FEMS Microbiology Ecology 44 (2003) 45^56
www.fems-microbiology.org
E¡ect of bulk density on the spatial organisation of
the fungus Rhizoctonia solani in soil
Kirsty Harris
a;b;
, Iain M. Young c , Christopher A. Gilligan b , Wilfred Otten b ,
Karl Ritz a;d
a
Soil-Plant Dynamics Unit, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
SIMBIOS Centre, School of Science and Engineering, University of Abertay Dundee, Bell Street, Dundee DD1 1HG, UK
d
National Soil Resources Institute, Cran¢eld University, Silsoe, Bedfordshire MK45 4DT, UK
b
c
Received 29 March 2002 ; received in revised form 28 October 2002; accepted 6 November 2002
First published online 3 December 2002
Abstract
The mycelial growth form of eucarpic fungi allows for a highly effective spatial exploration of the soil habitat. However, understanding
mycelial spread through soil has been limited by difficulties of observation and quantification of fungi as they spread through this matrix.
We report on a study on the effects of soil structure by altering the soil bulk density, on the spatial exploration of soil by the fungus
Rhizoctonia solani using a soil thin-sectioning technique. First we quantified fungal densities in microscopic images (0.44 mm2 ). At this
scale, hyphae were either absent, or present as minor fragments, typically occupying less than 1% surface area of the thin section. From
contiguous microscopic images we then produced large-scale (6.21 cm2 ) spatial distribution maps of fungal hyphae. These maps were
superimposed onto soil structural maps, which quantify the degree of porosity in each microscopic image. Alterations in soil structure by
changing the bulk density are shown to affect the distribution of the fungus within the soil. The volume of soil explored by the fungus
increased with increasing bulk density. This was associated with a shift from a few large pore spaces to more evenly distributed small-scale
pores. Fungal hyphae were present in all porosity classes within each bulk density, including areas that contain less than 5% visible pore
space. However, fungal hyphae were more often found in areas with a higher porosity, in particular at low soil bulk densities. The results
show that soil structure is a major component in the spatial exploration of soil by fungi.
< 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
Keywords : Soil structure ; Fungal spatial distribution; Bulk density ; Biological thin section
1. Introduction
A basic characteristic of eucarpic fungi is their mycelial
growth form, which enables a highly e¡ective spatial exploration of habitats [1]. This is particularly important for
saprotrophic and parasitic activity in soil [2,3]. As soils are
a complex three-dimensional physical framework, mycelia
must extend through the heterogeneous networks of pores,
to enable them to locate nutrients. Most studies with fungal growth in soil have been carried out with little atten-
* Corresponding author. Tel. : +44 (1382) 562731;
Fax : +44 (1382) 562426.
E-mail address : [email protected] (K. Harris).
tion to the soil structure within which the mycelia grow
and microbial interactions occur [4]. In this paper we report on growth patterns of the fungus Rhizoctonia solani
introduced into a mineral soil.
Prior studies mostly dealt with the e¡ects of temperature, water potential and other components on the dynamics of mycelial growth on arti¢cial surfaces [5] or over soil
surfaces [6]. Until recently, di⁄culties of observation and
quanti¢cation of fungi have limited our understanding of
mycelial spread through soil. Current studies have involved using a variety of techniques such as radiolabelled
isotopes [7] or baiting [8] to quantify fungal growth in soil.
Persson et al. [7] looked at the distribution of radiolabelled
isotopes which had been incorporated into the mycelium
of nematode-trapping fungi growing in sterile soil. Their
results showed that the radioactive tracing technique re£ected the growth of fungus from the sprinkle plate meth-
0168-6496 / 02 / $22.00 < 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
PII : S 0 1 6 8 - 6 4 9 6 ( 0 2 ) 0 0 4 5 9 - 2
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K. Harris et al. / FEMS Microbiology Ecology 44 (2003) 45^56
od, and that fungal growth was correlated with the size of
the food base. However, the method is destructive as the
soil had to be removed for detecting fungal presence and
also no information on the relationship with the structure
of the soil was provided. The baiting technique implemented by Andersson et al. [8] was a non-destructive
method to quantify the three-dimensional growth of
wood-rotting fungus in contaminated soil. This involved
using temporary baits of wood in the soil, which were
removed, grown on selective media and then the fungus
identi¢ed by polymerase chain reaction/restriction fragment length polymorphism. The results provide quantitative data on the three-dimensional growth rate and pattern
of the fungus in non-sterile soil. However, there is no
information on the spatial distribution of the fungus in
the context of the soil structure.
