remote sensing

Article
Prediction of Soil Physical and Chemical Properties
by Visible and Near-Infrared Diffuse Reflectance
Spectroscopy in the Central Amazon
Érika F. M. Pinheiro 1, *, Marcos B. Ceddia 1 , Christopher M. Clingensmith 2 , Sabine Grunwald 2
and Gustavo M. Vasques 3
1 Departamento de Solos, Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, BR 465,
km 7, Seropédica 23890-000, RJ, Brazil; [email protected]
2 Pedometrics, Landscape Analysis, and GIS Laboratory, Soil and Water Science Department,
University of Florida, 2181 McCarty Hall A, P.O. Box 110290, Gainesville, FL 32611-0290, USA;
[email protected] (C.M.C.); [email protected] (S.G.)
3 Embrapa Solos, Rua Jardim Botânico, 1024, Rio de Janeiro 22460-000, RJ, Brazil;
[email protected]
* Correspondence: [email protected]; Tel.: +55-21-3787-3772

Academic Editors: José A.M. Demattê, Lenio Soares Galvao, Clement Atzberger and Prasad S. Thenkabail
Received: 28 October 2016; Accepted: 12 March 2017; Published: 23 March 2017

Abstract: Visible and near-infrared diffuse reflectance spectroscopy (VIS-NIR) has shown levels of
accuracy comparable to conventional laboratory methods for estimating soil properties. Soil chemical
and physical properties have been predicted by reflectance spectroscopy successfully on subtropical
and temperate soils, whereas soils from tropical agro-forest regions have received less attention,
especially those from tropical rainforests. A spectral characterization provides a proficient pathway
for soil characterization. The first step in this process is to develop a comprehensive VIS-NIR soil
library of multiple key soil properties to be used in future soil surveys. This paper presents the first
VIS-NIR soil library for a remote region in the Central Amazon. We evaluated the performance of
VIS-NIR for the prediction of soil properties in the Central Amazon, Brazil. Soil properties measured
and predicted were: pH, Ca, Mg, Al, H, H+Al, P, organic C (SOC), sum of bases, cation exchange
capacity (CEC), percentage of base saturation (V), Al saturation (m), clay, sand, silt, silt/clay (S/C),
and degree of flocculation. Soil samples were scanned in the laboratory in the VIS-NIR range
(350–2500 nm), and forty-one pre-processing methods were tested to improve predictions. Clay
content was predicted with the highest accuracy, followed by SOC. Sand, S/C, H, Al, H+Al, CEC,
m and V predictions were reasonably good. The other soil properties were poorly predicted. Among
the soil properties predicted well, SOC is one of the critical soil indicators in the global carbon cycle.
Besides the soil property of interest, the landscape position, soil order and depth influenced in the
model performance. For silt content, pH and S/C, the model performed better in well-drained
soils, whereas for SOC best predictions were obtained in poorly drained soils. The association of
VIS-NIR spectral data to landforms, vegetation classes, and soil types demonstrate potential for
soil characterization.

Keywords: chemometrics; spectral pre-processing; partial least squares regression; soil organic
carbon; tropical soils

1. Introduction
Achieving food security with the given limited soil and water resources and a rising world
population set to breach breaching more than 9.5 billion within the next two decades will require

Remote Sens. 2017, 9, 293; doi:10.3390/rs9040293 www.mdpi.com/journal/remotesensing

Remote Sens. 2017, 9, 293 2 of 22

the adoption and expansion of digital soil mapping (DSM), precision agriculture, best management
practices, and geospatial spectral technologies [1]. Among the latter, visible and near-infrared (VIS-NIR)
diffuse reflectance spectroscopy (DRS) allows for fast, quantitative, cost effective and non-destructive
estimation of soil properties.
The quality of laboratory-based spectral models have been similar to traditional soil analytical
methods, though some variations occur in the prediction performance [2,3]. Visible and near-infrared
(350–2500 nm) DRS has been efficiently used to predict some physical (sand, silt and clay), chemical
(cation exchange capacity (CEC), pH, organic carbon), and mineral (kaolinite, gibbsite, montmorillonite
and iron oxides) soil properties [4–9]. The approach also allows estimation multiple soil properties
from the same spectral data, but is limited by the need for a reasonable number of samples to calibrate
and validate the predictive models. This is usually conducted using data-craving parametric and
non-parametric multivariate methods. Partial least squares regression (PLSR) is the most common
algorithm used to calibrate VIS-NIR spectra to predict soil properties [4]. Partial least squares
regression, in conjunction with the variable importance in the projection (VIP) metric, is an important
tool for identifying the most relevant explanatory variables for prediction [10]. In remote regions,
where field access is more difficult, a spectral characterization is especially important and provides a
proficient pathway for soil characterization. Once VIS-NIR soil models have been successfully built
through calibration and validation, they offer future cost-effective and less laborious pathways for
soil assessment. For instance, in the Central Amazon region, transportation is limited, expensive and
difficult (often sites are only accessible by boat and a few airplanes). Proximal sensors offer advantages
for soil measurement over remote sensing or traditional sampling and laboratory analysis [8,11].
One advantage of DRS is the capacity of computational storage in real-time of the measured spectra
allowing the creation of databases called spectral libraries [12]. The geographic and attribute domain
boundaries of these spectral libraries determine their applicability. Model predictions typically degrade
and uncertainties rise if spectral models are used outside of their calibration domain boundaries.
Soil chemical and physical properties have been predicted by reflectance spectroscopy successfully
in the past [5–8]. However, the focus has been on subtropical and temperate soils, whereas soils from
tropical agro-forest regions have received less attention, especially those from tropical rainforests [6–9].
Soils from the Amazon rainforest share common parent materials and formation processes
mediated geologically by the erosional processes that shaped the Amazon Sedimentary Basin,
regionally by climatic gradients, and locally by the relief and seasonal fluctuations of the rivers
forming the so-called várzea (lowland, floodplain) and terra firme (upland) forests. However, its size
and remoteness forbids ample soil sampling due to the high costs and human risks (e.g., contraction
of insect-borne diseases, attacks by wildlife, limited access pathways into the forest, etc.). Thus, few
opportunities exist to sample soils in the Amazon that are still relatively unknown. Associating
VIS-NIR spectral data to soil types, landforms characterized by specific terrain features, and vegetation
classes offer new avenues to complement and enhance traditional labor-intensive soil assessments.
Proximal soil sensing via VIS-NIR has been suggested to provide more comprehensive digital soil
models, specifically if they are combined with aboveground landscape features, such as vegetation
types, ecotypes or biome classes, often derived from remote sensing [1,13]. The objective of the study
was to evaluate the performance of VIS-NIR for the prediction of a suite of soil chemical and physical
properties in the Central Amazon, Brazil.

