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Article

Mapping the Depth-to-Soil pH Constraint, and the Relationship with Cotton and Grain Yield at the Within-Field Scale

by
Patrick Filippi
*,
Edward J. Jones
,
Bradley J. Ginns
,
Brett M. Whelan
,
Guy W. Roth
and
Thomas F.A. Bishop
School of Life and Environmental Sciences, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW 2006, Australia
*
Author to whom correspondence should be addressed.
Agronomy 2019, 9(5), 251; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9050251
Submission received: 20 March 2019 / Revised: 13 May 2019 / Accepted: 15 May 2019 / Published: 21 May 2019
(This article belongs to the Special Issue Precision Agriculture)
Browse Figures
Versions Notes

Abstract

:
Subsoil alkalinity is a common issue in the alluvial cotton-growing valleys of northern New South Wales (NSW), Australia. Soil alkalinity can cause nutrient deficiencies and toxic effects, and inhibit rooting depth, which can have a detrimental impact on crop production. The depth at which a soil constraint is reached is important information for land managers, but it is difficult to measure or predict spatially. This study predicted the depth in which a pH (H2O) constraint (>9) was reached to a 1-cm vertical resolution to a 100-cm depth, on a 1070-hectare dryland cropping farm. Equal-area quadratic smoothing splines were used to resample vertical soil profile data, and a random forest (RF) model was used to produce the depth-to-soil pH constraint map. The RF model was accurate, with a Lin’s Concordance Correlation Coefficient (LCCC) of 0.63–0.66, and a Root Mean Square Error (RMSE) of 0.47–0.51 when testing with leave-one-site-out cross-validation. Approximately 77% of the farm was found to be constrained by a strongly alkaline pH greater than 9 (H2O) somewhere within the top 100 cm of the soil profile. The relationship between the predicted depth-to-soil pH constraint map and cotton and grain (wheat, canola, and chickpea) yield monitor data was analyzed for individual fields. Results showed that yield increased when a soil pH constraint was deeper in the profile, with a good relationship for wheat, canola, and chickpea, and a weaker relationship for cotton. The overall results from this study suggest that the modelling approach is valuable in identifying the depth-to-soil pH constraint, and could be adopted for other important subsoil constraints, such as sodicity. The outputs are also a promising opportunity to understand crop yield variability, which could lead to improvements in management practices.

1. Introduction

Many soils possess a chemical or physical characteristic that constrains crop production, with the mechanism of growth inhibition varying depending on the nature of the constraint. The soils of the alluvial grain and cotton-growing valleys of eastern Australia have many desirable physical and chemical characteristics that make them highly suitable for cropping, but soil constraints are still widespread and can significantly reduce crop yields. Some of the most common soil constraints in this region are high levels of salinity, sodicity, alkalinity, and compaction [1], particularly in the subsoil, but still within the rooting zone of crops. Soil salinity [2,3], sodicity [4,5], and compaction [6,7], and their impact on crops in these regions have received much attention however, there has been little emphasis on soil alkalinity constraints.
While subsoil acidity is a widespread problem in other parts of Australia [8], subsoil alkalinity is a more localized issue, and has consequently received less consideration in the literature. Many of the soils in the cotton-growing valleys of eastern Australia are intrinsically alkaline due to the presence of calcium and sodium carbonates, and this generally increases with depth [9]. Soils with a high pH can limit the plant availability of certain nutrients, as well as cause toxicities [10]. At toxic levels, root growth is inhibited, decreasing the amount of water and nutrients that can be accessed, producing a detrimental impact on crop production [1]. The optimum pH (H2O) range for most crops is generally from 5.5 to 7, but this differs for individual crop types [11]. In soil with a pH (H2O) of nine or greater, it is likely that most crops would experience boron toxicity [12], as well as a considerable reduction in the availability of important macro and micronutrients, including phosphorus, nitrogen, calcium, magnesium, iron, copper, and zinc [13]. A pH (H2O) greater than nine also suggests the presence of sodium carbonates and high levels of soil sodicity, which indicates poor structural condition [12].
Soil pH, and the depth at which a soil pH constraint is reached, can significantly vary across fields [14], and this can result in spatially variable crop yields [15]. Digital soil mapping (DSM) has been used extensively for evaluating the spatial distribution of soil pH at a range of spatial extents, from the field [13], to the world [16]. Some studies solely produce pH maps for the topsoil (e.g., Kirk et al. [17]), which lacks important information about subsoil pH. Other studies create maps of several depth increments (e.g., Filippi et al. [18]), but this is often too much information from which to easily make management decisions. The typical broadacre farmer in Australia now has access to a plethora of data and information that relate to their farms [19], which is a great opportunity, but also a challenge to gain useful insights. For a farmer that is experiencing a subsoil pH constraint in parts of their farm, a single map of the depth at which that pH constraint begins would be invaluable. This would assist in identifying areas where crop rooting depth may be inhibited, and help farmers implement management practices to either rectify the issue or alter inputs according to the constrained production potential. It is important to know the depth at which a pH constraint is reached within a fine vertical resolution (e.g., 1 to 10 cm). However, most soil maps are produced at coarse resolutions, particularly deeper in the soil profile. For example, the Globalsoilmap specifications are at 0–5, 5–15, 15–30, 30–60, 60–100, and 100–200 cm [16], and this creates difficulty in identifying exactly at what depth pH is a limiting factor.
There has been limited focus in the literature on mapping the depth of soil constraints. The study reported here uses a novel modelling approach to predict and map the depth-to-soil pH constraint (high alkalinity: pH >9 (H2O)) on a dryland cotton and grain farm in the Namoi Valley in northern New South Wales (NSW), Australia. A collection of spatial and temporal datasets were used for modelling and mapping the depth-to-soil pH constraint, and the relationship with grain and cotton yield mapping data was assessed.

