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CHAPTER 2. SUBMICROSCOPIC EXAMINATION OF SOILS
E. B. A. BISDOM
techniques were also applied to weathered rocks and uncohesive geological
Thin-section studies of soils with the light microscope indicated that available
magmfkations were frequently insufficient to study the finer soil particles. The
TEM was initially used to investigate especially clayey material that had been
pretreated and was disturbed. In sifu studies using the TEM were first made on
replicas, and it has recently become possible to examine ultrathin sections of soft
soil constituents. Such in sifu studies became popular with the introduction of the
scanning electron microscope (SEM) (i.e., with the potential to study soil constituents in soil peds and to examine mineral grains with or without coatings).
“Three-dimensional” pictures were obtained and the morphologies of the soil
constituents were studied at various magnifications.
The investigation of very small particles in soils requires TEM and scanning
transmission electron microscope (STEM) investigation of ultrathin sections that
are transparent to the electron beam. Such ultrathin sections of organic matter
and clays have been prepared, but those from harder soil materials are still
difficult to obtain. Ultrathin sections also offer the possibility of electron diffraction of individual soil particles instead of X-ray diffraction of bulk samples that
have been pretreated and disturbed.
Submicroscopy with the SEM, especially after the introduction of new detector systems, can be used to study the form of pores and minerals in a thin section
if used in combination with equipment for image analysis. So far, however, thin
sections have been used more often to investigate chemical elements of soil
particles. Such microchemical analyses started with the EMA [also called EPMA
(electron probe microanalyzer)]. This instrument, as do most of the other instruments used in submicroscopy, requires a polished surface of a thin section or the
surface of a thin polished block. More recently, the SEM has been equipped with
an energy dispersive X-ray analyzer (EDXRA). This SEM-EDXRA allows in
situ analysis of soil materials in unhardened soil components and in thin sections.
A scanning electron microscope equipped with a wavelength dispersive X-ray
analyzer (SEM-WDXRA) can only analyze chemical elements in polished
Two problems remained with EMA and SEM-EDXRA-WDXRA analyses of
soil components; the lightest elements of the periodic system of chemical elements and trace elements could not be studied using electron microscopy. These
problems were solved with the introduction of ion microscopy. The instruments
involved use either primary ions for the excitation of secondary ions from materials in thin sections of soils [e.g., ion microprobe mass analyzer (IMMA) and
Cameca IMS 3F (ion microanalyzer)] or a laser for the excitation of primary ions
[e.g., LAMMA 500 and LAMMA lo00 (laser microprobe mass analyzers)].
Quantification of all chemical elements in soil constituents of a thin section
became possible with the Cameca IMS 3F.
SUBMICROSCOPIC EXAMINATION OF SOILS
The technical possibilities of in situ submicroscopic research are significant.
This young branch of soil science, together with light microscopy, allows us to
obtain knowledge on soil components in their natural environment and at a
variety of magnifications. Several examples of submicroscopic studies will be
given after discussing the capabilities of a number of machines.'
11. SUBMICROSCOPIC TECHNIQUES
I . Transmission and Scanning Transmission Electron
The transmission electron microscope is commonly used for the study of loose
and very small particles in soils using a static electron beam. A lateral resolution
of 0.2 nm can be achieved (Boekestein et al., 1981). If ultrathin sections can be
made with a thickness of about 1 pm, the TEM can be used because the electrons
can pass through the specimen. Ultrathin sections of clayey and of organic
material were prepared and studied with the TEM by Bresson (198 1) and Foster
The high-voltage electron microscope (HVEM) uses a much higher kinetic
energy than the TEM, about lo00 keV compared to 20-200 keV. The HVEM
can examine a specimen somewhat thicker than can the TEM but so far no results
have been published in soil micromorphology submicroscopy. The polyester
resin used for the embedding of soil material is expected to become brittle with
high voltage electron microscopy. Samples somewhat thicker than 1 pm can also
be studied with the STEM. The STEM (Fig. 1) can be used as a TEM, SEM, or
STEM. The instrument makes it possible to study an ultrathin section by a
Microchemical analysis is also possible with a TEM or an STEM that has a
'Abbreviations used in this paper: A E S , Auger electron spectroscopy; BESI, backscattered electron
scanning image; EDXRA, energy dispersive X-ray analyzer (analysis); EMA, electron microprobe
analyzer (analysis); EPMA, electron probe microanalyzer (analysis); ESCA, electron spectroscopy
for chemical analysis; HREM, high resolution electron microscope (microscopy); HVEM high
voltage electron microscope (microscopy); IMMA, ion microprobe mass analyzer (analysis);LAMMA, laser microprobe mass analyzer (analysis); LMA, laser microspectral analyzer (analysis); RS,
Raman spectroscopy; SEM, scanning electron microscope (microscopy);SIMS, secondary ion mass
spectrometer (spectrometry); STEM, scanning transmission electron microscope (microscopy);
TEM, transmission electron microscope (microscopy); WDXRA, wavelength dispersive X-ray analyzer (analysis); XRD, X-ray diffraction.
