Predicting and Mapping of Soil Organic Carbon

Using Machine Learning Algorithms in Northern

Iran
Mostafa Emadi 1, Ruhollah Taghizadeh-Mehrjardi 2,3, Ali Cherati 4, Majid Danesh 1, Amir
Mosavi 5,6,7,* and Thomas Scholten 2,8,9
1 Department of Soil Science, College of Crop Sciences, Sari Agricultural Sciences and Natural Resources
University, Sari 4818168984, Iran; [email protected] (M.E.); [email protected] (M.D.)
2 Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen,

Germany; [email protected] (R.T.-M.); thomas.scholten@uni-

tuebingen.de (T.S.)
3 Faculty of Agriculture and Natural Resources, Ardakan University, Ardakan 8951656767, Iran

4 Soil and Water Research Department, Mazandaran Agricultural and Natural Resources Research and

Education Center, AREEO, Sari 4849155356, Iran; [email protected]

5 Faculty of Civil Engineering, Technische Universität Dresden, 01069 Dresden, Germany

6 School of the Built Environment, Oxford Brookes University, Oxford, UK

7 Department of Informatics, J. Selye University, 94501 Komarno, Slovakia

8 CRC 1070 Ressource Cultures, University of Tübingen, 72070 Tübingen, Germany

9 DFG Cluster of Excellence “Machine Learning”, University of Tübingen, 72070 Tübingen, Germany

* Correspondence: [email protected]

Abstract: Estimation of the soil organic carbon (SOC) content is of utmost importance in
understanding the chemical, physical, and biological functions of the soil. This study proposes
machine learning algorithms of support vector machines (SVM), artificial neural networks (ANN),
regression tree, random forest (RF), extreme gradient boosting (XGBoost), and conventional deep
neural network (DNN) for advancing prediction models of SOC. Models are trained with 1879
composite surface soil samples, and 105 auxiliary data as predictors. The genetic algorithm is used
as a feature selection approach to identify effective variables. The results indicate that precipitation
is the most important predictor driving 14.9% of SOC spatial variability followed by the normalized
difference vegetation index (12.5%), day temperature index of moderate resolution imaging
spectroradiometer (10.6%), multiresolution valley bottom flatness (8.7%) and land use (8.2%),
respectively. Based on 10-fold cross-validation, the DNN model reported as a superior algorithm
with the lowest prediction error and uncertainty. In terms of accuracy, DNN yielded a mean
absolute error of 0.59%, a root mean squared error of 0.75%, a coefficient of determination of 0.65,
and Lin’s concordance correlation coefficient of 0.83. The SOC content was the highest in udic soil
moisture regime class with mean values of 3.71%, followed by the aquic (2.45%) and xeric (2.10%)
classes, respectively. Soils in dense forestlands had the highest SOC contents, whereas soils of
younger geological age and alluvial fans had lower SOC. The proposed DNN (hidden layers = 7,
and size = 50) is a promising algorithm for handling large numbers of auxiliary data at a province-
scale, and due to its flexible structure and the ability to extract more information from the auxiliary
data surrounding the sampled observations, it had high accuracy for the prediction of the SOC base-
line map and minimal uncertainty.

Keywords: soil organic carbon; carbon sequestration; machine learning; deep neural networks;
susceptibility; big data; mapping; soil informatics; geochemistry; remote sensing; deep learning;
data science; earth system science
1. Introduction
Soil organic carbon (SOC) is central to soil health as it plays a significant role in soil aggregation,
water holding capacity, cation/anion exchangeability, and nutrient availability, which promotes plant
growth. SOC can potentially affect both soil ecosystems and crop productivity due to its several
critical roles in soil functioning. Globally, the amount of carbon in the upper one meter of soil is about
three and two times higher than the amount of carbon found in the biosphere and atmosphere,
respectively [1–3]. Therefore, the contribution of SOC to the global C cycle by sequestering terrestrial
C is of great importance. Changes in SOC pools induced by soil management and land cover changes
affect global warming and, in turn, can significantly influence soil physical, chemical, and biological
properties [4–6]. As SOC is a good indicator of environmental quality [7], high-quality maps of the
spatial distribution of SOC can provide base-line data for SOC turnover and sequestration for C
management strategies at the province-scale. The spatial variability of SOC at the field to the regional
scale is highly related to the soil forming-factors including the climate (precipitation and
temperature); organisms (vegetation and human), relief (terrain attributes), parent materials, and
time [8].
Due to the global importance of SOC, digital soil mapping (DSM) approaches have become more
focused on SOC mapping in the last decade [4,9–12]. DSM describes the spatial variation of SOC by
taking the relations between SOC and environmental auxiliary variables into account [13–15]. The
auxiliary variables correlated with SOC are often obtained from digital elevation models [11,16],
remotely sensed data [16,17] and climatic data [18,19]. By using remotely sensed imagery and easy
accessibility of climatic and digital elevation model (DEM) data, the application of machine learning
(ML) techniques for predicting SOC is significantly increased [11,17,20].
Numerous ML algorithms have been applied in DSM for SOC prediction including artificial
neural networks (ANNs) [21–24], genetic programming [25], support vector regression (SVR)
[23,25,26], multivariate adaptive regression splines [27,28], Cubist [9,29,30], boosted regression tree
[16,31,32], and random forest (RF) [9,16,19,23,32–34]. In most cases, these approaches were much
more accurate than linear and geostatistical methods due to the higher ability to get a lot more
information for unsampled points by investigating nonlinear relationships between SOC and
environmental auxiliary variables.
Soils, especially SOC contents, which are the result of the actions and interactions of many
different processes and factors, vary from place to place with high complexity [35]. Thus, to predict
the behaviors and properties of such a complex environment, classical ML may encounter problems
[10,12,34,36]. A new approach that has received considerable attention as a sophisticated learning
algorithm with substantial learning capability and high performance is deep learning (DL) [37].
Recently, deep neural networks (DNNs) based on DL approaches have been proposed for
overcoming the shortages arising from the traditional ANNs [37,38], by adding more complexity
(deep) into the conventional models. This provides better learning capabilities to reveal the
complexity underlying the data, and thus results in a higher accuracy of the trained model [39]. The
hierarchical structure and high learning capacity make DNN models quite flexible and adaptable for
a wide variety of highly complex problems such as SOC prediction [11,39,40]. The DNNs have
recently been used for the prediction of soil properties [40–42] and particularly for SOC prediction
[43,44]. Xu et al. [43], for instance, indicated that the DNN method had a high performance for the
prediction of SOC with the effective abstraction of complex covariates for learning by using visible
and near-infrared soil spectra. DNNs are more complex and need further parametrization but
severely depend on the size of the training dataset.
To eliminate the multicollinearity of variables and exclude unimportant and redundant auxiliary
variables, numerous feature selection techniques have been developed for DSM including. Particle
swarm optimization [45], the genetic algorithm (GA) [25,32,46], hybrid GA-artificial neural network
[47], parallel GA [48], and the artificial bee colony algorithm [36] are among the notable feature
selection techniques. Such variable selection techniques can simplify modeling by lowering the
number of input variables and potentially improving the accuracy of soil predictions. There is no
universal feature selection method to reduce the number of covariates in the pool presented to an ML
algorithm. For instance, Behrens et al. [49] compared the two most common approaches for the
selection of covariates, namely supervised and unsupervised, and found that the supervised feature
selection approach was superior because the soil classes were predicted more accurately.
Taghizadeh-mehrjardi et al. [50] explored the effect of the reduction in dimension of feature space
with ant colony optimization (ACO) and correlation-based feature selection (CFS) on the accuracy of
prediction of spatial models for each particle size fraction. In this study, we decided to implement
the GA, one of the most advanced algorithms for feature selection [46]. GA can manage the datasets
with many features and do not need specific knowledge about the problem parallelizing easily in
computer clusters [46,51,52].
Although many ML algorithms have been developed for the prediction of soil properties, the
development of site-specific techniques is necessary for enhancing the quality of thematic soil maps
[53]. However, there is no best worldwide predictive algorithm for SOC mapping given that the
accuracy level of SOC predictions is highly related to the local geographic attributes of the study area
[54], the sampling size [9,55] and the selected auxiliary variates [14,19,56].
Mazandaran province, northern Iran, is located on the southern coast of the Caspian Sea. There
is a descending precipitation gradient from the west to east across the region, leading to a diversity
of soil moisture regime (SMR) and soil temperature regime (STR) classes [57]. Due to the changes in
SOC contents in northern Iran caused by the human activities and natural attributes (landslide,
flooding, depression) [58,59], the existence of a high-quality SOC prediction map with known
uncertainty in the Mazandaran province is crucial. This provides a base-line map for further temporal
monitoring of SOC at the province-scale. Despite the known advantages of feature selection, there
have been no insights into the important variables for SOC prediction in northern Iran given the
different predominant climatic and soil-forming conditions. Therefore, due to the lack of an SOC
base-line distribution map in Mazandaran province, the objectives of this research were (1) to
determine the important auxiliary variables driving the SOC contents in the province using GA as a
popular automatic method for feature selection, (2) to test the performance of six ML algorithms fed
with GA-selected auxiliary variables and (3) to predict the spatial distribution of SOC for mapping
with associated uncertainty and (4) to compare SOC contents in different geological units, soil classes
and land uses in Mazandaran province.