Recent studies have shown that mycelial exploration
through soil is in£uenced by soil physical characteristics
since hyphae must ramify through the complex heterogeneous network of pores [3,9,10]. The e¡ects of physical
conditions on hyphal spread are di⁄cult to ascertain because of the geometric complexity of the pore networks
[11]. Furthermore, soils are comprised of interdependent
solid, liquid and gaseous phases, where altering one of the
components could indirectly a¡ect the other phases or
associated processes. Many factors may modulate fungal
growth in soils, such as nutrient availability, pH, aeration,
and microbivory [12]. Previous studies of the spread of
fungi through soil have shown that soil physical conditions can also play a signi¢cant role in controlling the
growth of mycelia [3,4,10,13]. Glenn et al. [9,13] and Otten
et al. [3] argue that one of the principal limiting factors to
fungal growth in soil is the availability of air-¢lled pore
space. The connectivity and tortuosity of air-¢lled pore
networks are dictated by the architecture of the soil and
the interaction between the pore networks and water [14].
Field soil exhibits signi¢cant spatial heterogeneity on
many scales [15]. Even in controlled experimental systems
it is therefore di⁄cult to prescribe soil structure precisely.
In this paper we describe the use of aggregate size and
bulk density to manipulate soil structure as an experimental variable. This enabled us to de¢ne repeatable soil samples with identical air-¢lled pore volume in which the geometry of that pore volume was altered by aggregate size
and bulk density. The fungus R. solani, a ubiquitous soil
saprotroph and facultative parasite [16], was introduced
locally into the replicated samples. We produce high-resolution thin sections to quantify how soil structure a¡ected:
(i) the amount of hyphae at microscopic scales (0.44 mm2 ),
at which soil^hyphal interactions occur ; (ii) the total hyphal biomass at the colony scale (6.21 cm2 ); (iii) the spatial distribution of hyphal biomass. We obtained spatial
distribution maps of fungal hyphae from contiguous microscopic images, superimposed these maps onto soil
structural maps which quanti¢ed the degree of porosity
in each image, and tested if the microscopic heterogeneity
in soil a¡ects the spatial distribution of fungal hyphae.
2. Materials and methods
2.1. Production of fungal inoculum
Potato dextrose agar (PDA) plates were inoculated with
anastomosis group 4 isolate (R3) of R. solani Ku«hn and
incubated for 3 days at 23‡C. Poppy seeds (Papaver somniferum L.) were autoclaved at 120‡C at 1.1 atm for 1 h
twice with a 2-day interval. The sterilised seeds were subsequently sprinkled over the PDA plates previously colonised by R. solani, and incubated at 23‡C for 3 days.
2.2. Soil
An arable sandy loam (Caprow; organic matter, 2.6%;
sand, 71%; silt, 19%; clay, 10%; pH 6.2) from Bullion
Field, an experimental site at the Scottish Crop Research
Institute, was used in this study. The soil was air-dried,
sieved to an aggregate size of 1^2 mm, and sterilised by
autoclaving at 120‡C at 1.1 atm for 1 h twice with a 2-day
interval. The particle density (Qs = 2.52 Mg m33 [10]) of the
soil was used to calculate the porosity, O, for soil at dry
bulk densities, bb , of 1.2, 1.3, 1.4, 1.5 and 1.6 Mg m33
(O = 13bb /Qs ).
2.3. Preparation of soil cores
Appropriate masses of soil were packed into polypropylene cylinders (6 cm diameter, 5 cm high), to attain bulk
densities of 1.2, 1.3, 1.4, 1.5 and 1.6 Mg m33 , with an air¢lled pore volume of 0.17 for each bulk density. The bulk
properties of the samples are summarised in Table 1.
Three replicate cylinders per treatment were prepared.
Table 1
Physical characteristics of soil samples through which fungal growth was determined
Bulk density (Mg m33 )
Gravimetric water content (g g31 )
Volumetric water content
Total porosity
Air-¢lled pore volume
1.2
1.3
1.4
1.5
1.6
0.29
0.24
0.19
0.15
0.12
0.35
0.31
0.27
0.23
0.20
0.52
0.48
0.44
0.40
0.36
0.17
0.17
0.17
0.17
0.17
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To obtain identical air-¢lled pore volume, the soil was
wetted with an appropriate volume of sterile distilled
water and left for 24 h to equilibrate prior to packing.