E. B. A. BISDOM
FIG. 1. Scanning transmission electron microscope (Philips EM 400T/ST).
lateral resolution of about 5 nm. The instruments can be equipped with an
EDXRA. Analysis of the heavier chemical elements in ultrathin or somewhat
thicker thin sections thus becomes possible. Because of beam spot diameters that
are smaller than those present in conventional SEM instruments, it is possible to
analyze at magnifications which are larger than those possible with an SEMEDXRA (i.e., larger than X l0,OOO).
Very small particles can be analyzed and identified with the TEM and STEM
if equipment for electron diffraction is available. This technique is usually applied to study loose clay minerals but can also be used to study small particles in
ultrathin sections of soils. Work has been done with the STEM-EDXRA on thin
sections (5 pm thick) and at a maximum magnification of X50,OOO. Work with
the TEM-EDXRA and STEM-EDXRA on ultrathin sections, and diffraction
SUBMICROSCOPIC EXAMINATION OF SOILS
studies of these specimens, must yet be done. The principal difficulty is that we
still must learn how to prepare ultrathin sections of harder soil materials. Ionthinning techniques seem to give the best results at present. If ultrathin sections
have been prepared, TEM and STEM instrumenis are available for various types
of studies on an ultramicro scale.
2 . Electron Microprobe Analysis and Scanning Electron
The electron microprobe analyzer is the oldest machine used for microchemical analysis of soil materials in polished thin sections. It is used for microanalysis
only (i.e., for semiquantitative and quantitative measurements using a set of
standards with which to compare the results of the analyses). Older EMA instruments often caused localization problems for materials in a thin section of soil.
Modem machines, however, can be equipped in such a way that one can find soil
components in thin sections with relative ease, which is necessary for heterogeneous soils with fine particles and complicated fabrics.
The EMA is equipped with a WDXRA system. Wavelength dispersive analysis is done with a WD detector which contains a crystal that is used for Bragg
reflection and a gas-filled proportional counter (Boekestein et al., 1981). Only
one element can be measured at a time, unless more detectors are used. The WD
detector has a high efficiency, because of the thin entrance window of the
proportional counter, and a high peak-to-background ratio. This ratio is important because element-characteristic radiation is represented by the peaks and
noncharacteristic radiation is represented by the background. The detectable
elements are B-U (22 5 ) . The maximum magnification of the EMA is about
X500, which can be a problem (Bisdom et al., 1975, 1976); the lateral resolution
is about 1 pm.
The scanning electron microscope (Figs. 2 and 3) can also be equipped with a
WDXRA system, which allows magnifications up to X10,OOO. The SEMWDXRA and the SEM-EDXRA have lateral resolutions of about 1 pm, as does
the EMA. This means that the minimum diameter of a spot that is analyzed in a
thin section is 1 pm. The SEM-WDXRA, like the EMA, can only work with
polished surfaces, whereas both polished and rough surfaces can be examined
with the SEM-EDXRA. Consequently, materials in soil peds are now investigated microchemically, not only on the basis of morphology, by using the SEM. An
additional advantage of the EDXRA is that the current of the primary electron
beam on the specimen is lo-" A, whereas it is lo-' A for the EMA. Consequently, in EMA the polyester resin of the thin section is easier to damage than in
Energy dispersive X-ray analysis utilizes an ED detector which consists of a
lithium-drifted silicon crystal. If the detector has a beryllium window, very soft
E. B. A. BISDOM
FIG. 2. Scanning electron microscope (Jeol-JSM-35C).