2. Materials and Methods

2.1. Study Area

This research was conducted in Mazandaran province, northern Iran. The region is located at a
longitude of 50°31′21′′ E to 53°56′52′′ E and latitude of 36°38′06′′ N to 36°54′59′′ N and covers an area
of 2,388,179 ha. It borders the Caspian Sea in the north and the Alborz Mountain range in the south
(Figure 1). Most of the province is covered by dense, moderate, and low-density forest with each
forest type covering 39%, 4%, and 2% of the total area, respectively. There are several kinds of
cultivated lands in the study area. Paddy fields are the most common agricultural land use with about
210,000 ha, and orchards cover about 90,000 ha. Based on the De Martonne climate classification, the
western, central, eastern, and mountainous parts of the province have very humid, humid,
Mediterranean, and semihumid climates, respectively. The mean annual temperature ranges from 18
°C on the coastal plain to below 8 °C in the highlands. There is a gradient of the decreasing
precipitation from the west (around 1400 mm) to the east direction (around 450 mm) leading to the
diversity of soil moisture regime (SMR) and soil temperature regime (STR) classes across the
province. The xeric SMR class covers the largest area in the province, followed by the udic and aquic
classes, while thermic (66%) is the most abundant STR followed by mesic (33%) and cryic (1%) [57].
The variation of elevation ranges from the Caspian Sea coastal areas with elevations <−5 m to more
than 3000 m above sea level in the highlands of the Alborz Mountain range. Five USDS soil taxonomy
orders including Mollisols, Entisols Inceptisols, Alfisols, and Ultisols were in Mazandaran with a
total of 12 suborders. Mollisols are the most dominant soils forming on different landforms with
mollic epipedons. Mollisols have four main suborders including the aquolls, rendolls, udolls, and
xerolls mostly distinguishing based on soil moisture regime classes except for rendolls that have an
epipedon with less than 50 cm thickness overlies on a highly calcareous horizon. Alfisols are
characterized by a clay enriched endopedon with two main suborders, i.e., aqualfs and udalfs.
Ultisols with a single suborder, i.e., Humults occurring in a very limited area in Mazandaran province
with leached soils under native forest vegetation. Entisols with three main suborders, i.e., Orthents,
Fluvents, and Aquents are mostly used for paddy cultivation in the study area. Inceptisols in
Mazandaran province have a weakly developed B horizon with two main suborders, i.e., Aquept and
Xerepts.

Figure 1. (A) Geographical position of Iran on the world map, (B) geographical position of the
study area in Iran, and (C) spatial distribution of soil samples. The background is a false-color
composite image derived from Landsat.

2.2. Soil Data

The total dataset for SOC mapping is 1879 composite surface soil samples from two main sources
(Figure 1). More than half of the data (1055 samples) were derived from five Master of Science (M.Sc.)
research projects in the soil science department at Sari Agricultural Sciences and Natural Resources
University (SANRU) [60–64]. These samples were collected using a simple random sampling scheme
mostly in uncultivated areas. The rest of the dataset comes from soil surveys performed by the
Agricultural Research Education and Extension Organization (AREEO) and the Ministry of Jahad-e-
Keshvarzi in Sari, Northern Iran. These samples were mostly collected in cultivated areas spread
across the province using a grid sampling scheme with a 2000 m grid interval. Each composite soil
sample is collected within a 20 m radius surrounding each of the sampling points with at least 10
subsamples (cores). Samples were collected from a depth of 0–20 cm, and their geographical
coordinates were recorded with a global positioning system (GPS) device. After air-drying and
passing through a 2 mm sieve, the content of SOC was measured by the wet oxidation procedure
outlined by the Walkley and Black [65]. Figure 1 shows the spatial distribution of the sampling sites
across Mazandaran province.

2.3. Auxiliary Variables

The full set of 105 predictor variables initially considered is given in Table A1 in the Appendix
A. The auxiliary data included variables derived from remotely sensed imagery (60 variables from
Landsat 8 and MODerate-resolution Imaging Spectroradiometer, MODIS), terrain attributes (30
variables), climatic data (10 variables), and five categorical data (e.g., soil map and land use map).
The high contribution of SOC to soil color can be detected by the spectral signature of remotely
sensed data. The 60 environmental auxiliary variables derived from satellite imagery were developed
based on the median values of 8 satellite images of the Landsat 8 Operational Land Imager taken
from 2012 to 2016 to coincide with the dates of soil sampling. Following radiometric, geometric, and
atmospheric corrections digital numbers for the blue (B1), green (B2), red (B3), near-infrared (B4), and
shortwave IR-2 bands (B6) were extracted. Several indices were then calculated: the normalized
difference vegetation index (NDVI), enhanced vegetation index (EVI), combined spectral response
index (COSRI), land surface water index (LSWI), brightness index (BI), and other indices with a
spatial resolution of 30 m. The variables derived from MODIS imagery had a spatial resolution of 250
m. These included median values of two spectral reflectance bands: red (645 nm) and near-infrared
(858 nm) and the EVI, NDVI, and other indices. The daytime and nighttime land surface temperature
with a 1 km resolution were also derived from MODIS data. Overall, 60 auxiliary variables were
derived from Landsat 8 and MODIS data.
Thirty terrain attributes were derived from a DEM [66]. The DEM was obtained from shuttle
radar topography mission terrain (SRTM) data with 30 m grid cells. Terrain attributes, namely slope,
aspect, elevation, length and steepness (LS) factor, valley depth, openness, catchments area,
catchment slope, plane curvature, topographic wetness index (TWI), channel networks base level
(CNBL), distance to channel networks, the multiresolution valley bottom flatness index (MrVBF) and
other indices [67], were calculated using SAGA GIS.
Climatic factors have high potential to explain large parts of the variation of soil properties in
the northern part of Iran, due to the high degree of spatial variability in Mazandaran province. In this
study, 10 climatic variables were obtained using WorldClim. WorldClim version 2 [68] contains
reliable temperature and precipitation data at a spatial resolution of 1000 m. Categorical predictor
variables were derived from five choropleth maps, which were compiled at different cartographic
scales, e.g., soil map and land use map [69].
Figure 2 shows the spatial distribution of some auxiliary variables related to SOC including
precipitation, NDVI, MrVBF, and land use. The precipitation decreases from the north-west to the
north-east in the province, especially in shoreline areas (Figure 2). The southern parts of the province
have lower precipitation compared with the northern region where the Caspian Sea shoreline is
located. The NDVI values range from −0.5 to more than 0.8, indicating a high diversity of vegetation
cover spread across the province that has a potentially significant effect on SOC content due to large
differences in the number of falling leaves and plant residues. The MrVBF shows that flat valley
bottoms where sediments and outflows accumulate leading to higher clay and SOC contents [34,67].
All environmental variables which did not conform with SOC grid resolution of 30 × 30 m were
resampled to a 30 m spatial resolution using either the nearest neighbor or bilinear resampling
methods.
Figure 2. Four examples of auxiliary variates used for modeling soil organic carbon: (A)
multiresolution valley bottom flatness index (MrVBF), (B) normalized difference vegetation index
(NDVI), (C) precipitation, and (D) land use maps. The Crop.Or, Dense.Forest, Dry.Farm, Good.Range,
Low.Forest, Mod.Range, Poor.Range, Resident.L, Seashore.L, and Semi.Forest symbols in land use
map correspond to the land use type of croplands and orchards, dense forestlands, dry farming lands,
good rangelands, low dense forestlands, moderate rangelands, poor rangelands, residential lands,
seashore lands, and semidense forestlands, respectively.
2.4. Selection of Auxiliary Variables Using Genetic Algorithms (GA)
Instead of taking all 105 environmental auxiliary variables into consideration for a predictive
ML algorithm, the feature selection method reduces the number and collinearity of the auxiliary
variables. The most informative auxiliary variables should be inserted into the algorithms with the
aim of high accuracy of the ML algorithms for SOC prediction [9,16,25]. The selection of the
significant environment auxiliary variables is a preprocessing step for ML algorithms to remove
redundant and irrelevant variables. For this study, one of the most advanced algorithms for feature
selection, namely the genetic algorithm (GA), was used to select the most appropriate auxiliary data
to be fed as inputs to the ML algorithms [16]. GA is able to select those auxiliary data that are not
only essential but improve performance as well. Moreover, GA can manage the nonlinear
relationships between SOC and auxiliary data [70].
By mimicking natural biological evolution, the GA which is a heuristic search algorithm
provides the best value for a function [51]. A GA feature selection process starts with an initial
random population consisting of individuals. The individuals, representing subsets of auxiliary data,
are encoded as binary in which 1 represents if the feature is selected and 0 otherwise [71]. Then three
primary operations including selection, crossover, mutation repeat until a stopping criterion is
reached. The selection operations were for selecting the two fittest individuals for reproduction (i.e.,
the solutions providing the lowest root mean squared error, RMSE). The crossover recombines two
individuals to create new ones which may be better. The mutation operator introduces alteration in
a small number of individuals. The process of selection, crossover, and mutation continues until a
termination condition is satisfied [48,52]. Importantly, for each generation, it is necessary to assign a
fitness value to each individual in the population so that the RMSE values are calculated by fitting
the random forest model [46,48,52].
In this study, the GA procedure was performed with 10-fold cross-validation and 100 iterations
to select the smallest number of auxiliary variables important for SOC modeling using the caret
package in R [72]. The population size, crossover, and mutation rates used were 50, 0.6, and 0.001,
respectively, as outlined by Welikala et al. [52].

