Ernst Bekker final draft

i
VARIATION IN CLAY SURFACE MORPHOLOGY AND MINERALOGY
OF SOILS AFFECTED BY ACID AND SALINE MINE WATER
by
ERNST HENDRIK BEKKER
Submitted in partial fulfilment of the requirements for the degree
B.Sc. (Hons.) Environmental Soil Science
In the Department of Plant Production and Soil Science
University of Pretoria
Supervisor: Mr. C. de Jager
Co-supervisor: Dr. J van der Waals
October 2015

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DECLARATION
I hereby certify that this seminar is my own work, except where duly acknowledged. I
also certify that no plagiarism was committed in writing this thesis.
________________
Ernst Hendrik Bekker

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TABLE OF CONTENTS
LIST OF TABLES....................................................................................................... v
LIST OF FIGURES.....................................................................................................vi
ABSTRACT..............................................................................................................viii
CHAPTER 1: INTRODUCTION.................................................................................. 1
1.1 Literature review ............................................................................................... 1
1.2 Background to study ......................................................................................... 3
CHAPTER 2: METAL BALLANCES ........................................................................... 8
2.1 Background and literature review...................................................................... 8
2.2 Methodology ..................................................................................................... 9
2.2.1 Sample selection ........................................................................................ 9
2.2.2 Sample and solution preparation and procedure ........................................ 9
2.3 Theoretical soil loadings.................................................................................. 10
2.4 Results............................................................................................................ 11
2.4.1 Al, Fe and Mn extracts of BC soils............................................................ 12
2.4.2 Al, Fe and Mn extracts of RS soils............................................................ 12
2.5 Summary......................................................................................................... 13
CHAPTER 3: CHANGES IN SOIL MINERALOGY................................................... 15
3.1 Background and literature review.................................................................... 15
3.2 Methodology ................................................................................................... 17
3.2.1 Sample selection ...................................................................................... 17
3.2.2 Sample preparation .................................................................................. 17
3.2.3 Mineral identification ................................................................................. 17
3.3 XRD results and analysis for BC soils............................................................. 18
3.3.1 Diffractograms and mineral identification tables of BC Ori and BC MW. .. 18
3.3.2 The influence of ammonium acid oxalate treatment on mine water treated
BC soil. .............................................................................................................. 22
3.3.3 The influence of dithionite citrate extraction on mine water treated BC soil.
........................................................................................................................... 24
3.3.4 Diffractograms of RS original soil.............................................................. 27
3.4 Discussion....................................................................................................... 30
CHAPTER 4: CHANGES IN SOIL SURFACE MORPHOLOGY............................... 32
4.1 Background and literature review.................................................................... 32
4.2 Methodology ................................................................................................... 32

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4.2.1 Sample selection ...................................................................................... 32
4.2.2 Sample preparation and analysis.............................................................. 33
4.3 Results of photomicrographs of BC and RS selected samples....................... 34
4.4 Discussion....................................................................................................... 37
CHAPTER 5: SUMMARY AND CONCLUSIONS..................................................... 40
REFERENCES......................................................................................................... 41
APPENDIX A............................................................................................................ 44

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LIST OF TABLES
Table 1.1: Pyrite reaction with oxygen and water to various ions and finally ferric
hydroxide and acid…………………………………………………………………………2
Table 1.2: Approximations of the water qualities for the western, central and eastern
basin……………………………………………………………………………………..……3
Table 1.3: Water qualities for the western basin………………………………..….…..6
Table 2.1: Summary of soil metal loading (input), leached (removed) and attenuated
amounts……………………………………………………………………………………..11
Table 2.2: A summary of the AAO and DC soil concentrations of the BC Ori and BC
MW soil…………………………………………………………………………………..….12
Table 2.3: A summary of the AAO and DC soil concentrations of the RS Ori and RS
MW soil………………………………………………………………………………….…..13
Table 3.1 Diffractogram data analysis of figure 3.1…………………………….....….19
Table 3.2 Diffractogram data analysis of figure 3.3 and figure 3.4……….………...22
Table 3.3 Diffractogram data analysis of figure 3.7…………………………………...28
Table 3.4 Diffractogram data analysis of figure 3.9 and figure 3.10………………..30

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LIST OF FIGURES
Figure 1.1: Experimental methodology employed to investigate the effect AMD has
on mineral surfaces and mineralogy. Original soil refers to either the BC or RS
soil………………………………………………………………………………………….…7
Figure 3.1: Diffractograms of the BC MW and BC Ori for 5° - 30° (2θ). Peak 1:
gypsum, peak 2: montmorillonite, peak 3: gypsum, peak 4: quartz, peak 5:
montmorillonite, peak 6: gypsum, peak 7: microline and peak 8:
andesine…………………………………………………………………………………….18
Figure 3.2: Differential diffractogram of the BC MW intensity divided by the BC Ori
intensity for 5° - 30° (2θ). Peak 1: gypsum, peak 2: gypsum, peak 3: quartz and peak
4: gypsum……………………………………………………………………………......…20
Figure 3.3: Diffractograms of the BC MW soil and the BC Ori soil for 35° - 45° (2θ).
Peak 1: gypsum, peak 2: gypsum, peak 3: hematite, peak 4: quartz and peak 5:
quartz……………………………………………………………………………………..…21
Figure 3.4: Differential diffractogram of the BC MW and BW Ori soil for 35° - 45°
(2θ). Peak 1: gypsum, peak 2: gypsum, peak 3: hematite, peak 4: quartz and peak 5:
quartz……………………………………………………………………………………..…21
Figure 3.5: Diffractogram of the BC MW, BC Ori and BC MW AAO for 5° - 30° (2θ).
Peak 1: gypsum, peak 2: gypsum, peak 3: quartz and peak 4:
gypsum……………………………………………………………………………….……..23
Figure 3.6: Diffractogram of the BC MW, BC MW AAO and BC Ori and for 40° - 45°
(2θ) Peak 1: Hematite, peak 2: quartz and peak 3: quartz…………………………….24
Figure 3.7: Diffractogram of the BC MW, BC Ori and BC MW DC for 5° - 30° (2θ).
Peak 1: gypsum, peak 2: gypsum, peak 3: quartz and peak 4:
gypsum……………………………………………………………………………..……….25
Figure 3.8: Diffractogram of the BC MW, BC MW DC and BC Ori and for 40° - 45°
(2θ). Peak 1: Hematite, peak 2: quartz and peak 3: quartz.3.4 XRD analysis for RS
soil…………………………………………………………………………………………...26

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Figure 3.9: Diffractograms of the RS MW and the RS Ori soils for 5° - 30° (2θ). Peak
1: Gypsum, peak 2: montmorillonite, peak 3: gypsum, peak 4: quartz, and peak 5:
gypsum……………………………………………………………………………………...27
Figure 3.10: Diffractograms of the RS MW intensity divided by the RS Ori intensity
for 5° - 30° (2θ). Peak 1: gypsum, peak 2: gypsum, peak 3: quartz and peak 4:
gypsum……………………………………………………………………………………...28
Figure 3.11: Diffractograms of the RS MW and the RS Ori soils for 35° - 45° (2θ).
quartz………………………………………………………………………………………..29
Figure 3.12: Diffractogram of the RS MW intensity divided by the RS Ori intensity for
35° - 45° (2θ). Peak 1: gypsum, peak 2: gypsum, peak 3: hematite, peak 4: quartz
and peak 5: quartz……………………………………………………………………...….29
Figure 4.1: Photomicrographs (a) BC Ori, (b) RS Ori, (c) BC MW, (d) RS MW, (e) BC
MW (CaCO3) and (f) RS MW (CaCO3)……………………...………………...……...…35
Figure 4.2: Rod-like structures found on BC MW soil………………………………..36
Figure 4.3: White spot-like particles found on both (a) BC MW and (b) RS
MW……………………………………………………………………………….......……..37
Figure 4.4: (a) Clay and iron oxide 2:1 composite at a scale of 1 µm, (b) enlargement
of (a) at a 10 µm scale, (c) a sample of pure iron oxide at 1 µm scale…………….37
Figure 4.5: Hematite crystals on a large cristobalite particle 1 µm scale…………..38
Figure 4.6: (a) Sample of bassanite, (b) pure gypsum crystals. (c) and (d) are
photomicrographs taken of the BC MW soil…………………...………………………39

