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Foreword to ‘Linking Soil Structure and Soil Functions’

Article  in  Soil Research · January 2019

DOI: 10.1071/SRv57n6_FO

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University of Padova
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Soil Research, 2019, 57, i–iii
https://doi.org/10.1071/SRv57n6_FO

Foreword

A B
Céline Duwig , Karin Müller , Francesco Morari C, and Patrice Delmas D

A
Université Grenoble Alpes, CNRS, IRD, Grenoble INP, IGE, F-38000 Grenoble, France. Email: celine.duwig@ird.fr
B
Plant & Food Research, Bisley Road, Hamilton 3214, New Zealand. Email: karin.mueller@plantandfood.co.nz
C
Department of Agronomy, Food, Natural Resources, Animals and Environment, Agripolis, University of Padova, Viale
Dell’Università 16, 35020 Legnaro, Italy. Email: francesco.morari@unipd.it
D
Department of Computer Science, The University of Auckland, Auckland, New Zealand. Email: p.delmas@auckland.ac.nz

Soils and their protection have been recognised of paramount imaging techniques along with advances in imaging processing
importance by the Food and Agriculture Organization (FAO) by that allow visualising water and transport processes in soil were
declaring 2015 as the International Year of Soils (Martín et al. reviewed in the special section ‘Non-invasive imaging of
2017). Soils of natural and managed ecosystems deliver processes in natural porous media’ published in Vadose
several fundamental ecosystem services which, according to Zone Journal (Li et al. 2018). The breakthrough role of
the Millennium Ecosystem Assessment (2005), include X-ray CT in the understanding of the growth and activity of
provisioning services (e.g. production of food, fibre, fuel), microorganisms in soils and sediments was highlighted in
regulating services (e.g. contaminant filtering, carbon the special issue ‘Elucidating microbial processes in soils
sequestration, erosion control, flood protection), cultural and sediments: microscale measurements and modelling’
services (e.g. recreation, tourism) and supporting services published in Frontiers in Microbiology (Baveye et al. 2018).
(e.g. nutrient cycling processes) (Schwilch et al. 2016). This recent rich publishing activity, as also evidenced by an
The links between soil-related ecosystem services, soil analysis of papers published on the topic (Fig. 1), clearly
functions and properties have recently been reviewed by demonstrates the wide interest in X-ray CT applications and
Adhikari and Hartemink (2016). Depending on the dynamic the continuous and rapid advancement of imaging techniques.
interactions between physical, chemical and biological In comparison to the papers published only six years ago in
properties, soils generate a multitude of soil functions, which Anderson and Hopmans’ (2013) Special Issue, impressive
in turn support the delivery of ecosystem services. Among the advancements have been made in both X-ray CT technology
key soil properties and functions identified by these authors, and image processing. This highlights the potential that these
many of them are soil structure-dependant. Nowadays, it is techniques, with the exponential improvements in the
generally assumed that all processes in soils are directly or capabilities of X-ray CTs (e.g. with regard to resolution,
indirectly dependant on soil structure (Martín et al. 2017). power, and speed) and imaging approaches, can serve as
Indeed, soil structure affects retention and availability of common ground for interdisciplinary studies of the complex
water and nutrients, heat and air transport, root penetration, nature of soils.
and in turn, chemical and biological soil properties (Rabot et al. PROTINUS (PROviding new insighT into INteractions
2018). between soil fUnctions and Structure) was a project funded
In the last decade several Special Journal Issues have been between 2014 and 2018 by the European Union’s Horizon 2020
dedicated to new techniques and methods to advance the study research and innovation programme. It aimed to develop new
of soil structure, soil functions and their interactions. There is no experimental, imaging and modelling approaches in order to
research field dealing with the relations between soil structure evaluate the impact of soil structure on soil functions.
with abiotic (e.g. water, gas, particles) or biotic (e.g. roots, PROTINUS assembled a multi-disciplinary team that
microorganisms) factors, where X-ray computed tomography combined expertise in soil physics, biology and chemistry, as
(CT) has not been widely applied in the last twenty years. well as image acquisition and analysis and numerical
The special publication of the Soil Science Society of modelling.
America (Anderson and Hopmans 2013) ‘Soil–Water–Root A selection of the project’s results is presented in this Special
Processes: Advances in Tomography and Imaging’ Issue along with other related studies. The 14 papers of this
emphasised the role that X-ray CT and other imaging Special Issue contribute to improving current approaches of
techniques have played during the last 20 years in the study characterising soil structure and its evolution with internal or
of soil and root interactions. In Geoderma’s Special Issue external factors as well as discuss the effect of soil structure on
‘Structure and function of soil and soil cover in a changing functions associated to storage and filtering of water, mass and
word: characterization and scaling’ (Martín et al. 2017), authors gas transport, nutrients cycle and habitat for biological activity.
presented research on the parameterisation of structure being The scale investigated ranges from micropores to macropores,
scale-dependent and examples on how structure is related to as in these papers the main tool used to image soil structure is
processes in soils. The role of different 3D high resolution X-ray CT at micron resolution.

