Improving soil organic carbon predictions from a Sentinel–2 soil composite by assessing surface conditions and uncertainties

Soil organic carbon (SOC) prediction from remote sensing is often hindered by disturbing factors at the soil surface, such as photosynthetic active and non–photosynthetic active vegetation, variation in soil moisture or surface roughness. With the increasing amount of freely available satellite data, recent studies have focused on stabilizing the soil reflectance by building reflectance composites using time series of images. Although composite imagery has demonstrated its potential in SOC prediction, it is still not well established if the resulting composite spectra mirror the reflectance fingerprint of the optimal conditions to predict topsoil properties (i.e. a smooth, dry and bare soil). We have collected 303 photos of soil surfaces in the Belgian loam belt where five main classes of surface conditions were distinguished: smooth seeded soils, soil crusts, partial cover by a growing crop, moist soils and crop residue cover. Reflectance spectra were then extracted from the Sentinel–2 images coinciding with the date of the photos. After the growing crop was removed by an NDVI < 0.25, the Normalized Burn Ratio (NBR2) was calculated to characterize the soil surface, and a threshold of NBR2 < 0.05 was found to be able to separate dry bare soils from soils in unfavorable conditions i.e. wet soils and soils covered by crop residues. Additionally, we found that normalizing the spectra (i.e. dividing the reflectance of each band by the mean reflectance of all spectral bands) allows for cancelling the albedo shift between soil crusts and smooth soils in seed–bed conditions. We then built the exposed soil composite from Sentinel–2 imagery for southern Belgium and part of Noord-Holland and Flevoland in the Netherlands (covering the spring periods of 2016–2021). We used the mean spectra per pixel to predict SOC content by means of a Partial Least Squares Regression Model (PLSR) with 10–fold cross–validation. The uncertainty of the models was assessed via the prediction interval ratio (PIR). The cross validation of the model gave satisfactory results (mean of 100 bootstraps: model efficiency coefficient (MEC) = 0.48 ± 0.07, RMSE = 3.5 ± 0.3 g C kg–1, RPD = 1.4 ± 0.1 and RPIQ = 1.9 ± 0.3). The resulting SOC prediction maps show that the uncertainty of prediction decreases when the number of scenes per pixel increases, and reaches a minimum when at least six scenes per pixel are used (mean PIR of all pixels is 12.4 g C kg–1, while mean SOC predicted is 14.1 g C kg–1). The results of a validation against an independent data set showed a median difference of 0.5 g C kg–1 ± 2.8 g C kg–1 SOC between the measured (average SOC content 13.5 g C kg–1) and predicted SOC contents at field scale. Overall, this compositing method shows both realistic within field and regional SOC patterns

Soil organic carbon prediction using satellite imagery

The concern about the role of soils in the global carbon budget and the effects of soil organic carbon (SOC) decline on soil quality has been incorporated in international treaties. Initiatives such as ‘4 per 1000 Soils for Food Security and Climate’ or ‘The Farm to Fork’ strategy are being implemented in the context of the Paris Agreement to mitigate climate change. This requires a robust measurement, reporting and verification (MRV) system to track that the policy goals are being met. However, difficulties arise when implementing MRV systems, as cost-effective and accurate SOC maps that cover large areas with high spatial and temporal resolution are needed. This PhD thesis assessed the potential of remote sensing to provide a tool for a rapid, repeatable and cost-effective SOC monitoring in croplands. The process of deriving a final soil product is however hindered by the conditions of the soil surface, which needs to be bare, dry and smooth. Therefore, the first objective was to assess the effects of disturbing factors such as soil moisture, crop residues and soil crust on SOC prediction from Sentinel-2 satellite imagery. Secondly, we tested the potential of the created SOC maps as a tool for detecting areas under conservation agriculture. This resulted in an original work as we have: - Defined a methodology that allows obtaining pure soil pixels from Sentinel-2 imagery in Belgium, and - Used a Sentinel-2 derived SOC map and uncertainty map to evaluate the difference in SOC content of conservation agriculture fields from conventional agriculture fields(SC - Sciences) -- UCL, 202