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ABSTRACT
Underground mining on the Witwatersrand has produced a great deal of gold and to
a slighter extent other precious metals needed by both the consumer and industry
alike. This has however resulted in great underground voids which are slowly filling
up to environmental critical levels. As the water level rise within the voids more
reactions between the water and the ores take place, generating a great volume of
acidic mine water. One of the proposed methods of remediating acidic mine water is
to directly apply it as is to the soil with neutralising compounds such as limestone. In
a previous study, a black clay (BC) soil and a red sandy loam (RS) soil were used.
Both soils originate from farmland close to the Brakpan Dam tailings storage facility.
These soils were then treated with acidic mine water from the Western basin of the
Witwatersrand mines and found to have results worth investigating further. A
substantial amount of research has already been done, however, there is still a lot to
be gained on how acidic mine water affects soils at a micro and nano-scale. Acid
ammonium oxalate (AAO) and dithionite citrate (DC) extractions are considered to
be two of the five most widely used methods of extracting different forms of Al, Fe
and Mn. AAO extracted Fe is considered to be “active” Fe, also referred to as the
non-crystalline or amorphous Fe while DC extracted Fe is considered to be “free” Fe
or non-silicate Fe. This provides a basis of what to expect in the XRD and SEM
analyses. Fe, Al, Ca, Mg, Mn and SO4 are the main focus as they can form oxides,
hydroxides or can associate with SO4 in acid mine waters if concentrations permit.
From the AAO and DC extractions it was deduced that the BC soil had more
amorphous Fe whereas the RS soil seemed to have more crystalline Fe. Both soils
showed an increase in Fe content. X-ray diffraction (XRD) was used to differentiate
changes in soil mineralogy caused by acid mine water. All of the diffractograms
generated by the XRD had a distinct background profile which was most probably
due to the high content of poorly crystalline material in the samples. The mine water
treated samples all showed an increase of poorly crystalline material between 5 –
7.5 degrees 2 theta. The hematite peaks formed after treating the soils with acidic
mine water were all short and broad indicating that they are poorly crystalline which
is also an indication of nano-sized particles of Fe oxides. Some of the gypsum
peaks, those found at <30 degrees 2 theta, were found to have formed more
crystalline than those found between 35 – 45 degrees 2 theta. Scanning electron

ix
microscopy (SEM) was employed to assess the variation in clay surface morphology
caused by acid mine water. SEM analyses found that the samples treated with acidic
mine water gained charged nano-sized spheroids on top of the clay. These are
thought to be nano-hematite particles. No typical linear gypsum crystals were found
on any of the samples even though XRD analyses did pick it up. Structures
resembling bassanite, a hemihydrate form of gypsum were however found.

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CHAPTER 1
INTRODUCTION
1.1 Literature review
Underground mining on the Witwatersrand has produced a great deal of gold and to
a lesser extent other precious metals needed by both the consumer and industry
alike. Some of these underground voids have become as vast as 400 Mm3
such as
the Eastern basin. The other two, the Western and Central basins have void volumes
of 43 Mm3
and 280 Mm3
respectively (Akcil and Koldas 2006). These voids were
initially thought not to present a problem at the time partly due to the sheer size of
the voids and the assumption that the water would naturally dissipate into the
environment without a problem. The reality however was that the voids were slowly
filling up to environmental critical levels (ECL). The ECL is defined as “the mine
water level below which, the risk of negative impacts on the shallow economically
exploitable groundwater resources and the surrounding surface water resources is
small” (BKS (Pty) Ltd. 2011). The water was also undergoing various reactions due
to the great surface area within the voids. The reactions between the water and the
ores generated a great volume of acidic mine water which is often referred to as acid
mine drainage (AMD). AMD is defined to be water with a pH of 5.0 or less,
containing sulphates and iron largely as well as various other metals.
Numerous ore minerals have been identified within the conglomerates that contain
contributing sulphide and various heavy metals. The most abundant being pyrite,
uraninite (UO2), brannerite (UO3Ti2O4), arsenopyrite (FeAsS), cobaltite (CoAsS),
galena (PbS), pyrrhotite (FeS), gersdofite (NiAsS) and chromite (FeCr2O4). Pyrite is
by far the greatest contributor to the AMD on the Witerwatersrand and will thus be
the main focus from here on forward (Naicker et al. 2003). The primary ingredients
for acid generation are as follows: (1) sulphide minerals, (2) water or a humid
atmosphere and (3) an oxidant, particularly oxygen from chemical sources or the
atmosphere. Bacteria can also play a major role in accelerating the rate of acid
generation, specifically Acidithiobacillus ferrooxidans which can oxidise pyrite if
conditions are favourable (Akcil and Koldas 2006). The primary factors that
determine the rate of acid generation are: pH; temperature; oxygen content of the
gas phase, if saturation is less than 100%; oxygen concentration in the water phase;

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degree of saturation with water; chemical activity of Fe3+
, chemical activation energy
required to initiate acid generation and bacterial activity.
As table 1.1 shows, the first important reaction is the oxidation of pyrite into
dissolved iron, sulphate and hydrogen ions. The dissolved ions represent an
increase in the total dissolved solids and acidity of the water lowering the pH. If the
surrounding environment is sufficiently oxidising then much of the ferrous iron will
oxidize to ferric iron as per the second equation. At pH values of between 2.3 and
3.5, ferric iron precipitates as ferric hydroxide, leaving little Fe3+
in solution while
simultaneously lowering pH (Coetzee et al. 2007).
Table 1.1: Pyrite reaction with oxygen and water to various ions and finally ferric
hydroxide and acid (Coetzee et al. 2007).
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Pyrite oxidises to form an acidic solution of ferrous iron and sulphate:
4FeS2 (s) + 14O2 (g) + 4H2O (l) → 4Fe
2+
(aq) + 8SO4
2-
(aq) + 8H
+
(aq)
2
Oxidation of the ferrous ion to ferric ion:
4Fe
2+
(aq) + O2 (g) + 4H
+
(aq) → 4Fe
3+
(aq) + 2H2O (l)
3
Ferric iron precipitates as ferric hydroxide, producing more acid:
4Fe
3+
(aq) + 12H2O (l) → 4Fe(OH)3 (s) + 12H
+
(aq)
The Witwatersrand basins each have very high Total Dissolved Solids (TDS) which
consist to a great extent of sulphates followed by calcium carbonates, calcium, iron
manganese and aluminium. The basins do each have quite different amounts of
each dissolved solid. As seen in table 1.2, the western basin has the most TDS, the
lowest pH, highest conductivity, the highest sulphate and iron content of all of the
basins. It is considered the most polluted of the three. The central basin has a similar
pH value to that of the western basin yet has lower TDS, sulphate or iron than any of
the other basins. The eastern basin has an almost neutral pH yet has TDS and other
relevant values between that of the western and central basins.

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Table 1.2: Approximations of the water qualities for the western, central and eastern
basin (DWA 2012).
Water Quality Parameters Units
Basin within greater Witwatersrand
Western Central Eastern
pH - 3 3.2 7.1
TDS mg/ℓ 5388 3888 4248
Conductivity Ms/m 426 354 367
Acidity/Alkalinity (CaCO3) mg/ℓ 1255 125 541
Aluminium (Al) mg/ℓ - 44 2
Calcium (Ca) mg/ℓ 823 483 421
Chloride (Cl) mg/ℓ - 69 253
Iron (Fe) mg/ℓ 799 177 206
Magnesium (Mg) mg/ℓ - 161 165
Manganese (Mn) mg/ℓ 114 20 6
Sodium (Na) mg/ℓ 243 185 264
Sulphate (SO4) mg/ℓ 3410 2464 2581
Uranium (U) mg/ℓ 0.1 0.2 0.5
For the Western basin in table 1.2, Ca, Fe and SO4 are considerably high relative to
the other elements. Ca come from the chemical weather of calcite [CaCO3], dolomite
[CaMg(CO3)2] and plagioclase [NaAlSi3O8 and CaAl2Si2O8] (Lottermoser 2010). Fe
and SO4 are primarily derived from the oxidation of pyrite as discussed earlier. Other
elements such as Al, Cl, Mg, Mn, Na and U are either leached from rocks or brought
into solution once their minerals are dissolved by the acidity of the water.
1.2 Background to study
Currently there is a lack in the capacity to treat the acid mine water decanted from
the basins as the sheer volume of the problem is just too big to be sustainably
treated with current water treatment methods. Its sustainability is hampered by the
immense cost to run the treatment plants yet it is essential for the future of Gauteng

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drinkable water supply as well as the surrounding environment. If the water is not
decanted and treated, it will start to surface at lower lying areas and become an
environmental disaster.
Some studies have proposed to first neutralise the acidic mine water and then use it
to irrigate crops. Other proposed methods of remediating acidic mine water is to
directly apply it as is to the soil with neutralising chemicals such as limestone. A lot
of research has already been done on both approaches but there is still a lot to be
gained on how acidic mine water affects soils at a micro and nano-scale.
The method of applying untreated acidic mine water directly to soil is considered a
viable approach as it exploits the natural integral characteristics of the soil. These
characteristics include buffering capacity, natural alkalinity, cation exchange capacity
(CEC) and sorption capacity to aid in the remediation of acidic mine water (Fey et al.
2014).
There are various elements, compounds and minerals associated with AMD. The
main element of focus for the study will be Fe. Al, Ca Mg, Mn and SO4 will however
also be looked at in certain areas where applicable. These elements can form
oxides, hydroxides or can associate with SO4 in acid mine waters if concentrations
permit.
In these conditions, Fe is most abundant in its Fe3+
form. Fe minerals formed usually
formed in acidic mine water conditions include: ferrihydrite [Fe2OH3 · 2H2O], goethite
[FeO(OH)], hematite [Fe8O8], jarosite [KFe3(SO4)2(OH)6], and schwertmannite
[Fe16O16(OH)12-10(SO4)2-3] (Hudson-Edwards et al. 1999).
In the case of Al it is in its only soluble form as Al3+
. Gibbsite [Al(OH)3] and kaolinite
[Al2Si2O5(OH)4] are considered to control its solubility in soil but under acidic
conditions the presence of SO4 can dramatically alter these solubilities. Other, less
soluble minerals then control the aqueous geochemistry of Al. The likely candidates
include: alunite [KAl3(SO4)2(OH)6], alunogen [Al2(SO4)3 · 17H2O], basaluminite
[Al4(SO4)(OH)10 · 5H2O] and jurbanite [Al(SO4)(OH) · 5H2O] according to Nordstrom
(1982).

