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Comment on “Speciation and fate of toxic cadmium in contaminated paddy soils and rice using
XANES/EXAFS spectroscopy”
Geraldine Sarret, Hester Blommaert, Matthias Wiggenhauser
To cite this version:
Geraldine Sarret, Hester Blommaert, Matthias Wiggenhauser. Comment on “Speciation and fate of toxic cadmium in contaminated paddy soils and rice using XANES/EXAFS spectroscopy”. Journal of Hazardous Materials, Elsevier, 2020, 401, pp.123240. �10.1016/j.jhazmat.2020.123240�. �hal-02988771�
Comment on “Speciation and fate of toxic cadmium in contaminated paddy
1
soils and rice using XANES/EXAFS spectroscopy”
2 3
Géraldine Sarret1*, Hester Blommaert1, Matthias Wiggenhauser2 4
5
1 Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, IRD, IFSTTAR, ISTerre, 38000 6
Grenoble, France 7
2 Institute of Agricultural Sciences, ETH Zurich, Eschikon 33, CH-8315 Lindau, Switzerland 8
9 10 11 12
* Corresponding author: geraldine.sarret@univ-grenoble-alpes.fr 13
14 15
16
17
Graphical abstract 18
19 Abstract 20
Kunene et al. recently published a paper in the Journal of Hazardous Materials 383 (2020) 21
121167 on the speciation of cadmium in contaminated paddy soils and rice using 22
XANES/EXAFS spectroscopy. This paper included experimental procedures and data 23
processing steps that were partly erroneous, especially in regard to the synchrotron 24
speciation measurements. We address these issues in this comment and provide the reader 25
with a brief overview of the paper to avoid future misconceptions.
26 27
Highlights 28
The soil studied cannot be considered as contaminated based on its Cd concentration.
29
The reported interatomic distances for Cd in soils and rice kernels are unrealistic.
30
The use of appropriate reference compounds is necessary in EXAFS analysis.
31 32 33
Dear Editor, 34
We read Kunene et al.’s article, “Speciation and fate of toxic cadmium in contaminated 35
paddy soils and rice using XANES/EXAFS spectroscopy,” published in the Journal of 36
Hazardous Materials, with great interest (https://doi.org/10.1016/j.jhazmat.2019.121167).
37
Rice is a major food source of Cd for humans, especially in Asian countries. To improve 38
agricultural practices and mitigate Cd transfer into grains, there is a need for a better 39
understanding of the processes that control the mobility of Cd in soil-rice systems. The 40
paper’s strategy for achieving this goal, i.e., studying Cd speciation in a contaminated soil 41
and in the kernels of rice plants that grew on this soil using X-ray absorption spectroscopy 42
(XAS), seems appropriate. However, the paper contains erroneous and inaccurate methods 43
of data acquisition, treatments, and interpretations that are addressed in the following 44
sections and in the Supplemental Information (SI).
45 46
Detailed comments 47
First, the measurements and the interpretation of Cd concentrations in the soil samples are 48
questionable. The mean Cd concentration in the soil that is characterized as “contaminated”
49
(0.06 mg kg-1, measured after acidic digestion) is in the range of Cd that naturally occurs in 50
soil (0.01-1 mg kg-1) (Smolders and Mertens, 2013). The concentration in the “contaminated”
51
soil is a factor of five less than the permissible limit in China (0.3 mg kg-1) mentioned in 52
Kunene et al.’s introduction (2020). Furthermore, Cd measurements in the contaminated 53
and non-contaminated soil (0.06 ± 0.6 and 0.02 ± 0.3 mg kg-1, respectively) show high 54
uncertainties (a factor ten greater than the mean) and did not seem significantly different 55
from each other (although no statistical tests were applied). The combination of low Cd 56
concentration and high uncertainty may indicate that the soil measurements were 57
conducted close to the detection limit. The ICP-OES’s is limit of quantification was not 58
reported, and no certified material was used to assure the accuracy and precision of the 59
reported concentration measurements. It is likely that ICP-OES, unlike ICP-MS, was not 60
sensitive enough to adequately measure Cd concentrations in soils that were near 61
background Cd levels (McBride, 2011). Based on the data presented in the article, the soil 62
studied cannot be considered as being contaminated by Cd and the reported concentrations 63
are questionable. However, the Cd concentration presented in Figure 4 for rice leaves, 64
stems, and roots seems to be comparable to Cd concentrations measured in the straw of 65
various rice cultivars grown in a soil contaminated with 2 mg kg-1 Cd (Bai et al., 2018; Yan et 66
al., 2016). Thus, it is possible that the soil that was defined as contaminated was actually 67
enriched in Cd, and that the reported soil Cd concentration was underestimated.