FIG. 3. Scanning electron microscope (Philips SEM 505).
SUBMICROSCOPIC EXAMINATION OF SOILS
X rays are absorbed and the characteristic radiation of elements with low atomic
numbers is not detected. Elements Na-U (22 11) are detected in this way. If an
ECON detector is used without a beryllium window, the radiation of C, N, 0,
and F can also be measured. The ED detector has very small processing times
and can give information on a range of elements simultaneously. However, the
energy resolution is rather poor, which affects the peak-to-background ratio and
the minimal detectable concentration. Ideally, SEM-EDXRA is used for reconnaissance and semiquantitativework and EMA and SEM-WDXRA for quantitative and semiquantitative work. Trace elements are usually not measurable
with electron microscopes. However, under ideal conditions, lo-'* g of an
element [approximately 0.1%can be measured (Boekestein et al., 1981)].
B. ION MICROSCOPY
Various instruments for the analysis of secondary ions, excited from the sample by primary ions, have been tested on soil samples, including the IMMA of
ARL, Cameca IMS 300 (ion microscope), Cameca IMS 3F (Fig. 4), and LAS of
Riber [an apparatus in which SIMS, ESCA, and Auger (see later discussion)
analysis can be done]. Only polished thin-section material which has been removed from the support glass can be used in these instruments. The IMMA uses
a scanning primary ion beam and a mass spectrometer for mass analysis of
sputtered ions (Bisdom et al., 1977). The primary electron beam of the electron
FIG. 4, Ion microanalyzer (Cameca IMS 3F).
E. B. A. BISDOM
microscope has been replaced in the IMMA by a primary ion beam and secondary ions are produced instead of secondary electrohs. In the IMMA the sample
can be viewed during analysis through a binocular microscope (Henstra et af.,
1981a), whereas this is not possible with the Cameca instruments. Localization is
done in the latter machines with a low-power optical microscope. A viewport is
present in the LAS series of instruments.
All four instruments are used for secondary ion mass spectrometry (SIMS).
Such spectra of secondary ions give information on all chemical elements that are
present in a sample including hydrogen. Both trace and major elements can be
measured. Background problems, such as are present in electron microscopy, are
virtually absent. Background readings are usually below 5 counts/sec, with total
count rates on the order of lo8 counts/sec (Liebl, 1975). Trace concentrations
can therefore be analyzed, usually down to the
range and in many cases
even down to the
range. Trace amounts (10-I8 g) of sample material are
measurable. The sentitivity of SIMS is much better than that of X-ray analytical
techniques (i.e., 1OOO-10,OOO times) (Henstra er al., 1981a).
All elements can be detected with SIMS but the secondary ion yield differs for
various elements. Also, the same element in a different matrix may give a
different secondary ion yield. The secondary ion yield of the sample can be
strongly enhanced by bombarding with a reactive species such as oxygen or
nitrogen. The primary ions used for bombarding the sample can be charged either
positively or negatively. The sample is continuously eroded under ion bombardment; consequently, the determination of concentration as a function of depth is
important. Depth-concentration profiling with a resolution of about 5 nm is
possible. Probe diameters on the surface of the sample range from 500 to 1-2
FmIsotopic analysis is possible in SIMS, and isotopic abundance ratios can be
measured with high accuracy. This should allow in siru age dating of materials in
thin sections of soils and in horizons of soil profiles. Another possibility is to
label chemical elements with stable isotopes, which should allow the study of
transport phenomena in soils by measuring the position of these labeled isotopes
in thin sections. Secondary ion mass spectrometry offers a large variety of
measurement possibilities which can be added or compared to those of electron
microscopy. As ion microscopy is a younger field than is electron microscopy,
various measurement techniques are still being developed. Experiments have
indicated, however, that quantitative and semiquantitative measurements of soil
materials in thin sections of soils are now possible (see Section IV).