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Ca in its only soluble form Ca2+
, forms gypsum with SO4
2-
. Gypsum is considered to
be the most common sulphate salt found in acidic mine water environments. Its
solubility is not affected by pH (Lottermoser 2010).
Epsomite [MgSO4 ·7H2O] is formed if concentrations of Mg and SO4 are sufficient
and is commonly precipitated in acidic mine waters (Lottermoser 2010).
Birnessite [(Na, Ca, K) x (Mn4+
, Mn3+
)2O4 · 1.5H2O] is considered to be one of the
most common Mn minerals in soil environments, while manganite [MnO(OH)] is said
to be the most stable and abundant mineral among those in the MnO(OH) group. It
should however be noted that it is challenging to identify Mn minerals in fresh
precipitates since these materials are typically fine-grained, poorly crystalline, and
contain multiple valence states of Mn (Lee et al. 2002).
The soils used in this study were acquired from a previous study which focussed on
simulating a land treatment method for decontaminating metalliferous mine water. A
black clay soil (BC) and a red sandy loam soil (RS) were used. Both soils originate
from farmland close to the Brakpan Dam tailings storage facility. Both soils were said
to be selected based on their unique properties. The BC soil was classified as
melanic A top soil horizon with a strong structure. The soil is considered to be
dominated by smectite clay with a permanent negative charge. It is also considered
to have a high base status, large CEC and a good ability to retain water. The RS soil
was identified as an orthic A top soil horizon which forms part of a Hutton form. It is
considered to be dominated by kaolinite clay. Consequently it also has a much
smaller CEC and have better drainage relative to soil BC. Both soils were found to
successfully retain and sequestrate the metals and salts to a confident extent. The
BC soil was found to be a better option relative to the RS soil due to it being able to
treat great amounts of mine water more effectively (Storm 2014).
The mine water used came from the Western basin of the Witwatersrand mines as it
has the highest Al, Fe and Mn water qualities of the three basins. The water used in
that study was found to have slightly different concentrations than those of table 1.2
and can be found in table 1.3 of which calculations for this study will also be based
on.

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Table 1.3: Water qualities for the western basin (Fey et al. 2014).
pH EC (dS·m
-1
)
mg·ℓ
-1
Al Ca Cl Fe Mg Mn Na SO4 Total
3.38 0.520 54 696 31 342 232 64 92 3494 4942
There are no standard methods in literature on how to approach microscale analysis
of soils probably due to the vast differences in soil properties and the almost infinite
numbers of soil compositions. There are however some generic approaches which
have been proposed and proven over the past few decades with a trial and error
approach. X-ray diffraction (XRD) and scanning electron microscopy (SEM) are
currently considered to provide a manner to assess the variation in clay surface
morphology and mineralogy of soils affected by acid mine water. SEM provides
visual information in surface morphology where as XRD provides information on
mineralogy.
In terms of mineralogical and morphological changes, it was expected that various
metal oxides and hydroxides of Al, Fe and Mn could form. It is also important to
know if formed, how much of these newly formed minerals were crystalline and
amorphous. In order to obtain these quantitative answers acid ammonium oxalate
(AAO) and dithionite citrate (DC) were used to make this separation. AAO extracted
Fe is considered to be “active” Fe, also referred to as the non-crystalline or
amorphous Fe. DC extracted Fe is considered to be “free” Fe or non-silicate Fe
according to the Food and Agriculture Organization of the United Nations (1998).
This method was chosen above the similar citrate bicarbonate dithionite (CBD)
extraction method as the DC method has been found to be more effective by other
research scientist (personal communication with Ms. Leushantha Mudaly).
The overarching aim was to understand what would result when Al, Fe and Mn were
administered. This lead to the following two objectives: 1) To determine if any
minerals had formed, what they look like and what had happened to the clay
surfaces using XRD and SEM; 2) To quantitatively determine the distribution
between amorphous and crystalline forms particularly of Fe administered. It was
hypothesised that some of the clay minerals will dissolve and reconstitute with
elements found in the AMD. It is also hypothesised that some of the elements,
particularly Fe will be adsorbed or precipitated onto the mineral surfaces.

7
A visual outline of the study (Fig 1.1) shows the approach as well as what the train of
thought was throughout as there is no formal approach for such work yet.
Figure 1.1: Experimental methodology employed to investigate the effect AMD has
on mineral surfaces and mineralogy. Original soil refers to either the BC or RS soil.

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CHAPTER 2
METAL BALLANCES
2.1 Background and literature review
The AAO extraction method consists of a solution made of ammonium oxalate and
oxalic acid. The oxalic acid lowers and buffers the pH to about 4, while the oxalate
chelates the metals dissolved by the acidic solution. This extraction is effective at
removing organically complexed and amorphous inorganic compounds of Al, Fe and
to a slighter extent Mn. It should also be carried out in the dark to prevent
photodecomposition of the oxalate solution (Carter and Gregorich 2007).
In the DC extraction, the dithionite creates a reducing environment which dissolves
the metallic oxides. The citrate then chelates the dissolved metals and buffers the pH
to roughly 7 units as to avoid the precipitation of FeS compounds. This extraction is
effective at removing organically complexed and amorphous inorganic compounds of
Al, Fe and Mn. Al extractions should however be interpreted cautiously while the
treatment is considered to be particularly effective at extracting “free” Fe from soils. It
is also often used for removing sesquioxide coatings from soils and clays prior to x-
ray analysis (Carter and Gregorich 2007).
AAO is effective at extracting poorly crystalline and non-crystalline aluminosilicates
while DC is said to be much less effective at extracting these compounds. Both
extractions are said to attack crystalline oxide forms of Mn to some extent but the
differences between the two extracts are not easy to interpret. The DC method is
also effective at extracting finely divided minerals including hematite, goethite and
ferrihydrite while AAO only slightly attacks crystalline Al and Fe oxides. AAO does
however dissolve considerable amounts of magnetite while DC does not (Carter and
Gregorich 2007). AAO treatment is also said to preferentially dissolve ferrihydrite
over goethite (Schwertmann et al. 1982).
It is thus expected that the DC extracts will most probably have higher
concentrations relative to oxalate extracts for Al and Fe while Mn could be higher for
the AAO extracts. These results should also give a better indication of the
crystallinity of the minerals.

9
2.2 Methodology
2.2.1 Sample selection
The samples comprised of the BC original soil sample (BC Ori), BC mine water
treated soil sample (BC MW), RS original soil sample (RS Ori) and RS mine water
treated soil sample (RS MW) of which each were replicated three times for statistical
viability.
2.2.2 Sample and solution preparation and procedure
The soil samples were first homogenously mixed after which a generous amount
was finely ground using a mortar and pestle to get the sample as fine as possible.
This would thus remove some variability among the replicates and samples.
The AAO and DC solution extracts were prepared according to the procedures found
in Soil Sampling and Methods of Analysis by Carter and Gregorich (2007). It is
however recommended that more solution (eg. 3-4 times more) is used for the
extract and that a control extract of different concentrations of the element of interest
is also carried out as the solution may become saturated which would require you to
repeat the experiment.
Acid ammonium oxalate extraction:
The AAO solution was prepared completely in the dark. It comprised of a 0.2 M
solution of ammonium oxalate [(NH4)2C2O4·H2O] and a 0.2 M solution of oxalic acid
[H2C2O4·2H2O] and which were mixed in a 1.3:1 ratio respectively. The pH must then
be measured and be around 3, if not then either one of the solutions should be used
to achieve this before carrying on. A sample size of 1.0 g was used instead of the
suggested 0.5 g and 150 mL of solution per extraction instead of the suggested 20
mL per 0.5 g of sample. The samples were then shaken at 150 rpm for 4 hours.
Dithionite citrate extraction:
The dithionite citrate solution was prepared by making a 0.68 M solution of tri-sodium
citrate [Na3C6H5O7·2H2O] and adding 1.3 g of dithionite [Na2S2O4] to each sample
tube before the soil sample was added. A sample size of 0.5 g was used and 80 mL
of solution per extraction instead of the suggested 40 mL per 0.5 g of sample. The
samples were then shaken at 150 rpm for 8 hours (until the soil particles were
bleached white).