2. Materials and Methods

2.1. Study Area

The sample set consisted of 434 soil samples from the Central region of the Amazon state, Brazil
(Figure 1). The study site is located in the Urucu municipality. The area is located within the Içá
Geologic Formation and encompasses an area of 80 km2 [14]. The climate is equatorial (Af, according
Remote Sens. 2017, 9, 293 3 of 22

to Köppen climate classification), with the temperature of the coldest month greater than 20 ◦ C,
and mean annual precipitation of 2500 mm, with no pronounced dry period.
Remote Sens. 2017, 9, 293 3 of 22

Figure 1. Location and shape of the study area in the Central Amazon, Brazil.
Figure 1. Location and shape of the study area in the Central Amazon, Brazil.
The Içá Geologic Formation is part of the Solimões Sedimentary Basin, which encompasses an area
The Içá Geologic Formation is part of the Solimões Sedimentary Basin, which encompasses an
of about 450,000 km2 . The basin contains rocks of Paleozoic age, covered by deep sedimentary rocks of
area of about 450,000 km2. The basin contains rocks of Paleozoic age, covered by deep sedimentary
Cretaceous to Quaternary origin [15]. In general, the lithology is composed of sandstones, siltstones
rocks of Cretaceous to Quaternary origin [15]. In general, the lithology is composed of sandstones,
and claystones
siltstones deposited under
and claystones high-energy
deposited underhydrologic
high-energyconditions
hydrologicand arid climate
conditions [16].
and arid Soil orders
climate [16].
in the area include: Argisols, Spodosols, Neosols, Planosols and Cambisols (Table 1).
Soil orders in the area include: Argisols, Spodosols, Neosols, Planosols and Cambisols (Table Parent material,
1).
relief and local
Parent climaterelief
material, are heterogeneous
and local climateinare
theheterogeneous
Amazon region, thus
in the forming
Amazon manythus
region, types of soils
forming manywith
diversetypes
properties, depths,
of soils with drainage
diverse characteristics,
properties, and so
depths, drainage on. Most soils
characteristics, andhave low
so on. chemical
Most fertility,
soils have low
with low activity clays (1:1 phyllosilicates and Fe and Al oxy-hydroxides, predominantly), and high
chemical fertility, with low activity clays (1:1 phyllosilicates and Fe and Al oxy-hydroxides,
predominantly), and high Al content.
Al content.
Remote Sens. 2017, 9, 293 4 of 22

Table 1. Number of soil profiles (n), and frequency of soil suborders, according to the Brazilian Soil
Classification System (SiBCS) and Soil Taxomony.

SiBCS Soil Taxonomy n Frequency (%)

Yellow Argisols Oxyaquic Hapludults 27 28
Red Argisols Typic Hapludults 2 2
Red-Yellow Argisols Typic Hapludults 21 22
Greyish Argisols Typic Endoaquults 3 3
Haplic Cambisols Typic Dystrudepts 39 41
Spodosols Humods 1 1
Quartzarenic Neosols Quartzipsamments 2 2
Haplic Planosols Aquults 1 1
Total 96 100

2.2. Soil Sampling and Laboratory Analysis

Between the years of 2008 and 2009, a soil survey was conducted in the Geólogo Pedro de Moura
Oil Province, close to the Urucu River, resulting in a detailed soil map (1:10,000) [17], which covers an
area of 80 km2 (Figure 1; Table 1). Throughout the soil survey, 96 soil profiles (Table 1) were described
and sampled by horizon, totaling 434 horizons/samples. Due to the access limitations imposed by the
dense native vegetation, sampling sites were spread across, and restricted to, the region surrounding
the access roads along a pipeline of the Brazilian Petroleum Corporation (Petrobras). The pipeline
is about 120 km long and spans longitudinally across the Içá Geologic Formation, which is part of
the Solimões Geologic Domain. The soils were classified according to the Brazilian Soil Classification
System [18], and Soil Taxonomy [19], respectively, and comprised five soil orders according to the
Brazilian system (Table 1).
The soil samples were air dried, milled and then passed through a 2-mm sieve. Chemical and
physical analyses were performed according to [20]. Measured soil chemical properties included
pH (in water, soil/solution ratio of 1:2.5), exchangeable cations (Ca, Mg, Al and H extracted using
1 N KCl and determined titulometrically; and K and Na extracted using diluted HCL and measured
using a flame photometer), available phosphorus (P) determined using the colorimetric method [21],
and organic carbon (SOC) determined by wet combustion [22]. The sum of bases (SB = Ca + Mg +
Na + K), cation exchange capacity (CEC = SB + (H+Al)), percentage of base saturation (V = 100 ×
SB/CEC), and percentage of Al saturation (m = 100 × Al/[Al + SB]) were calculated from the chemical
analytical results.
The pipette method was used for soil particle size analysis to measure the total (dispersed in
0.1 N NaOH) and natural clay (dispersed in water) contents [20]. The sand content was separated
by sieving (0.53-mm sieve) and the silt fraction was calculated by difference from the total soil mass.
The following indices were calculated: silt/clay ratio (S/C), and degree of flocculation (F = 100 × [total
clay − natural clay]/total clay).

2.3. Laboratory Spectral Analysis and Pre-Processing

Laboratory-based VIS-NIR spectral measurements were obtained using a QualitySpec® Pro
spectroradiometer (Analytical Spectral Devices Inc., Boulder, CO, USA) with a spectral resolution of
10 nm and sampling interval of 1 nm in the spectral range of 350–2500 nm. In preparation for scanning,
the soil samples were thoroughly mixed and placed into 47-mm wide Petri dishes forming a 5-mm
thick layer. The Petri dishes were placed in an oven at 45–50 ◦ C for 24 h to equalize moisture, and then
in a desiccator to cool down prior to analysis.
For each soil sample, four spectral measurements were obtained by rotating the Petri dish by
90◦ and then averaged in order to obtain a representative spectrum. Each spectral measurement was
the average of 100 internal replicate scans made by the instrument. Soil samples were scanned in
Remote Sens. 2017, 9, 293 5 of 22

sets of ten. Prior to scanning each set, a white reference scan was acquired from white Spectralon®
(LabSphere, North Sutton, NH, USA).
Forty-one pre-processing methods were compared to improve soil properties predictions.
The pre-processing treatments were applied using the ‘signal’ and ‘pls’ R packages [23]. The treatments
included multiplicative scatter correction (MSC), standard normal variate transformation (SNV),
pseudo-absorbance transformation (log[1/reflectance]), and Savitzsky-Golay (SG) smoothers, 1st
and 2nd derivatives using different polynomial degrees and window sizes, ranging from 3 to 11.
Multiplicative scatter correction was applied after the dataset was split into calibration and validation
sets. The details about these spectral transformations can be found in [23]. After the application of
treatments, the dimensionality of the spectra was reduced by averaging over 10-nm bands. Finally,
the spectral range included in the analysis was reduced slightly to exclude potential noise at the limits
of the detectors. The ranges of 350–399, 986–1015, 1786–1815, and 2476–2500 nm were thus removed
from the spectra.

2.4. Statistical Analysis

Descriptive statistics were derived to characterize the soil data set variability and evaluate
outliers, as well as to assess data normality. In addition, linear correlation analysis was
performed among transformed soil properties with 95% confidence level to understand their
interrelationships. The normality of the data was evaluated by the skewness and kurtosis coefficients,
and Kolmogorov-Smirnov test. For data without normal distribution, the Box-Cox transformation [24]
was applied using the software Action Stat 2.4 [25] to approximate normal distribution, and its inverse
function used to back-transform the predicted values before external validation. For non-negative
values of the variable x,s the Box-Cox transformation is defined as (Equations (1) and (2)):

xT = (xβ − 1)/β, for β 6= 0 (1)

xT = ln(x), for β = 0 (2)

where: xT is the transformed value of x, and β is the transformation parameter.