68 69
Second, there are major issues concerning synchrotron XAS data acquisition, treatment, and 70
interpretation. The exact Cd concentration in rice kernels is difficult to deduce from Figure 4, 71
but it was probably in the range of a 0-10 mg kg-1. Kunene et al. state that the spectra were 72
recorded in transmission mode. More details should be provided to better document this 73
unprecedented sensitivity of EXAFS in transmission mode. For “diluted” samples, such as Cd- 74
contaminated soils and sediments, fluorescence mode has been previously used because of 75
its higher sensitivity (Fulda et al., 2013 ; Furuya et al., 2016; Hashimoto and Yamaguchi, 76
2013; Huguet et al., 2015). Transmission mode is generally employed for samples that have a 77
high concentration of the target element, such as reference compounds. Newville et al.
78
(2014) state that, as a rule of thumb, a sample needs to have a concentration of 10% weight 79
(i.e., 100 g kg-1, fourorders of magnitude higher than Kunene et al.’s study) to be measured 80
in transmission mode. However, from our experience, and personal communication with 81
EXAFS beamline scientists, EXAFS spectra can be recorded in transmission mode on very 82
stable beamlines and on samples that have lower concentrations, typically down to 1000 mg 83
kg-1 to 1% Cd. A theoretical calculation using XAFSmass 1 shows that it is theoretically 84
possible to record EXAFS spectra in transmission mode on diluted samples, but under very 85
unusual conditions. For example, 30g of carbon containing 74 mg kg-1 Cd, i.e., roughly 20 cm 86
thick, would provide acceptable measurement conditions (edge jump of 0.1, beam intensity 87
attenuation of 92%).
88
In order to interpret the XAS spectra of environmental samples, they are generally compared 89
to reference spectra as part of a first step of the analysis. It is essential that all possible forms 90
of Cd inorganic and organic complexes are covered by the Cd standards that may appear in 91
the system under investigation. Based on previous studies on Cd speciation in soils, relevant 92
Cd standards include Cd sorbed on minerals, Cd complexed to O- and S-containing groups of 93
organic compounds, and Cd sulfide (CdS) in the case of soils in anoxic conditions (Fulda et al., 94
2013 ; Furuya et al., 2016; Hashimoto and Yamaguchi, 2013; Huguet et al., 2015). For plant 95
samples, relevant Cd standards include Cd bound to O/N-containing and S-containing groups 96
of organic molecules (Isaure et al., 2015; Küpper et al., 2004). In Kunene et al., only two 97
reference spectra were recorded and compared to the soil and rice kernel spectra: metallic 98
Cd and Cd oxide (CdO). By limiting the study to these two standards, Kunene et al. did not 99
cover the abovementioned major inorganic and organic complexes that are expected to 100
occur in soil-rice systems. Based on the comparison of the XANES spectra, the authors 101
discussed the valence of Cd (0 versus II). It is well known that Cd is divalent in environmental 102
compartments (Maret and Moulis, 2013; Shahid et al., 2017) and, to our knowledge, there is 103
no report of elemental Cd in soils or plants.
104
After comparing the spectra of the samples and standard spectra, Kunene et al. treated the 105
EXAFS spectra for the soil and rice kernel by shell fitting. The EXAFS data presented in Figure 106
9 reveal major inconsistencies. If Figures 9c and 9d show Fourier transformed (FT) EXAFS 107
spectra, then the abscissa and ordinates are wrong (they should be Å and FT magnitude, 108
respectively). The y-axes for the EXAFS spectra shown in Fig 9e and 9f are labeled with 109
[k3χ(k)] while the legend describes the y-axis as [k2 χ(k)]. These inconsistencies require 110
clarification. The kx weight is used to enhance the amplitude of EXAFS oscillations in the high 111
k region. In Figure 9e and f, the amplitudes at high k (10-15 Å-1) are extremely high.