10
All of the samples were then centrifuged for 30 min and immediately suction filtered
through 0.45 μm PES membrane filters. Their concentrations, including the blanks,
were then determined a few hours later using the ICP-OES of the Department of
Plant Production and Soil Science of the University of Pretoria by Mr. Charl Hertzog.
2.3 Theoretical soil loadings
Al, Fe and Mn are part of the fabric of soil and naturally quite abundant. The aim, in
part, of the theoretical calculations was to determine if the accumulation of Al, Fe
and Mn were appreciably enough to be analytically separated from the natural (or
background) levels of the soil. Table 2.1 is a summary of how much Al, Fe and Mn
was loaded to the soils based on the respective volume of mine water added, the
amount that leached, and concentration of mine water added. These value were then
divided by the soil mass and a mass concentration loading was calculated. The
leached amounts were based on a cumulative leached volume for that respective
treatments. This was reported by Mr. Ignus Storm during the previous study.
Subtracting the elemental quantities of the soil treated with mine water from the
natural soil should give an indication of what has been theoretically attenuated by the
soil. The BC soil should thus had sorbed 748 mg·kg-1
, 4711 mg·kg-1
and 739 mg·kg-1
of Al, Fe and Mn respectively. The RS soil on the other hand should theoretically
have sorbed 422 mg·kg-1
, 2832mg·kg-1
and 23.4 mg·kg-1
of Al, Fe and Mn
respectively. The calculated enrichment of Al Fe and Mn was expected to be
analytically detectable.

11
Table 2.1: Summary of soil metal loading (input), leached (removed) and attenuated
amounts.
Input Leached
Soil BC RS BC RS
Mine water concentration (mg·ℓ
-1
)
Al 54 2 74
Fe 342 50 314
Mn 64 207 544
Al, Fe and Mn loading per treatment (mg · 250g
-1
soil)
Al 187 125 0.36 19.3
Fe 1186 790 9.00 82.0
Mn 222 148 37.3 142
Al, Fe and Mn loading per treatment (mg · kg
-1
)
Al 750 499 1.44 77.3
Fe 4747 3160 36.0 327
Mn 888 591 149 568
Al, Fe and Mn attenuated by soil (mg · kg
-1
)
Soil BC RS
Al 748 422
Fe 4711 2832
Mn 739 23
2.4 Results
Please note that It is expected that there will be some error regarding the values of
the extracts as this part of the study was only carried out after a small fraction
(roughly 2-3 g) of the soil fraction <63 μm had been removed and lost which
removed a significant effect on the amount of <63 μm fraction of the soil. The original
soil sample size was 250 g. The soil samples have thus been slightly compromised
overall but should still be able give some indication of the crystallinity of Fe. A full
summary of the soil data and statistics can be found in appendix A.

12
2.4.1 Al, Fe and Mn extracts of BC soils
In table 2.2, Al concentrations for both the AAO and DC extracts are quite similar for
the BC Ori and BC MW soils. The AAO Al concentrations are however more than
twice the concentration of that of the Al DC concentrations which suggests there is a
fair amount of poorly crystalline and non-crystalline aluminosilicates present. This is
however not for certain as literature suggests Al extract concentrations should be
considered with caution.
The BC Fe concentrations for both extraction methods were found to be high. The
AAO Fe concentrations are lower than that of the DC Fe concentrations which is
expected. There is almost no difference between the AAO and DC extractions for the
BC MW soils which suggests the crystalline Fe attenuated in the soil was largely
poorly crystalline or of small crystal size with fairly large surface to volume ratios
making them more susceptible to extraction. The difference between BC Ori and BC
MW soils also suggested this. The Δ BC (4062 mg·kg-1
) and theoretical Fe
enrichment (4711 mg·kg-1
) was reasonably close.
AAO Mn extracts were found to be almost double that of the DC and suggests that
roughly half of the Mn extracted from both soil treatments could be in the form of
manganite.
Table 2.2: A summary of the AAO and DC soil concentrations of the BC Ori and BC
MW soil (in mg kg-1
).
Soil BC Ori BC MW Δ BC
Treatment AAO DC AAO DC AAO DC
Al 1768 851 1631 974 -137 123
Fe 7590 9616 11652 11830 4061 2214
Mn 1983 1052 1851 1126 -132 73
2.4.2 Al, Fe and Mn extracts of RS soils
The AAO and DC RS Ori and RS MW Al concentrations have fairly similar values
which suggests there is not much poorly crystalline and non-crystalline
aluminosilicates present in either treatment.

13
Similar to the BC soil, the DC extracts of the different RS treatments have higher
concentrations than that of the AAO. The DC difference is however greater than that
of the AAO difference unlike the BC soils. It should also be noted that there is a lot
more crystalline than amorphous Fe in both the original soil and the mine water
treated soil. The original soil is naturally red indicating the presence of Fe-oxides.
There is a noticeable decrease in Mn content for RS MW relative to RS Ori to. As
with the BC samples, the RS Ori AAO extract is high and the DC low but these
values are fairly similar for the RS MW extracts.
Table 2.3: A summary of the AAO and DC soil concentrations of the RS Ori and RS
MW soil (in mg·kg-1
).
Soil RS Ori RS MW Δ RS
Treatment AAO DC AAO DC AAO DC
Al 1595 1506 1187 1167 -408 -339
Fe 4739 18510 3960 19391 -779 871
Mn 1184 657 326 262 -858 -396
2.5 Summary
There are noticeable error regarding the values of the extracts as some
concentrations after being treated with mine water decreased instead of increasing.
This effect was also more prominent in the RS soils than in the BC soils which could
be due to the fact that the BC soil has more clay than the RS soil. Given that the RS
MW values for AAO and DC had both decreased, it would suggest that a
considerable amount of the Al, Fe and Mn was situated in the <63 μm fraction of the
soil.
The BC soil seems to have a lot more amorphous Fe whereas the RS soil seems to
have a lot more crystalline Fe. Both soils do however show an increase in Fe
content.
Given the circumstances of the data, only minor conclusions can be drawn. For all of
the samples, the Fe content was <1.5 % (kg·kg-1
) which is below the detection limit
of an XRD, these soil samples are however representative of the whole soil, or at
least intended to be, given a small fraction of the finer material had already been

14
removed. Fortunately, the samples analysed using the XRD were of the <63 μm
fraction. There was thus a chance that crystalline Fe oxides may have formed
sufficiently to be detected.

15
CHAPTER 3
CHANGES IN SOIL MINERALOGY
XRD is considered to be a crucial method in understanding soil mineralogy and is
the technique most heavily relied on presently. It is however important to understand
the nature of XRD data before any interpretations can be made. A powder
diffractometer is said to be the most applicable to analyse soil mineralogy. Powder
diffractometer results are generally plotted as 2θ degrees on the x axis from 0° to 90°
and X-ray intensity per second on the y axis (Harris and White 2007). Clay minerals
occur between 2° to 30° (2θ) whereas oxides occur at higher degrees 2θ.
Relative peak intensities and d-spacing are then used to identify minerals. Peaks
should then be marked and their corresponding 2θ angles converted to d-spacing
values. To convert to d-spacing values, Bragg’s Law is used as in equation (3.1):
2d Sin θ = n λ (3.1)
Where,
d = d-spacing value in Angstroms (Å)
θ = Radians (2 θ°)
n = 1
λ = Element wavelength (Co-Kα) = 1.789 Å
Given the nature of the experiments performed for this study, there will be various
mixtures of minerals which are said to produce complex XRD patterns. Quartz is
often used to correct data shifts between samples however this should be done with
caution as samples high in and containing different mixtures of clays can shift strong
pronounced peaks of well-defined crystal structures of quartz (Harris and White
2007). These present a great challenge in identifying the different minerals.
Intensity on the y-axis is usually expressed in counts per second and is considered a
relative measurement at most which is affected by various conditions which include
current and voltage at which the X-ray tube is operating as well as the counter

16
efficiency. The relative intensity of a diffraction peak produced by a given set of
atomic planes in a crystal, assuming all atomic planes are equally represented
(random orientation), is dictated by the composition and arrangement of atoms in the
unit cell. Thus, relative intensity does not provide a simple 1:1 index of the mass
fraction of minerals in a mixture (Harris and White 2007). Minerals have multiple d-
spacing at different temperature and chemical treatments and must thus also be
considered if resources permit it.
It is already known that the BC Ori soil is a dark, clay rich soil with swelling
properties. It is thus expected that there will be some clays detected, specifically
swelling clays such as smectites. The RS Ori is however a red well drained soil and
contains far less clay than the BC Ori soil and could already contain Fe-oxide peaks.
It is expected that the BC MW soil might gain enough crystalline Fe-oxides to be
detected but if not it could indicate that the Fe is in fact mostly amorphous. Similarly
for the RS MW soil, there is an expectation to find Fe-oxides. These expectations are
based on conclusions drawn from chapter 2.
XRD is better suited to crystalline materials but poor crystalline materials are also
identified to some extent. These are given as low but broad peak intensities and a
background profile (Stunda et al. 2011).
If there are in fact Fe-oxide peaks detected then these peaks may have different
shapes and sizes. These may either be short and broad or thin and tall. If they are
short and broad then it is an indication of nano-sized particles of Fe oxides according
to Cheng et al. (2010). If the peaks are however thin and tall then the Fe-oxides are
larger more micro-sized.