2.5. Machine Learning Techniques

In this study, six ML algorithms including support vector machines (SVM), artificial neural
networks (ANNs), regression tree (Cubist), random forest (RF), extreme gradient boosting (XGBoost),
and deep neural networks (DNN) were chosen. Each algorithm can discover complex relationships
between SOC content and auxiliary covariables. Table 1 summarizes the hyperparameters of the six
ML algorithms used in this study. A brief description of the ML techniques used in this study follows.

Table 1. Hyperparameters of machine learning algorithms used in this study.

ML Algorithms Hyperparameters Definition Defined Parameters

SVM Kernel type the kernel function RBF
(support vector C the penalty parameter 0.01–100
machines) 𝜎 the bandwidth parameter 0.01–100
Cubist committees the number of model trees 1–100
(regression tree) neighbors the number of nearest neighbors 0–9
the type of model
booster gbtree
the depth of tree
max_depth 3–10
XGBoost the minimum sum of weights of all
min_child_weight 0–5
(extreme gradient observations
colsample_bytree 0.5–1
boosting) the number of variables supplied to a tree
subsample 0.5–1
the number of samples supplied to a tree
eta 0.01–0.5
learning rate
RF Mtry the number of input variables 1–30
(random forest) Ntree the number of trees 100–3000
ANN
decay learning rate 0.001–0.05
(artificial neural
size the number of neurons in the hidden layer 1–10
networks)
DNN hidden the number of hidden layers 2–10
 (deep neural networks) size the number of neurons in the hidden layer 15–200
network weight the initialized weight of networks uniform/he_normal
initialization that controls adjusting the weights of the 0.001–0.05
learning rate network 0.2–0.8
dropout the amount of the neurons that are
regularization randomly dropped
ML: machine learning; SVM: support vector machine; Cubist: regression tree; XGBoost: extreme
gradient boosting; RF: random forest; ANN: artificial neural networks; DNN: deep neural networks.

2.5.1. Support Vector Machines (SVMs)

Initially, SVMs were developed as a methodology for resolving problems of classification into
two attributes using a threshold value. Connected with the earlier development of SVMs as a
classification method, the regressive type of support vector machines was proposed. This caused the
spread of the philosophy of support vectors machines being used to solve regression problems. The
algorithm was formulated as a linear method and then it was generalized to (1) the presence of noise
in the data using slack variables following the soft-margin philosophy, and (2) a nonlinear model
through the conversion of the input space into a larger dimension, as done for classification [73].
Hence, SVM is used for classification and regression processes with a set of connected supervised
learning algorithms and they have an excellent ability to be universal predictors of any multivariate
function to any specified degree of accuracy [20]. In this study, the SVM algorithm was employed by
improving the range of its components (C: 0.01–100; σ: 0.01–100) based on the input data (Table 1).

2.5.2. Artificial Neural Networks

Artificial neural networks (ANNs) stand out among the different types of models because they
are calculative techniques with mathematical models simulated from the human’s brain neural
function [74]. ANNs as vigorous data-modeling tools attain knowledge by way of experience. They
are able to detect patterns and draw results, therefore they can be used for data prediction with
correlation, such as soil properties. The ability for handling and modeling multiple outputs
simultaneously is a primary benefit of ANN techniques [75]. The development of an ANN model
mainly consists of three main stages: the generation of data for the training/testing of the model, the
selection of the optimal configuration, and the validation of the model on an independent data set.
Additionally, ANNs are interconnected by structures called perceptrons and consist of input, output,
and hidden layers that transform the input into something that the output layer can utilize [76]. ANN
models allow one to attribute lower weight to samples that deviate from a standard, since ANNs can
identify patterns in data distribution, which is not observed in linear and nonlinear regression [77].
As a result, ANN models can lead to a higher accuracy than linear and nonlinear regression [78]. The
present neural networks of this study were made based on a learning rate of 0.001–0.05 and the
number of hidden layer neurons was 2–10 (Table 1). The sigmoid function is the activation function
in the nnet package [79] for the MLP with one hidden layer which we used in this study.

2.5.3. Regression Tree (Cubist)

Cubist is an ML estimating tool that is similar in approach to regression trees [80]. However,
unlike classification and regression tree models, linear models are often well structured rather than
having end values [81]. Additionally, the Cubist and other regression tree algorithms have a clear
difference, that is the linear regression model is fitted to the leaf nodes of the trees in the Cubist [82].
Overall, the Cubist approach makes multivariate models that are made of sets of rules, and the
prediction model will be chosen based on the rules [83]. In this research, the ptoposed regression tree
models are based on Cubist regression models [84]. Cubist models were improved by defining the
number of model trees, and nearest neighbors using the data set shown in Table 1.
2.5.4. Random Forest (RF)
The random forest (RF) consists of a series of binary rule-based decisions that define
relationships between input and its dependent variables. It comprises a large number of individual
tree algorithms trained from bootstrap samples of the data [85]. The single prediction will be made
by accumulating the results of all trees. One of the main benefits of random forests is that they can
precisely explain the compound connections between the independent variables and the dependent
variables. So when composite environmental systems and ecological supplementary variables are
introduced, RF can be helpful [86]. Two important parameters in RF algorithms are the number of
trees (Ntree) and the number of variables (Mtry) which are available for selection in each split [87].
These two main parameters (Mtry and Ntree) were adjusted for the best result. The range of values
used is shown in Table 1.