Prior to regression analysis using PLSR [26], the dataset (434 samples) was randomly split into
calibration (70% of the samples, 304 samples) and validation (30%, 130 samples) sets. The calibration
set was used to create the regression models and the validation set was used to independently validate
the models. The performance of the models was evaluated by the coefficient of determination (R2 ), root
mean squared error (RMSE), residual prediction deviation (RPD), ratio of performance to inter-quartile
range (RPIQ), and bias (Equations (3)–(7)):
n n
R2 = ∑ (ŷi − y)2 / ∑ (yi − y)2 (3)
i =1 i =1
s
n
RMSE = ∑ (ŷi − yi )2 /n (4)
i =1

RPDval = sdval /RMSEval (5)

RPIQval = Q3 − Q1/RMSEval (6)

Bias = y − ŷi (7)

where: ŷi is the predicted value of the ith observation, y is the mean observed value, yi is the observed
value of the ith observation, n is the number of samples, sdval is the standard deviation of the validation
set, RMSEval is the RMSE of validation, and Q3 and Q1 are 3rd and 1st quartiles of the validation
set, respectively.
Remote Sens. 2017, 9, 293 6 of 22

The six levels of interpretation of the RPD given by [27] was adopted, as follows: RPD < 1.0
indicates very poor predictions, unsuitable for analysis; 1.0 < RPD < 1.4 indicates poor predictions;
1.4 < RPD < 1.8 indicates fair predictions, suitable for assessment and correlation; 1.8 < RPD < 2.0
indicates good predictions, suitable for quantitative assessment; 2.0 < RPD < 2.5 indicates very good,
quantitative predictions; and RPD > 2.5 indicates excellent predictions.
The PLSR models were derived using the ‘pls’ package in R. The maximum number of latent
variables was set at 20 and the type of model used was the classical orthogonal scores algorithm [28].
Ten-fold cross-validation was used to determine the optimal number of latent variables to be included
as predictors in the models based on the RMSE of calibration.

2.5. PLSR-VIP Method

In order to assess the influence of each VIS-NIR reflectance band (explanatory variable) on the
model results, we calculated the VIP metric for each band, as described by [10] and implemented
by [29] (Equations (8) and (9)). For each variable y, the VIP was calculated by:
v
h 2 ! h
wjk
u 
∑ ∑ SS(bk tk )
u
V IPj = t p SS(bk tk ) / (8)
k =1
kwk k k =1

SS(bk tk ) = bk2 t0k tk (9)

where j is the index of the explanatory variables, p is the number of explanatory variables, h is the
number of latent variables, SS is the sum of squares, bk is the y-scores for the k-th latent variable, t is
the loading scores for the k-th latent variable, wjk is the k-th value for the j-th explanatory variable
from the weight matrix, and wk is the weights for the k-th latent variable.
Essentially, the numerator contains the explained sum of squares of y by the PLSR model, and the
denominator contains the total sum of squares of y. A spectral band is then considered important
in the model if its VIP score is considerably large. In this study, we used the VIP threshold of 1 put
forth by [10].

3. Results

3.1. Descriptive Statistics and Correlations among Soil Properties

The descriptive statistics of the soil chemical and physical properties are shown in Table 2.
All variables showed a non-normal distribution according to the Kolmogorov Smirnov test, and the
following variables were transformed to approximate normality: sand, silt, clay, F, pH, Al, H+Al, P, SB,
and m. The β parameter values of the Box Cox transformations are also shown in Table 2.
Soil particle size contents showed a predominance of sand and silt fractions, reflecting the
characteristics of the parent material (Table 2). The base saturation was low (mean: 19%), whereas the
Al (mean: 4 cmolc ·kg−1 ) and H+Al (mean: 8 cmolc ·kg−1 ) contents were high, which are characteristic
of these tropical acidic soils. This is the result of a combination of nutrient-poor parent materials, high
rainfall in the tropical rainforest, and low nutrient retention capacity, since the properties affecting
nutrient retention are also low [30]. This was confirmed by the low CEC (mean: 9.6 cmolc ·kg−1 ),
the dominance of Fe and Al oxides and kaolinite in the clay fraction, the low SOC (mean: 7.99 g·kg−1 ),
and the low pH (mean: 4.5) of these soils (Table 2).
In terms of the linear correlations among soil properties, the SOC was significantly correlated
(p < 0.05) to chemical properties, including H (correlation of 0.67), H+Al (0.51), pH (−0.53), and others
(Table 3). Exchangeable Ca and Mg were strongly correlated to SB (0.86 and 0.70, respectively),
V and m. As expected, exchangeable Al and H+Al were negatively correlated with V (−0.65 and −0.58,
respectively), and Al was strongly correlated with m (0.79). The clay content, showed high correlations
with chemical properties representing acidity, including Al (correlation of 0.70) and m (0.70), which
confirms the dominance of Al in the cation exchange sites in these soils (the average Al saturation was
68% (Table 1). The clay content also showed a high negative correlation (−0.77) with S/C.
Remote Sens. 2017, 9, 293 7 of 22

Table 2. Descriptive statistics of the soil properties.

Soil Property Min. Mean Max. Median SD Variance Skewness Kurtosis β

Sand (g·kg−1 ) 22 397 884 385 177.5 31,512.3 0.42 −0.27 0.58
Silt (g·kg−1 ) 50 344 660 341.5 118.8 14,122.8 0.04 −0.02 0.93
Clay (g·kg−1 ) 10 257 640 251.5 133.1 17,720.2 0.24 −0.68 0.68
F (%) 2 58 100 56 25.8 666.9 −0.02 −1.09 0.83
S/C (unitless) 0.1 2.0 13.2 1.4 1.9 3.65 2.58 8.27 -
pH (unitless) 3.2 4.5 6.5 4.7 0.4 0.20 0.04 0.63 0.93
Ca (cmolc ·kg−1 ) 0.2 1.0 3.2 0.8 0.6 0.39 0.77 −0.44 -
Mg (cmolc ·kg−1 ) 0.1 0.56 2.2 0.5 0.4 0.15 1.59 2.85 -
H (cmolc ·kg−1 ) 0.1 4.0 63.5 2.5 5.0 25.26 5.39 48.93 -
Al (cmolc ·kg−1 ) 0.1 4.0 12 3.8 1.9 3.80 0.38 0.16 0.73
H+Al (cmolc ·kg−1 ) 0.35 8.0 66.5 7.4 5.2 27.32 4.45 39.05 0.33
P (mg·kg−1 ) 0 1.37 13 1 1.7 3.00 2.48 9.13 2.50
SOC (g·kg−1 ) 0.1 7.99 105.6 6.2 8.1 65.9 5.45 51.74 -
CEC (cmolc ·kg−1 ) 1 9.6 69.6 8.8 5.6 31.56 4.04 32.76 -
SB (cmolc ·kg−1 ) 0.3 30.6 2924 1.4 251.2 63,126.4 8.96 82.54 −0.48
V (%) 3 19 100 17 11.7 138.1 2.66 12.18 -
m (%) 7 68 96 72 18.2 332.2 −0.99 0.70 2.04
Min., minimum; Max., maximum; SD, standard deviation; β, Box-Cox transformation parameter; F, degree of flocculation; S/C, silt/clay ratio; SOC, soil organic carbon content; CEC,
cation exchange capacity; SB, sum of bases; V, percentage of base saturation; m, percentage of Al saturation.
Remote Sens. 2017, 9, 293 8 of 22

Table 3. Linear correlation coefficients among soil properties, with significant correlations (p < 0.05) highlighted in bold.