17
3.2 Methodology
Samples were selected on their relevance toward understanding the changes in
mineralogy and each of which were replicated three times. Sample selection was as
follows: BC Ori, BC MW, BC MW AAO, BC MW DC, RS Ori and RS MW.
The rationale for only subjecting the BC MW AAO and BC MW DC was to see
whether the changes obtained between the XRD of the BC original and the BC mine
water treated soils was due to a metal adsorbed on the surface, particularly Fe-
oxides.
3.2.2 Sample preparation
All the samples used were first placed in a sieve shaker with multiple sieve
diameters with the smallest being a <63 µm sieve. This approach was followed as
opposed to a chemical separation as any contact with a solution risked to influence
the mineral concentrations. The <63 µm fraction consist of both silt and clay. For the
BC soil this fraction consists of course silt, fine silt and clay as 19.8%, 30.8% and
29.2% respectively. While for the RS soil, the values are 24.5%, 10.3% and 9.5% in
the same respective order. These fractions thus represent 78.8% and 44.3% of the
BC and RS soil particle sizes correspondingly (Storm 2014).
Once the BC MW fraction samples were treated with AAO and DC, they were dried
for 72 hours in a 30 °C oven after which they were then powered using a mortar and
pestle.
All of the selected samples powders were then set into XRD specimen holders. This
was done by compressing the samples into the holders until the top of the
specimens were completely flat. This is done to keep all specimens as consistent as
possible and to minimise variables as rough surfaces can have an effect on the
results.
3.2.3 Mineral identification
The samples were prepared according to the standardized Panalytical backloading
system, which provides nearly random distribution of the particles. The samples
were then analysed using a PANalytical X’Pert Pro powder diffractometer in θ–θ
configuration with an X’Celerator detector and variable divergence- and fixed

18
receiving slits with Fe filtered Co-Kα radiation (λ=1.789Å). The data was then
analysed for inconsistencies using Microsoft Excel which originated when the data
was transformed from its original .asc file format to .xls (MS Excel) format. These
inconsistencies are in the form of majorly patterned peak increases which are easily
removed by deducting an established error value. This ‘fix’ is then confirmed by
assessing the smoothness of the data where there are known to not be peaks. The
peaks were identified using the American Mineralogist Crystal Structure Database
with assistance from Ms. Wiebke Grote from the Department of Geology at the
University of Pretoria X-Ray Diffraction unit.
3.3 XRD results and analysis for BC soils
3.3.1 Diffractograms and mineral identification tables of BC Ori and BC MW.
The main minerals identified in the <63 μm fraction of the BC Ori soil were andesine,
microcline, montmorillonite and quartz. The same minerals were again found in the
soil treated with acidic mine water but also gained hematite and gypsum. Andesine
was identified at peak 8, microline at peak 7, montmorillonite at peaks 2 and 5 and
quartz at peak 4 (Fig 3.1). Gypsum has three peaks, these are peak 1, 3 and 6.
Gypsum and quartz both have two lower order peaks between 35 – 45 degrees 2
theta (Fig 3.4). The identification data for figure 3.1 and 3.4 can be found in table 3.1
and 3.4 respectively.
Figure 3.1: Diffractograms of the BC MW and BC Ori for 5° - 30° (2θ). Peak 1:
gypsum, peak 2: montmorillonite, peak 3: gypsum, peak 4: quartz, peak 5:
montmorillonite, peak 6: gypsum, peak 7: microline and peak 8: andesine.
0
3000
6000
9000
12000
15000
5 10 15 20 25 30
Counts(s-1)
Position (2θ)
BC MW
BC Ori
2
3
4
5 6 7 8
1

19
The diffractogram data analysis of figure 3.1 (Table 3.1) shows that the d-spacing’s
for the peaks and their respective minerals are not exactly the same, which occurs
when there are other elements in the crystal structure (Harris and White 2007). This
trend does however change as the relative intensity values decrease.
Table 3.1: Diffractogram data analysis of figure 3.1
Peak 2θ (°) Peak d-spacing (Å) Mineral Mineral d (Å)
a
1 13.5001 7.61 Gypsum 7.60
2 23.1321 4.46 Montmorillonite 4.45
3 24.2441 4.26 Gypsum 4.28
4 24.2601 4.25 Quartz 4.25
6 27.1801 3.80 Gypsum 3.80
7 27.6201 3.75 Microcline 3.75
8 28.4041 3.64 Andesine 3.64
(a) Mineral d-spacings as reported by American Mineralogist Crystal Structure Database
To isolate the differences between the BC Ori and the BC MW XRD spectrums, the
intensity of BC MW was divided by the intensity of the BC Ori soil (Fig 3.2). This
differential intensity (IBC MW / IBC Ori) shows that only gypsum formed (peak 1, 2 and 4)
for “spectrum” < 30 degrees 2 theta. All the other minerals remained the same.
There is no definite explanation for the decrease in quartz (peak 3), however, it is
thought to be due to the mix of clay present in the sample. There is also a noticeable
increase in background noise (between 5 - 7.5 degrees 2 theta) which is due to an
increase in amorphous material.

20
Figure 3.2: Differential diffractogram of the BC MW intensity divided by the BC Ori
intensity for 5° - 30° (2θ). Peak 1: gypsum, peak 2: gypsum, peak 3: quartz and peak
4: gypsum.
The higher degrees 2 theta (Fig 3.3) also showed prominent peaks appearing after
the mine water treatment. Gypsum (peak 1 and 2) is present again in the BC MW
sample. Peak 3 has a low yet broad profile at where hematite is usually found. There
is a noticeable shift again between quartz (peak 4 and 5) of the treatment differences
(Fig 3.3). These low yet broad peak observations are indicative of poorly crystalline
minerals. The peaks and their relevant information are summarised in table 3.2.
23 24 25 26 27 28
2
3
4
0
1
2
3
4
5
6
7
8
5 10 15 20 25 30
IBCMW/IBCOri
Position (2θ)
1

21
Figure 3.3: Diffractograms of the BC MW soil and the BC Ori soil for 35° - 45° (2θ).
quartz.
The differential diffractogram (Fig 3.4) isolates the gypsum (peak 1 and 2) and
hematite (peak 3) that was formed after the soil was treated with acidic mine water.
Quartz has again shifted slightly.
Figure 3.4: Differential diffractogram of the BC MW and BW Ori soil for 35° - 45°
(2θ). Peak 1: gypsum, peak 2: gypsum, peak 3: hematite, peak 4: quartz and peak 5:
quartz.
0
500
1000
1500
2000
2500
35 37 39 41 43 45
Counts(s-1)
Position (2θ)
BC Ori
BC MW
1
2
3
4
5
0.7
0.8
0.9
1
1.1
1.2
1.3
1.4
1.5
1.6
35 36 37 38 39 40 41 42 43 44 45
IMW/IBCOri
Position (2θ)
1
2 3
4
5

22
It should be noted that the peak d-spacing and the mineral d-spacing are the same
where they are slightly different at lower degrees 2 theta.
Table 3.2: Diffractogram data analysis of figure 3.3 and figure 3.4.
a
1 36.2601 2.87 Gypsum 2.87
2 38.9401 2.68 Gypsum 2.68
3 41.5081 2.52 Hematite 2.52
4 42.6841 2.46 Quartz 2.45
5 42.7721 2.45 Quartz 2.45
3.3.2 The influence of ammonium acid oxalate treatment on mine water treated BC
soil.
The aim of treating the sample with AAO was to extract the gypsum and more
importantly the Fe oxides. Poorly crystalline Fe oxides should be soluble in AAO and
it was expected that especially peaks related to ferric iron minerals will either
disappear or become less pronounced. The AAO almost completely dissolved the
gypsum formed), as shown by its peaks all but disappearing (Fig 3.5). All the other
minerals remain unaffected. There also seems to be a shift in the data as peak one
and two seem slightly shifted. The quartz (peak 3) for the BC MW is also broadened
to the left.