2.5.5. Extreme Gradient Boosting (XGBoost)

The algorithm for extreme gradient boosting (XGBoost) was proposed by Chen and Guestrin
[88]. It is an algorithm for improving the performance for gradient boosting machines and especially
for regression trees and K classification methods [89]. By the supplemental training strategies, the
“boosting” as a basic idea of this method extends a “strong” learner from a set of “weak” learners.
The XGBoost technique is supposed to improve calculation but also reduce over-estimation events.
The XGBoost simplifies the objective functions and improves the calculation speed to an optimum by
allowing the combination of estimative and adjustment terms. In addition, in the XGBoost approach,
during the training step, simultaneous computations will be done automatically for the functions
[89]. More information can be obtained about the XGBoost algorithm from the work of [88]. Table 1
shows the XGBoost algorithm parameters used to do this research including the type of algorithm,
the depth of trees, the minimum sum of weights of all observations, the number of variables provided
to a tree, the number of samples provided to a tree, and the learning rate.

2.5.6. Deep Neural Networks (DNN)

The performance of conventional DNN as an estimation algorithm for remote sensing
applications has been extensively explored during the past few years [90]. DNN has been reported
as a reliable and efficient approximation function for delivering insight into the relationship (whether
a linear or a nonlinear relationship) between input and output variables [91]. DNN has shown
promising results in a wide and diverse range of applications from digital signal processing and
control systems to hazard susceptibility mapping [92,93]. Figure 3 illustrates the architecture of a
conventional DNN. The networks are configured by passing several layers for learning the
probability of the outputs.

Figure 3. Illustration of the architecture of conventional deep neural network (DNN).

 In this study, conventional DNN is a feedforward learning network where there is no looping
back from the output layer to input. In this case, the DNN produces a map of virtual neurons and
random weights. The inputs and weights will be multiplied and would deliver outputs within the
range of 0 and 1. The algorithm would adjust the weights to accurately identify a particular learning
pattern to fully process the data. The DNN includes L hidden layers, the input layer (vector X), and
the output layer (vector Y). As recently formulated by Wang et al., [94], the estimation of Y can be
presented as follows.
𝐳1 = 𝜎1 (𝐖1 𝐗 + b1 ) (1)
2
𝐳 = 𝜎2 (𝐖 2 1
𝐳 +b 2 ), 𝐿
𝐳 = 𝜎𝐿 (𝐖𝐿 𝐿−1
𝐳 𝐿 ),
+b 𝐘=𝐖 𝐿+1 𝐿 𝐿
𝐳 +b , 𝜃 = {𝐖 𝑖 , b𝑖 }𝐿+1
𝑖=1 (2)

where b𝑖 and 𝜎𝑖 are the bias and the activation function of the ith layer. Here, 𝐖 𝑖 represents the
weights. In Equation (2), the 𝐿 + 1 represents the output layer. Therefore, Y can be presented as
follows.

𝐘 = 𝑁𝑁(𝐗; 𝜃) (3)
Eventually, through calculating the mean square error (MSE) of output and input values, loss
function L can be estimated as follows.
𝑁
1
𝑀𝑆𝐸𝐷𝑎𝑡𝑎 = 𝐿(𝜃) = ∑|𝑁𝑁(𝐗 𝑖 ; 𝜃) − 𝐘𝑖 |2 (4)
𝑁
𝑖=1

where N represents the sequence of data. Here, the GA is used to minimize the 𝐿(𝜃) function for the
training. A trained DNN is further used for the estimation of the new variables. The predictive ability
of neural networks is possible by learning large amounts of data. Generally, input data create the
training datasets, and similar output data will be entered into a neural network algorithm. This
algorithm can detect the basic rules in the data entered and compose an interior model that is suitable
to estimate the new input data using several training repetitions during the process. The model can
be computed by the interactions and connections between neurons, whereas any physical or clear
mathematical relationships cannot be supplied [90]. The neural network structure can affect the
precision of the predictive models. Each latent layer of the DNN algorithm consists of some
calculative neurons that are interconnected to the next calculative neurons in the adjoining latent
layers. To finalize the DNN model, the neurons of each latent layer measure the calculative neuron
outputs of the prior layer, and after the computation procedure of the activation function, the outputs
are generated for the subsequent layer [42].
Table 1 shows the specifications used for DNN, which are hidden layers, size, network weight
initialization, learning rate, dropout regularization. In this study, for the DNN method, the H2O
package [92] with the rectifier function as a nonlinear transformation was used for DNNs in this
study [95]. It is worth mentioning that adhering to a balanced ratio of training and testing is of utmost
importance in modeling with machine learning [96]. Several methods in a wide range of applications
are introduced to identify the correct balance for testing [97]. Nevertheless, the evaluation metrics
have been shown to be reliable measures to maintain a sufficient number of elements for a training
dataset in soil research [37–40]. It is often observed that by decreasing the amount of training data,
the error increases, which accurately indicates the worth of data for models. The amount of training
data, in this study, is optimally tuned to ensure the lowest errors. The total dataset is divided into 10
datasets that are sequentially used for training and testing. The DNN is calibrated 10 times to assure
each data point was used as validation at least once.

2.6. Evaluation of Algorithm Performance

Ten-fold cross-validation was implemented for testing the performances of six ML prediction
algorithms for estimating the SOC contents in Mazandaran province. In this regard, the total dataset
was split into 10 datasets that were sequentially used as training and testing datasets for a given
prediction algorithm. Each prediction model is calibrated 10 times, guaranteeing each data point was
used as validation at least once. Then, the 10 prediction errors can be obtained for each prediction
algorithm. The four evaluation criteria used in this study are the coefficient of determination (R2) [98],
Lin’s concordance correlation coefficient (CCC) [99], mean absolute error (MAE) [100] and root mean
squared error (RMSE) [100] with following formulas:

2
∑𝑛𝑖=1(𝑂𝑖 − 𝑝)2
𝑅 =1−( ) (5)
∑𝑛𝑖=1(𝑂𝑖 − 𝑂´)2
2 𝑟 𝜎𝑜 𝜎𝑝
𝐶𝐶𝐶 = (6)
𝜎𝑜2 + 𝜎𝑝2 + [𝑂´ − 𝛲´]2
𝑛
1
𝑀𝐴𝐸 = ∑|𝑃𝑖 − 𝑂𝑖| (7)
𝑛
𝑖=1

𝑛
1
𝑅𝑀𝑆𝐸 = √ ∑(𝑃𝑖 − 𝑂𝑖)2 (8)
𝑛
𝑖=1

where, n is the number of samples, Oi and Pi are observed and predicted SOC contents, respectively.
O’ and P’ are the means for the observed and predicted SOC contents, respectively. Furthermore, σo
and σp are the variances of observed and predicted values. Four criteria of the validation datasets in
10-fold validation in each prediction algorithm were averaged and used for selecting the best
performing prediction algorithms. The prediction algorithm with the lowest MAE and RMSE, and
highest R2 and CCC values are determined as the best for SOC prediction.

2.7. Uncertainty Assessment

The spatially explicit quantification of the uncertainty of SOC prediction is analyzed in this
study. The SOC maps generated by each model were used to calculate the mean and standard
deviation (SD) of the SOC for each pixel in 10-fold realization [101]. It was assumed that six ML
models follow the normal distribution for each raster cell. The confidence interval (CI) was calculated
with the mean as ±1.64 SD for a given 90% CI. The upper and lower limit of the 90% CI were mapped.
The mean of the SOC contents in each pixel and the 90% CI was calculated by retrieving the 5th and
95th percentiles of prediction. Finally, three maps of the SOC were produced for the best performing
model: the mean prediction, lower CI (5%), and higher CI (95%).

3. Results and Discussions

3.1. Summary Statistics

Table 2 shows the summary statistics for topsoil SOC for the 1879 sampling sites. SOC contents
ranged from 0.02% to 11.48% with a mean and standard deviation of 2.19% and 1.27%, respectively.
The lower SOC contents correspond to highly degraded lands where the surface soil is eroded and
the maximum SOC contents were observed in dense forestlands. The coefficient of variation of 58.23%
demonstrates the high variability of SOC contents within the study area. The values of skewness
(2.33) and kurtosis (8.2) indicate that the SOC data is highly skewed and in turn, violates assumptions
of normality. SOC data were anchored at 1.00 and then, transformed by the natural logarithm to make
the distribution less skewed. The skewness and kurtosis values of the log-transformed SOC values
were 0.59 and 1.50, respectively, and the Kolmogorov–Smirnov test showed that the distribution of
these log-transformed values was not significantly different from normal. Further analysis was
performed on the log-transformed data; and the predicted SOC values were back-transformed to the
original scale.
 Table 2. Descriptive statistics of SOC (%) in this study (n = 1879).