Properties Sand Silt Clay F S/C pH Ca Mg SB Al H H+Al CEC V m P SOC

Sand (g·kg−1 ) 1.00
Silt (g·kg−1 ) −0.64 1.00
Clay (g·kg−1 ) −0.74 0.02 1.00
F (%) −0.07 0.09 0.02 1.00
S/C (unitless) 0.28 0.43 −0.77 0.03 1.00
pH (unitless) −0.14 −0.08 0.19 −0.23 −0.11 1.00
Ca (cmolc ·kg−1 ) 0.24 0.01 −0.30 −0.03 0.24 −0.37 1.00
Mg (cmolc ·kg−1 ) 0.20 0.11 −0.35 0.09 0.32 −0.32 0.52 1.00
SB (cmolc ·kg−1 ) 0.19 0.07 −0.29 0.00 0.26 −0.38 0.86 0.70 1.00
Al (cmolc ·kg−1 ) −0.64 0.16 0.70 0.11 −0.50 −0.09 −0.13 −0.21 −0.17 1.00
H (cmolc ·kg−1 ) 0.16 0.10 −0.26 0.13 0.19 −0.50 0.43 0.42 0.43 0.00 1.00
H+Al (cmolc ·kg−1 ) −0.17 0.16 0.10 0.21 −0.07 −0.50 0.31 0.27 0.29 0.51 0.79 1.00
CEC (cmolc ·kg−1 ) −0.15 0.17 0.06 0.19 −0.02 −0.51 0.47 0.41 0.45 0.47 0.80 0.96 1.00
V (%) 0.39 −0.08 −0.44 −0.16 0.35 0.06 0.49 0.43 0.54 −0.65 −0.26 −0.58 −0.44 1.00
m (%) −0.56 0.06 0.70 0.07 −0.55 0.17 −0.61 −0.62 −0.65 0.79 −0.26 0.17 0.06 −0.79 1.00
P (mg·kg−1 ) 0.31 −0.13 −0.27 −0.03 0.14 −0.18 0.09 0.06 0.07 −0.20 0.26 0.15 0.12 −0.01 −0.20 1.00
SOC (g·kg−1 ) 0.26 0.10 −0.39 0.14 0.32 −0.53 0.50 0.47 0.51 −0.13 0.67 0.51 0.52 0.09 −0.42 0.33 1.00
F, degree of flocculation; S/C, silt/clay ratio; SB, sum of bases; CEC, cation exchange capacity; V, percentage of base saturation; m, percentage of Al saturation; SOC, soil organic
carbon content.
Remote Sens.Sens.
Remote 2017, 9, 293
2017, 9, 293 9 of 922of 22

3.2. 3.2. Qualitative

Qualitative Description
Description of ofthe
theSoil
SoilSpectra
Spectra

TheThe VIS-NIR
VIS-NIR spectral
spectral reflectancecurves
reflectance curvesof
of the
the main
main soil
soilorders
ordersininthe
thestudy
studysite areare
site presented in in
presented
Figure 2. In a soil survey, the properties of different soil horizons are important for
Figure 2. In a soil survey, the properties of different soil horizons are important for soil characterization soil
andcharacterization and the
classification, thus, classification, thus, the spectral
spectral reflectance reflectance
of different of different
soil horizons soil horizons
are presented. are
In general,
presented. In general, the different soil orders showed similar spectral signatures in the VIS-NIR
the different soil orders showed similar spectral signatures in the VIS-NIR region, except for the
region, except for the Spodosols. In addition, in each soil class, the curve shape and reflectance
Spodosols. In addition, in each soil class, the curve shape and reflectance intensity was similar across
intensity was similar across horizons (Figure 2). The soil spectra of all soil orders showed prominent
horizons (Figure 2). The soil spectra of all soil orders showed prominent absorption features at 1400,
absorption features at 1400, 1900 and 2200 nm, however for the Spodosols these absorption features
1900were
andless
2200 nm, however for the Spodosols these absorption features were less evident.
evident.

Figure 2. VIS-NIR spectral curves of the horizons of a Red Argisol (A), Yellow Argisol (B), Greyish
Figure 2. VIS-NIR spectral curves of the horizons of a Red Argisol (A), Yellow Argisol (B), Greyish
Argisol (C), Red Cambisol (D), Neosol (E), and Spodosol (F).
Argisol (C), Red Cambisol (D), Neosol (E), and Spodosol (F).
Differences in the absorption peaks were observed between the soil horizons. For example,
Differences
goethite showsinstrong
the absorption
absorption peaks were
features nearobserved
480 and 900between the soil
nm (Figure horizons.
2). The 900-nm Forbandexample,
was
more evident in the Bt
goethite shows strong absorption features near 480 and 900 nm (Figure 2). The 900-nm band was in
1 and Bt2 -horizons of Argisols and Cambisols. A-horizons of all soil orders more
the study
evident in thesite
Bt1didandnotBthave prominent
2 -horizons absorption
of Argisols andfeatures in these
Cambisols. typical mineral-related
A-horizons VIS-NIR
of all soil orders in the
regions.
study site did not have prominent absorption features in these typical mineral-related VIS-NIR regions.
The number of selected wavelengths (bands) and its distribution varied strongly depending on
the pre-processing method that was used (Table 4). Overall, the best pre-processing methods, based
on the R2, RMSE, RPD and RPIQ, were Savitzky Golay smoothing and derivatives, which were chosen
for ten out of the seventeen soil properties (Table 4).
Remote Sens. 2017, 9, 293 10 of 22

The number of selected wavelengths (bands) and its distribution varied strongly depending on
the pre-processing method that was used (Table 4). Overall, the best pre-processing methods, based on
the R2 , RMSE, RPD and RPIQ, were Savitzky Golay smoothing and derivatives, which were chosen for
ten out of the seventeen soil properties (Table 4).

3.3. Predictions of Soil Chemical and Physical Properties

Clay content was predicted with the highest accuracy (R2 : 0.78, RPD: 2.14), followed by soil
organic carbon (R2 : 0.71, RPD: 1.84) (Table 4). Sand, S/C, H, Al, H+Al, CEC, m and V predictions were
moderately well predicted from VIS-NIR spectra. H, Al, H+Al and m had a R2 of 0.59–0.75 and RPD of
1.4–1.8. V value and CEC had a R2 of 0.50 and 0.68, RPD of 1.40 and 1.17, respectively. VIS-NIR also
indicates limitations to predict specific soil properties, such as Ca, Mg, P, pH, SB, silt and F, with RPD
between 1.0 and 1.4 (Table 4). The observed versus predicted values for soil chemical and physical
properties are shown in Figure 3.

Table 4. Validation results of the best partial least squares regression models according to the best fitted
pre-processing method.