23
Figure 3.5: Diffractogram of the BC MW, BC Ori and BC MW AAO for 5° - 30° (2θ).
Peak 1: gypsum, peak 2: gypsum, peak 3: quartz and peak 4: gypsum.
There seems to be a slight decrease of hematite (peak 1) once the BC MW soil was
treated with AAO (Fig 3.6). It therefore seems that the hematite is fairly crystalline.
The hematite peak looks better defined after the oxalate treatment. Given that AAO
is considered not to effectively dissolve crystalline Fe oxides this result is expected
(the y-axis is in counts per second but on different axis and thus not included).
23.5 24.5
32
26 27 28 29
4
-3000
-1000
1000
3000
5000
7000
9000
11000
13000
15000
5 10 15 20 25 30
Counts(s-1)
Position (2θ)
1
Legend:
BC MW
BC MW AAO
BC Ori

24
Figure 3.6: Diffractogram of the BC MW, BC MW AAO and BC Ori and for 40° - 45°
(2θ) Peak 1: Hematite, peak 2: quartz and peak 3: quartz.
3.3.3 The influence of dithionite citrate extraction on mine water treated BC soil.
The aim of treating the sample with DC was to completely extract the Fe oxides and
see if it had had an effect on the soils. Treating the BC MW sample with DC (Fig 3.7)
completely dissolves the formed gypsum (peak 1, 2 and 4). All the other minerals
remain unaffected. Quartz (peak 3) for the BC MW is also again broadened to the
left.
40 41 42 43 44 45
Position (2θ)
BC MW
BC MW AAO
BC Ori
1
2 3

25
Figure 3.7: Diffractogram of the BC MW, BC Ori and BC MW DC for 5° - 30° (2θ).
Peak 1: gypsum, peak 2: gypsum, peak 3: quartz and peak 4: gypsum.
Similar to the AAO treatment, there is again a slight decrease of hematite (peak 1)
once the BC MW soil is treated with DC (Fig 3.8). The DC treatment effectively
dissolve Fe oxides yet in this result this is not the case. One possible reason for this
could be that the solution was supersaturated and no more Fe oxides could be
further extracted.
23.5 24.5
2 3
26 27 28 29
4
-3000
-1000
1000
3000
5000
7000
9000
11000
13000
15000
5 10 15 20 25 30
Counts(s-1)
Position (2θ)
1
Legend:
BC MW
BC MW DC
BC Ori

26
Figure 3.8: Diffractogram of the BC MW, BC MW DC and BC Ori and for 40° - 45°
(2θ). Peak 1: Hematite, peak 2: quartz and peak 3: quartz.3.4 XRD analysis for RS
soil.
40 41 42 43 44 45
Position (2θ)
BC MW
BC MW DC
BC Ori
1
2
3

27
3.3.4 Diffractograms of RS original soil
The main minerals identified in the RS Ori soils (Fig 3.9) were only montmorillonite
and quartz. The same minerals were again found for the soil treated with acidic mine
water with the addition of gypsum. Montmorillonite (peak 2) and quartz (peak 4) and
gypsum (peak 1, 3 and 5). Gypsum and quartz both have two more peaks on figure
3.10 (35° - 45°). Gypsum and quartz both have two lower order peaks between 35 –
45 degrees 2 theta (Fig 3.9). The identification data for figure 3.9 and 3.10 can be
found in table 3.7 and 3.9 respectively.
Figure 3.9: Diffractograms of the RS MW and the RS Ori soils for 5° - 30° (2θ). Peak
1: Gypsum, peak 2: montmorillonite, peak 3: gypsum, peak 4: quartz, and peak 5:
gypsum.
The diffractogram data analysis of figure 3.7 (Table 3.3) shows that the d-spacing’s
for the peaks and their respective minerals are exactly the same except for
montmorillonite meaning their crystal structures are well formed.
0
3000
6000
9000
12000
15000
5 10 15 20 25 30
Counts(s-1)
Position (2θ)
RS Ori
RS MW1
2
3
4
5

28
Table 3.3 Diffractogram data analysis of figure 3.7
a
1 13.5081 7.60 Gypsum 7.60
3 24.1161 4.28 Gypsum 4.28
4 24.2921 4.25 Quartz 4.25
5 27.2201 3.80 Gypsum 3.80
A similar approach used to isolate the effect the mine water had on the BC soil was
used on the RS soil, by dividing the RS MW data with the RS Ori. Similarly than for
the BC soil, gypsum formed at <30 degrees 2 theta (Fig 3.8) while quartz peaks also
showed. Again there is a decrease in quartz peak which is in fact a shift.
Figure 3.10: Diffractograms of the RS MW intensity divided by the RS Ori intensity
for 5° - 30° (2θ). Peak 1: gypsum, peak 2: gypsum, peak 3: quartz and peak 4:
gypsum.
23 23.5 24 24.5 25 25.5 26 26.5 27 27.5 28
2
3
4
0
1
2
3
4
5
6
7
8
9
5 10 15 20 25 30
Counts(s)
Position (2θ)
1

29
Gypsum is present again in the RS MW sample and there is a noticeable shift again
between the quartz peaks in figure 3.11, similar to what happened in the BC soils.
Gypsum peaks, peak one and two, are also less pronounced compared to the same
peaks for the BC MW soil.
Figure 3.11: Diffractograms of the RS MW and the RS Ori soils for 35° - 45° (2θ).
quartz.
The differential diffractogram (Fig 3.10) again emphasise the formation of gypsum
and hematite.
2000
3000
4000
5000
35 37 39 41 43 45
Counts(s-1)
Position (2θ)
RS MW
Ori
1 2 3
4
5
0.8
0.9
1
1.1
1.2
1.3
1.4
35 36 37 38 39 40 41 42 43 44 45
IRSMW/IRSOri
Position (2θ)
1
2 3
4
5

30
Figure 3.12: Diffractogram of the RS MW intensity divided by the RS Ori intensity for
35° - 45° (2θ). Peak 1: gypsum, peak 2: gypsum, peak 3: hematite, peak 4: quartz
and peak 5: quartz.
The d-spacing values of the peaks and minerals (Table 3.4) are similar to at least
two decimal places where as some of the BC soil d-spacings were not. An
explanation for this could be that the crystal structures are better formed and also
that the RS soils contain less clay.
Table 3.4 Diffractogram data analysis of figure 3.9 and figure 3.10
a
1 36.2441 2.87 Gypsum 2.87
2 38.9161 2.68 Gypsum 2.68
3 41.6181 2.52 Hematite 2.52
4 42.6601 2.45 Quartz 2.45
5 42.7401 2.45 Quartz 2.45
3.4 Discussion
The BC Ori soils were found to contain andesine, microcline, montmorillonite and
quartz while the RS Ori soils were found to contain montmorillonite and quartz.
These are however not considered to be the only clays in these soils.
The diffractograms all have a distinct background profile which are most probably
due to the high content of poorly crystalline material in the samples (Stunda et al.
2011).
The hematite peaks formed are also short and broad indicating they are poorly
crystalline (Carlson and Schwermann 1980). This is also an indication of nano-sized
particles of Fe oxides according to Cheng et al. (2010). There was no evidence
found of other Fe-oxides such as ferrihydrite, goethite, jarosite, and schwertmannite
although they may just be under detection limit.
Some of the gypsum peaks, those found at <30 degrees 2 theta, were found to have
formed more crystalline than those found between 35 – 45 degrees 2 theta. The
formation of gypsum is due to the mine water having high concentrations of both
Ca2+
and SO4
2-
which have precipitated (Lottermoser 2010).

31
The two highest intensity gypsum peaks of BC MW’s d-spacing’s were slightly off
and are thought to be a transition interference caused by bassanite before it
becomes gypsum. This is however very speculative but might be due to a
mechanism hypothesised by Wang et al. (2012) who reported a multistep process
which precipitated gypsum via hemihydrate using Ca2+
and SO4
2-
as starting solution.
If this is indeed true, the bassanite is so little that it cannot be picked up by the XRD
instrument as a minimum of 1.5 % of it is needed mass/mass. There is also no trace
of any bassanite in any of the other samples using XRD.
All of the RS MW gypsum d-spacings were found to be exact to those in literature
which suggests their crystalline structures are well formed. In contrast to the BC soil
this could suggest that gypsum could have formed via a mass precipitation.

32
CHAPTER 4
CHANGES IN SOIL SURFACE MORPHOLOGY
A fundamental part of the study was to establish whether morphological changes
occurred on the clay surfaces due to the treatment with acidic mine water. SEM is
considered to be uniquely suited for this challenge as it magnifies the surface of the
clays, giving a three-dimensional view of the surface with great depth focus.
Fundamentally, the process works by scanning the sample with a focused beam of
electrons. The electrons interact with atoms in the sample, producing numerous
signals which are then again received by the instrument and used to produce an
image. The signals are unique to different elements and can give compositional
information about specific points or areas of interest if the machine has the additional
hardware and the points/areas of interest are of great enough size (Bohor and
Hughes 1970).
It is however necessary for clays to either be coated with a thin metallic or carbon
coating. This is applied in a vacuum evaporator. The coating is said to prevent a
build-up of electrons on the surfaces by conducting away static electricity and are
usually between 2-3 nm thick (Frost et al. 2002). There are currently no known
universal standard methods of preparing and analysing soil clays but there are
however various successful attempts by scientists in the past with specific clay
materials.
It is expected that there will be some gypsum crystals formed and perhaps
derivatives thereof (BC MW samples). There is also a good chance of hematite
crystals (in both BC MW and RS MW) having formed, more specifically poorly
crystalline forms thereof as found by the XRD.
4.2 Methodology
Both the BC Ori and the RS Ori soils were chosen to serve as the controls. Their
acidic mine water treated counterparts, BC MW and RS MW respectively, to see how
the acidic mine water had affected the clay surfaces. Finally, the same soils treated
with acidic mine water and CaCO3 were then also added to see what affect the