112
Regardless of the k-weights chosen, the shape of the EXAFS spectra and of the FTs differ 113
from those previously reported for compounds in which Cd is bound to oxygen ligands (see 114
for example, Grafe et al., 2007; Pokrovsky et al., 2008; Fulda et al., 2013; Huguet et al., 2015;
115
Furuya et al., 2016). The shell fitting results presented in Table 3 also show major 116
inconsistencies. For metallic Cd (“Cd” in Table 3), the shell of Cd (i.e., the neighboring atoms) 117
should be Cd instead of O. For the rice kernels, a first O shell at 2.83 Å is unrealistic.
118
Although there can be long Cd-O/N bonds (up to 2.8 Å, Carballo et al., 2013), typical average 119
first shell Cd-O/N distance ranges between 2.20 and 2.35 Å, as shown in the Cambridge 120
structural database (Bruno et al., 2002) and in several articles on Cd in soils, sediments and 121
living organisms (Grafe et al., 2007; Fulda et al., 2013; Huguet et al., 2015; Pokrovsky et al., 122
2008). First shell average Cd-O/N distances are shorter than Cd-S distances, which range 123
between 2.5 and 2.6 Å (Bruno et al., 2002; Fulda et al., 2013; Huguet et al., 2015; Pokrovsky 124
et al., 2008) due to the shorter ionic radius of O compared to S. The first shell Cd-O distance 125
of 2.83 Å reported in Kunene et al. is even longer than typical Cd-S distances. The fact that 126
there was more than a 1 Å difference between the position of the first peak of the FT EXAFS 127
spectra (positioned at about 1.0 and 1.2 Å in Figure 9c and 9d, respectively) and the 128
distances determined by shell fitting in Table 3 (2.35 and 2.83 Å, respectively) provoked 129
further inquiry. The difference between actual interatomic distance and the position of the 130
peak on the FT EXAFS spectra, which is due to the energy dependence of the phase functions 131
in the sine function, should be about 0.2–0.5 Å (Koningsberger and Prins, 1988).
132 133
Third, there are instances of inappropriate citations. For example, in the sentence, 134
“Moreover, Cd in rice was found in a form of CdS (Fan et al., 2016; Siripornadulsil and 135
Siripornadulsil, 2013; Furuya et al., 2016),” the cited references concern soils and bacteria, 136
not rice. Furuya et al. (2016) measured CdS in flooded soils using EXAFS spectroscopy, Fan et 137
al. (2016) measured Zn in soils, and Siripornadulsil and Siripornadulsil (2013) used XANES 138
spectroscopy to measure Cd speciation in bacteria. Additional examples of erroneous 139
citations can be found in the SI.
140 141
Lastly, ample questionable expressions were used throughout the manuscript (the SI 142
provides some examples), which confirmed our overall impression that the paper was not 143
sufficiently elaborate to be accepted in a high quality peer reviewed journal.
144 145
Conclusions 146
Several lessons can be learned from Kunene et al’s paper. Most importantly, a reliable peer 147
review process is essential. It is the duty of editors to assign submitted manuscripts to 148
reviewers who possess the appropriate expertise, and reviewers should assess the quality 149
and accuracy of the manuscript.Including raw data with each article, a requirement that in 150
more and more common in peer reviewed scientific journals, should be the norm. Doing so 151
provides several advantages, including facilitating the checking of the data quality.
152
In regard to synchrotron measurements, non-expert users should take advantage of the 153
various training courses available at many synchrotron facilities, and obtain assistance 154
during data acquisition and data treatment by collaborating with beamline staff. Regarding 155
EXAFS spectroscopy, developing open databases of reference spectra (like the initiatives of 156
individual beamlines, such as FAME 2 and ID21 3 at the ESRF) enhances data output and 157
quality for researchers that apply this technique to study pollutants such as Cd in the 158
environment.