2. Methods

2.1. Study Site

This study was conducted on a mixed farming property—L’lara (30°15′18″ S, 149°51′39″ E), which is located near Narrabri in the Namoi Valley in northern NSW, Australia. Summers in Narrabri are very hot, while winters are cool. The long-term average precipitation for the study area is 658.5 mm, and is summer-dominant [20]. The farm consists of 780 hectares of uncropped dryland grazing on primarily native perennial pastures, and 1070 hectares of summer and winter dryland broadacre cropping (Figure 1). The cropped area was the focus of this study, where cotton (Gossypium hirsutum L.), and winter wheat (Triticum aestivum L.) are the dominant crops grown, with additional rotations of canola (Brassica napus L.), and chickpea (Cicer arietinum L.). The soils of the cropping fields at L’lara are classed as grey or brown Vertosols according to the Australia Soil Classification [21]. These soils are primarily derived from alluvial deposits of basaltic sediments from the western side of the Nandewar range.

2.2. Legacy Soil Data

Soil data from 80 locations sampled across the cropping fields in July 2017 were available. Two subsamples were extracted from the 0–0.1- and 0.4–0.5-m depth increments of each sampling location, resulting in a total of 160 subsamples. All soil subsamples were air dried, and ground to <2 mm fraction. Soil pH was analyzed in 1:5 soil:water extracts using a Mettler Toledo S220 SevenCompact™ pH/Ion meter (Mettler Toledo, Colombus, OH, USA).

2.3. Additional Soil Data

Soil samples at an additional 30 sites were also collected. The locations of these soil sampling sites were determined with a stratified random sampling methodology utilizing k-means clustering for strata identification [22]. The spatial and temporal data used and the details of the clustering analysis and sampling/analysis are described in the following two subsections.

2.3.1. Data Used in Clustering Analysis

To guide where additional soil samples would be taken, spatial clusters were created using publicly available data. These data consisted of digital soil maps, a digital elevation model, air-borne gamma radiometric data, and remotely sensed satellite imagery. Digital maps of soil clay content at 90-m resolution for the 0–5-, 5–15-, 15–30-, 30–60-, and 60–100-cm depth increments were obtained from the Soil Landscape Grid of Australia (SLGA) [23]. Hydrologically corrected digital elevation model (DEM) data was used from the Shuttle Radar Topography Mission (SRTM) [24]. Air-borne gamma radiometrics data for the study area at 90-m spatial resolution were obtained from Geoscience Australia. Low-pass filtering was used on all radiometric products [25]. Google Earth Engine (GEE) [26] was used to access Landsat 7 Tier 1 surface reflectance satellite imagery. A cloud-masking filter was applied to remove all pixels that were affected by cloud cover, and the 10th, 50th and 90th percentile statistics were calculated from all images that fell within 1 January 2000, to 31 December 2017. These statistics were selected to not only represent the most common value, but the lower and upper distribution of the imagery. From this, two outputs were extracted; (1) the Normalized Difference Vegetation Index (NDVI), and (2) the red band. The NDVI was used to map changes in biomass throughout the production history and build a pattern of production potential across the farm. The red band was used separately as a representation of topsoil color. All spatial data were extracted onto a single 30-m grid using the nearest neighbor method.