33
CaCO3 had had on the surface of the clays as the water was neutral. All six of the
samples were replicated three times for consistency.
4.2.2 Sample preparation and analysis
All the samples used were firstly placed in a sieve shaker with multiple sieve
diameters in, the smallest being a <63 µm sieve. The samples were purposefully
extracted to 63 µm and smaller to see what it would look like under the SEM. The
<63 µm extracts were then kept separately to be used further for further analysis and
comprised of fine quartz particles, silt and clay. To get the samples to almost pure
clay (<2 µm) without using chemical treatments is nearly impossible. Given that
sample morphological and amorphous changes want to be detected a
water/chemical treatment of any sort would compromise the integrity of the samples
and was thus not considered. A degree of trial-and-error is said to be required as
SEM clay analysis is still a new field and thus does not have defined guidelines on
how to approach it as mentioned.
To analyse the samples in the SEM, a powder mount was used. The powder mount
was done by pressing the sample onto conducting carbon adhesive tape and then
coating it with carbon to insure that the low conducting clay does not build up charge
as this could blur the image of the SEM. An epoxy coating was considered to smooth
the surface of the clay topography but was inevitably decided against as it would not
make a significant difference due to the particle sizes analysed being small enough.
An epoxy coating would also take weeks to dry which given circumstances was not
an option.
The instruments used were a Joel JSM 5800LV SEM for low resolution imaging and
a Zeiss ULTRA Plus FESEM for high resolution imaging. Field emission scanning
electron microscope (FESEM) enables high resolution electron imaging with low
acceleration voltages which makes it possible to analyse also delicate biological
samples and nanostructures.

34
4.3 Results of photomicrographs of BC and RS selected samples
All samples were replicated three times and all were found to have the same visual
appearance. Both the original BC and RS soils were found to have no “white spots”
on them as seen in figure 4.1 (a) and (b) respectively. As soon as the samples were
treated with acidic mine water, both BC and RS soils gained a white spot-like
appearances on top of the clay as seen in figure 4.1 (c) and (d). Figure 4.1 (e) and (f)
are the BC and RS soils treated with the acidic mine water and CaCO3 respectively.
They both have a similar spot-like appearance as in figure 4.1 (c) and (d). These
white spots are caused by a charge difference relative to the surrounding particles
due to the nature of the machine.
These spot-like appearances are considered far too small to do an elemental
analysis using Energy-dispersive X-ray spectroscopy (EDS) on them (verbally
communicated by SEM technician) and would give an inaccurate representation of
the spot composition.

35
Figure 4.1: Photomicrographs (a) BC Ori, (b) RS Ori, (c) BC MW, (d) RS MW, (e) BC
MW (CaCO3) and (f) RS MW (CaCO3).
a b
c d
e f
200nm
200nm
200nm200nm
200nm
200nm

36
The structures within the red rectangles in figure 4.2 were found to have formed on
the BC MW soil but not on any of the other soils.
Figure 4.2: Rod-like structures found on BC MW soil.
1µm

37
4.4 Discussion
Figure 4.3: White spot-like particles found on both (a) BC MW and (b) RS MW.
Due to the high iron content in the acidic mine water used to treat the soils it was
hypothesised that the iron had sorbed/precipitated onto the surface of the clay. In
study conducted by Oliveira et al. (2003) on clay-iron oxide composites (Fig 4.4 a)
the clay surface resulted. Figure 4.4 (b) is magnification of the white square in figure
4.4 (a). Figure 4.4 (c) is a sample of pure iron oxide. A much greater size than that of
the results obtained which is due to the higher temperature used to synthesise the
iron oxides which was at 70 °C. It is hypothesised that the white spot-like particles
(Fig 4.3) are likely to be small iron oxides, specifically nano hematite particles. The
smaller size could be due to a slow formation as the temperature of the samples
never rose above 30 °C during the experiment which produced the samples nor did
they during this study.
Figure 4.4: (a) Clay and iron oxide 2:1 composite at a scale of 1 µm, (b) enlargement
of (a) at a 10 µm scale, (c) a sample of pure iron oxide at 1 µm scale (Oliveira et al.
2003).
a b
200nm200nm

38
A sample of hematite crystals (Fig 4.5) attached to a large cristobalite (a polymorph
of quartz) particles, according to a study conducted by Scheidegger et al. (1993).
These particles have similar morphologies to that of the BC MW and RS MW soils
but are at a greater size scale.
Figure 4.5: Hematite crystals on a large cristobalite particle 1 µm scale (Scheidegger
et al. 1993).
The precipitation of gypsum from solution is considered to be a single phase direct
precipitation, however Wang et al. (2012) has reported a multistep process and Van-
Driessche et al. (2012) has synthesised gypsum from a solution of 150 mM solution
of CaSO4 at room temperature and pressure. Wang and Meldrum (2012) observed
an aggregation-based mechanism, where the hemihydrate (bassanite) nanorods
aggregate to form rod-like structures which subsequently recrystallize to gypsum.
The rod-like structures found on only the BC MW soils (Fig 4.5 c and d) have a
similar appearance to that of bassanite (Fig 4.5 a) while Fig 4.5 b is a sample of
gypsum crystals (Wang and Meldrum 2012).

39
Figure 4.6: (a) Sample of bassanite, (b) pure gypsum crystals (Wang and Meldrum
2012). (c) and (d) are photomicrographs taken of the BC MW soil.
a b c
d
500nm
1 µm

40
CHAPTER 5
SUMMARY AND CONCLUSIONS
As expected, there are noticeable errors regarding the values of the extracts as
some concentrations after being treated with mine water decreased instead of
increasing. This effect was also more prominent in the RS soils than in the BC soils
which could be due to the fact that the BC soil had more clay than the RS soil. Given
that the RS MW values for AAO and DC had both decreased, it would suggest that a
considerable amount of the Al, Fe and Mn was situated in the <63 μm fraction of the
soil. The BC soil seems to have a lot more amorphous Fe whereas the RS soil
seems to have more crystalline Fe , which could be due the removal of colloidal
particles. Both soils showed an increase in Fe content.
All of the samples analysed using the XRD were of t<63 μm fraction of the soil.
There was thus a good chance that crystalline Fe-oxides formed would be of
sufficient concentration to be detected. Hematite was the only Fe-oxide found in the
soil samples treated with mine water. All of these had low broad peaks indicating that
they were poorly crystalline and of nanoparticle size. Gypsum was also identified in
the soil samples treated with mine water. Gypsum peaks <30 degrees 2 theta were
found to be narrower and of higher intensity than peaks than peaks found at >30
degrees 2 theta. The two highest intensity gypsum peaks of BC MW’s d-spacing’s
were slightly off and are thought to be a transition interference caused by bassanite
before it becomes gypsum or due to impurities within the gypsum crystal structure.
This is however this is very speculative. In contrast, all of the RS MW gypsum d-
spacings were found to be exact to those in literature which suggests their crystalline
structures are well formed.
For SEM, both the original BC and RS soils were found to have no white spots on
them. The samples treated with acidic mine water gained white nano-sized particles
on top of the clay which are thought to be nano-hematite particles. No gypsum
structures were found on any of the samples but structures resembling deviations
thereof (BC MW only), such as bassanite, a hemihydrate mineral of gypsum were.
It is thus suggested that various amorphous Fe-oxides may have formed in smaller
than detectible concentrations, however enough nano-sized poorly crystalline
hematite has formed to concentrations detectable by both XRD and SEM.

41
REFERENCES
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studies. Journal of Cleaner Production 14: 1139-1145.
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(Phase 1). Report No. J01599/05.
Bohor BF. 1970. Scanning electron microscopy of clays and clay minerals. Clays
And Clay Minerals 19: 49-54
Carlson L, Schwermann U. 1980. Natural occurrence of feroxyhite (8'-FeOOH).
Clays and Clay Minerals 4: 272-280
Carter MR, Gregorich EG. 2007. Soil Sampling and Methods of Analysis (2nd edn).
CRC Press. pp 307-311
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Van Driessche AES, Benning LG, Rodriguez-Blanco JD, Ossorio M, Bots P, García-
Ruiz JM. 2012. The Role and Implications of Bassanite as a Stable Precursor
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8 November 2015].
Department of Water Affairs (DWA). 2012. Feasibility study for a long-term solution
to address the acid mine drainage associated with the East, Central and West
Rand underground mining basins. Assessment of the water quantity and
quality of the Witwatersrand mine voids. Report No. P RSA 000/00/16512/2.
Pretoria.