159 160
1 K. V. Klementiev, XAFSmass, freeware:
161
www.cells.es/Beamlines/CLAESS/software/xafsmass.html 162
2 https://www.sshade.eu/db/fame 163
3 https://www.esrf.eu/home/UsersAndScience/Experiments/XNP/ID21/php.html 164
165
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R. (2002) New software for searching the Cambridge Structural Database and visualising 168
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169
Carballo, R., Castiñeiras, A., Domínguez-Martín, A., García-Santos, I. and Niclós-Gutiérrez, J.
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(2013) Solid State Structures of Cadmium Complexes with Relevance for Biological Systems, 171
in: Sigel, A., Sigel, H., Sigel, R.K.O. (Eds.), Cadmium: From Toxicity to Essentiality. Springer 172
Netherlands, Dordrecht, pp. 145-189.
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Fan, T.-T., Wang, Y.-J., Li, C.-B., He, J.-Z., Gao, J., Zhou, D.-M., Friedman, S.P. and Sparks, D.L.
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(2016) Effect of Organic Matter on Sorption of Zn on Soil: Elucidation by Wien Effect 175
Measurements and EXAFS Spectroscopy. Environmental Science & Technology 50, 2931- 176
2937.
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Fulda, B., Voegelin, A. and Kretzschmar, R. (2013) Redox-Controlled Changes in Cadmium 178
Solubility and Solid-Phase Speciation in a Paddy Soil As Affected by Reducible Sulfate and 179
Copper. Environmental Science & Technology 47, 12775-12783.
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Furuya, M., Hashimoto, Y. and Yamaguchi, N. (2016) Time-Course Changes in Speciation and 181
Solubility of Cadmium in Reduced and Oxidized Paddy Soils. Soil Science Society of America 182
Journal 80, 870-877.
183
Grafe, M., Singh, B. and Balasubramanian, M. (2007) Surface speciation of Cd(II) and Pb(II) on 184
kaolinite by XAFS spectroscopy. J Colloid Interface Sci 315, 21-32.
185
Hashimoto, Y. and Yamaguchi, N. (2013) Chemical Speciation of Cadmium and Sulfur K-Edge 186
XANES Spectroscopy in Flooded Paddy Soils Amended with Zerovalent Iron. Soil Science 187
Society of America Journal 77, 1189-1198.
188
Huguet, S., Isaure, M.-P., Bert, V., Laboudigue, A., Proux, O., Flank, A.-M., Vantelon, D. and 189
Sarret, G. (2015) Fate of cadmium in the rhizosphere of Arabidopsis halleri grown in a 190
contaminated dredged sediment. Sci. Tot. Environ. 536, 468-480.
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Isaure, M.-P., Huguet, S., Meyer, C.-L., Castillo-Michel, H., Testemale, D., Vantelon, D., 192
Saumitou-Laprade, P., Verbruggen, N. and Sarret, G. (2015) Evidence of various mechanisms 193
of Cd sequestration in the hyperaccumulator Arabidopsis halleri, the non-accumulator 194
Arabidopsis lyrata, and their progenies by combined synchrotron-based techniques. J. Exp.
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Koningsberger, D. and Prins, R. (1988) X-Ray Absorption: Principles, Applications, Techniques 197
of EXAFS, SEXAFS, and XANES. Wiley, New York.
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Kunene, S.C., Lin, K.-S., Mdlovu, N.V., Lin, Y.-S. and Mdlovu, N.B. (2020) Speciation and fate 199
of toxic cadmium in contaminated paddy soils and rice using XANES/EXAFS spectroscopy.
200
Journal of Hazardous Materials 383, 121167.
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McBride, M.B. (2011) A comparison of reliability of soil cadmium determination by standard 209
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Supplemental information
1
Comment on “Speciation and fate of toxic cadmium in contaminated paddy
2
soils and rice using XANES/EXAFS spectroscopy”
3
Géraldine Sarret, Hester Blommaert, Matthias Wiggenhauser 4
5 6
In addition to the major critiques on data quality, data treatment, and data interpretation that 7 are presented in the main manuscript, other inconsistencies and inadequate uses of 8 expressions are point by point listed below.