2.3.2. Clustering Analysis and Site Selection

To create clusters of the study area with the data sources described above, k-means clustering for strata identification was implemented using the statistical program JMP® Pro 11 (SAS Institute, Cary, NC, USA). The optimum number of clusters for the study area was found to be eight (Figure 2), and this was determined via the elbow method [27]. The elbow method looks at the relationship between the number of clusters and the proportion of variance explained and helps to identify the point where adding another cluster would provide marginal gain. The area of each cluster varied from 39 to 228 ha. The 30 soil sampling locations were selected randomly within each cluster, with the number of sites per cluster proportional to the area of each cluster (Figure 2).

2.3.3. Sampling Details

Soil cores at the 30 sites were extracted to a 1.0-m depth in July 2018. The cores were then subdivided into five depth intervals (0–0.1, 0.1–0.3, 0.3–0.6, 0.6–0.8, and 0.8–1.0 m), resulting in a total of 150 subsamples. Equally to the legacy data, the subsamples were then air dried, and ground to <2 mm fraction, and soil pH analyzed in 1:5 soil:water extracts with a Mettler Toledo S220 SevenCompact™ pH/Ion meter (Mettler Toledo, Colombus, OH, USA).

2.4. Vertical Depth Modelling/Resampling of Profiles

Equal-area quadratic smoothing splines were fitted to the soil pH data for each of the 110 individual soil sampling sites [28,29]. This was implemented using the ‘ithir’ package in R [30]. Rather than aggregating this for a few standard depth intervals as is common, data were stored at the 1-cm resolution in which it was fitted. This produced estimates of pH at 1-cm increments down each soil profile. Data were only predicted between the surface and deepest depth sampled. Consequently, the 30 soil profiles with 100 cm extracted resulted in 100 pH estimates per profile, and the 80 sites extracted to 50 cm resulted in 50 pH estimates per profile.

2.5. Modelling and Mapping of Soil pH

2.5.1. Data used for Modelling/Mapping Soil pH

The data used for modelling/mapping soil pH across the study area consisted of data collected on-farm, and data from publicly available databases (Table 1; Figure 3). A proximal soil sensing survey was conducted to collect high-resolution apparent soil electrical conductivity (ECa) and gamma radiometrics data. Soil ECa was measured via electromagnetic induction using a DUALEM-21S instrument (Dualem Inc., Milton, ON, Canada). Gamma radiometric data were recorded using an RSX-1 gamma radiometric detector with a 4 L sodium iodine crystal (Radiation Solutions Inc., Mississauga, ON, Canada). The proximal soil sensing survey was conducted on 24-m swaths, and the position was recorded with differential GPS (DGPS) equipment. Continuous surface layers were obtained by kriging with local variograms [31] onto a standard 5-m grid through the software VESPER [32]. A 5-m resolution DEM was also obtained from Spatial Services, NSW Government [33]. The 90th percentile red band image from Landsat 7 described in the previous section was also used in this analysis. All spatial data were then extracted onto a single 5-m resolution grid using the nearest neighbor method.

2.5.2. Modelling/Mapping Procedure

At each of the 110 soil sampling locations, the corresponding on-farm and publicly available data described in Table 1 were collated. A model to predict the relationship between soil pH at 1-cm increments and these covariates was then created using a random forest model [34]. The ‘ranger’ package in the software R was used to create the model, which is essentially a fast implementation of random forests for high dimensional data [35]. Instead of one model for each depth increment, all were modelled together. This was possible, as each depth (at a 1-cm increment) was stacked in the data frame, and depth was then included as a predictor variable. More specifically, the central depth between the upper and lower depths was used (e.g., 0.5 cm for the 0–1-cm depth interval, and 99.5 for the 99–100-cm depth interval). This model was then used to predict onto the 5-m grid of the study area using the spatially distributed covariate dataset. This was done at each 1-cm increment down to 100 cm, resulting in 100 maps. The depth in which the pH first reached a value of 9 or greater was then identified for each 5-m grid point. A pH of 9 (H2O) was selected, as this is an indicator of when significant constraints to growth for most crops is reached as described previously. This information was then mapped across the study area, showing the depth-to-high soil pH constraint.