Cylinders were packed using ¢ve 1-cm layers, and one
pre-colonised poppy seed was centrally placed onto the
surface of each successive compressed layer except for
the ¢nal layer. The cores were sealed in polypropylene
bags and incubated at 23‡C for 5 days. This temperature
was chosen, as it is the optimum temperature for this isolate and to ensure consistency with previous work involving the same isolate [4,17].
2.4. Preparation of soil thin sections
Soil thin sections were prepared according to the basic
method of Nunan et al. [18] and Tippko«tter and Ritz [19].
After incubation of the soil cores, they were placed into
250-ml polypropylene beakers raised from the base by two
wooden rods.
2.4.1. Fixation and staining
A ¢ltered (Whatman GF/F) aqueous solution of glutaraldehyde (2.5%) and £uorescent brightener 28 (0.2%) (Sigma, UK) was poured gently into the bottom of each
beaker until the soil sample was immersed to ¢x and stain
the mycelia. The beakers were then placed in a desiccator
and a pressure of 0.6 bar applied for 10 min. The beakers
were left to incubate at room temperature for a further
1.5 h at the end of which the solution was removed from
the base of the beakers by gentle suction.
2.4.2. Dehydration
The samples were subsequently dehydrated with a
graded series of acetone:water solutions, comprising 70%
acetone for 24 h, twice in 90% acetone for 24 h each, three
times in 100% acetone for 2 days each, and 100% dry
acetone for 2 days. Dry acetone was obtained by adding
molecular sieve type 3A pellets to a bottle of 100% acetone. Each solution was poured gently into the bottom of
each beaker until the sample was immersed. After each
acetone change the beakers were placed in a desiccator
and a pressure of 0.6 bar applied for 10 min, then left
to incubate at room temperature for the speci¢c time interval allocated for each acetone concentration (as above).
2.4.3. Resin impregnation
The ¢nal acetone solution was removed and a formulation of Crystic XB52n9 resin, catalyst ‘M’ and accelerator
‘G’ (Scott Bader, Northants, UK), mixed at ratios of
100:0.6:0.3, by volume, was gently poured into the bottom of each beaker until the sample was immersed. The
beakers were placed in a desiccator and a pressure of 0.6
bar applied overnight at room temperature. The beakers
were removed from the desiccator and left to polymerise
for 10 days at room temperature, and then at 40‡C for
4 days to harden.
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47
2.4.4. Sectioning
Sections were produced in the horizontal plane through
the middle of the cured soil/resin samples. Rectangular
blocks were cut from the impregnated and cured samples
with a diamond saw (Buehler, Coventry, UK), using para⁄n oil as a coolant. Blocks of approximately 3U4U2 cm
were produced. A face of each block was £attened and
polished using diamond then silicon carbide papers on a
Metaserv 2000 grinder/polisher (Buehler). The polished
surfaces were cleaned with Ecoclear, a non-solvent cleaning £uid (Logitech, Glasgow, UK), and isohexane. The
clean surfaces were attached to a microscope slide
(50U76 mm) using the resin mixture, prepared as above
except at ratios of 50:0.6:0.3, by volume, and left to cure
for 48 h. The bonded blocks were cut to a thickness of
approximately 800 Wm using a Petro-thin (Buehler, Illinois, USA), ground evenly to approximately 30 Wm on
the Metaserv 2000 grinder/polisher and polished by hand
on paper coated with a 6-Wm, followed by a 1-Wm, diamond paste to ¢nish. Finally, coverslips were bonded to
the thin sections using Eukitt quick hardening mounting
medium (Agar Scienti¢c, Essex, UK).
