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Biologia, Bratislava, 61/Suppl. 19: S339—S343, 2006

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Impact of plant roots and soil organisms on soil micromorphology
and hydraulic properties
Radka Kodešová1, Vít Kodeš2, Anna Žigová3 & Jiří Šimůnek4
1

Czech University of Agriculture in Prague, Department of Soil Science and Geology, Kamýcka 129, CZ–16521 Prague,
Czech Republic; e-mail: kodesova@af.czu.cz
2Czech Hydrometeorological Institute, Department of Water Quality, Na Šabatce 17, CZ–14306 Prague, Czech Republic3
Academy of Sciences of the Czech Republic, Institute of Geology, Rozvojová 269, CZ–16502 Prague, Czech Republic
4
University of California Riverside, Department of Environmental Sciences, Riverside, CA 92521, USA

Abstract: A soil micromorphological study was performed to demonstrate the impact of soil organisms on soil pore
structure. Two examples are shown here. First, the inﬂuence of earthworms, enchytraeids and moles on the pore structureof a Greyic Phaeozem is demonstrated by comparing two soil samples taken from the same depth of the soil proﬁle thateither were aﬀected or not aﬀected by these organisms. The detected image porosity of the organism-aﬀected soil sample
was 5 times larger then the porosity of the not-aﬀected sample. The second example shows macropores created by roots
and soil microorganisms in a Haplic Luvisol and subsequently aﬀected by clay coatings. Their presence was reﬂected in
the soil water retention curve, which displayed multiple S-shaped features as obtained from the water balance carried out
for the multi-step outﬂow experiment. The dual permeability models implemented in HYDRUS-1D was applied to obtainparameters characterizing multimodal soil hydraulic properties using the numerical inversion of the multi-step outﬂow
experiment.
Key words: soil micromorphology, soil organisms, pore-sizes, soil hydraulic properties

Introduction

the direct impact of the weather and management practices.

Soil pore structure and subsequently soil hydraulicproperties are inﬂuenced by many factors, including themineralogical composition, stage of disintegration, organic matter, soil water content, transport processes
within the soil proﬁle, weather, plant roots, soil organisms, and management practices. Shapes and sizesof soil pores may be studied on images of thin soil
sections, taken at varying magniﬁcations. Macropores
form major transport pathways in soil and their impact on saturated hydraulic conductivities, Ks , was previously explored by Bouma et al. (1977). Diﬀerently
shaped pores in soils under diﬀerent management practices and their Ks values were studied by Pagliai etal. (1983, 2004). A soil micromorphological study presented here was performed to demonstrate the impact
of soil microorganisms on soil pore structure. Their activity is reﬂected not only in the presence of macroporesand subsequently high Ks values and preferential ﬂow
in these macropores, but also in the entire shapes ofthe soil hydraulic properties. Two examples presented
in this study illustrate pore structure of soil samples
collected from the soil depth of 60 cm and below affected dominantly by soil organisms and roots, without

Material and methods
Undisturbed large soil aggregates and undisturbed 100 cm3
soil samples were taken from each horizon of a Haplic Luvisol and Greyic Phaeozem. Micromorphological properties
characterizing the soil pore structure were studied on thinsoil sections prepared from large soil aggregates. Thin sections were prepared according to the methods presented
by CATT (1990). The soil pore structure was analyzed using a similar procedure to that presented by RÖSSLEROVÁKODEŠOVÁ & KODEŠ (1999). Images were taken at one
magniﬁcation at a resolution of 300 dpi. To detect pores,
image-processing ﬁlters were used. The ArcGIS raster processing tools were used to analyze pore areas and perimeters. The shape factors [perimeter2 /(4π area2 )] proposed by
PAGLIAI et al. (1983) were calculated to divide pores into
diﬀerent shape groups.
The soil hydraulic properties were studied in the laboratory on the undisturbed 100 cm3 soil samples. Soil water
retention curves were determined for matric potentials to–10 kPa using a sand table and the pressure plate apparatus for more negative matric potentials. Saturated hydraulic conductivities were measured using the constanthead method. The multi-step outﬂow method was applied





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a)b)Fig. 1. Micromorphological images of the soil sample characterizing the Ck horizon at depths of 45–125 cm (a) and the image of the
krotovina at the depth of 100–110 cm (b) in the Greyic Phaeozem. A – pores, B – amorphous forms of CaCO3 , C – calcite needles,
D – earthworm and enchytraeid excrements, and E – clay coatings.