Min Max Mean SD CV Skewness Kurtosis

0.02 11.48 2.19 1.27 58.23 2.33 8.2
SOC: soil organic carbon; Min: minimum; Max: maximum; SD: standard deviation; CV: coefficient of
variation; K-S p-value: significance level of Kolmogorov–Smirnov test.

3.2. Selected Auxiliary Data

In this study, the GA procedure with 10-fold cross-validation and 100 iterations (i.e., GA was
executed 1000 times) was used to select the minimum number of important auxiliary variables for
SOC modeling. The results of GA for 1000 generations are presented in Figure 4. The average of the
internal out-of-bag RMSE estimates as well as the average of the external performance estimates
calculated. Based on these results, the generation associated with the best external RMSE estimate
was 0.86. The GA selected 35 predictors out of 105 environmental variables, as the most relevant
driving factors for SOC mapping in Mazandaran province (Table 3). These variables comprised 13
terrain attributes, 18 remotely sensed variables, two climatic variables, and two categorical data
layers. The resolution and origins of the 35 predictors are given in Table 3. Getting more information
about the contribution of each variable to SOC variability is of great importance. Therefore, the
significance of each environmental auxiliary variable was analyzed using a sensitivity analysis and
was represented as an attribute percentage. Figure 5 indicates the order of the relative importance of
the selected predictors on SOC spatial variability using the procedure outlined by [45].

Figure 4. Internal and external validations of GA.

Table 3. The selected auxiliary data using genetic algorithms for predicting SOC.

Definition Res. Ref.

Selected Terrain Attributes
Aspect 30 m SRTM
Slope Gradient 30 m SAGA GIS
Elevation 30 m SAGA GIS
Slope Length Factor 30 m SAGA GIS
Valley Depth 30 m SAGA GIS
Openness (PosOpen) 30 m SAGA GIS
Openness (NegOpen) 30 m SAGA GIS
Catchment Slope (CaSLOP) 30 m SAGA GIS
Plane Curvature (Plan.Curv) 30 m SAGA GIS
Topographic Wetness Index (TWI) 30 m SAGA GIS
 Channel networks base level (CHNL.BASE) 30 m SAGA GIS
Multiresolution ridge top flatness index (MRRTF) 30 m Gallant and Dowling (2003)
Multiresolution Valley Bottom Flatness Index (MrVBF) 30 m
Selected RS data
Blue band of Landsat-8 (B1) 30 m Wulder et al. (2016)
Green band of Landsat-8 (B2) 30 m
Red band of Landsat-8 (B3) 30 m
Near-infrared band of Landsat-8 (B4) 30 m
Shortwave IR-1 band of Landsat-8 (B5) 30 m
Shortwave IR-2 band of Landsat-8 (B6) 30 m
Normalized difference vegetation index (NDVI) 30 m Rouse et al. (1974)
Enhanced vegetation index (EVI) 30 m
Combined Spectral Response Index (COSRI) 30 m
Transformed SAVI (TSAVI) 30 m
Soil adjusted vegetation index (SAVI) 30 m
Brightness Index 30 m Metternicht and Zinck (2003)
Clay Index 30 m Boettinger et al. (2008)
Carbonate index
MODIS Red 250 m
MODIS Near Infrared (MODIS Nir) 250 m
MODIS Night Temperature(MODIS.Night.Temp) 1000 m
MODIS Day Temperature (MODIS.Day.Temp) 1000 m
Selected climatic data
Annual precipitation (mm) 1000 m Fick and Hijmans (2017)
Annual mean temperature (°C) 1000 m Fick and Hijmans (2017)
Selected categorical data
Land use 125 m Banaei et al. (2005)
Soil map 500 m
Abr.: abbreviation; Res.: resolution; Ref: references.

As can be seen in Figure 5, precipitation is the most crucial feature (14.9%) driving the spatial
variability of SOC contents in Mazandaran province followed by the NDVI (12.5%), MODIS day
temperature (10.6%), MrVBF (8.7%), land use (8.2%), valley depth (7.2%), and MODIS night
temperature, respectively. In Mazandaran province, as previously thought, the precipitation
significantly affects SOC contents by enhancing vegetation coverage and the rate of organic matter
inputs. Together precipitation and temperature (MAT) explain 18.9% of the variation in SOC contents
demonstrating the high dependencies of SOC contents in the province-scale to the climatic variables.
Lamichhane et al. [14] reviewed several studies and pointed out that climate is the most influential
factor for the variation of SOC at large extents. The high precipitation is mostly combined with lower
temperatures and slower SOC decomposition rates at higher altitudes [102,103]. Falahatkar et al. [104]
reported that the most important auxiliary predictors for SOC stocks for surface soil in Guilan
province, northern Iran are land use, NDWI, silt, clay, and elevation. Along with our findings, the
surface temperature data derived from remotely sensed data (Landsat) was found to be influential
for improving SOC prediction [66].
The NDVI is the second most important feature explaining SOC variability, indicating that the
SOC contents were highly influenced by vegetation variation. SOC content was highly dependent on
the natural vegetation cover intensity, and the plant residue left after plant harvesting [4,36,105]. Due
to the dependency of SOC on vegetation cover, NDVI has frequently been used as a predictor for
mapping SOC in several studies [16,25,33,106]. Additionally, NDVI has more importance to SOC
contents compared to other remotely sensed vegetation indices like EVI. Although the EVI performs
better than the NDVI in many applications, our results indicated that NDVI is more important for
explaining SOC contents compared to EVI. It might be related to the topographic conditions as
Matsushita et al. [107] reported that EVI is more sensitive to topographic conditions than is the NDVI.
Meanwhile, the green band of Landsat-8 (B2) showed a higher contribution to SOC than B3 and B4.
The high contribution of the MrVBF (8.7%) to SOC variability in this study could be attributed
to the deposition of fine organic-enriched particles and sediment [58] from the highlands in the lower
valleys with flat and low-lying areas. Land use data is considered as the fifth important variable for
SOC variation. Land use effects on SOC variation is related to the land-use conversion in the last two
decades in Mazandaran province that have led to the exposure of soils and the rapid decomposition
of SOC [58].
The TWI only contributed 3% SOC contents showing that SOC tends to accumulate in wetter,
low-lying areas in Mazandaran province. Taghizadeh-Mehrjardi et al. [25] demonstrated that the
wetness index is the most important terrain variable for the prediction of SOC in subsoils (>30 cm
depth). Plan curvature (Plan.Curv), soil map, slope, aspect, channel networks base level
(CHNL.BASE), LS factor and other variables ranked in Figure 4 made only a small contribution to
SOC spatial variability at the province-scale used in this study but still need to be considered as input
variables for SOC modeling by ML techniques.

Figure 5. Relative importance of auxiliary data using genetic algorithms. (Refer to Table 3 for a
definition of auxiliary data).

3.3. Machine Learning Performances

The average MAE, RMSE, R2, and CCC for SOC prediction by 10-fold cross-validation are shown
in Table 4. The proposed ML models showed different abilities to predict SOC contents at unsampled
locations at the province-scale. This could be related to the various mathematical functions of each
algorithm [2]. The mean R2 values indicate that the SVM, ANN, Cubist, RF, and XGB models deliver
53%, 55%, 57%, 58%, and 57% of SOC variability, respectively. However, the DNN model
outperforms other models by delivering 65% of the SOC variability. In all ML models, the RMSE
values are reported more significant than the MAE, indicating that there is a contribution of the errors
in SOC predictions [108]. The DNN algorithm showed the lowest mean MAE value (0.59%) of the six
studied ML algorithms. The SVM algorithm had the highest error with mean RMSE values of 0.87%
compared with other ML models, meanwhile, the DNN outperformed with the lowest mean RMSE
value (0.75%). ANN, Cubist, RF, and XGB showed a similar ability to predict SOC in Mazandaran
province. Based on the performance criteria used, SVM was always a weaker ML algorithm than the
other algorithms, while DNN was the most consistently robust algorithm.
One of the main advantages of DNN is that the step of feature extraction was performed by the
DNN model itself [10]. Our results confirm previous research on the performance of DNN in soil
modeling. For instance, a recent research study introduces the DNN as an effective and robust
modeling method to capture the complex nonlinearity between auxiliary variables and soil moisture
[40] and SOC prediction [11,42]. DNN models by using the multiple hidden layers of the neural
network improve the SOC prediction. Padarian et al. [11] reported that using deep learning models
for digital soil mapping offers a simple and effective framework for future soil mapping. The DNN
algorithm needs a large number of parameters to be fitted so that it performs well with a large dataset
like the one used in this study. Importantly, the sample size is a critical issue for training in the DNN
[41].