C. A D D ~ O N ASUBMICROSCOPY
Various additional submicroscopic techniques are available, but only a few
(those which seem to be the most promising for research of soil materials) have
SUBMICROSCOPIC EXAMINATION OF SOILS
been tested so far, namely, Raman spectroscopy (RS), laser microprobe mass
analysis (LAMMA), electron spectroscopy for chemical analysis (ESCA), and
Auger electron spectroscopy (AES). Raman spectroscopy has been tested for soil
materials by Jeanson (1981). Illumination of the soil sample is done with a laser
beam. The Raman spectrum is obtained when monochromatic light is passed
through a transparent substance. The light is scattered by the transparent substance and undergoes energy transformations. The frequency of some of the light
is therefore changed, resulting in the addition of certain lines to the Raman
spectrum. The lines of the spectrum are thus characteristic of the molecular
structure of the examined area in a thin section or soil ped. An important aspect
of RS is that it is nondestructive.
Laser microprobe mass analysis, which is destructive, has been done with the
LAMMA 500 of Leybold-Heraeus (Henstra et al., 1980a; Bisdom et al., 1981).
An optical microscope is used to focus a high-power pulsed laser onto an area of
the thin section or soil ped less than 1 pm in diameter. A microvolume of about
10- '*-lo- l 4 cm3 is evaporated and ionized. These ions are detected by a mass
spectrometer, also used in ion microscopy. The difference between the two
methods is that excitation of the ions takes place with a laser beam in LAMMA
and with primary ions in ion microscopes. The LAMMA 500 was made for the
investigation of ultrathin specimens of 0.1- 1 pm, and the light optical and ion
detection systems were therefore placed on opposite sides of the piece of ultrathin section. Thicker thin sections of about 15 pm could therefore only be
analyzed by applying laser milling, in which the laser shots evaporate soil material from the edges of the piece of thin section inward. So far, in the LAMMA
lo00 (Fig. 5), the optical and ion systems are placed on the same side of the
sample. Consequently, our common thin sections can now remain on their support glass during analysis.
Electron spectroscopy for chemical analysis uses X rays or uv photons to
irradiate materials in thin sections (Henstra et al., 1981b). Ultraviolet and X-ray
electromagneticradiation can be used to excite outer- or inner-shell electrons and
this causes the ejection of electrons (McCrone and Delly, 1973). Ultraviolet
radiation, with its long wavelength and lower energy, can eject the outermost
electrons, whereas X-ray radiation, which has a short wavelength and higher
energy, can eject inner-shell electrons. The energies of the ejected electrons can
be used to distinguish pure elements and elements in a bonded state; the difference can be observed as different peaks in an energy spectrum. Electron
spectroscopy for chemical analysis is mainly used for chemical bonding studies
in situ. Tables by Wagner el al. (1979) are available for ESCA studies; all
elements except hydrogen can be studied. The depth of analysis is 2-10 nm, and
the minimal detectable concentration is about 0.1%. Electron spectroscopy for
chemical analysis will usually succeed for soil materials that are homogeneous
over fairly great distances; the lateral resolution of analysis is about 3 mm, which
E. B. A. BISWM
FIG.5. Laser microprobe mass analyzer (LAMMA 10o0, bybold-Heraeus).
FIG. 6. AES (Auger electron spectroscopy), ESCA (electron spectroscopy for chemical analysis), and SIMS (secondary ion mass spectrometry) are possible with the LAS 3000 (Riber).
SUBMICROSCOPIC EXAMINATION OF SOILS
is too large for heterogeneous samples with small particles. Bemer and Holdren
(1977) have used this technique for the study of weathered feldspar.
Auger electron spectroscopy is a typical surface analytical technique. Primary
electrons are used to obtain Auger electrons from the sample. The energy of the
Auger electrons is recorded in an energy spectrum which can be used for quantitative and qualitative chemical analysis of soil materials up to a depth of 1-2
nm below the surface of the thin section. All elements except H and He can be
analyzed, and the lateral resolution of analysis is about 0.1 pm. The minimal
detectable concentration is about 0.1%(Henstra et al., 1981b). Experiments with
LAS (see section II,B) gave results on iron-coated organic material from the
Netherlands, but no information was obtained on nonconductive clayey material.