2.5.3. Model Quality and Validation

The quality of the model was tested by using leave-one-site-out cross-validation (LOSOCV). This entailed iteratively removing all soil data from each site, which ensured that data from different depth increments of the same soil core were not included in both the calibration and validation datasets. This LOSOCV was performed at all 110 sites, with 109 sites used to predict the remaining site each time. The results of the validation at every site were then combined, and the Lin’s concordance correlation coefficient (LCCC) [36] and the RMSE (root-mean-square error) were used to assess the quality of the model predictions. This cross-validation procedure was performed in two ways: (1) at 1-cm vertical resolution (the splined observed pH data vs. the independently predicted pH data) and (2) at the original sampling depths of the observed data (observed pH data vs. predicted pH data at a 1-cm resolution aggregated to the original sampling depths). The rationale for this was that the splining procedure introduces some amount of uncertainty to the data [37] and validating by the second approach avoids this limitation as the predicted data are compared to the original, un-splined soil pH data. To test the importance of different predictor variables in the model, the mean decrease in accuracy was used, which is based on the mean square error (MSE). This shows the amount by which the random forest model prediction accuracy would decrease if that particular variable is excluded. The larger the mean decrease in accuracy for a predictor variable, the more important that variable is deemed. All data analysis was performed in the open-source software R [38].

2.6. Crop Yield Data and the Relationship with Depth-to-Soil pH Constraint

2.6.1. Crop Yield Data

Yield data from an on-harvester monitoring system was used to analyze the relationship with the depth-to-soil pH constraint. This yield monitor data consisted of a variety of broadacre crops from two fields—Campey 4/5 (C4/5) which is 61 ha in size, and L’lara 2 (L2) which is 183 ha. For C4/5, canola was grown in 2016, and chickpea in 2017 (Figure 4a). For L2, wheat was grown in 2016, and a summer cotton crop in 2017/2018 (Figure 4b). The raw yield monitor data were processed by removing spurious and extreme values following the method of Taylor et al. [39]. VESPER software was then used to krige the yield data onto the same 5-m grid as the soil modelling/mapping covariate data. The final surfaces were corrected and standardized using field total yields (grain weight at silo, or sum of bales of cotton harvested). A 30-m internal buffered zone was applied around the paddock boundaries to remove the low-yielding edge effects, and a 20-m buffer was also placed on the contour banks in L2 (Figure 4a,b). The rationale for removing these yield values was because the cause of low yield in these areas would likely be related to other factors as well as potential high soil pH.

2.6.2. Relationship of Crop Yield Data with Depth-to-Soil pH Constraint Data

The predicted depth-to-high soil pH constraint data and the yield data were mapped on the same 5-m grid, allowing the relationship to be easily analyzed. Boxplots were used to assess this, where data were grouped in 10-cm intervals (depth-to-soil pH constraint), showing how the distribution of yield data changed as the depth-to-soil pH constraint changed for each paddock and crop/season. The Spearman rank-order correlation coefficient, rs, was also used to assess this relationship. Spearman’s correlation is a nonparametric measure of the direction and strength of a relationship that exists between two variables based on their ordered ranks. The median yield value was calculated for each 1-cm depth interval, and the rs was then reported.

3. Results

3.1. pH Variability in the Study Area

Soil pH values varied considerably across the study area in the top 100 cm, with a low of 6.1 at 0–10 cm, and a high of 10.2 at 30–60 cm (Figure 5). As depth increased, median soil pH values increased, and the variability of observations decreased. Soil pH was generally alkaline, with a mean soil pH of 8.2 in the shallowest layer (0–10 cm), rising to a mean pH of 9.3 in the deepest layer (80–100 cm).

3.2. Depth-to-Soil pH Constraint

The depth-to-high soil pH constraint map showed considerable spatial variability across the study area (Figure 6). In total, 77% of the cropping fields had a strongly alkaline pH of nine somewhere within the top 100 cm (Table 2). The eastern section of the study area was largely unconstrained, with much of the middle section becoming constrained at 31–40 cm. The south-western section of L’lara had high spatial variability in constraint conditions, with areas that were constrained in the top 1–10 cm, and unconstrained within 100 cm, all within a short distance.

3.3. Model Quality and Variable Importance

For the random forest model, the validated results showed an LCCC of 0.63, and an RMSE of 0.47 using LOSOCV when tested on the splined 1 cm data, and an LCCC of 0.66 and RMSE of 0.51 using LOSOCV when tested on the aggregated data at the original sampling depths (Table 3). These statistics suggest that the model could spatially predict soil pH accurately (within ~0.5 pH units). Visual examples of the validation of soil pH predictions at 1-cm increments are shown in Figure 7, where Figure 7a shows the mean observed and predicted soil pH of all sampling sites, and Figure 7b for a single randomly selected sampling site (Site 16). The soil pH predictions in these figures were created using an independent calibration. This demonstrates that the random forest model can predict the vertical distribution of soil pH.
The plot of the predictor variable importance showed that proximally sensed gamma radiometric K was the most important predictor of soil pH (Figure 8). This was closely followed by depth, and then other horizontally variable predictors, such as DEM, and soil ECa. Landsat 7 data of the 90th percentile red band from the period 2000–2017 proved to be the least important predictor of soil pH, suggesting that this only represents a small component of soil spatial variation.