Soil Property Pre-Processing R2 RMSE RPD RPIQ Bias

Sand (g·kg−1 ) SG.Q.3.0 0.62 114.74 1.61 2.05 −17.37
Silt (g·kg−1 ) SNV 0.36 95.15 1.25 1.68 3.20
Clay (g·kg−1 ) SG.L.3.1 0.78 61.70 2.14 3.35 −1.75
S/C (unitless) SG.Q.9.1 0.62 1.09 1.63 1.42 −0.03
F (%) SG.C.5.1 0.16 22.83 1.08 1.73 −1.61
pH (unitless) SNV 0.40 0.34 1.18 1.49 0.03
Ca (cmolc ·kg−1 ) SG.C.5.0 0.40 0.52 1.26 1.92 −0.08
Mg (cmolc ·kg−1 ) SG.L.3.1 0.33 0.34 1.21 1.46 −0.05
H (cmolc ·kg−1 ) MSC 0.79 4.40 1.45 0.70 0.32
Al (cmolc ·kg−1 ) LOG 0.63 1.22 1.62 2.36 −0.18
H+Al (cmolc ·kg−1 ) SNV 0.70 3.61 1.80 1.08 0.15
P (mg·kg−1 ) SG.L.9.1 0.11 1.98 1.05 1.01 −0.32
SOC (g·kg−1 ) SNV 0.71 5.69 1.84 1.05 0.07
CEC (cmolc ·kg−1 ) SNV 0.68 5.86 1.17 0.82 0.75
SB (cmolc ·kg−1 ) SG.L.11.2 0.17 296.39 1.00 0.00 −35.55
V (%) SG.L.3.0 0.50 9.13 1.40 1.31 −1.51
m (%) SG.C.7.1 0.59 11.65 1.57 2.10 −0.38
R2 , coefficient of determination; RMSE, root mean square error; RPD, residual prediction deviation; RPIQ, ratio of
performance to inter-quartile range; S/C, silt/clay ratio; F, degree of flocculation; SOC, soil organic carbon content;
CEC, cation exchange capacity; SB, sum of bases; V, percentage of base saturation; m, percentage of Al saturation;
SG.Q.3.0, Savitzky Golay, quadratic, window: 3, derivative: 0; SNV, standard normal variate; SG.L.3.1, Savitzky
Golay, linear, window: 3, derivative: 1; SG.Q.9.1, Savitzky Golay, quadratic, window: 9, derivative: 1; SG.C.5.1,
Savitzk Golay, cubic, window: 5, derivative: 1; SG.C.5.0, Savitzky Golay, cubic, window: 5, derivative: 0; SG.L.3.1,
Savitzky Golay, linear, window: 3, derivative: 1; MSC, multiplicative scatter correction; LOG, log(1/reflectance);
SG.L.9.1, Savitzky Golay, linear, window: 9, derivative: 1; SG.L.11.2, Savitzky Golay, linear, window: 11, derivative: 2;
SG.L.3.0, Savitzky Golay, linear, window: 3, derivative: 0; SG.C.7.1, Savitzky Golay, cubic, window: 7, derivative: 1.
Remote Sens. 2017, 9, 293 11 of 22
Remote Sens. 2017, 9, 293 11 of 23

Figure 3. Validation results for observed vs. predicted values for soil chemical and physical properties
Figure 3. Validation results for observed vs. predicted values for soil chemical and physical properties
including: sand content (g·kg−1); silt content (g·kg−1−);1 clay content (g·kg−1);−S/C (silt/clay ratio); F
including: sand content (g·kg−1 ); silt content −1 (g·kg ); clay content (g·kg 1 ); S/C (silt/clay ratio);
(flocculation degree); pH; Ca content (cmolc·kg ); Mg content (cmolc·kg−1); H content (cmolc·kg−1); Al
F (flocculation degree); pH; Ca content (cmolc ·kg −1 Mg content (cmol ·kg−1 ); H content (cmol ·kg−1 );
content (cmolc·kg−1); H+Al content (cmolc·kg −1); P); content (cmolc·kg−1c); SOC; CEC (cmolc·kg−1c); SB
Al(cmol
content (cmol · kg − 1 ); H+Al content (cmol · kg −1 ); P content (cmol ·kg−1 ); SOC; CEC (cmol ·kg−1 );
c c c
c·kg−1); V (%); m (%). The solid line is the line of regression and the dotted lines is the 1:1 line.
c
SB (cmolc ·kg−1 ); V (%); m (%). The solid line is the line of regression and the dotted lines is the 1:1 line.
Remote Sens. 2017, 9, 293 12 of 22

3.4. Explanatory Variable Importance

Remote Sens. 2017, 9, 293 12 of 23
The VIP scores from the PLSR models for the 15 soil properties are presented in Figure 4. The sum
of bases
3.4.(SB) and degree
Explanatory of flocculation
Variable Importance (F) were not included in the VIP analysis due to poor model
performance. The VIP scores from the sand PLSR model are greater than one in the spectral regions
The VIP scores from the PLSR models for the 15 soil properties are presented in Figure 4. The
400–830,
sum 1890–1980, 2110–2240
of bases (SB) andof2330–2470
and degree flocculationnm,
(F) with
were a peak
not at 740innm,
included the double peaks
VIP analysis at to
due 560/610
poor nm
and 1900/1940
model performance. The VIP scores from the sand PLSR model are greater than one in the spectralmodel
nm, and a triple peak at 2150/2200/2230 nm. The VIP scores for the clay
are greater
regionsthan one 1890–1980,
400–830, in the spectral regions
2110–2240 500–610, nm,
and 2330–2470 760–850, 1370–1400,
with a peak 1420–1430,
at 740 nm, double peaks1870–1900,
at
and 2130–2220
560/610 nm nm.
andThe VIP peak
1900/1940 nm, around 800peak
and a triple nm at may be linked tonm.
2150/2200/2230 hematite
The VIPand/or
scores forgoethite
the claywhile
the VIPmodel
peaks arearound
greater 1380/1420
than one in the
andspectral regions 500–610,
2150/2190/2210 nm 760–850, 1370–1400,
are likely 1420–1430,
the influence 1870–1900,
of –OH and Al-OH
and 2130–2220 nm. The VIP peak around 800 nm
groups, respectively, on the model from kaolinite and illite. may be linked to hematite and/or goethite while the
VIP peaks around 1380/1420 and 2150/2190/2210 nm are likely the influence of –OH and Al-OH
The silt VIP score graph has features of both the sand and clay VIP graphs. Moreover, the silt/clay
groups, respectively, on the model from kaolinite and illite.
VIP score graph highly resembles the clay VIP graph, indicating the importance of clay mineral features
The silt VIP score graph has features of both the sand and clay VIP graphs. Moreover, the
on its prediction.
silt/clay VIP score graph highly resembles the clay VIP graph, indicating the importance of clay
For chemical
mineral predictions,
features the VIP graph for SOC shows scores greater than one in the spectral
on its prediction.
regions 400–500, 540–890,
For chemical 1390–1410,
predictions, the 2170–2220,
VIP graph for and 2350–2470
SOC nm.greater
shows scores The VIP scores
than one infor
thethe remaining
spectral
regions 400–500,
soil properties (V, pH,540–890,
Al and1390–1410,
combined2170–2220, and 2350–2470
exchangeable H and Al) nm.contain
The VIP features
scores for found
the remaining
in the sand,
soilSOC
clay, and properties (V, pH,
VIP score Al and
plots, combined exchangeable
highlighting the complexHrelationships
and Al) containthese
features found inhave
properties the sand,
with soil
clay, and SOC VIP score plots, highlighting the complex relationships these properties have with soil
mineralogy and chemistry. Other soil chemical properties do not exhibit spectral response features.
mineralogy and chemistry. Other soil chemical properties do not exhibit spectral response features.

Figure 4. Cont.
Remote Sens. 2017, 9, 293 13 of 22
Remote Sens. 2017, 9, 293 13 of 23

Figure 4. VIP scores from PLSR model for soil chemical and physical properties in the Central
Figure 4. VIP scores from PLSR model for soil chemical and physical properties in the Central Amazon.
Amazon.