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Food and Agriculture Organization of the United Nations. 1998. World Reference
Base for Soil Resources. International Society of Soil Science.
Fey MV, van der Laan M, van der Burgh G, de Jager PC, Annandale JG, du Plessis
HM. 2014. Alternatives for decontaminating water from Witwatersrand gold
mines: sulfate and metals removal using soils, mine tailings and chemical
amendments. Water Research Commission. Project No. K8/1058//3. Pretoria,
South Africa.
Frost RL, Van Der Gaast SJ, Zbik M, Kloprogge JT, Paroz GN. 2002. Birdwood
kaolinite: a highly ordered kaolinite that is difficult to intercalate - an XRD,
SEM and Raman spectroscopic study. Applied Clay Science 20: 177– 187
Harris W, White N. 2007. X-ray Diffraction Techniques for Soil Mineral Identification
In: Methods of Soil Analysis. Soil Science Society of America. pp 1-35.
Hudson-Edwards KA, Schell C, Macklin MG. 1999. Mineralogy and geochemistry of
alluvium contaminated by metal mining in the Rio Tinto area, southwest
Spain. Applied Geochemistry 14: 1015-1030
Lee G, Bighamb JM, Faurea G. 2002. Removal of trace metals by coprecipitation
with Fe, Al and Mn from natural waters contaminated with acid mine drainage
in the Ducktown Mining District, Tennessee. Applied Geochemistry 17: 569-
581
Lottermoser BG. 2010. Mine Wastes: Characterization, Treatment and
Environmental Impacts. Springer Science & Business Media.
Naicker K, Cukrowska E, McCarthy TS. 2003. Acid mine drainage arising from gold
mining activity in Johannesburg, South Africa and environs. Environmental
Pollution 122: 29-40.
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Sulfate Weathering. Soil Science Society of America. pp 37-56.

43
Oliveira LCA, Rios RVRA, Fabris JD, Sapag K, Garg VK, Lago RM. 2003. Clay–iron
oxide magnetic composites for the adsorption of contaminants in water.
Applied Clay Science 22: 169– 177
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preparation and analytical identification. Geoderma 1-2: 43-65
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Dissolution Kinetics, Differential X-ray Diffraction, and Mössbauer
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Decontaminating metalliferous mine water. Honours thesis, University of
Pretoria, South Africa.
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Parameters on Poorly Crystalline Material Difractogram. University of Latvia,
Lativa.
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hemihydrate intermediates. Journal of the Chemical Society 48: 504-506
Wang YW, Meldrum FC. 2012. Additives stabilize calcium sulfate hemihydrate
(bassanite) in solution. Journal of Materials Chemistry 22: 22055-22062

44
APPENDIX A
BC Ori soil
Raw data Average
Al Fe Mn Al Fe Mn
mg/l mg/l
BC DC 1 52.3 320 36.7 BC DC 5.3 60.2 6.60
BC DC 2 50.5 306 37.4 BC AAO 11.8 50.7 13.2
BC DC 3 49.7 306 35.3
BC AAO 1 178 500 94.4 Standard deviation
BC AAO 2 148 430 88.8 Al Fe Mn
BC AAO 3 106 328 61.1 mg/l
BC DC 0.10 0.53 0.11
(Raw data) - (Blanks) BC AAO 0.53 1.91 0.39
Al Fe Mn
mg/l Coefficient of variance
BC DC 1 5.35 60.7 6.52 Al Fe Mn
BC DC 2 5.23 60.3 6.72 %
BC DC 3 5.42 59.7 6.55 BC DC 1.79 0.88 1.63
BC AAO 1 12.3 52.5 13.6 BC AAO 4.47 3.77 2.95
BC AAO 2 11.9 50.8 13.4
BC AAO 3 11.3 48.7 12.8 Average
Al Fe Mn
(Raw data) - (blanks) mg/kg
Al Fe Mn BC DC 851 9616 1053
mg/kg BC AAO 1769 7591 1984
BC DC 1 854 9695 1040
BC DC 2 835 9629 1073 Standard deviation
BC DC 3 864 9524 1046 Al Fe Mn
BC AAO 1 1842 7861 2030 mg/kg
BC AAO 2 1777 7614 2002 BC DC 14.9 86.4 17.5
BC AAO 3 1686 7297 1919 BC AAO 78.2 283 57.6
Blank average Coefficient of variance
Al Fe Mn Al Fe Mn
mg/l %
AAO B Ave 0.44 0.48 0.10 BC DC 1.75 0.90 1.66
DC B Ave 0.48 1.08 0.10 BC AAO 4.42 3.73 2.91

45
BC MW soil
Raw data Average
Al Fe Mn Al Fe Mn
mg/l mg/l
BC DC 1 6.39 73.7 6.91 BC DC 6.10 74.1 7.05
BC DC 2 6.74 76.3 7.32 BC AAO 10.9 77.8 12.4
BC DC 3 6.61 75.6 7.23
BC AAO 1 12.1 80.3 12.9 Standard deviation
BC AAO 2 9.79 73.3 11.6 Al Fe Mn
BC AAO 3 12.1 81.2 12.9 mg/l
BC DC 0.18 1.35 0.21
(Raw data) - (Blanks) BC AAO 1.33 4.34 0.74
Al Fe Mn
BC DC 1 5.91 72.6 6.81 Al Fe Mn
BC DC 2 6.26 75.2 7.22 %
BC DC 3 6.14 74.5 7.13 BC DC 2.93 1.82 3.04
BC AAO 1 11.6 79.8 12.8 BC AAO 12.2 5.58 6.00
BC AAO 2 9.35 72.8 11.5
BC AAO 3 11.7 80.7 12.8 Average
Al Fe Mn
Al Fe Mn BC DC 974 11830 1126
mg/kg BC AAO 1631 11652 1851
BC DC 1 944 11603 1088
BC DC 2 997 11990 1150 Standard deviation
BC DC 3 980 11896 1138 Al Fe Mn
BC AAO 1 1740 11970 1916 mg/kg
BC AAO 2 1401 10900 1723 BC DC 27.3 202 33.0
BC AAO 3 1751 12079 1914 BC AAO 198 648 111
Al Fe Mn Al Fe Mn
mg/l %
AAO B Ave 0.44 0.48 0.10 BC DC 2.80 1.70 2.93
DC B Ave 0.48 1.08 0.10 BC AAO 12.2 5.56 5.99

46
RS Ori soil
Raw data Average
Al Fe Mn Al Fe Mn
mg/l mg/l
RS DC 1 9.05 111 3.84 RS DC 9.43 116 4.12
RS DC 2 10.2 119 3.91 RS AAO 10.6 31.6 7.90
RS DC 3 10.5 121 4.89
RS AAO 1 12.1 33.5 8.41 Standard deviation
RS AAO 2 11.1 32.3 8.09 Al Fe Mn
RS AAO 3 10.1 30.5 7.48 mg/l
RS DC 0.77 5.36 0.59
(Raw data) - (Blanks) RS AAO 0.98 1.48 0.47
Al Fe Mn
RS DC 1 8.57 110 3.74 Al Fe Mn
RS DC 2 9.67 118 3.81 %
RS DC 3 10.1 120 4.79 RS DC 8.13 4.62 14.3
RS AAO 1 11.6 33.0 8.31 RS AAO 9.21 4.68 5.97
RS AAO 2 10.6 31.8 7.99
RS AAO 3 9.66 30.1 7.38 Average
Al Fe Mn
Al Fe Mn RS DC 1506 18510 657
mg/kg RS AAO 1594 4738 1183
RS DC 1 1366 17517 596
RS DC 2 1543 18766 608 Standard deviation
RS DC 3 1609 19246 767 Al Fe Mn
RS AAO 1 1740 4941 1244 mg/kg
RS AAO 2 1595 4767 1198 RS DC 125 893 95.4
RS AAO 3 1449 4508 1107 RS AAO 146 218 69.9
Al Fe Mn Al Fe Mn
mg/l %
AAO B Ave 0.44 0.48 0.10 RS DC 8.33 4.82 14.5
DC B Ave 0.48 1.08 0.10 RS AAO 9.14 4.60 5.90

47
RS MW soil
Raw data Average
Al Fe Mn Al Fe Mn
mg/l mg/l
RS DC 1 7.76 124 1.76 RS DC 7.30 121 1.64
RS DC 2 8.00 124 1.65 RS AAO 7.95 26.5 2.18
RS DC 3 7.59 119 1.78
RS AAO 1 8.50 26.1 2.38 Standard deviation
RS AAO 2 8.91 28.2 2.29 Al Fe Mn
RS AAO 3 7.76 26.7 2.18 mg/l
RS DC 0.20 2.89 0.08
(Raw data) - (Blanks) RS AAO 0.59 1.07 0.10
Al Fe Mn
RS DC 1 7.28 123 1.66 Al Fe Mn
RS DC 2 7.51 123 1.55 %
RS DC 3 7.11 118 1.70 RS DC 2.78 2.39 4.65
RS AAO 1 8.06 25.7 2.28 RS AAO 7.39 4.02 4.40
RS AAO 2 8.47 27.7 2.19
RS AAO 3 7.31 26.2 2.08 Average
Al Fe Mn
Al Fe Mn RS DC 1166 19381 262
mg/Kg RS AAO 1187 3960 326
RS DC 1 1163 19615 265
RS DC 2 1201 19687 248 Standard deviation
RS DC 3 1136 18840 272 Al Fe Mn
RS AAO 1 1206 3836 341 mg/kg
RS AAO 2 1266 4139 327 RS DC 32.9 469 12.1
RS AAO 3 1090 3904 311 RS AAO 89.4 159 15.0
Al Fe Mn Al Fe Mn
mg/l %
AAO B Ave 0.44 0.48 0.10 RS DC 2.82 2.42 4.61
DC B Ave 0.48 1.08 0.10 RS AAO 7.53 4.00 4.60

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