Table 4. Comparisons of the accuracy of six machine learning models for validation dataset by 10-
fold cross-validation (means ± standard deviation).

ML Algorithms MAE RMSE R2 CCC

SVM 0.69 ± 0.07 0.87 ± 0.05 0.53 ± 0.05 0.76 ± 0.05

ANN 0.67 ± 0.08 0.85 ± 0.07 0.55 ± 0.05 0.77 ± 0.06

Cubist 0.66 ± 0.06 0.83 ± 0.04 0.57 ± 0.04 0.78 ± 0.04

RF 0.65 ± 0.03 0.82 ± 0.03 0.58 ± 0.05 0.78 ± 0.03

XGB 0.66 ± 0.04 0.83 ± 0.04 0.57 ± 0.03 0.78 ± 0.04

DNN 0.59 ± 0.06 0.75 ± 0.06 0.65 ± 0.05 0.83 ± 0.06

ML: machine learning; SVM: support vector machine; Cubist: regression tree; XGBoost: an extreme
gradient boosting; RF: random forest; ANN: artificial neural networks; DNN: deep neural networks;
MAE: mean absolute error; RMSE: root mean square error; R 2: the coefficient of determination; CCC:
Lin’s concordance correlation coefficient.

underestimated. The CCC statistic quantified the level of agreement between predicted and
measured SOC values according to the 1:1 line. It is based on CCC values (Table 4). The The lower
performance of other ML algorithms except for the DNN could be related to taking a large number
of auxiliary variables into account and the original data having multiple-scales of variation, as well
as different sources and sampling times, all of which increase the uncertainty.
The 1:1 scatterplots of actual vs. predicted SOC using the six ML algorithms are shown in Figure
6. It is now much easier to understand the prediction efficiency of the DNN algorithm as most
predictions follow the 1:1 line with the exception of large observed SOC contents, which were slightly
DNN algorithms with a 0.83 value were superior and the SVM (CCC = 0.76) was inferior.
 Figure 6. Actual vs. predicted values of soil organic carbon using six machine learning algorithms:
(A) SVM, (B) ANN, (C) Cubist, (D) RF, (E) XGB, and (F) DNN. (SOC: soil organic carbon; SVM:
support vector machine; Cubist: regression tree; XGBoost: extreme gradient boosting; RF: random
forest; ANN: artificial neural networks; DNN: deep neural networks).

As the deep learning method is sensitive to the size of the training dataset, DNN apparently
yielded the best result in this study due to the large data for training. Using a deep convolutional
neural network trained with a smaller dataset was not effective for the prediction of soil properties
by spectral data [41].
 The DNN algorithm has a more flexible structure and is explicitly able to extract more
information from the environmental auxiliary variables and the SOC content and this is consistent
with the results of [11,42]. Therefore, we could recommend the DNN algorithm as the best ML
algorithm for the prediction of SOC content with reliable uncertainty in Mazandaran province. The
DNN model in this study was successfully trained with a large number of covariates due to its more
flexible neural structure and in turn was able to effectively combine with multiscale properties. This
algorithm uses the data imputation for taking the missing values into account thereby the better
model performance could be achievable especially for subsurface DSM [11].
The observed mean value of R2 and RMSE in the DNN algorithm can be compared to the other
studies at the regional scale [109–111]. Wang et al. [16] only achieved an R2 mean value of 48% of the
total spatial SOC variability using the RF algorithm in semiarid pastures of eastern Australia.

3.4. Spatial Prediction of SOC with Uncertainty Estimates

The numbers and percentages of SOC contents that fall within the 90% CI are shown in Table 5.
The uncertainty analysis also showed to some extent the same trend to the ability of the ML
algorithms to predict SOC. The DNN had the maximum percentage of observations (~88%) that fell
within the defined CI. The spatial prediction of mean SOC content with a 5% lower confidence limit
and 95% upper confidence limit values in Mazandaran province produced by the DNN algorithm
are shown in Figure 7. It is clear that the combined influence of selected auxiliary variables controls
the SOC contents. It is evident that the SOC contents tend to be higher in a strip from the west (more
than 3%) to the east (lower than 1%) in the middle of the Mazandaran province. The precipitation
gradient and NDVI index, which were the most highly correlated variables, were greatly responsible
for SOC variations. The SOC content coincided in a systematic way with increasing the precipitation
gradient, NDVI, and MrVBF indices (Figure 2). It was clear from the predicted SOC map that the
amounts were higher in the area with high NDVI values ranging from 0.71 to 0.81 (the central part of
the study area). The higher rainfall favors higher net primary production of plant residues and
explains the higher SOC contents in the middle portion of the province. There is some uncertainty in
the predicted map that may be related to the high variability in SOC data, low precision of predictors,
inherently poor relationships between SOC and auxiliary variables, and errors in modeling [112].
Considering the multiple scales of auxiliary variables and the good resolution of soil
erosion/deposition data, such data can potentially [32] reduce the spatial prediction uncertainty in
future studies.
The SOC contents change over time, thus the predicted map can be used as a base-line to indicate
temporal changes. Together with the estimation of uncertainty, the prepared maps are more reliable
and could be useful for future SOC inventories and province-scale accounting and carbon balance
studies.

Table 5. The numbers and percentages (%) of SOC that fall within the 90% prediction intervals
predicted by machine learning models for 10-fold cross-validation.

Number of Points %
ML Models All Inside CI Outside CI Inside CI Outside CI
5 to 95% <5% >95% 5 to 95% <5% >95%
SVM 1879 1490 187 202 79.30 9.95 10.75
ANN 1879 1524 165 190 81.11 8.78 10.11
Cubist 1879 1580 155 144 84.09 8.25 7.66
RF 1879 1559 150 170 82.97 7.98 9.05
XGB 1879 1587 140 152 84.46 7.45 8.09
DNN 1879 1650 110 119 87.81 5.85 6.33
ML: machine learning; SVM: support vector machine; Cubist: regression tree; XGBoost: extreme
gradient boosting; RF: random forest; ANN: artificial neural networks; DNN: deep neural networks;
CI: confidence interval.
 Figure 7. Spatial prediction of (A) upper, (B) mean, and (C) lower confidence limits of soil organic
carbon (SOC) using a deep neural network model.

3.5. SOC Contents in Soil Classes and Geological Eras

The mean comparison of the SOC contents within different soil orders and suborders is shown
in Table 6. The Ultisols and Mollisols with mean SOC contents of 4.04% and 3.20%, respectively, had
higher surface SOC compared with other soils. Most Ultisols and Mollisols were found in the dense
forest in Mazandaran province showing the higher C inputs into the soils. The high precipitation
with a relatively low MAT in the center of the Mazandaran province leads to higher SOC
accumulation at the soil surface and in turn higher clay content in a Bt horizon [6,113] and the deeper
Bk horizon [6,113,114]. Entisols had the highest SOC variability (CV = 40.66%) followed by the
Inceptisols (33.94%), Alfisols (CV = 33.64%), and Mollisols (30.55%). The SOC under Mumults had
the highest SOC with the lowest SOC variability (CV = 15.63) whereas Fluvents had significantly the
lowest SOC due to the higher SOC decomposition caused by the exposure (tillage) and loss of SOC
by erosion.
 Table 6. The SOC changes in different soil orders and suborders in Mazandaran province.

Soil Orders Mean a CV (%) Soil Suborders Mean a CV (%)

Aquept 2.85 C 20.11

Inceptisols 2.45 B 33.94
Xerepts 2.06 B 36.26

Aqualfs 1.94 C 21.17

Alfisols 2.55 B 33.64
Udalfs 3.17 B 27.44

Aquents 2.51 BC 14.91

Entisols 2.78 AB 40.66 Fluvents 1.91 C 22.81

Orthents 3.93 A 23.52

Aquolls 2.43 BC 21.64

Rendols 4.03 A 22.43

Mollisols 3.20 A 30.55
Udolls 3.33 B 24.08

Xerolls 2.31 BC 34.97

Ultisols 4.04 A 12.63 Humults 4.04 A 15.63

a: Values with different letters in each column indicate significant differences (p < 0.05); CV: coefficient
of variations.