4. Discussion
4. Discussion

4.1. Correlations between

4.1. Correlations SoilSoil
between Properties
Properties
The matrix
The matrix of linear
of linear Pearson
Pearson correlations
correlations (Table
(Table 3) 3) showedthat
showed thatchemical
chemical properties
properties suggesting
suggesting soil
soil acidity, such2 as H (R 2: 0.67), H+Al (R2: 0.51), pH H2O (R2: −0.53) and m (R2: −0.42) had considerable
2 2 2
acidity, such as H (R : 0.67), H+Al (R : 0.51), pH H2 O (R : −0.53) and m (R : −0.42) had considerable
correlation with SOC. CEC (0.52) and SB (0.51) also correlated with SOC suggesting the important
correlation with SOC. CEC (0.52) and SB (0.51) also correlated with SOC suggesting the important
role of organic content at the charge generation of tropical soils. It is well recognized that soil organic
role ofmatter
organic content at the charge generation of tropical soils. It is well recognized that soil organic
has a substantial contribution to the CEC of the whole soil and to the retention of exchangeable
mattercations
has a substantial contribution
[30]. Humic substances to the
(fulvic CEC
acids, of the
humic whole
acids and soil andare
humin) to formed
the retention of exchangeable
contributing to the
cationssoil
[30]. Humic
acidity substances
through their high (fulvic
amountsacids, humic
of acidic acids and
functional humin)
groups. Theseare formedgroups,
functional contributing
such as to the
soil acidity through
the –COOH their high
(carboxylic) andamounts
the –OHof acidic functional
(phenolic groups.HThese
groups), dissociate functional
+ (contributing groups,
to soil such as
acidity)
and thus
the –COOH exchangeable
(carboxylic) andcations can be(phenolic
the –OH chemicallygroups),
bound [31].dissociate H+ (contributing to soil acidity)
Exchangeable H
and thus exchangeable and H+Al
cations can were strongly correlated
be chemically bound [31].with CEC (R2: 0.80 and 0.96, respectively).
It is common to have high Hand Al content in the Amazon Forest soils (Table 3). Al content had a
Exchangeable H and 2H+Al were strongly correlated with CEC (R2 : 0.80 and 0.96, respectively).
positive correlation (R : 0.70) with clay content and a negative correlation with SOC. Amazon soils
It is common to have high Hand Al content in the Amazon Forest soils (Table 3). Al content had a
positive correlation (R2 : 0.70) with clay content and a negative correlation with SOC. Amazon soils
are often highly weathered and therefore possess low plant-available nutrient contents [29]. 30 Basic
cations such Ca, Mg, Na and K are easily leached by the usually high precipitation (2500 mm/year)
Remote Sens. 2017, 9, 293 14 of 22

contributing to the lower CEC (mean 9.6 cmolc ·kg−1 ). Hand Al are preferably linked to the soil colloids
due to its lower ionic ray and higher valence, respectively.
Phosphorous presented low correlation with spectrally detectable ones (clay content, soil organic
carbon). Terra et al. [32] observed that the order of prediction modeling for other non-spectrally
detectable soil properties is dependent on their correlation with the detectable ones.
According to Terra et al. [32] soil properties directly detectable by VIS-NIR spectroscopy such as
clay, iron and aluminum oxides, hydroxide contents and SOC can be modeled by first-order predictions;
however, the order of prediction modeling for other non-spectrally detectable soil properties will be
dependent on their correlation with the detectable ones. For example, other properties indicating soil
acidity, fertility and mineralogy can be modeled by second-order or even third-order predictions due to
the significant correlation with clay and organic carbon content [33]. It is important to notice the role of
soil organic matter in generating charges in tropical soils even with low content and under weathering
conditions which have influence on the adsorption of ions and, consequently on their predictions.
The matrix of linear Pearson correlations (Table 3) showed that SOC had considerable correlation with
H (r: 0.67), H+Al (r: 0.51), pH H2 O (r: −0.53), m (r: −0.42), CEC (r: 0.52) and SB (r: 0.51).

4.2. Predictions of Soil Chemical Properties

Soil organic carbon showed one of the best predictions among the soil properties in our study
with a RPD of 1.84, RMSE of 5.69 g·kg−1 , RPIQ of 1.05, and R2 of 0.71. In [34],a literature review
showed that SOC predicted with PLSR had a RPD ranging from 0.23 to 5.75, bias from −0.45 to 1.6,
and the highest RMSE was 9.0 g·kg−1 . Additionally, when SOC was predicted using standard normal
variate (SNV) pre-processing, the following results were observed: RMSE of 5.7–6.8, bias of 0.6–1.9 and
RPD of 2.2–2.7 [34]. Viscarra Rossel et al. [27] reported average R2 for SOC prediction as 0.81 in the
near infrared (NIR) region, 0.78 in the VIS region and 0.96 in the MIR region. Although MIR spectra
generally produced more accurate results, especially for SOC, due to its stronger direct relation with
MIR spectral data produced by fundamental vibrations, the technology is more complex and expensive
than that used for VIS and NIR measurements [27]. Recently, Terra et al. [32] observed a R2 of 0.65 and
a RMSE of 0.16 for SOC predictions in the VIS-NIR region, for four states in the Brazilian tropical soils.
In our study SOC varied from 0.1 to 105.6 g·kg−1 (Table 2), with lowest SOC observed in Neosols,
Yellow Argisols and Greyish Argisols, and highest SOC observed in Red Argisols and Yellow Argisols.
These results are in agreement with other findings in this region [2]. The highest SOC values were
observed in the O and A-horizon, due to the high litter input by the forest. All the outliers, reducing
SOC prediction, were observed in the O and A-horizon (Figure 3). The presence of non-degraded
or partly degraded organic material in the topsoil can increase the prediction uncertainty [30–35].
The model was more efficient to predict in the subsurface horizons due to more humified (humic acids)
organic matter that has absorption in the VIS-NIR region. Therefore, stratification of soil order and
horizons can produce more a homogeneous group and may improve the model performance [2].
Soil properties suggesting acidity, such as m, H, Al and H+Al performed moderately well, with
2
R of 0.59–0.75 and RPD of 1.4–1.8 (Table 4). According to the six level interpretations of RPD in [27],
these models/predictions were classified as fair and may be used for assessment and correlation.
Terra et al. [32] predicted physical, chemical and mineralogical soil properties using VIS-NIR and MIR
spectroscopy, on 1259 soil samples from four Brazilian states. The authors observed fair predictions
only for potential acidity(R2 : 0.54, RPIQ: 2.01), while other predictions of acidity were unreliable in the
VIS-NIR region.
Other chemical properties suggesting soil reactivity and fertility, such as Ca, Mg, P, pH, and SB
could not be well predicted from the VIS-NIR spectra, with RPD between 1.0 and 1.4. On the other
side, the V value could be predicted moderately well (R2 : 0.50, RPD: 1.40) by VIS-NIR spectroscopy
in our study (Table 4). Terra et al. [32] could not predict well Ca, Mg, P, K, pH, SB and V value in the
VIS-NIR region for four States in the Brazilian soils. For instance, the P model in our study had an R2
Remote Sens. 2017, 9, 293 15 of 22

of 0.11, comparable to that presented by Janik et al. [36] (R2 of 0.07) and Araújo et al. [37] (R2 of 0.05)
using MIR spectra, whereas high R2 (0.81) was obtained by Daniel et al. [38] using VIS-NIR spectra.
The average R2 for CEC in our study was 0.68, a RPD of 1.17 and the RMSE was 5.86 (Table 4).
According to the six levels of interpretations of RPD given by [27], 1.0 < RPD < 1.4 indicates poor
predictions. Viscarra-Rossel [27] also observed a good R2 (0.73) for CEC prediction in the VIS-NIR and
0.82 in the MIR region in Australian soils. Terra et al. [32] also observed R2 values (0.72) very close to
this study of and RMSE of 0.14 for CEC prediction in Brazilian tropical soils. The calibration models
for P, K, and SOC did not provide good predictions for Amazon Dark Earths [37], showing very low
R2 and RPD from both MIR and VIS-NIR spectra. The reason why certain soil properties were or not
accurately predicted using VIS-NIR is that the fundamental molecular vibrations of soil components
occur in the mid-IR, while only their overtones and combinations are detected in the NIR [27]. Hence,
soil VIS-NIR spectra display fewer and much broader absorption features compared to MIR spectra.