3.4. The Relationship with Crop Yield and the Depth-to-Soil pH Constraint

Two fields, C4/5 and L2, were used to assess the relationship between yield monitor data and the predicted depth-to-soil pH constraint data. These fields were selected due to the availability of yield data, and the variation in the depth in which a pH of 9 was predicted across the field (Figure 6). Boxplots were used to describe this relationship, with the grouping of yield data at 10-cm depth-to-soil pH constraint intervals (Figure 9a,b). The 1–10 and 11–20 cm (to constraint) data are not used due to the very few locations reaching a pH greater than 9 in the upper 20 cm. It was clear that as a soil pH constraint (>9) was deeper in the soil profile, the yield of most crops increased (Figure 9a,b). For all grain crops, the lowest median yield was observed where a soil pH constraint was reached in the shallowest, well-observed layer (21–30 cm), and the highest median yield was observed where soil was deemed unconstrained by pH in the top 100 cm. A clear spatial correlation can also be seen between the grain crop yield maps (Figure 4a,b) and the depth-to-soil pH constraint map (Figure 6). For cotton, the lowest median yield was observed where a soil pH constraint was reached in the shallowest layer (21–30 cm), and an increase in median yield was observed as the depth-to-soil pH constraint increased to 61–70 cm. However, this plateaued and slightly declined after this depth. The Spearman’s correlation analysis revealed that the relationship between the predicted depth-to-soil pH constraint data and yield monitor data ranged from strong to weak (Table 4). The strongest relationship was found with wheat (rs = 0.75), followed by canola (rs = 0.66), chickpea (rs = 0.58), and then cotton (rs = 0.37).

4. Discussion

4.1. Soil Alkalinity and Depth-to-Soil pH Constraint

Soil pH was generally alkaline and increased with depth. This is typical of Vertosols in the cotton-growing valleys, and other studies in similar areas concur [18,40]. The depth in which a soil pH greater than nine was reached was shown to be highly spatially variable across the study area. Over half of the total area reached a pH of 9 within the shallow subsoil (21–40 cm), and approximately 77% of the area possessed an alkalinity constraint somewhere in the top 100 cm of the soil profile. Soil alkalinity is often an inherent feature of the soils in these landscapes. However, it is possible that the distribution of soil pH is being impacted by cultivation practices, which could be bringing the more alkaline subsoils closer to the surface. Alkalinity in these soils are generally due to the presence of calcium carbonates, but the extremely high pH values (>9) also indicate that sodium carbonates are present. The presence of sodium carbonates also suggests that these soils possess high levels of soil sodicity [41]. While alkalinity can reduce nutrient accessibility, cause toxicities, and inhibit root growth for crops, soil sodicity is also known to have adverse impacts on crop productivity through waterlogging and soil structural decline.

4.2. Modelling/Mapping

4.2.1. Modelling/Mapping Approach and Validation

The random forest model could predict the spatial distribution of soil pH well, and the approach proved successful in identifying the depth-to-soil pH constraint at a 1-cm vertical resolution to a 100-cm depth. The LOSOCV on the splined 1-cm data showed an LCCC of 0.63, and an RMSE of 0.47, and an LCCC of 0.66 and RMSE of 0.51 when tested on the data at the original sampling depths. The fact that these two cross-validation techniques showed very similar validation statistics is optimistic. The second cross-validation approach validates predictions with the original, un-splined data, which suggests that the splining procedure is creating a relatively small amount of uncertainty in the data, giving confidence in the developed mapping approach.
While this study was performed on a 1070-ha farm, there is promise for implementing this approach over larger areas. However, the fine-resolution splining of soil property data results in a much larger amount of data compared to typical DSM methods, and implementing this with very large datasets could become computationally restrictive. One opportunity to reduce the computational load of this approach is to fit the soil property at 5-cm increments with the splines as opposed to 1-cm increments. This would still be at a fine enough vertical resolution to inform management decisions for land managers but would significantly reduce the dataset size. An alternative would be to use the approach of Orton et al. [37] who presented a geostatistical approach to predict in 3D at any vertical resolution using observations from different vertical supports (e.g., soil horizons). This would remove the need for using splines to create the finely spaced vertical dataset. Adopting the approach by Orton et al. [37] also bypasses the uncertainty introduced by the splining process, although, as discussed, the results in the current study suggested that this was relatively small (Table 3). The uncertainty in imputed values is commonly ignored in DSM studies that use splined soil data.
Few studies have used DSM approaches to map the depth-to-soil constraints, but there has been considerable research in mapping the depth to bedrock [42,43,44]. The methods used in these studies are essentially traditional DSM approaches, and differ significantly from the current study. For example, data for the depth to which bedrock is reached is commonly available from mining exploration and bore hole drilling exercises, and Wilford et al. [44] used a database of these observations to create depth-to-bedrock maps of Australia using a Cubist model. In contrast, rather than use direct observations of the depth of the target variable/constraint, the current study uses splined soil pH data, and machine learning to predict the depth in which an alkalinity constraint is reached at each 1-cm vertical increment, which is then combined to create a depth-to-soil pH constraint map. It is typically not easy to identify the depth at which a soil constraint occurs in the field, but this approach helps overcome this. Another advantage of the approach used in this study is that it could be applicable to any soil property, not just soil alkalinity.