The LAS instrument (Fig. 6) was able to perform SIMS and ESCA analyses.
Ill. APPLICATIONS OF ELECTRON MICROSCOPY
Applied electron microscopy has been subdivided into studies of unhardened
samples (Section II1,A) and thin sections (Section II1,B) because most of the in
situ submicroscopic literature describes unhardened materials in soil peds. These
studies were usually performed with an SEM that had no equipment for microchemical analysis. The main goal was the study of the morphology of soil
particles in the peds and the arrangement of the soil into certain fabric patterns.
Thin sections were used for microchemical analysis with the EMA, an instrument which was specifically built for this purpose. Analysis by the
SEM-EDXRA and the SEM-WDXRA followed later. Currently, microchemical analyses can also be done in soil peds with the SEM-EDXRA, and the
morphology of soil particles and certain types of fabrics can also be studied in
thin sections. It remains true, however, that quantitative analysis of the chemical
elements in soil constituents requires a polished surface and must be done with an
EMA or an SEM-WDXRA. The most impressive three-dimensional morphology of soil components is found in unhardened soil peds using the SEM.
Several review articles have been written on electron microscopy as applied to
soils. The use of TEM, SEM, and EMA in pedology was discussed by Bocquier
and Nalovic (1972). The use of light microscopy, TEM, and SEM in micropedology was treated by Stoops (1974). A number of submicroscopic techniques
which can be applied to soil micromorphology were given by Smart (1974), and
details of TEM and SEM techniques as applied to soils and sediments are discussed by Smart and Tovey (1981, 1982). Published studies using SEM and
EMA were indicated by Bisdom et al. (1976). Two review papers have been
published in which TEM, SEM, SEM-EDXRA-WDXRA, EMA, and nonelectron microscopic work on thin sections of soils (i.e., ion microscopy, laser
E. B. A. BISWM
analysis, and electron spectroscopy for chemical analysis) are discussed
(Bisdom, 1981a,b) .
The submicroscopic study of unhardened soil samples can be done by TEM,
STEM,and SEM. The TEM and STEM can give magnificationsover X 1,OOO,OOO
depending on the type of soil particles that are studied. The TEM and STEM are
usually used for very small soil particles that are present in ultrathin sections or in
pretreated and disturbed samples. Ultrathin sections are discussed in Section
III,B, but pretreated and disturbed samples form no significant part of this article.
The SEM can reach magnifications of more than X100,OOO. The maximum
magnification is again dependent on the type of soil particle that is investigated.
The SEM is an ideal instrument for three-dimensional studies of soil constituents
and therefore it is frequently used for morphological examination. Much attention
has also been paid by specialists in soil mechanics and soil microscopy to the
spatial relationships between individual constituents in soil peds.
2 . Clay Minerals
Individual clay minerals in soil peds or aggregates are usually difficult to
recognize with the SEM because they commonly form stacks that can be partly or
wholly coated with other fine soil constituents. X-raypowder diffractograms of
bulk and disturbed samples and TEM studies of pretreated and disturbed individual clay minerals are usually performed simultaneously with SEM studies of
materials in soil peds.
Keller (1976a,b,c, 1977a,b, 1978a) and Keller and Haenni (1978) studied
kaolinite in various deposits around the world and were able to classify these
deposits into transported and residual types on the basis of texture differences
found in scanning electron micrographs. Gillott (1974) and Tessier and Berrier
(1978) recognized that the in situ investigation of clay minerals in soil peds
required ‘special preparation techniques such as freeze-drying or critical-point
drying if air-drying does not give the required results. Smart and Tovey (1982)
discuss these and other techniques for electron-microscopic work.
Spherulitic halloysite in volcanic deposits was examined with the SEM and
TEM by Sudo and Yotsumoto (1977) and Violante and Violante (1977). Differences in shape and mineralogical properties were found to exist between the
spherulitic halloysite bodies. Sudo and Yotsumoto (1977) called the bodies
“chestnut-shell-like” on a morphological basis and “allophane-halloysite-