4.3. Predictions of Soil Physical Properties

Clay content showed a good fit (R2 of 0.78), very good quantitative predictions (RPD of 2.14),
low bias (−1.75 g·kg−1 ), and an RMSE of 61.70 g·kg−1 . The modeling performance for clay and
sand in our study are in agreement with the results found by [32,39–41] which ranged from 0.51
to 0.86 (R2 ) and 31 to 120 g·kg−1 (RMSE) for both soil fractions. However, all these studies used
different soils, methodologies, prediction algorithms and soil properties were not back-transformed
in some situations. The low performance of the silt content prediction can be explained by the error
associated with the laboratory method. In this case, the silt content was computed after measuring
the clay and sand content. It means that the most part of the analytical error is computed in the silt
fraction. The silt/clay ratio was moderately well predicted in our study with an R2 of 0.62, RPD
of 1.63 and RMSE of 1.09 (Table 4). Most of the S/C ratio outliers (62%) belong to moderate to an
imperfectly drained soil (Figure 3). According to Bellon-Maurel and McBratney [34], high bias should
be avoided as it cannot be removed by averaging the measurements. Chang et al., Shepherd and Walsh,
Cozzolino and Moron [42–44] obtained good R2 (0.67, 0.78 and 0.86, respectively) for clay content
models from VIS-NIR spectra using principal components regression (PCR) models. Terra et al. [32]
found significantly higher performance for clay and sand content in the MIR region compared to the
VIS-NIR region in Brazilian tropical soils. Greater predictive performance for particle size is usually
observed in the MIR compared to the VIS-NIR region. It can be explained by the stronger interaction
between mid-infrared reflection spectra and soil particles by fundamental vibration processes when
compared to the VIS-NIR [27,39,40].

4.4. PLSR-VIP Method

The VIP scores from the PLSR model for 15 soil properties are presented in Figure 4. Sum of bases
(SB) and flocculation level (F) were not included due to poor model performance but soil phosphorus
was included to compare to other soil elements. Any spectral band with a VIP score greater than one is
thought to contribute to the model prediction [29].
The VIP scores from the sand PLSR model in the first region (400–830 nm) correspond to electronic
transition within the visible portion of the spectrum. Hematite has strong absorbance peaks at 400 and
855 nm and a reflectance peak at 750 nm, which gives its red color [40,45]. The high VIP score at 400 nm
and the peak at 740 nm likely indicates that the presence of hematite is contributing to sand model
performance. This would make sense since hematite would exist on sand particles as a coating agent.
The double peak at 560/610 nm is likely due to overall soil color as this region does not correspond
directly to mineralogical spectral features. The VIP score double peaks at 1890/1980 nm are related to
structural water and the triple peak at 2150/2200/2230 is due to Al-OH groups [45]. This indicates
that clay mineralogy also had an influence on the sand PLSR model. The incorporation of hematite
and clay mineral spectral features may be one reason the sand model performed more poorly than the
Remote Sens. 2017, 9, 293 16 of 22

clay model (R2 : 0.62 vs. 0.78). The other reason may be that quartz, the dominant mineral in the sand
fraction, does not have spectral features in the 400–2500 nm region.
The silt VIP score graph has features of both the sand and clay VIP graphs, perhaps indicating the
mixed mineralogy of this particle size fraction (combination of primary and secondary minerals) and
the difficulty of the PLSR model to predict it (R2 : 0.36). The silt/clay VIP score graph highly resembles
the clay VIP graph, indicating the importance of clay mineral features on its prediction.
For SOC, the first two regions are broadly related to soil color, primarily to organic matter (humic
acids), hematite, and goethite [45]. The VIP score peak at 1400 nm is due to water hydroxyl (–OH)
groups that may be adsorbed to soil organic matter. It is possible that clay mineral features (–OH from
kaolinite and illite) are acting as a proxy predictor for SOC as was observed by [45]. The VIP peak at
2200 nm appears to be related more to kaolinite/illite Al-OH groups rather than to organic functional
groups whereas the spectral region 2350–2470 nm corresponds to spectral absorption features of several
organic functional groups [45].
Other soil chemical properties like Ca, CEC, and H resemble the VIP scores for SOC potentially
indicating that SOC is an importance factor for these properties. CEC in highly weathered soils
typically results from organic matter, where carboxyl and alcohol groups deprotonate and contribute
to the CEC, rather than from clay minerals because Fe and Al oxides and, to a lesser extent, kaolinite
tend to become protonated and contribute more to the anion exchange capacity due to positive surface
charge. Ca would remain in soils with SOC, where the CEC would prevent it from being leached from
the soil. Exchangeable H also seems to be associated with SOC where it can protonate carboxyl and
alcohol sites.
However, the VIP scores for available soil P, exchangeable Mg and percentage of Al saturation (m)
resemble the VIP scores for clay suggesting that the clay fraction of the soil is influencing the models
for these soil properties. Soil P would exist as the phosphate anion (PO4 3− ) in soils that can adsorb
to anion exchange sites on Fe and Al oxides and kaolinite. Despite the poor performance, the PLSR
model was still able to extract the relationship between soil P and clay from the spectra. In contrast,
it would be expected that exchangeable Mg would follow the same pattern as Ca since they have
similar behavior in soil.
The reason why the clay fraction, namely the clay mineralogy, would influence the PLSR model is
not clear but exchangeable Mg does have a stronger negative relationship with clay than exchangeable
Ca (Table 3). It would also be expected that the percentage of Al saturation follows the pattern of SOC,
where most of CEC lies, but the clay-sized fraction and its mineralogy seems to be the main factor in
the PLSR model. From the linear correlation matrix, it is noted that m has a stronger relationship with
clay (0.70) than SOC (0.09) and the PLSR model may be taking advantage of that relationship.
The pH of soil is a result of the organic and inorganic components and this relationship has been
demonstrated via spectral modeling before [45]. The VIP graph for base saturation is complex, perhaps
showing the influence of sand, clay, and SOC on the model. The graphs for H+Al and Al show a
smaller influence from clay mineralogy with the visible region of the spectrum contributing most to
the model, likely due to the factors influencing soil color such as SOC and iron oxides.

4.5. Relationships between Spectral Reflectance and Soil Type

In general, the reflectance intensity increased from the surface to the deeper soil horizons in
all soil orders in the study site (Figure 2). Topsoil horizons have more soil organic matter, which
absorbs energy and promotes lower reflectance intensity throughout the entire spectrum [46–48].
The absorption features produced by the organic compounds occurred at 2316 and 2382 nm [47–49].
Spectral reflectance curves for Red Argisols presented the same shapes in all horizons, although
with different intensities, except for the 900 nm region. The curve concavity at 900 nm was sharp
only for the subsurface horizons (BA, Bt1 and Bt2 ), which may be attributed to the iron content in
the B horizons, as soil organic matter is masking the effect of the iron in the surface horizon [50–52].
According to Viscarra Rossel et al. [27], peaks near 900 nm may represent absorption caused by
Remote Sens. 2017, 9, 293 17 of 22