4.2.2. Predictor Variables

Only four spatial predictor variables were used for modelling and mapping (Table 1), whereas most other DSM studies use a much larger suite of predictor variables. The rationale for this was that the variables used in the current study were of a fine spatial resolution (5–30 m), with the on-farm collected data (ECa and gamma radiometrics) known to reflect soil spatial variability very well. The most important covariate for the soil pH random forest model was proximally sensed gamma radiometrics K (5 m). This covariate is often highly correlated with soil type and represents fine-scale soil spatial variability due to intensive measurements collected in this study. The second most important covariate for the soil pH random forest model was depth, which is logical, as pH in these soils increases as depth increases. The model could predict the vertical distribution of soil pH well, and this is due to the inclusion of depth as a predictor variable. This concept is demonstrated in Figure 7. The DEM data (5 m) represented broader trends across the study area and possessed lower short-range spatial variability (Figure 4), but this proved to be an important predictor variable. The ECa data (5 m) was the second least important predictor, as the high spatial variability (Figure 4) did not seem to represent the spatial variation of soil pH particularly well. The least important predictor was the 90th percentile red band (30 m), which could be due to the coarser spatial resolution compared to the other predictor variables, and that it did not sufficiently reflect the spatial distribution of soil pH.

4.3. Relationship between Depth-to-Soil pH Constraint and Crop Yield

The relationship between the depth-to-soil pH constraint map and cotton and grain yield was explored for fields C4/5 and L2. It was clear that the deeper in the soil profile a pH constraint greater than nine was reached, the yield of all crops generally increased. The relationship between yield and the depth-to-soil pH constraint data was stronger for the grain crops than for cotton. The Spearman’s correlation was highest for wheat (rs = 0.75), followed by canola (rs = 0.66), chickpea (rs = 0.58), and then cotton (rs = 0.37). This suggests that cotton was relatively unaffected by an alkalinity constraint compared to the grain crops. Cotton is almost solely grown in the alkaline Vertosols of the alluvial valleys of eastern Australia and is therefore well-accustomed to these soils. This could be a possible reason for the weaker relationship. However, crop yield is a function of climate, soil, and management, and their interaction, and this could vary from season to season [45]. Future research should focus on using a longer time-series of yield data to assess the variation in the relationship between yield and the depth-to-soil pH constraint to account for this. The approach developed in this study should also be applied to a larger spatial extent in the future, as this information could be useful in identifying constraints to yield at a broader scale to guide policy decisions.
In field C4/5, similar spatial patterns were observed for canola in 2016 and chickpea in 2017. In contrast, the wheat yield maps in 2016 and the cotton yield maps in 2017/2018 showed some differing spatial patterns, with some of the highest yielding areas for cotton being the lowest yielding for wheat. These inconsistently yielding or flip-flop patterns have been commonly observed in other studies [45,46,47], and often point to a temporary constraint, rather than a permanent soil constraint such as high soil pH levels. Despite the important role that soil pH plays on crop productivity, few studies have looked at the impact of within-field soil pH variability on crop yield, let alone how the depth-to-soil pH constraint relates to this. Shatar and McBratney [48] assessed the relationship between soil pH (15–30 cm) and sorghum yield, and found that pH was a limiting factor in some areas of the field. A study by Schepers et al. [49] also found that management zones (MZ) with varying pH levels within a field displayed a marked difference in corn grain yield over several seasons. The MZ with the lowest mean pH (6.41) showed the highest yield, and the MZ with the highest mean pH (7.43) displayed the lowest yields. In contrast, Adeoye and Agboola [50] saw a significant positive correlation between the soil pH and the relative yield of maize.
The results found in this study suggest that the depth-to-soil pH constraint can directly influence crop yield. However, as aforementioned, these very high levels of soil pH are a strong indicator that soil sodicity is also an issue. Soil sodicity is a common issue in the alluvial Vertosols of eastern Australia [4,51,52] and is deemed to be one of the biggest constraints to crop production in these regions [1]. High sodicity levels of soil have a greater capacity to inhibit root growth than high pH levels. This results in a smaller volume of soil that is accessible to crops, and consequently a smaller amount of water and nutrients available for crop development [53]. Further research should look at soil sodicity and the impact it has on crop yield variability in the study area. Future work should also use the approach presented to estimate the reduction in the soil water holding capacity and therefore yield potential, caused by soil constraints.