to estimate soil water retention curves and unsaturated hydraulic conductivity functions using numerical inversion andassuming either the single-porosity, dual-porosity or dualpermeability models in HYDRUS-1D (ŠIMŮNEK et al., 2003,
2005). The van Genuchten functions (1980) were used to describe both soil hydraulic properties in all cases.
Two examples were chosen to show the impact of plantroots and varying organisms, and subsequent aﬀects of different coatings and ﬁllings on the soil pore structure. First,
the inﬂuence of earthworms, enchytraeids and moles on thesoil pore structure in a Greyic Phaeozem is presented. The
impact of such soil porous systems on transport processes
within the soil proﬁle was presented by KOČÁREK et al.
(2005). Micromorphological images were taken, and image
porosities and pore shape factors were calculated to provide
the evidence of very diﬀerent pore structures in soil samples characterizing the Ck horizon at depths of 45–125 cm
and krotovina (the soil transported by a mole from the A
horizon) discovered at the depth of 100–110 cm.
The second example shows the impact of roots andsoil organisms on the soil pore structure in the Haplic
Luvisol. Two micromorphological images of the soil sample characterizing the Bt horizon at depths of 75–102 cm
are presented. Image porosities were analyzed and thesingle-porosity and dual-permeability models in HYDRUS1D were used to reveal the impact of multimodality of soil
porous systems on the soil hydraulic properties.

Results
The micromorphological image taken for the soil sample
characterizing the Ck horizon in the Greyic Phaeozem
is shown in Fig. 1a. The image illustrates a relatively
homogeneous structure with many pores less than 100µm and few larger pores created by small soil organisms. The image of krotovina in the same soil horizon is documented in Fig. 1b. Krotovina consists ofmineral grains, earthworm and enchytraeid excrements,
clay coatings, amorphous forms of CaCO3 , and calcite
needles. All these structural components resulted in avery heterogeneous soil pore structure with higher measured porosity and with a very diﬀerent pore-size distri-bution compared to the bulk soil. The detected image
porosity (pore diameter greater than 40 µm) of krotovina (17.3%) was 5 times higher than the porosity of the
Ck horizon (3.4%). Using the shape factor (SF) classiﬁcation proposed by Pagliai et al. (1983) [regular SF =1–2, irregular SF = 2–5, and elongated SF > 5], thepercentages of diﬀerent shape groups were also very
diﬀerent: regular pores represented 49.0% and 59.4%of the pores in krotovina and the Ck horizon, respectively, irregular pores 45.1% and 37.9%, and elongatedpores 5.9% and 2.7%, respectively. The pore irregularity increased with increasing pore sizes. The majority
of detectable pores corresponded to a matric potential
range between –0.2 and –7 kPa. It is evident from presented images that analyses of pores smaller than 40µm would require higher magniﬁcation (ﬁner resolution) and thinner sections. It is likely that a diﬀerent
pore-size distribution would be obtained for pressure
heads below –70 cm. Soil water retention curves obtained on the soil sample characterizing the Ck horizon(not shown here) have therefore a slightly multimodal
character. The soil hydraulic properties and numericalinversion for such porous system is discussed in detailbelow only for the Haplic Luvisol. The soil hydraulicproperties of krotovina were not studied since the shapeand size of krotovina did not allow taking undisturbed
100 cm3 samples.
The micromorphological images of the soil sample characterizing the Bt horizon in the Haplic Luvisol are presented in Fig. 2. The ﬁgures show the relatively homogeneous matrix structure with many poresless than 100 µm and a system of larger pores createdby roots and soil organisms. These pores are aﬀected
additionally by clay coatings and inﬁllings that control the water ﬂow interaction between the larger poresand pores of the matrix structure. The image porosities were 9.8% and 5.5%. The percentages of diﬀerent
shape groups were as follows: regular pores represent
64.5% and 62.2% of the pores, irregular pores 33.6%
and 35.6%, and elongated pores 1.9% and 2.2%. The



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Fig. 2. Micromorphological images of the soil sample characterizing the Bt horizon at depths of 75–102 cm in the Haplic Luvisol.
A – pores, B – external part of ﬁlling with amorphous forms of CaCO3 , C – clay coatings, and D – internal part of ﬁlling with clay
coatings.

a)

b)





Fig. 3. Soil water retention curves (a) and multi-step outﬂow data (b) obtained on the soil sample characterizing the Bt horizon at
depths of 75–102 cm in the Haplic Luvisol.

pore irregularity again increases with increasing poresizes.
Corresponding soil water retention data points obtained using the water balance calculated for the soil
sample subject to the multi-step outﬂow experimentis shown in Fig. 3a. The soil pore structure displayed
multi-modality of the pore-size distribution that resulted in a multiple S-shaped curve. Soil water retention curves obtained using the numerical inversion of
the multi-step outﬂow experiment are also shown inthis ﬁgure. The single-porosity model in HYDRUS-1D
was used ﬁrst to analyze multi-step outﬂow data andto obtain soil hydraulic parameters assuming uniformﬂow (single continuum approach). Points of the soil water retention curve were also utilized in the inversion.
While the saturated soil water content, θs , was set tothe measured value of 0.401 m3 /m3 , the soil hydraulicparameters θr (the residual water content), α (reciprocal of the air entry pressure), n (related to the slopeof the retention curve at the inﬂection point), and Ks(the saturated hydraulic conductivity) were optimized(Tab. 1). The resulting soil water retention curve does
not ﬁt the experimental data satisfactorily (Fig. 3a).