10 9
Introduction:
11 12
• ‘Amongst the heavy metals, Cd has been reported to be the major contaminant of 13 agricultural soil quality, particularly paddy soils’
14 Cd is one of the major contaminants in agricultural soils. Otherwise, the authors should 15 precisely cite literature that reports the strong statement ‘the major contaminant’.
16 • ‘Additionally, Cd can be deposited into the soil, leached with waste water or taken up 17 by plant roots. As a result, it is speedily transported to the edible plant parts, from 18 where it enters the human food chain (Boussen et al., 2013; Ke et al., 2015; Chen et al., 19 2018).’
20 ‘Waste water’ is not an appropriate term to describe water that is leached from the 21 soil profile (alternatively: seepage water). Furthermore, does ’speedily’ suggest a Cd 22 uptake rate that is faster than for the other elements. This statement should be backed 23 up by literature.
24 25
Methods:
26 27
• The authors did not give any information about sample replicates and how statistical 28 differences of the mean values were determined. For instance, in section 3.1 the 29 authors state: ‘In comparison, the difference between concentration of absorbed 30 elements in contaminated and non-contaminated plants was not significant.’ This 31 statement is not comprehensible based on the given method. The same applies for the 32 following sentence in the Results section ‘The difference was not significant in terms 33 of the particle sizes.’
34 • ‘The toxicity characteristic leaching procedure (TCLP) extraction was performed 35 according to Taiwan Environmental Protection Administration (TEPA) NIEA R201.12C 36 Method (Hashimoto et al., 2016). Before extraction, centrifugation was used to remove 37 excess water from the soil and rice samples.’
38 The method for TCLP extraction was not found in the cited article (Hashimoto et al., 39 2016). The TCLP proposed by the EPA is an extraction method to determine the 40 mobility of organic and inorganic analytes present in liquid, solid, or multiphasic 41 wastes, using acetic acid at different pHs (EPA, 1002). The protocol used by the authors 42 is an acidic digestion. Moreover, some critical details are missing. It is not clear 43 whether dry weights were determined or not, so whether concentrations are 44
expressed as dry of fresh weight. Other information such as temperature and 45 instruments for digestion are not reported.
46 47
• ‘Cationic exchange capacities (CEC) were measured following Colzato et al. (2017) 48 method (Colzato et al., 2017). Carbonates in soil samples were characterized using a 49 titration method (Metal standard for ICP TraceCERT®, 2019).‘
50 The CEC determination referred to is a method for highly weathered soils (Gillman 51 1979). The authors should have given a justification for their choice of extraction 52 method. Concerning the titration method for the determination of carbonates, a 53 wrong citation is given.
54 55
Results:
56 57
• ‘The results depict the presence of trace amount of S (2%) … due to its trace amount, S 58 could not be dictated by EXAFS/XANES analyses (Siripornadulsil and Siripornadulsil, 59 2013)’.
60 The expression ‘trace amounts’ is inadequate. The S concentration (20 g kg-1) was 61 lower than the C and N concentration, but it was still about 1000 times higher than 62 concentrations of trace metals in the studied system (e.g. Zn ~ 50-150 mg kg-1, Cd < 40 63 mg kg-1). Furthermore, the sentence is not clear. Supposing that the authors refer to 64 the possibility to detect S in the Cd coordination shell by XANES/EXAFS: It depends on 65 the ratio between total S and total Cd content, not on total S content. If the Cd content 66 is in the mg kg-1 range (presumably 10 mg kg-1 , Figure 4) and the S content is 2%, then 67 the S/Cd ratio equals 2000. Thus, there is a huge excess of S relative to Cd which could 68 potentially bind Cd. Supposing the authors refer to the possibility to study S speciation 69 by XANES spectroscopy: This is feasible with a concentration of 2% S.
70 • In the text, the terms “clay soil”, sandy soil”, silty soil” are employed instead of clay, 71 silt and sand fraction.
72 • Most of the Cd concentrations are not reported in a readable manner. In Figure 4, the 73 authors report the concentration of Cd, Cr, Ni, Cu, As, and Pb in the same Figure as 74 barplot. Since the Cd concentration is much lower than e.g. the Zn or the As 75 concentrations, the reader can hardly see the Cd concentration which is most central 76 in this study. The exact Cd concentrations are also not given in the text although the 77 authors discuss the toxicity of Cd for plants and humans (section 3.1). Furthermore, 78 the bars in Figure 3 and 4 also have no error bars which shows (as mentioned in the 79 method section) that it is not clear how the samples were replicated and statistically
80 evaluated.