Journal compilation Ó CSIRO 2019 www.publish.csiro.au/journals/sr

ii Soil Research C. Duwig et al.

800 The pore system of the fragipan is heterochronous: the mainly

700 closed micropores were formed at the time of structural
Number of articles

600 collapse while fissures appeared later.

500 In the third section of this Special Issue, the authors
400
demonstrate how X-ray CT data can improve our
understanding and modelling of hydrodynamic functions.
300
Shiota et al. (2019, this issue) predict the drainage water
200
retention curve by applying the voxel percolation method
100 (VPM). VPM is a morphological approach under the
0 assumption of capillary-dominated quasi-static flow. X-ray
2000 2004 2008 2012 2016
CT was used during a drainage experiment. The resulting
Publishing year
images were segmented for solid, air and water phases.
Fig. 1. Evolution of the number of journal articles including the terms Permeability is another key soil function that is dependent
‘X Ray CT and soil science’ from 2000 to 2018. Source: Scopus, Elsevier, on soil structure. Ortega Ramírez et al. (2019, this issue)
accessed 30 July 2019. compute the permeability by solving the Navier-Stokes
equation into the 3D structure of Fontainebleau sand and
The papers are arranged in five sections: a methodological virtual pack of spheres obtained at different resolutions. The
section, followed by a section on the studies of soil structure conflict between the need of good resolution, the computational
characterisations and three sections on the links between soil power requirement and the size of the sample increases the
structure and physical, chemical and biological functions. difficulty inherent to direct numerical simulation in real 3D
The first two papers describe the development and porous structure. Müller et al. (2019a, this issue) found that
application of new methodologies related to the use of X-ray structural parameters derived by X-ray CT were significantly
CT in soil sciences, a novel image segmentation technique and a related to indicators of preferential flow and that they can predict
new approach to visualise the distribution of particulate organic solute transport. In soils under different land uses and
matter (POM) in soils are introduced. Several image processing anthropogenic pressures, Yi et al. (2019) also found significant
steps are necessary to obtain parameters quantifying soil positive influence of soil macropore properties derived by X-ray
structure from X-ray CT 3D reconstructions. The choice of CT on the pore water velocity or the solute dispersion coefficient.
the image processing techniques will impact the resulting pore The subtle interactions between soil structure, chemical
network. In particular, the segmentation to distinguish the pores properties and management were investigated in the fourth
from the solid is a crucial step (Smet et al. 2018). Azhar et al. section. Indeed, agricultural management such as tillage,
(2019, this issue) provide an automated image segmentation irrigation, crop type or animal treading modifies soil
strategy, use more robust than current state-of-the art methods. structure. Andosols are characterised by unique soil physical
Soil organic matter is a key component of soil structure and an properties such as high water retention capacity, low bulk
integrative indicator of land degradation. Piccoli et al. (2019, density and high permeability due to the presence of
this issue) demonstrate that, thanks to the use of contrast agents, amorphous compounds that can be lost by inadequate
POM can be discriminated from the mineral fraction and its agricultural practices (Duwig et al. 2019, this issue). Baniya
content successfully estimated. et al. (2019, this issue) and Müller et al. (2019b, this issue)
In the second section of this Special Issue, soil structure found that pore structural parameters derived from X-ray CT,
evolution due to internal and external factors is characterised by were affected by compaction and that these allowed a fair
means of X-ray CT and other imaging techniques. Soil structure prediction of several important mass transport parameters
is a dynamic property at different time scales and evolves with such as saturated hydraulic conductivities, soil-gas diffusion
pedogenesis, root growth and different soil management coefficients and soil-air permeabilities.
practices. Amato et al. (2019, this issue) show that mucilage Soil structure is also affected by compaction, for example
produced by myxodiaspores during seed germination alters soil through grazing of crops in situ. This modifies soil aeration
structure and strongly binds soil. This is a transient but crucial conditions and can lead to high emissions of nitrous oxide and
time of crop production when the soil is totally or partially bare leaching of nitrate to aquifers (Thomas et al. 2019, this issue).
and soil stability depends on the relation between germination Soil water repellency (SWR) is another transient process
mechanisms and microorganisms. At larger time scale, linked with soil structure through microbial activities. SWR
Pogosyan et al. (2019a and 2019b, this issue) studied two implications on soil properties were addressed in the last section
types of subsoil horizons: one indurated subsoil from of this Special Issue. Some enzymes activities were strongly
volcanic origin (Tepetates) and one high density horizon correlated with the development of SWR and could help the
from a Luvisol (fragipan). These hard layers usually prevent development of treatments to remediate SWR and improve
root growth and water infiltration but little is known about their water infiltration and soil water storage (Simpson et al.
genesis. The 2D and 3D quantitative studies of the pore spaces 2019, this issue).
show that pores of different sizes were formed at distinct These results of the PROTINUS project plus the
stages: the small homogeneously distributed pores of the reinforcement of international research networks through the
Tepetates were formed during the primary compaction, and project set the base for future investigations of soil structure and
large crack pores appeared later, while the clay coating soil functions in a world under much climate and anthropogenic
infilling the cracks participated in a secondary compaction. pressure. Soils are among the key resources to overcome some
 Foreword Soil Research iii