Also the measured and simulated outﬂow data do notcorrespond well (Fig. 3b). The dual permeability modelin HYDRUS-1D was then applied to improve numericalinversion results and to obtain parameters characterizing two ﬂow domains deﬁned as matrix (m) and larger
pore (f) (two continuum approach). The fraction of thelarger pore domain was estimated based on the micromorphological images (elongated pores corresponding
to pressure heads between –0.2 and –7 kPa). Values ofθs,m and θs,f (saturated water contents of the matrix
and larger pore domains, respectively) were set assuming that the sum of their values multiplied by domains
ratios (wm = 0.925, wf = 0.075) was equal to the measured θs value. Values of θr,m and θr,f (residual watercontents of the matrix and larger pore domains, respectively) were set equal to θr for the single porosity modeland zero, respectively. Considering that the larger porescontrol saturated ﬂow, the saturated hydraulic conductivity of the larger pore domain, Ks,f , was deﬁned as theratio of the Ks value (0.496 cm/h), obtained using theconstant head experiment on the same soil sample andthe domain ratio (wf ). The nf parameter was set equal
to 3 assuming a step-like shape of the soil water reten-



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Table 1. Parameters of the van Genuchten functions for the single-porosity and dual-permeability models for the soil sample characterizing the Bt horizon at depths of 75–102 cm in the Haplic Luvisol.
Model – Flow Domain

Single Porosity
Dual Permeability – Larger Pore
Dual Permeability – Matrix

θs[cm3 /cm3 ]θr[cm3 /cm3 ]α[1/cm]

n[–]Ks[cm/h]

0.401*
0.410*
0.400*

0.254*
0*0.253*

0.041
0.036
0.009

1.214
3*
1.240

0.310
6.5*
0.0032* not optimized

tion curve for the larger pore domain. The eﬀective saturated hydraulic conductivity, Ke , for the mass transfer
between the matrix and the larger pore domains was set
equal to a low value of 10−5 cm/h due to the presence ofclay coatings. Parameters αm , nf , nm , Ks,m were optimized (Tab. 1). The resulting total soil water retention
curve was obtained as the sum of soil water retention
curves for the matrix and larger pore domains multiplied by their corresponding fractions. The total soil
water retention curve and simulated outﬂow data arepresented in Fig. 3. Agreement between the measured
and optimized retention curves and outﬂow data using
the dual-permeability model exhibited signiﬁcant improvement, especially for the pressure head range corresponding to pores detected in the micromorphologicalimage.
Discussion
The micromorphological study of soil pore structure
discovered in all cases the multimodality of the poresystem that was caused by roots and diﬀerent soil organisms. The soil pores were aﬀected by a varying degree of clay coatings or by amorphous forms of CaCO3
and calcite needles. The soil water retention curves also
displayed multimodality for both soil types studied, especially for the Haplic Luvisol. This may be due to thepresence of clay coatings that limited the interaction between the matrix pores and pore domain originated byroots and soil organisms. Another reason for ﬂow limitation between the two pore domains may be the soil
densiﬁcation around the roots that was described by
Bruand et al. (1996). The impact of a proper description of the multimodal ﬂow domain on water and herbicide transport was shown by Kodešová et al. (2005).
While the soil water regimes in the soil proﬁle simulatedusing the single-porosity and dual-permeability models
with similar total soil hydraulic properties were almost
the same, the solute transport was signiﬁcantly diﬀerent. The multimodality of soil hydraulic properties was
also previously discussed by Durner (1994). However,
he only compared the multimodal concept for description of the soil hydraulic properties with the single continuum approach, without considering ﬂow and transport. On the other hand the two continuum approach
is applied by Dušek et al. (2006) to preferential ﬂow
and cadmium transport through biopores under heavy
rainfall. The soil porous system is highly aﬀected byplant roots and soil organisms. The soil micromorphology helps describe pore conﬁguration and explain ﬂow
processes in diﬀerent ﬂow domains and possible interactions between these ﬂow domains.
Acknowledgements
Authors acknowledge the ﬁnancial support of the grants No.
GA CR 103/05/2143, MSM 6046070901 and GA AS CR
A300130504.
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