The mean SOC contents spread across the Mazandaran province differed in soils under different
soil SMR and STR classes as shown in Figure 8. The SOC mean value was the highest in the udic SMR
class with mean values of 3.85% followed by the aquic (2.45%) and xeric (2.10%), respectively. The
high precipitation for soils with the udic SMR class [57] led to the high aboveground biomass
production inputs. The greater SOC contents in soils having the aquic SMR class compared to the
xeric SMR could be related to anaerobic (reducing) conditions decreasing the rates of organic matter
decomposition [115].
The soils having mesic STR classes have high SOC content with a mean value of 2.75%, which
was significantly higher than the thermic (2.20%) and cryic (1.25%) STR classes, respectively (Figure
8). Soils in the thermic STR class with higher MAT in low-lying areas had lower SOC contents
compared with mesic STR classes reflecting a negative effect of MAT on SOC contents in Mazandaran
province due to the high SOC decomposition rate. The small area of the province with a cryic STR
class has low vegetation cover in high-altitude lands accompanied by unsuitable temperature
conditions for plant growth leading to low inputs of plant residues and biomass. Overall, SOC has
been increased with precipitation and decreased with temperature associated with a given altitude
in the study area. Moreover, soils formed on younger geological formation have lower SOC contents.
The mean SOC contents in soils under the Cenozoic geological era (2.35%) had significantly lower
SOC contents compared with soils under Mesozoic (3.12%), Paleozoic (3.35%) and Proterozoic
(3.29%) eras, respectively. The higher observed SOC developed on the older geological formations
could be attributed to the increased time for SOC to develop and aboveground carbon inputs by the
dense vegetation cover inducing the SOC accumulation.
Figure 8. Mean comparison of soil organic carbon values within (A) soil moisture regime, soil
moisture regime (SMR), classes, (B) the soil temperature regime, soil temperature regime (STR),
classes, and geological eras in the Mazandaran province. Values with different letters in each column
indicate significant differences (p < 0.05). The maps of SMR and STR classes were produced by Emadi
et al. [57] according to the Newhall model.
3.6. SOC Contents in Landform Units and Land Uses
The soils formed on mountainous landforms had the highest SOC (3.11%) values with forest
land use, while there was little difference in SOC contents for the other landforms except for the soils
developed on alluvial fans that had significantly the lowest SOC contents (1.57%) with high coarse
fractions (soil particles greater than 2 mm) (Figure 9). The alluvial fans with unstable landforms, have
a high susceptibility to erosion and have little water holding capacity providing the lowest
aboveground biomass production in the study area. The high degrees of stability in mountain
landforms especially in the summit areas [6] showed more developed soils including the Ultisols,
Mollisols, and Alfisols. These are closer to the steady-state conditions relative to the younger
landforms (Fluvents) leading to greater humification and SOC accumulation on mountain landforms
that are currently covered by dense forest. On more geomorphically dynamic/unstable landforms,
organic layers can be removed from the developing surface inducing the SOC losses through erosion
[115].

Figure 9. Mean comparison of soil organic carbon values within (A) physiographic units and (B) land
uses in the Mazandaran province. Values with different letters in each column indicate significant
differences (p < 0.05). I indicates the error bar (SD) in all columns.
 The disturbed soils in croplands and orchards had significantly lower SOC compared with
forests and rangelands except for poor rangelands. Soils in residential, dry farming, poor rangelands,
and seashore areas had SOC mean values of 2.08%, 1.78%, 1.71%, and 0.75%, respectively.
Unsurprisingly, the dense forestlands have significantly the highest SOC content with mean values
of 3.77% (Figure 9) followed by the semidense forestlands (2.90%), low dense forestlands (2.50%),
good rangelands (2.57%), and moderate rangelands (2.03%), respectively. Emadi et al. [58] reported
that the cultivation of virgin forest and pasturelands in Mazandaran province led to about 35 and
30% reduction of SOC content, respectively. The conversion of forest and rangelands into the
croplands induces SOC oxidation whereby the topsoil SOC decreases.

4. Conclusions
The objective of this study was to determine a reliable algorithm for predicting the SOC contents
in Mazandaran province through consideration of six different ML algorithms and using 105
environmental auxiliary variables derived from terrain attributes, remote sensing, and climatic data.
Thirty-five auxiliary predictors were selected by the GA method. Precipitation, NDVI, MODIS day
temperature, MrVBF, and land use were the most important predictors. The results show that the
DNN algorithm outperformed other ML algorithms in terms of the power of the prediction
uncertainty at the province scale demonstrating that DNN is suitable for use as a robust estimator for
SOC mapping in Mazandaran province. The SOC was lower in soils under late geological age
(Cenozoic era), while it is accumulated in more developed Ultisols and Mollisols with virgin forest
and rangelands in udic SMR classes spread across the middle strip of Mazandaran province. The
mesic STR class has significantly higher SOC with high vegetation cover and biomass and probably
with a lower C decomposition rate. The predicted SOC map could be used as a base-line for further
studies and projects related to the C sequestration development both locally in soils of the
Mazandaran province and globally at the worldwide scale. Although the DNN algorithm was found
to be the best algorithm to map SOC contents more accurately than other studied ML algorithms, the
search for optimized spatial interpolation algorithms is still in its early stages in this province.
Moreover, further investigation should be conducted to test the potential of other combination
algorithms in this province and test the reliability of DNN reliability for other regions in Iran with
different climate and agro-ecological structures.
Author Contributions: Conceptualization, M.E., and R.T.-M.; methodology, R.T.-M., and T.S.; software, R.T.-M.;
validation, M.E., A.M., and T.S.; formal analysis, R.T.-M., and T.S.; investigation, M.E., and R.T.-M.; resources,
A.C.; data curation, A.C., and M.D.; writing—original draft preparation, M.E., and R.T.-M.; writing—review and
editing, A.M., and T.S.; visualization, R.T.-M.; supervision, M.E., and R.T.-M. All authors have read and agreed
to the published version of the manuscript.

Funding: This study is financially supported by the Sari Agricultural Sciences and Natural Resources University
(SANRU) (under grant no.T161-1368). The work of Ruhollah Taghizadeh-Mehrjardi has been supported by the
Alexander von Humboldt Foundation under the grant number: Ref 3.4-1164573-IRN-GFHERMES-P. Thomas
Scholten thanks the German Research Foundation (DFG) for supporting this research through the Collaborative
Research Center (SFB 1070) ‘Resource Cultures’ (subprojects Z, S and B02) and the DFG Cluster of Excellence
‘Machine Learning—New Perspectives for Science’, EXC 2064/1, project number 390727645. We thank Ruth
Kerry, Geography Department, Brigham Young University, USA, who thoroughly revised the technical English
of the paper.

Acknowledgments: This study is financially supported by the Sari Agricultural Sciences and Natural Resources
University (SANRU) (under grant no.T161-1368). The work of Ruhollah Taghizadeh-Mehrjardi has been
supported by the Alexander von Humboldt Foundation under the grant number: Ref 3.4-1164573-IRN-
GFHERMES-P. Thomas Scholten thanks the German Research Foundation (DFG) for supporting this research
through the Collaborative Research Center (SFB 1070) ‘Resource Cultures’ (subprojects Z, S and B02) and the
DFG Cluster of Excellence ‘Machine Learning—New Perspectives for Science’, EXC 2064/1, project number
390727645. We thank Ruth Kerry, Geography Department, Brigham Young University, USA, who thoroughly
revised the technical English of the paper.

Conflicts of Interest: The authors declare no conflicts of interest.

Appendix A

Table A1. Environmental auxiliary data initially considered for predicting the distribution of SOC.