2.5. Production and analysis of hyphal distribution maps
The system for image acquisition consisted of an epi£uorescence microscope (Zeiss, Axiophan 2), with a highpressure mercury bulb (HBO 103 W/2), ¢lter block 1 (BP
365/12, FT 395, LP 397) and Plan-Neo£uar U10 lenses
(magni¢cation 100U) (Zeiss), and a digital video camera
(JVC, model KY F55B) linked to a PC. By means of a
computer-controlled scanning stage, the entire central area
of 27U23 mm of each thin section was imaged at this
magni¢cation as a series of 1400 contiguous ¢elds of
view, each 0.77U0.58 mm (Fig. 1). The inoculum was
situated in the centre of these sections. The image sets
were stored onto CD-R for subsequent analysis. Hyphae
were clearly present in images due to their distinct blue
£uorescence as a result of staining by the £uorochrome
(Fig. 1). To establish an appropriate classi¢cation for the
degree of hyphal colonisation, 100 single images were selected at random for each bulk density. Each image was
visually scored for hyphae and allocated to one of the
following classes : 0 (no hyphae) ; 1 (minor fragments of
hyphae) ; 2 (low hyphal density, c. 1^5% of image area
containing hyphal fragments) ; 3 (medium hyphal density,
c. 5^15%) ; 4 (very high density, c. 15^100%); or unscorable, where assessment was not possible due to crystallisation of the stain, resulting in a high degree of background £uorescent £are (Table 2). Since on average 90%
of these 1500 images fell into classes 0, 1 or unscorable,
the classi¢cation system was simpli¢ed to absence, presence or unscorable. For each replicated section, 1400 contiguous ¢elds of view were then scored visually using this
scheme, resulting in a series of maps of hyphal distribution
within each section (Fig. 1).
Cyaan Magenta Geel Zwart
48
K. Harris et al. / FEMS Microbiology Ecology 44 (2003) 45^56
Fig. 1. The production of large-scale hyphal distribution map from contiguous microscopic images. Black kernels denote hyphae present and white kernels denote hyphae absent. The expanded microscopic image (0.77U0.58 mm) shows the occurrence of soil matter (dark regions), pore space s 30 Wm
(light region) and fungal hyphae, which appear as white strings. The section shows typical low densities of fungal hyphae that are mainly observed in
the pore space between more dense soil mass.
2.6. Production of pore network distribution maps
Pore maps for the corresponding central (27U23 mm)
area of each thin section were obtained by successively
imaging the areas using bright-¢eld and cross-polar transmitted illumination. These sections were imaged in one
pass, i.e. at a lower magni¢cation, using a stereo microscope (Olympus MO21, Olympus Optical, London, UK)
and digital colour video camera (JVC, model TK-1280E).
The cross-polar image was subtracted from the bright ¢eld
to segment transmission pore spaces (i.e. pores that penetrated the depth of the thin sections, c. 30 Wm). The images
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were then thresholded using Zeiss KS300 Imaging System
3.0 to produce binary pore maps, where white represents
pore space and black represents soil matter with pores of
diameters less than 30 Wm. In order to match the spatial
resolution of the mycelial maps (i.e. 0.77U0.58 mm), the
pore maps were then deresolved by dividing the images
into 1400 contiguous quadrats, and calculating the mean
pixel value to within 1% within each quadrat: this equates
to the average porosity of each quadrat (Fig. 2). At this
experimental scale we denote the average porosity hereafter as porosity class. The hyphal distribution and deresolved porosity maps were then overlain (Fig. 2). Thus it
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K. Harris et al. / FEMS Microbiology Ecology 44 (2003) 45^56
49
Table 2
Hyphal densities that occur within a fungal colony spreading through soil
Class
0, no fungal hyphae
1, minor fragments
2, low hyphal density
3, medium hyphal density
4, very high hyphal density
Crystals
Approximate density (surface area covered %)
0
0^1
1^5
5^15
15^100
N/A
was possible to associate the presence of hyphae with the
porosity of the soil at each location.
2.7. Analysis of spatial distribution of hyphae
The spatial distribution of hyphae was tested for departure from complete spatial randomness using Ripley’s K
function [20] within the statistical package S+ SPATIAL
STATS (S-PLUS Corp., Mathsoft, Seattle, WA, USA).
The K function for the hyphal distribution maps was compared with the upper and lower K functions of 100 simulations of complete spatial randomness. Where the hyphal
distribution maps lay within the complete spatial randomness envelope, the distribution was considered to be random. The distribution was considered clustered above the
envelope and regular, below.
For each treatment the fraction of each porosity class
that contained fungal hyphae, ph , was calculated as the
ratio of the number of microscopic images (0.77U0.58
mm) that contain hyphae and the total number of images
in a thin section belonging to a speci¢c porosity class.