Sentinel-2 Exposed Soil Composite for Soil Organic Carbon Prediction

Pilot studies have demonstrated the potential of remote sensing for soil organic carbon (SOC) mapping in exposed croplands. However, the use of remote sensing for SOC prediction is often hindered by disturbing factors at the soil surface, such as photosynthetic active and non-photosynthetic active vegetation, variation in soil moisture or surface roughness. With the increasing amount of freely available satellite data, recent studies have focused on stabilizing the soil reflectance by building image composites. These composites tend to minimize the disturbing effects by applying sets of criteria. Here, we aim to develop a robust method that allows selecting Sentinel-2 (S-2) pixels with minimal influence of the following disturbing factors: crop residues, surface roughness and soil moisture. We selected all S-2 cloud-free images covering the Belgian Loam Belt from January 2019 to December 2020 (in total 36 images). We then built nine exposed soil composites based on four sets of criteria: (1) lowest Normalized Burn Ratio (NBR2), (2) Normalized Difference Vegetation Index (NDVI) 0.25). We then built a partial least square regression (PLSR) model with 10-fold cross-validation to estimate the SOC content based on 137 georeferenced calibration samples on the nine composites. We obtained non-satisfactory results (R² 2.50 g C kg–1, and RPD 68) for all composites except for the composite in the ‘greening-up’ stage with a NBR2 < 0.07 (R² = 0.54 ± 0.12, RPD = 1.68 ± 0.45 and RMSE = 2.09 ± 0.39 g C kg–1, n = 49). Hence, the ‘greening-up’ method combined with a strict NBR2 threshold allows selecting the purest exposed soil pixels suitable for SOC prediction. The limit of this method might be its coverage of the total cropland area, which in a twoyear period reached 62%, compared to 95% coverage if only the NDVI threshold is applied

Soil Organic Carbon Mapping from Remote Sensing: The Effect of Crop Residues

Since the onset of agriculture, soils have lost their organic carbon to such an extent that the soil functions of many croplands are threatened. Hence, there is a strong demand for mapping and monitoring critical soil properties and in particular soil organic carbon (SOC). Pilot studies have demonstrated the potential for remote sensing techniques for SOC mapping in croplands. It has, however, been shown that the assessment of SOC may be hampered by the condition of the soil surface. While growing vegetation can be readily detected by means of the well-known Normalized Difference Vegetation Index (NDVI), the distinction between bare soil and crop residues is expressed in the shortwave infrared region (SWIR), which is only covered by two broad bands in Landsat or Sentinel-2 imagery. Here we tested the effect of thresholds for the Cellulose Absorption Index (CAI), on the performance of SOC prediction models for cropland soils. Airborne Prism Experiment (APEX) hyperspectral images covering an area of 240 km2 in the Belgian Loam Belt were used together with a local soil dataset. We used the partial least square regression (PLSR) model to estimate the SOC content based on 104 georeferenced calibration samples (NDVI < 0.26), firstly without setting a CAI threshold, and obtained a satisfactory result (coefficient of determination (R2) = 0.49, Ratio of Performance to Deviation (RPD) = 1.4 and Root Mean Square Error (RMSE) = 2.13 g kgC−1 for cross-validation). However, a cross comparison of the estimated SOC values to grid-based measurements of SOC content within three fields revealed a systematic overestimation for fields with high residue cover. We then tested different CAI thresholds in order to mask pixels with high residue cover. The best model was obtained for a CAI threshold of 0.75 (R2 = 0.59, RPD = 1.5 and RMSE = 1.75 g kgC−1 for cross-validation). These results reveal that the purity of the pixels needs to be assessed aforehand in order to produce reliable SOC maps. The Normalized Burn Ratio (NBR2) index based on the SWIR bands of the MSI Sentinel 2 sensor extracted from images collected nine days before the APEX flight campaign correlates well with the CAI index of the APEX imagery. However, the NBR2 index calculated from Sentinel 2 images under moist conditions is poorly correlated with residue cover. This can be explained by the sensitivity of the NBR2 index to both soil moisture and residues

Improving SOC predictions from Sentinel-2 soil composites by assessing surface conditions and uncertainties