5. Conclusions

High levels of soil alkalinity were observed in the study area, particularly at depth. The random forest model to predict soil pH distribution showed high quality predictions when testing with LOSOCV, with an LCCC of 0.63–0.66, and an RMSE of 0.47–0.51. The overall approach to identify the depth at which a pH alkalinity constraint (>9) occurred at fine vertical resolution (1 cm) at a farm scale proved successful and showed promise for identifying other important subsoil constraints. The study revealed that the shallower in the soil profile a pH constraint was reached, the generally smaller the crop yield. A strong relationship was found for wheat, canola, and chickpea, with a weaker relationship for cotton. The output of a single map showing the depth at which a soil alkalinity constraint occurs is a valuable, concise piece of information for farmers and land managers, and is a promising avenue to guide the remediation of soil constraints, or the tailoring of crop management inputs to account for these constraints.

Author Contributions

Conceptualization, P.F. and T.F.A.B.; Formal analysis, P.F., E.J.J. and B.J.G.; Investigation, B.J.G.; Methodology, P.F., E.J.J., B.M.W. and T.F.A.B.; Project administration, P.F.; Resources, G.W.R.; Validation, P.F. and T.F.A.B.; Writing—original draft, P.F. and B.J.G.; Writing—review and editing, P.F., E.J.J., B.M.W., G.W.R. and T.F.A.B.

Funding

This research was partly funded by grants provided by the Cotton Research and Development Corporation (DAN1801, US1802), the Grains Research and Development Corporation (US00087), and the University of Sydney.

Acknowledgments

Thank you to the two anonymous reviewers for their helpful feedback, and to the Commercial Cropping Supervisor of L’lara—Kieran Shephard, for his assistance in gathering the data.

Conflicts of Interest

The authors declare no conflict of interest.