Assuming a binomial distribution for this fraction, the
generalised linear model procedure within the statistical
package GENSTAT (Numerical Algorithms Group, Oxford, UK) was used to test for a correlation between the
fraction of fungal presence and the porosity class, using a
M2 test at a level of signi¢cance of 0.05.
3. Results
3.1. Characterisation of the pore networks within
the soil matrix
The soil thin sections were examined at two scales:
(i) the mesoscopic scale (27U23 mm), corresponding to
the size of a fungal colony, and (ii) the microscopic scale
(approx. 0.77U0.57 mm), which is a scale suitable for
quanti¢cation of hyphal density in soil (see below). Sections di¡ered in visible pore space at the mesoscopic scale
amongst the bulk density treatments. For all treatments,
only the fraction of the pore space that contained transmission pores larger than 30 Wm was visible. About 39% of
the pore volume was visible in the sections (Table 3). The
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Relative frequency
1.2 Mg
m33
1.3 Mg
m33
1.4 Mg
m33
1.5 Mg
m33
1.6 Mg
m33
Mean
0.85
0.09
0.02
0
0
0.04
0.54
0.30
0.03
0
0
0.13
0.25
0.51
0.13
0.01
0
0.09
0.35
0.44
0.19
0.01
0
0.01
0.46
0.44
0.10
0
0
0
0.49
0.36
0.09
0.01
0
0.05
black areas in the section were interpreted as areas containing porosity with pore diameters smaller than 30 Wm.
The bulk density also a¡ected the small-scale structure
of the soil (Fig. 3). Soil packed at the lowest bulk density
contained large gaps surrounded by more dense areas.
Increasing the bulk density led to a progressive reduction
in large voids. A quantitative measure of the small-scale
heterogeneity in soil structure was obtained by quantifying
the porosity in contiguous microscopic images (0.77U0.57
mm) throughout each section. The majority of these microscopic images contained less than 5% visible pore
space, for all treatments. However, the proportion of microscopic images that contained s 95% pore space within
each section (comprising 1400 images) decreased from
4.5% at a bulk density of 1.2 Mg m33 to 6 0.2% for
densities of 1.4 Mg m33 and higher, indicating the signi¢cant di¡erences in pore geometry amongst the bulk density
treatments.
3.2. Microscopic quanti¢cation of fungal hyphae in soil
Fungal hyphae of R. solani were easily detected by microscopic observation of the thin sections (magni¢cation
100U, ¢eld of view 0.77U0.57 mm). At this scale, R. solani
was visible under £uorescent light as fragments of fungal
hyphae in the soil matrix (Fig. 1). Typically, hyphae were
present in void spaces between more dense solid mass (Fig.
1). Closer and thorough observation of the soil matrix at
higher magni¢cations did not reveal fungal hyphae within
these structural elements, indicating that R. solani preferentially followed the larger pores usually provided by inter-aggregate pore space. With the exception of a few
areas close to the inoculum source, all ¢elds of view contained either no hyphae, or small fragments ( 6 1%, cf.
Fig. 1 and Table 2). At the scale of observation the hyphal
density classes were therefore e¡ectively the same, and
hence it is reasonable to use the proportion of sites occupied by the fungus as a qualitative measure of hyphal
density within the di¡erent treatments.
Sterile soil was used in this study to facilitate the detection of R. solani. In preliminary studies, autoclaved sterile
soil was not inoculated with R. solani. Analysis of thin
sections derived from these soils at 100U magni¢cation
showed that there was no fungal presence and images
Cyaan Magenta Geel Zwart
50
K. Harris et al. / FEMS Microbiology Ecology 44 (2003) 45^56
Fig. 2. Diagram illustrating the stages in superimposing maps for pore and hyphal distributions.
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K. Harris et al. / FEMS Microbiology Ecology 44 (2003) 45^56
51
Table 3
Visible pore space in the two-dimensional sections in relation to soil bulk density
Bulk density (Mg m33 )
Mean visible pore volume
Ratio of mean visible pore volume to total porosity (Table 1)
1.2
0.20
0.38
1.3
0.21
0.43
1.4
0.18
0.42
1.5
0.15
0.37
1.6
0.13
0.35
At each bulk density, the mean value (n = 3) of visible pore space in a thin section, given as a fraction of the area of the thin section transmitting light,
is compared with the porosity in the three-dimensional soil sample. The total three-dimensional porosity is calculated from the bulk density using a particle density of 2.52 Mg m33 . The ratio gives the fraction of the three-dimensional pore volume that is visible in a two-dimensional section.
viewed at 630U con¢rmed an absence of other microbial
cells. Observation at high-power magni¢cation con¢rmed
that the cores remained axenic with respect to Rhizoctonia.