SOC prediction from remote sensing is often hindered by disturbing factors at the soil surface, such as photosynthetic active and non-photosynthetic active vegetation, variation in soil moisture or surface roughness. With the increasing amount of freely available satellite data, recent studies have focused on stabilizing the soil reflectance by building reflectance composites using time series of images. Even if SOC predictions from composite images are promising, it is still not well established if the resulting composite spectra mirror the reflectance fingerprint of the optimal conditions to predict topsoil properties (i.e. a smooth, dry and bare soil). We have collected 303 photos of soil surfaces in the Belgium loam belt where five main classes of surface conditions were distinguished: smooth seeded soils, soil crusts, vegetation, moist soils and soils covered by crop residues. Reflectance spectra were then extracted from the Sentinel-2 images coinciding with the date of the photos. The Normalized Burn Ratio (NBR2) was calculated to characterize the soil surface, and a threshold of NBR2 < 0.05 was found to be able to separate wet soils and soils covered by crop residues from dry bare soils. Additionally, we found that normalizing the spectra (i.e. dividing the reflectance of each band by the mean reflectance of all spectral bands) allows for cancelling the albedo shift between soil crusts and smooth soils in seed-bed conditions. We then built the exposed soil composite from Sentinel-2 imagery (covering the spring periods of 2016-2021), and used the reflectance information to predict SOC content by means of a Partial Least Square Regression Model (PLSR) with 10-fold cross-validation. The uncertainty of the models (expressed as q0.05+q0.95/q0.50) was assessed via bootstrapping, where each model was repeated 100 times with a slightly different calibration dataset. The cross validation of the model gave satisfactory results (R² = 0.49 ± 0.10, RMSE = 3.4 ± 0.6 g C kg-1 and RPD = 1.4 ± 0.2). The resulting SOC prediction maps show that (1) the uncertainty of prediction decreases when the number of scenes per pixel increases, and reaches a minimum when more than six scenes per pixel are used (median uncertainty of all pixels is 28% of predicted SOC value) and (2) the uncertainty of prediction diminishes if SOC predictions are aggregated per field (median uncertainty of fields is 22% of predicted value). The results of a validation against an independent data set showed a median difference of 0.5 g C kg-1 ± 2.8 g C kg-1 SOC between the measured and predicted SOC contents at field scale. Overall, this compositing method shows both realistic SOC patterns at the field scale and regional patterns corresponding to the ones reported in the literature

UAV Remote Sensing for Detecting within-Field Spatial Variation of Winter Wheat Growth and Links to Soil Properties and Historical Management Practices. A Case Study on Belgian Loamy Soil

Intra-field heterogeneity of soil properties, such as soil organic carbon (SOC), nitrogen (N), phosphorous (P), exchangeable cations, pH, or soil texture, is a function of complex interactions between biological factors, physical factors, and historic agricultural management. Mapping the crop growth and final yield heterogeneity and quantifying their link with soil properties can contribute to an optimization of amendment/fertilizer application and crop yield in a management variable zones (MVZ) approach. To this end, we studied a field of 17 ha consisting of four former fields that were merged in early 2017 and cropped with winter wheat in 2018. Historical management practices data were collected. The topsoil characteristics were analyzed by grid-based sampling and kriged to create maps. We tested the capacity of a multispectral MicaSense® RedEdge-MTM camera sensor embedded on an unmanned aerial vehicle (UAV) to map in-season growth of winter wheat. Relating several vegetation indices (VIs) to the plant area index (PAI) measured in the field highlighted the red-edge NDVI (RENDVI) as the most suitable to follow the crop growth throughout the growing season. The georeferenced final grain yield of the winter wheat was measured by a combine harvester. The spatial patterns in RENDVI at three phenological stages were mapped and analyzed together with the yield map. For each of these images a conditional inference forest (CI-forest) algorithm was used to identify the soil properties significantly influencing these spatial patterns. Historical management practices of the four former fields have induced significant heterogeneity in soil properties and crop growth. The spatial patterns of RENDVI are rather constant over time and their Spearman rank correlation with yield is similar along the growing season (r ≃ 0.7). Soil properties explain between 87% (mid-March) to 78% (mid-May) of the variance in RENDVI throughout the growing season, as well as 66% of the variance in yield. The pH and exchangeable K are the most significant factors explaining from 15 to 26% of the variance in crop growth. The methodology proposed in this paper to quantify the importance of soil parameters based on the CI-forest algorithm can contribute to a better management of amendment/fertilizer inputs by stressing the most important parameters to take into consideration for site-specific management. We also showed that heterogeneity induced by the soil properties can be described by a crop map early in the season and that this crop map can be used to optimize soil sampling and thus amendment/fertilizer management