References

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Figure 1. The arrangement of the cropping fields at L’lara, and the location within northern New South Wales (NSW), Australia.
Figure 1. The arrangement of the cropping fields at L’lara, and the location within northern New South Wales (NSW), Australia.
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Figure 2. The distribution of the eight clusters derived from a k-means clustering analysis, and the locations of the soil sampling sites across the study area.
Figure 2. The distribution of the eight clusters derived from a k-means clustering analysis, and the locations of the soil sampling sites across the study area.
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Figure 3. The data sources used for digital soil mapping. (a) Soil ECa (0–3.0 m) from a Dual EM-21S, (b) Gamma radiometrics K, (c) DEM, and (d) the 90th percentile (2000–2017) red band from Landsat 7.
Figure 3. The data sources used for digital soil mapping. (a) Soil ECa (0–3.0 m) from a Dual EM-21S, (b) Gamma radiometrics K, (c) DEM, and (d) the 90th percentile (2000–2017) red band from Landsat 7.
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Figure 4. (a), Canola yield for the 2016 season (left), and chickpea yield for the 2017 season (right) from a yield monitor for field Campey 4/5 (C4/5). (b), Wheat yield for the 2016 season (left), and cotton yield for the 2017/18 season (right) from a yield monitor for field L’lara 2 (L2).
Figure 4. (a), Canola yield for the 2016 season (left), and chickpea yield for the 2017 season (right) from a yield monitor for field Campey 4/5 (C4/5). (b), Wheat yield for the 2016 season (left), and cotton yield for the 2017/18 season (right) from a yield monitor for field L’lara 2 (L2).
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Figure 5. Boxplots of the distribution of soil pH (1:5 H2O) with depth for 110 soil cores taken from cropping fields at L’lara. Solid black lines inside boxes represent median values, and the dashed, vertical grey line indicates the pH (H2O) threshold of nine, deemed to have potential constraining effects on crop growth.
Figure 5. Boxplots of the distribution of soil pH (1:5 H2O) with depth for 110 soil cores taken from cropping fields at L’lara. Solid black lines inside boxes represent median values, and the dashed, vertical grey line indicates the pH (H2O) threshold of nine, deemed to have potential constraining effects on crop growth.
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Figure 6. Digital soil map of the depth in which soil pH constraint (>9) is reached across the study area.
Figure 6. Digital soil map of the depth in which soil pH constraint (>9) is reached across the study area.
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Figure 7. Observed soil pH data splined using equal-area quadratic smoothing splines (black circles), and independently validated predicted data from the random forest model (blue circles) for the mean of all soil sites (a) and an example soil profile, Site 16 (b). The observed soil pH data at the sampled depth increments (solid black lines) for Site 16 is also shown in (b). The red dashed line represents the pH threshold of nine (H2O).
Figure 7. Observed soil pH data splined using equal-area quadratic smoothing splines (black circles), and independently validated predicted data from the random forest model (blue circles) for the mean of all soil sites (a) and an example soil profile, Site 16 (b). The observed soil pH data at the sampled depth increments (solid black lines) for Site 16 is also shown in (b). The red dashed line represents the pH threshold of nine (H2O).
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Figure 8. Mean decrease in accuracy showing the predictor variable importance in predicting soil pH.
Figure 8. Mean decrease in accuracy showing the predictor variable importance in predicting soil pH.
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Figure 9. (a) Boxplots of the relationship of crop yield data with the predicted depth-to-high soil pH constraint data for field Campey 4/5. (b) Boxplots of the relationship of crop yield data with the predicted depth-to-high soil pH constraint data for field L’lara 2.
Figure 9. (a) Boxplots of the relationship of crop yield data with the predicted depth-to-high soil pH constraint data for field Campey 4/5. (b) Boxplots of the relationship of crop yield data with the predicted depth-to-high soil pH constraint data for field L’lara 2.
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Table
Table 1. Description of the data sources used in the mapping analysis.
Table 1. Description of the data sources used in the mapping analysis.
Data TypeData DescriptionResolution
On-farmECaDual EM-21S (0–3.0 m)5 m
Gamma radiometricsPotassium (K) 5 m
PublicElevation DEM5 m
Landsat 7—red band90th percentile (2000–2017)30 m
Table
Table 2. The area constrained at various depth intervals where pH >9 is first observed.
Table 2. The area constrained at various depth intervals where pH >9 is first observed.
Depth (cm)0–1011–2021–3031–4041–5051–6061–7071–8081–9091–100Unconstrained within 100 cm
Area (ha)1116183339128512332374245
Area (%)1.01.517.131.712.04.82.23.03.50.323.0
Table
Table 3. Validation prediction statistics for the soil pH model using leave-one-site-out cross-validation (LOSOCV) at a splined 1-cm resolution, and at the original sampling depth resolution.
Table 3. Validation prediction statistics for the soil pH model using leave-one-site-out cross-validation (LOSOCV) at a splined 1-cm resolution, and at the original sampling depth resolution.
Validation ResolutionLin’s Concordance Correlation Coefficient (LCCC)Root Mean Square Error (RMSE)
Splined 1 cm0.630.47
Original sampling depth0.660.51
Table
Table 4. The Spearman’s correlation (rs) of the relationship between the depth-to-soil pH constraint map data and the median yield value for each 1-cm depth increment to 100 cm.
Table 4. The Spearman’s correlation (rs) of the relationship between the depth-to-soil pH constraint map data and the median yield value for each 1-cm depth increment to 100 cm.
Campey 4/5L’lara 2
Canola ‘16Chickpea ‘17Wheat ‘16Cotton ‘17/18
rs0.660.580.750.37

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Filippi, P.; Jones, E.J.; Ginns, B.J.; Whelan, B.M.; Roth, G.W.; Bishop, T.F.A. Mapping the Depth-to-Soil pH Constraint, and the Relationship with Cotton and Grain Yield at the Within-Field Scale. Agronomy 2019, 9, 251. https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9050251

AMA Style

Filippi P, Jones EJ, Ginns BJ, Whelan BM, Roth GW, Bishop TFA. Mapping the Depth-to-Soil pH Constraint, and the Relationship with Cotton and Grain Yield at the Within-Field Scale. Agronomy. 2019; 9(5):251. https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9050251

Chicago/Turabian Style

Filippi, Patrick, Edward J. Jones, Bradley J. Ginns, Brett M. Whelan, Guy W. Roth, and Thomas F.A. Bishop. 2019. "Mapping the Depth-to-Soil pH Constraint, and the Relationship with Cotton and Grain Yield at the Within-Field Scale" Agronomy 9, no. 5: 251. https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy9050251

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