Bacteria, clearly visible at high magni¢cation [18], were
never observed. All hyphae observed were of similar appearance and their morphology was characteristic of that
of Rhizoctonia spp., i.e. hyphal diameter between 3 and 17
Wm and branches produced at right and acute angles to the
main hypha [16]. Therefore, we are con¢dent that the fungal fragment observed in the thin sections did belong to
R. solani.
The £uorescent brightener used stained L1,4-glucan
links [21] and hence is not a vital stain. However, the
study above provided evidence that any dead hyphae
present in the soil, prior to growth of Rhizoctonia, do
not normally stain.
of this proportion against porosity class on the logit scale,
decreased with bulk density (Fig. 6a), indicating that predominance in areas with more pore space was more apparent at low bulk densities. To illustrate this more clearly
we back-transformed the data and plotted the relative predominance against bulk density (Fig. 6b). The relative
predominance is here de¢ned as the ratio of the proportion of fungal presence at the highest porosity class (sections with 95^100% visible pore space) and the proportion
of fungal presence in the lowest porosity class (sections
with 6 5% visible pore space). The relative predominance
is in agreement with the visual observation of the hyphal
distribution maps (Fig. 5), and shows that fungal hyphae
are predominantly located in larger void spaces when soil
is packed at low bulk densities.
3.3. The e¡ect of bulk density on the distribution of hyphae
within the soil matrix
4. Discussion
At the mesoscopic scale, the bulk density of the soil had
a signi¢cant impact on the spread and spatial distribution
of R. solani hyphae. The percentage of the mapped areas
containing hyphae increased as the bulk density of the
soils increased from 1.2 to 1.4 Mg m33 , but stabilised
thereafter at around 60% (Fig. 4). The spatial distribution
of hyphae was patchy at lower soil bulk densities (Fig. 5).
Analysis of hyphal distribution using Ripley’s K function
showed randomness in the distribution of hyphae in the
soil sections when large-scale distribution maps of fungal
hyphae were superimposed onto the deresolved porosity
map (Fig. 5). It was apparent that hyphae were situated
in fewer sites within the available pore space, and appeared to be associated more with the edges of larger
void spaces at low bulk densities (Fig. 5a,b). An association between small-scale porosity and fungal presence was
less apparent at higher bulk densities, possibly because
areas of large void spaces were not present, and overall
hyphal density was higher (Fig. 5c^e).
To quantify the relationship between small-scale porosity class and fungal presence we calculated the proportion
of images in each porosity class that contained hyphae.
This revealed that: (i) fungal hyphae were present in all
porosity classes, including images that contained 6 5%
visible pore space ( s 30 Wm), and (ii) there was more often
fungus in areas with lower porosity classes. The strength
of the relationship, measured by the regression coe⁄cient
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The growth of fungi through soil involves spreading
through a heterogeneous three-dimensional framework of
tortuous pores [4,22]. Manipulation of the soil framework
is one of the principal means by which microbial dynamics, in particular fungi, can be regulated at the small scale
with e¡ects that may be realised in the ¢eld [23]. Regulation of microbial dynamics by this means occurs through
the fragmentation in habitat space, water and substrate
distribution and the spatial arrangement of pore pathways
[14].
In this study, we changed the soil bulk density to alter
the geometry of the pore volume as clearly illustrated by
the pore network maps (Fig. 3). The water content was
also selected to ensure that the air-¢lled pore volume
through which R. solani predominantly spreads is identical
amongst the bulk density treatments.
