ca4b6e96cff5cc8c0314eee91eCAS |
Warner GS, Nieber JL, Moore ID, Geise RA (1989) Characterising macropores in soil by computed tomography. Soil Science Society of America Journal 53, 653–660.
| Characterising macropores in soil by computed tomography.Crossref | GoogleScholarGoogle Scholar |
Wong PTW, Griffin DM (1976) Bacterial movement at high matric potentials 1. Artificial and natural soils. Soil Biology & Biochemistry 8, 215–218.
| Bacterial movement at high matric potentials 1. Artificial and natural soils.Crossref | GoogleScholarGoogle Scholar |
Young IM, Ritz K (2000) Tillage, habitat space and function of soil microbes. Soil & Tillage Research 53, 201–213.
| Tillage, habitat space and function of soil microbes.Crossref | GoogleScholarGoogle Scholar |
Young IM, Crawford JW, Rappoldt C (2001) New methods and models for characterising structural heterogeneity of soil. Soil & Tillage Research 61, 33–45.
| New methods and models for characterising structural heterogeneity of soil.Crossref | GoogleScholarGoogle Scholar |
Young IM, Crawford JW, Nunan N, Otten W, Spiers A (2008) Microbial distribution in soils: physics and scaling. Advances in Agronomy 100, 81–121.
| Microbial distribution in soils: physics and scaling.Crossref | GoogleScholarGoogle Scholar |