electronic transitions in goethite. Red Argisols (soil color 5YR) was located on the highest position of
the toposequence, followed by Yellow Argisols (soil color 10YR) located on the Tabular interfluves,
and then Greyish Argisols (low chrome) located on the footslopes (Figure 5). From Red Argisols to
Greyish Argisols there was a gradual reduction in the curve concavity at 900 nm in the subsurface
horizons. Again, this can be attributed to the different contents and forms of iron, which distinctly
affect the concavity in this region; crystalline iron forms present concavity, whereas amorphous iron
forms do not [46]. In fact, Greyish Argisols presented no concavity shape at 850–900 nm, since its
iron is in the reduced form (Fe2+ ). Absorptions due to electronic transition are primarily associated
with minerals that contain iron (e.g., hematite) and their fundamentals may be found in the VIS-NIR
region [27].
A-horizons in Red Argisols showed lower reflectance intensity compared to A-horizons of Yellow
and Greyish Argisols (Figure 4). The flooded lowland open tropical rainforest and upland open tropical
rainforest are the main vegetation types on Greyish Argisols, since their species are more adapted to
soil aeration restrictions, mainly at the surface. According to Ceddia et al. [14], the carbon stocks are
lower in Greyish Argisols, especially in the lower horizons, because the input of carbon from leaves,
trees, trunks and roots is lower, and is concentrated at the surface layers (Figure 4). For Cambisols,
the reflectance intensity increased (Figure 2d) from the surface (A-horizon) to the deeper soil horizons
(Bi3 ) because of the lower organic matter content in subsurface layers. The characteristic curve
concavity at 900 nm present in Argisols did not appear in any of the Cambisol horizons because of
their low iron contents.
All suborders in the study site showed a pronounced shoulder at 2200 nm, except for the Spodosols.
This shoulder is associated with the di-octahedral layers of the kaolinite mineral structure [52] and is
more pronounced in subsurface horizons, indicating greater proportions of 1:1 minerals. The Spodosol
spectra showed weak absorption peaks (Figure 2f). The AE, EA, E and EB horizons have high sand
contents with predominantly quartz in the sand fraction, which in turn do not have prominent
absorption features in the UV-VIS-NIR region [27]. Their intense fundamental vibrations occur in the
mid infrared around (10,000 nm) [53]. It is likely that sand particles (mostly quartz) act like a blank
template, diluting other components that control the reflectance of the soil [52].
In general, considering all soil properties studied, there was a consistent pattern for a given soil
property and a particular landscape position, soil order and depth in the model performance. For pH
value, silt content and S/C ratio, the model performed better in well-drained soils. The Spodosol and
Greyish Argisol order were considered outlier in the pH model, whereas for silt content and S/C ratio,
the Argisol was the outlier (Figure 3).
For soil chemical properties, exchangeable Ca and Mg and SOC content, the Argisol and Cambisol
classes were the outliers in the model performance (Figure 3). For SOC content, 60% of the outliers
belongs to well-drained sites (Yellow and Red-Yellow Argisol). These soil classes are also contributing
with higher SOC content. By the other side, for Ca and Mg content, the model performed worst in
moderate and poorly drained soils.
There was also a consistent pattern for a given soil property and a particular soil depth. Most of
the outliers (84%) were observed in the superficial depth (O and A-horizon), especially for T value and
SOC content. This is due to the presence of non-degraded or partly degraded organic material in the
topsoil, which increases the prediction uncertainty [34]. For phosphorous content, V value, S/C ratio,
pH and Al content, the B-horizon was the outlier. Therefore, stratification of soil order and horizons
could produce more homogeneous group and may improve the model performance [2].
 Remote Sens. 2017, 9, 293 18 of 22
Remote Sens. 2017, 9, x FOR PEER REVIEW 19 of 22

Figure 5. Schematic representation of the soil, relief and vegetation classes and the respective soils spectral data in the study site.
Figure 5. Schematic representation of the soil, relief and vegetation classes and the respective soils spectral data in the study site.
Remote Sens. 2017, 9, 293 19 of 22

We believe that this VIS-NIR soil study provides the first step towards spectral mapping in the
larger tropical Amazon region. The spectral fingerprinting of the highly weathered, hydric soils
in the Central Amazon allows discernment of soil properties that can be predicted from VIS-NIR
and those that still require traditional soil mapping using classical analytical lab-based methods in
the future. Understanding of the implicit relationships between VIS-NIR hyperspectral data and
specific soil properties will also support future remote sensing studies in this region as new sensor
technologies, filtering algorithms and noise removal (e.g., removal of canopy interference to map the
soil surface) emerge.

5. Conclusions
Diffuse reflectance spectroscopy is an effective technique with high applicability in quantitative
analysis of tropical Central Amazon soils, especially for prediction of properties useful in soil survey,
classification, fertility management, climate change monitoring and soil security. Soil properties
directly detectable by reflectance spectroscopy, such as clay and SOC content were predicted with the
highest accuracy. Sand, S/C ratio, H, Al, H+Al, CEC and m were moderately well predicted from
VIS-NIR spectra. VIS-NIR also indicates limitations to predict specific soil properties, such as Ca, Mg,
P, pH, SB, silt and F.
The very good performance of clay and the moderately performing of sand models using VIS-NIR
spectral data suggests that at least soil particle sizes can be efficiently replaced by DRS VIS-NIR. In the
same manner, SOC was also very well predicted by VIS-NIR spectroscopy with significance in soil
carbon assessments, global carbon cycling, global climate change and ecosystem service assessment.
This is profoundly important for the rapid and urgent demand for SOC stocks predictions in the
Amazon Forest that have not been reliably assessed at this point in time.
There was a consistent pattern for a given soil property and a particular landscape position, soil
order and soil depth in the model performance. For silt content, pH value and S/C ratio, the model
performed better in well-drained soils whereas for SOC content, the model performed better in
poorly-drained soils. Most of the outliers (84%) were observed in the superficial depth (O and
A-horizon), especially for T value and SOC content. Therefore, stratification of soil order and horizons
could produce more homogeneous group and may improve the model performance.
Finally, VIS-NIR and the methodology we tested is a powerful tool to be used for rapid and
cost-efficient assessment of soil properties in the Central Amazon and for generating datasets of soil
properties. Specifically, associating VIS-NIR spectral data to landforms, vegetation classes, and soil
types hold much promise for soil characterization, because above-ground landscape features can be
more readily mapped using remote sensing. We recommend the calibration and validation of these
soils spectral models to other landscapes that englobe the complexity of the Amazon biome.

Acknowledgments: The authors acknowledge Petróleo Brasileiro S.A. for the technical and financial support
(Petrobrás/UFRRJ/FAPUR Contract No. 0050.0036944.07.2). We also thank the Conselho Nacional de Desenvolvimento
Científico e Tecnológico (CNPq Project No. 249594/2013-7) and the Coordenação de Aperfeiçoamento de Pessoal
de Nível Superior (CAPES Project No. 1574-14-0) for the Post-Doctoral Scholarships granted to Pinheiro and
Ceddia. Moreover, they also appreciated all the support of the Pedometrics, Landscape Analysis and GIS
Laboratory, supervised by Sabine Grunwald, as well, Soil and Water Science Department, in University of Florida.
Author Contributions: Érika Pinheiro analyzed soil samples by visible and near-infrared diffuse reflectance
spectroscopy and wrote the article. Marcos Bacis Ceddia was the project supervisor and participated in all stages
of the article. He also described the soils profiles and collected soils samples in the Brazilian Amazon Forest.
Christopher M. Clingensmith was responsible for modeling algorithm coding, as well all data pre-processing
and statistical analysis. Sabine Grunwald contributed writing the article and with materials and analysis tools.
Gustavo M. Vasques contributed to the writing of the article and also in analyzing the spectral results and
their interpretation.
Conflicts of Interest: The authors declare no conflict of interest.
Remote Sens. 2017, 9, 293 20 of 22

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