Soil bulk density had a signi¢cant impact upon the spatial organisation of R. solani growing through the soil
volume. The spatial distribution of hyphae was patchy at
lower bulk densities and the volume of soil that contained
hyphae increased with bulk density, between 1.2 and 1.4
Mg cm33 . Generalisation of these results must be done
cautiously: the results are concerned with a central radial
region of the fungal colony (20 mm) in which density of
hyphae is expected to be high in non-sterile soil. Nevertheless, the results are consistent with previous studies
with R. solani by Glenn and Sivasithamparam [9] and
Otten et al. [3]. Glenn and Sivasithamparam [9] demon-
Cyaan Magenta Geel Zwart
52
K. Harris et al. / FEMS Microbiology Ecology 44 (2003) 45^56
(a) 1.2 Mg m-3
(b) 1.3 Mg m-3
(c) 1.4 Mg m-3
(d) 1.5 Mg m-3
Key:
Transmission pores
Soil matter & pores with
diameters < 30 µm
5 mm
(e) 1.6 Mg m-3
Fig. 3. Typical distribution of pore networks for pores s 30 Wm within the soil matrix generated by di¡erent bulk densities.
strated that the density of hyphae within soil di¡ered with
bulk density, with more hyphae per gram of soil in compacted than in uncompacted soil. Otten et al. [3] showed
that small colonies with high biomass densities are formed
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when the spread of the fungus is restricted by blockage of
pores with water. Higher hyphal densities were also reported for the take-all fungus Gaeumannomyces graminis
when spreading through compacted soil [13]. We conjec-
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K. Harris et al. / FEMS Microbiology Ecology 44 (2003) 45^56
Percentage of mapped area
containing hyphae (%)
80
70
60
50
40
30
20
10
0
1.2
1.3
1.4
1.5
1.6
Bulk Density (Mg m-3)
Fig. 4. Presence of hyphae of R. solani within mapped areas of thin sections (27U23 mm) at di¡erent bulk densities (point show means, n = 3;
S.E.M. shown).
ture that this is caused by a reduction in the continuity of
the macro- and meso-pore space as the soil is compacted
(Fig. 3).
The spatial architecture of the pore networks and the
distribution of water within the pore volume can also restrict the £ow of gases, such as oxygen and carbon dioxide. The aeration of the soil plays an important role in the
distribution of soil micro-organisms, especially fungi [14].
R. solani is known to be more sensitive to carbon dioxide
accumulation than most other soil microbes [9]. The rate
of di¡usion of oxygen is 104 times faster through air than
water ; therefore the amount and spatial distribution of
water has serious consequences for the di¡usion rate of
oxygen [24]. Glenn and Sivasithamparam [9] and Otten
et al. [3] demonstrated that the air-¢lled pore volume is
a signi¢cant factor in dictating fungal spread. Further
work is necessary to discriminate between soil structural
and other physical processes, such as gaseous di¡usion, on
the growth of soil fungi.
The technique of soil thin sectioning was used for this
study as it allowed for the visualisation of hyphae within
the context of the soil matrix. The ¢delity of the system, in
terms of preserving the mycelial network, is high. Visual
observations of the thin sections show that the mycelial
networks appear intact and that they are characteristic of
living mycelial systems observed in undisturbed soil microcosms. Small fragments of hyphae were predominantly
present in the images from the thin sections. However,
the mycelia were observed to be structurally intact as hyphae were clearly visible across the pore space; therefore
loss during preparation is unlikely.
Hyphae might not be visualised due to ine¡ective staining. This could be due to the predominant presence of
older mycelia and melanised hyphae, as £uorescent brightener reacts more e¡ectively with actively growing fungi
and bacteria [21,25,26]. However, in this study, fungal
growth occurred over 5 days resulting in a prevalence of
young hyphae, which bind stain more e⁄ciently. From the
visual observations of the thin sections the results obtained
are qualitatively similar to Otten et al. [3], where they use
monoclonal antibody-based immunosorbent assay to
FEMSEC 1483 7-4-03
53
quantify the amount of active fungal biomass in a soil
sample. The thin section technique provides novel information about the spatial distribution of the fungus and
soil structure, and a visual representation of where micro-organisms reside within the pore network at high resolution [18,27]. However, the technique is time-consuming
to produce the ¢nal sections and only transmitted pores
above 30 Wm in diameter are visible, thus compared to
other techniques such as the dispersal method [28] it is
not appropriate for estimating the amount of fungal biomass present.
The distribution and size of the pore pathways generated by di¡erent bulk densities had a signi¢cant impact on
the distribution of hyphae within the soil matrix. Increasing the bulk density led to a shift from a few large pore
spaces to more evenly distributed small-scale pores and
hyphae becoming more abundant. This suggests that there
is a degree of association between mycelial distribution
and pore networks.