81 82
Discussion:
83 84
• ‘Although Cd concentration was low in the contaminated edible parts, many 85 researchers have reported that Cd is harmful for plants and humans even at low 86 concentrations. It has been reported that when Cd concentrations in the body of human 87 being reaches levels considered harmful (> 200 μg/g wet weight in the kidney cortex), 88 it can induce kidney damage, cancer, skeletal disorders, and other diseases. The 89 bearable daily consumption of Cd is 1 μg/kg per body weight (Kjellström and Nordberg,
90 1978; Page et al., 1987; Haghiri, 1987).’
91
It is not defined what ‘low concentration‘ means and the Cd concentrations that were 92 measured in this study were not well related with how Cd harms plants and humans.
93 The authors report limits for daily Cd intake per kg body weight [μg (kg body weight)- 94 1], but no concentration limits for rice were reported [mg (kg dry weight)-1].
95 Furthermore, it is impossible for the reader to relate daily Cd intake to the Cd 96 concentrations that are given in Figure 4. The FAO set a threshold for Cd in rice at 0.4 97 mg kg-1 (Codex Alimentarus, CODEX STAN 193–1995 2009). This value could be 98 compared with the Cd concentrations that were measured in the rice kernels.
99 Furthermore, one of the critical issues about Cd is that the critical Cd concentrations 100 in edible plant parts are about one order of magnitude below the Cd concentrations 101 that induce stress for the plant (Ismael et al., 2019; White, 2012). The authors just 102 stated that Cd is toxic for humans and plants which does not sufficiently describe the 103 critical issue with Cd in the soil-rice systems.
104 105
• ‘The heavy metals were more concentrated in the root-soils. This phenomenon was 106 observed due to the process of filtration or detoxification occurring in rice crops.’
107 As for Figure 4, it is impossible to see the difference between ‘root-soil’ and the soil 108 samples at different depths in Figure 5. Neither mean values nor standard deviation 109 are given in the text. In addition, the explanation why the ‘root-soils’ were more 110 concentrated than the other soils is not clear. It is not clear what the authors mean 111 with ‘process of filter’, and how detoxification leads to this difference in Cd 112 concentration in the soil.
113 114
• ‘The presence of O ligands for Cd is in line with the results obtained by Cheng et al.
115 (2016), who reported that Cd formed a co-ordination compound with O bonds (Cheng
116 et al., 2016).’
117 Cheng et al. studied hyperaccumulator plants, this should be mentioned because these 118 plants cope differently with Cd than non-hyperaccumulating plants, which might also 119 affect Cd speciation (Verbruggen et al, 2009). In addition, the statement above is not 120 precise, even not correct. Cheng et al. showed that Cd in shoots and xylem sap was to 121 substantial fractions present as Cd-S and Cd-O.
122 123
• ‘Hashimoto and Yamaguchi (2013) reported that flooded paddy soils amended with 124 zero-valent iron (ZVI) is an effective way of reducing or decontaminating Cd in the soil.
125 Moreover, the use of bacteria to transform soluble and toxic cadmium chloride into less 126 toxic and insoluble cadmium sulfide is also a possible decontamination route. These 127 methods have been reported to be available, cost effective, and easy to prepare 128 (Hashimoto and Yamaguchi, 2013; Siripornadulsil and Siripornadulsil, 2013; Mdlovu et
129 al., 2019).’
130 Numerous papers reviewed the knowledge on mitigation strategies to reduce the Cd 131 transfer from soil to plant/grain (e.g. Kirkham, 2006; Puschenreiter et al., 2011; Rizwan 132 et al., 2016; Li et al., 2017). The authors should consider this knowledge in a more 133 exhaustive way. It is as well unclear why Mdlovu et al., 2019 is cited here. This paper 134 reports ‘In-situ reductive degradation of chlorinated DNAPLs in contaminated 135 groundwater using polyethyleneimine-modified zero-valent iron nanoparticles.’
136 137
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