of the threats humanity is facing, such as improving soil Millennium Ecosystem Assessment (2005) Living Beyond Our Means:
management to ensure food security for the world’s rising Natural Assets and Human Well-Being. A Statement from the
global population and increasing carbon storage in soils to Board, 28 pp. Available at: https://www.millenniumassessment.org/
documents/document.429.aspx.pdf [verified 22 August 2019].
lower the threat of climate change (Schlesinger and
Müller K, Duwig C, Tinet AJ, Gastelum Strozzi A, Spadini L, Morel MC,
Amundson 2019). It also demonstrated that X-ray CT may
Charrier P (2019a) Orchard management and preferential flow in
serve as a common ground for interdisciplinary studies in soil Andosols – comparing two kiwifruit orchards in New Zealand. Soil
soils, combining expertise in research fields only apparently far Research 57, 615–628. doi:10.1071/SR18293
from each other. Müller K, Dal Ferro N, Katuwal S, Tregurtha C, Zanini F, Carmignato S,
Wollesen de Jonge L, Moldrup P, Morari F (2019b) Effect of long-term
Conflict of interest irrigation and tillage practices on X-ray CT and gas transport derived
The authors declare no conflict of interest pore-network characteristics. Soil Research 57, 657–669. doi:10.1071/
SR18210
Funding statement Ortega Ramírez MP, Oxarango L, Gastelum Strozzi A (2019) Effect
of X-ray CT resolution on the quality of permeability
European Union’s Horizon 2020 research and innovation computation for granular soils: definition of a criterion based on
programme 645717. morphological properties. Soil Research 57, 589–600. doi:10.1071/
SR18189
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