There are many factors that can in£uence fungal
growth, such as resource availability and microbivory
[12]. The system used in our study was axenic. However,
in non-sterile soil other organisms are present which compete with each other for oxygen, nutrients and habitat
space. Competition is high for nutrients within non-sterile
environments and almost invariably, introduced micro-organisms, such as R. solani, are outcompeted by adapted
and established indigenous organisms [4,29]. As well as the
other organisms regulating each other, they are also being
regulated by the structure of the soil and the distribution
of water within the pore network.
The distribution, size and quality of substrate present in
the soil can a¡ect the activity of soil-borne fungal mycelia
[30]. The quality and quantity of substrate was unlikely to
be the limiting factor in fungal spread, as the soil was
sterilised by autoclaving. Autoclaving causes the soil to
release large quantities of soluble carbon as well as ammonium N and amino acids [31], therefore providing an
abundant source of nutrients. A larger total quantity of
substrate would have been present at the higher soil bulk
densities since a larger mass of soil was packed into the
cores. However, the distribution of nutrients within the
pore networks may also have varied and could a¡ect the
spread of the mycelium as mycelial growth (energy expenditure) is often proportional to substrate availability
[30,32]. The results here were consistent with studies of
fungal colony growth using non-sterile soil, suggesting
that substrate availability was unlikely to be the dominant
factor in our experiments [4,9,13]. The correlation between
spatial distribution of mycelium and the microscopic
structure of the soil further indicates that the soil structure
had an e¡ect on the fungal exploration of soil (Fig. 5).
Fungi play an essential role in maintaining critical ecological balances in soil, upon which many environmental
processes depend. Until now, our understanding of fungal
dynamics in soil has been limited by di⁄culties of obser-
Cyaan Magenta Geel Zwart
54
K. Harris et al. / FEMS Microbiology Ecology 44 (2003) 45^56
Fig. 5. Distribution maps of mycelia of R. solani overlaying porosity maps at di¡erent bulk densities.
vation, identi¢cation and quanti¢cation of these micro-organisms as they grow through the complicated structure of
soil and in bridging the gaps between the microscopic scale
and the larger scale processes. In this paper we have linked
experimentation in soil physics (to control and quantify
FEMSEC 1483 7-4-03
soil structure) with soil microbiology (to quantify hyphal
and colony growth in situ) in order to quantify soil^fungal
interaction at scales ranging from millimetres to centimetres. We showed that soil structure is a major component governing the spatial exploration of soil by fungi.
Cyaan Magenta Geel Zwart
K. Harris et al. / FEMS Microbiology Ecology 44 (2003) 45^56
A
B
relative predominance
0.012
0.010
regression slope
55
0.008
0.006
0.004
0.002
0.000
-0.002
-0.004
1.1
1.2
1.3
1.4
1.5
1.6
1.7
2.4
2.2
2.0
1.8
1.6
1.4
1.2
1.0
0.8
0.6
0.4
0.2
0.0
1.1
-3
hyphae predominantly in
areas high in porosity
hyphae predominantly in
areas low in porosity
1.2
1.3
1.4
1.5
1.6
1.7
-3
bulk density (Mg m )
bulk density (Mg m )
Fig. 6. Summary of the analysis of the relationship between fungal presence and the small-scale porosity for soil samples that were packed at mean
bulk densities ranging from 1.2 to 1.6 Mg m33 . The mean strength of the relationship (n = 3) is given by a regression coe⁄cient on a logit scale (a). A
regression coe⁄cient larger than 0 indicates that the fungus predominantly is found in areas high in porosity. The relative predominance of the fungus
for high-porosity areas declines for soils packed at increasing bulk density (b). The relative predominance here equals the ratio of the proportion of sites
containing fungus in the highest porosity class ( s 95% visible porosity) and the lowest porosity class ( 6 5 visible porosity). A value s 1 indicates a
preference for sites with a higher porosity.
Acknowledgements
This work is part of a linked research grant between the
Scottish Crop Research Institute (SCRI) and the Epidemiology and Modelling Group in the University of Cambridge, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), which we gratefully
acknowledge. SCRI receives grant-in-aid from the Scottish
Executive Environment and Rural A¡airs Department.
We would like to thank Dr Naoise Nunan from SCRI
for his advice and assistance in the use of the spatial statistics.
[8]
[9]
[10]
[11]
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