No. Covariates Definition

1 Aspect The compass direction of the maximum rate of change
2 Catchment Slope Average gradient above flow path
3 Channel networks base level The interpolated channel network base level elevations
It calculates an index of convergence/divergence regarding to
4 Convergence Index
overland flow
The surface normal and a tangent to the contour—perpendicular to
5 Cross-Sectional Curvature
maximum gradient direction
6 Diffuse Insolation Calculate the diffuse incoming solar radiation
7 Direct Insolation Calculate the direct incoming solar radiation
Calculates the local curvature of a cell as sum of the gradients to its
8 Downslope Curvature
neighbor cells
9 Elevation Height above sea level (m)
10 Flow Accumulation Calculates accumulated flow
The distance from any point in the watershed to the watershed
11 Flow Path Length
outlet
12 Local Curvature The degree to which a curve deviates from a straight line
13 Mass Balance Index Balance between soil mass deposited and eroded
Multiresolution Ridge-top
14 Measure of flatness and lowness
Flatness Index
Multiresolution Valley Bottom
15 Measure of flatness and lowness
Flatness Index
16 Normalized Height Normalized height is defined by slope height and valley depth
17 Openness (NegOpen) How wide a landscape can be viewed from any position
18 Openness (PosOpen) How wide a landscape can be viewed from any position
The curvature of a contour line formed by intersecting a horizontal
19 Plan curvature
plane with the surface
20 Relative Slope Position The position of one point relative to the ridge and valley of a slope
21 Slope Gradient Average gradient above flow path
22 Slope Length Calculate the length of slope
23 Slope Length factor Slope Length and Steepness factor
24 Topographic Wetness index Ln (FA/SG)
25 Total Insolation Calculate the total incoming solar radiation
The distance weighted average local curvature in a cell’s upslope
26 Upslope Curvature
contributing area
27 Valley Depth The vertical distance to a channel network base level
28 Vector Terrain Ruggedness Measures terrain ruggedness
Vertical distance to channel
29 The altitude above the channel network
networks
30 Wind Effect The Wind Effect is a dimensionless index
31 Blue Wavelength of 0.450–0.515 μm of Landsat 8 spectral band
32 Green Wavelength of 0.525–0.600 μm of Landsat 8 spectral band
33 Red Wavelength of 0.630–0.680 μm of Landsat 8 spectral band
34 Near infrared Wavelength of 0.845–0.885 μm of Landsat 8 spectral band
35 Shortwave infrared-1 Wavelength of 1.560–1.660 μm of Landsat 8 spectral band
36 Shortwave infrared-2 Wavelength of 2.100–2.300 μm of Landsat 8 spectral band
37 Principal Component 1 The first principal component of Landsat 8 spectral band
38 Principal Component 2 The second principal component of Landsat 8 spectral band
39 Principal Component 3 The third principal component of Landsat 8 spectral band
40 TASSELED CAP 1 The overall brightness of the image
41 TASSELED CAP 2 The overall greenness of the image
42 TASSELED CAP 3 The overall wetness of the image
Wetness brightness difference
43 TASSELED CAP 3/TASSELED CAP 1
index
 Atmospherically Resistant
44 (−0.18 + 1.17 (NIR − RED/NIR + RED))
Vegetation Index
Blue-Wide Dynamic Range
45 (0.1 × NIR − BLUE)/(0.1 × NIR + BLUE)
Vegetation Index
46 Brightness Index ((RED)2 + (NIR)2)0.5
47 Canopy Index (SWIR-1-GREEN)
48 Carbonate Index (RED/GREEN)
49 Chlorophyll vegetation index (NIR × RED/(GREEN)0.5
50 Clay Index (SWIR-1/SWIR-2)
51 Coloration Index (RED − GREEN/RED + GREEN)
52 Differenced Vegetation Index (NIR − RED)
53 Enhanced Vegetation Index (NIR − RED)/(NIR + C1 × RED − C2 × BLUE + L)
54 Ferrous Minerals (SWIR-1/NIR)
Green Atmospherically
55 (NIR − (GREEN − (BLUE − RED))/(NIR − (GREEN + (BLUE − RED))
Resistant Vegetation Index
56 Green Leaf Index (2 × GREEN − RED − BLUE)/(2 × GREEN + RED + BLUE)
Green Normalized Difference
57 (NIR − GREEN/NIR+ GREEN)
Vegetation Index
58 Green Vegetation Index (0.29 × GREEN − 0.56 × RED + 0.6 × SWIR-1 + 0.49 × GREEN)
59 Green-Blue NDVI (NIR − (GREEN + BLUE)/NIR + (GREEN + BLUE))
60 Green-Red Vegetation Index (GREEN − RED)
61 Gypsum index (SWIR-1 − NIR)/(SWIR-1 + NIR)
62 Hue Index (2 × (RED − GREEN − BLUE))/(GREEN − BLUE)
Infrared Percentage Vegetation
63 (NIR/(NIR+RED))
Index
64 Iron Oxide (RED/BLUE)
65 Leaf Water Content (SWIR-1/SWIR-2)
Modified Soil Adjusted
66 (0.5 × ((2 × (NIR + 1)) − (((2 × NIR) + 1)2 − 8 × (NIR − RED))0.5))
Vegetation Index
67 Near Infrared Ratio (NIR/RED)
68 Norm GREEN (GREEN/(NIR + RED + GREEN))
69 Norm NIR (NIR/(NIR + RED + GREEN))
70 Norm RED (RED/(NIR + RED + GREEN))
71 Normalized Based ((NIR − (BLUE + GREEN)/(NIR + (BLUE + GREEN)))
72 Normalized Canopy Index (SWIR-1 − GREEN/SWIR-1 + GREEN)
Normalized Difference
73 (NIR − SWIR-1)/(NIR + SWIR-1)
Moisture Index
Normalized Difference Salinity
74 (RED − NIR)/(RED + NIR)
Index
Normalized Difference
75 (NIR − RED)/(NIR + RED)
Vegetation Index
Perpendicular Vegetation
76 (NIR − r) cos µ − RED × sin µ
Index
77 Ratio Vegetation Index (NIR/RED)/(GREEN + RED)
78 Redness Index (RED^2/BLUE × GREEN)
79 Reflectance Absorption Index (NIR/(RED + SWIR-1))
Renormalized difference
80 (NIR − RED)/((NIR + RED) ^ 1/2)
Vegetation Index
81 MODIS Red Wavelength of 0.620–0.670 μm of MODIS spectral band
82 MODIS Near Infrared Wavelength of 0.841–0.876 μm of MODIS spectral band
83 MODIS Night Temperature Land Surface Temperature/Emissivity Daily L3 Global 1 km
84 MODIS Day Temperature Land Surface Temperature/Emissivity Daily L3 Global 1 km
MODIS Normalized Difference
85 (MODIS NIR − MODIS RED)/(MODIS NIR + MODIS RED)
Vegetation Index
86 MODIS Brightness Index ((MODIS RED)2 + (MODIS NIR)2)0.5
87 Soil Adjusted Vegetation Index (1+ L) × (NIR − RED)/(NIR + RED + L)
Specific Leaf Area Vegetation
88 (NIR/RED + SWIR-1)
Index
 89 Stress Related ((BLUE× GREEN)/RED)
90 Vegetation Index (SWIR-2 − SWIR-1/SWIR-2 + SWIR-1)
91 Annual Precipitation It is derived from the monthly rainfall values
Precipitation Seasonality
92 It is derived from the monthly rainfall values
(Coefficient of Variation)
93 Precipitation of Wettest Month It is derived from the monthly rainfall values
94 Precipitation of Driest Month It is derived from the monthly rainfall values
95 Mean Annual Temperature It is derived from the monthly temperature values
96 Mean Annual Wind Speed It is derived from the monthly wind speed values
Mean Annual Water Vapor
97 It is derived from the monthly water vapor pressure values
Pressure
Mean Annual Actual Evapo-
98 It is derived from the monthly actual evapo-transpiration values
Transpiration
Mean Annual Potential Evapo-
99 It is derived from the monthly potential evapo-transpiration values
Transpiration
100 Global Aridity Index It shows the rainfall deficit for potential vegetative growth
101 Soil Map Soil and Water Research Institute of Iran
102 Geology Map Soil and Water Research Institute of Iran
103 Land Use Map Soil and Water Research Institute of Iran
104 Physiography Map Soil and Water Research Institute of Iran
105 Erosion Classes Map Soil and Water Research Institute of Iran

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