Bare Earth's Surface Spectra as a Proxy for Soil Resource Monitoring

Metagenomic approaches and opportunities in arid soil research

Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.

Increasing and fluctuating resource availability enhances invasional meltdown

Exotic plant invaders can promote others via direct or indirect facilitation, known as "invasional meltdown." Increased soil nutrients can also promote invaders by increasing their competitive impacts, but how this might affect meltdown is unknown. In a mesocosm experiment, we evaluated how eight exotic plant species and eight Eurasian native species responded individually to increasing densities of the invasive plant Conyza canadensis, while varying the supply and fluctuations of nutrients. We found that increasing density of C. canadensis intensified competitive suppression of natives but intensified facilitation of other exotics. Higher and fluctuating nutrients exacerbated the competitive effects on natives and facilitative effects on exotics. Overall, these results show a pronounced advantage of exotics over native target species with increased relative density of C. canadensis under high nutrient availability and fluctuation. We integrate these results with the observation that exotic species commonly drive increases in soil resources to suggest the Resource-driven Invasional Meltdown and Inhibition of Natives hypothesis in which biotic acceleration of resource availability promotes other exotic species over native species, leading to invasional meltdown.

Geotechnologies on the phosphorus stocks determination in tropical soils: General impacts on society

Phosphorus (P) is a critical nutrient for primary production in terrestrial and aquatic ecosystems. As P mineral reserves are finite and non-renewable, there is an increasing discussion on its sustainable utilization to safeguard food security for future generations. Understanding the spatial distribution of soil P is central in advancing effective phosphorus management and fostering sustainable agricultural practices. This study aims to digitally map the stocks of available P (AP) and total P (TP) in Brazil at a fine resolution (30 m). Using the Random Forest machine learning algorithm and a database of topsoil (0-20 cm) with 28,572 samples for AP and 3154 for TP, we predicted P stocks based on environmental covariates related to soil formation processes. By dividing Brazil into two sub-regions, representing areas with native coverage and anthropogenic ones, we built independent predictive models for each sub-region. Our results show that Brazil has a TP stock of 531 Tg and an AP stock of 17.4 Tg. The largest soil TP stocks are in the Atlantic Forest biome (73.8 g.m2), likely due to higher organic carbon stocks in this biome. The largest AP stocks were in the Caatinga biome (2.51 g.m2) because of younger soils with low P adsorption capacity. We also found that fertilizer use significantly increased AP stocks in agricultural areas compared to native ones. Our results indicated that AP stocks strongly influenced Brazil's agricultural production, with a correlation coefficient ranging from 0.20 for coffee crops to 0.46 for soybean. The maps generated in this study are expected to contribute to the sustainable use of P in agriculture and environmental systems.

A novel framework for improving soil organic matter prediction accuracy in cropland by integrating soil, vegetation and human activity information

Remote sensing is an important tool for monitoring soil information. However, accurate spatial modeling of soil organic matter (SOM) in areas with high vegetation coverage, typically represented by agroecosystems, remains a challenge for field-scale estimation using remote sensing. To date, studies have focused on using single-period or multi-temporal vegetation information to characterize SOM. Thus, the relationship between SOM content and time-series vegetation biomass has not yet been fully explored. In addition, most studies have ignored the effects of critical soil properties and human activities (e.g., soil salinization, soil particle size fractions, history of land-use changes) on SOM. By integrating information on vegetation, soil, and human activities, we propose a novel framework for assessing SOM in cotton fields of artificial oases in northwest China, where returned straw is one of the primary sources of SOM coming from vegetation. We developed an Annual Maximum Biomass Accumulation Index (AMBAI) using time-series Landsat images from 1990 to 2019. Subsequently, we quantified the information of the planting years (PY) of cropland using spectral index threshold and incorporated proximal sensing data (soil hyperspectral and apparent conductivity data) and soil particle size fractions to establish a predictive model of SOM using partial least squares regression (PLSR), random forest (RF), and convolutional neural network (CNN). The results revealed that AMBAI had the highest correlation coefficient (r) with SOM (0.76, P < 0.01). AMBAI, soil hyperspectral data, and PY were the most relevant predictors for estimating SOM. The CNN model integrating vegetation, soil, and human activity information performed best, with coefficient of determination (R2), relative analysis error (RPD), and root mean square error (RMSE) of 0.83, 2.38 and 1.38 g kg-1, respectively. This study confirmed that AMBAI and PY had great potential for characterizing SOM in arid and semi-arid regions, providing a reference for other relevant studies.

Scale-Specific Prediction of Topsoil Organic Carbon Contents Using Terrain Attributes and SCMaP Soil Reflectance Composites

There is a growing need for an area-wide knowledge of SOC contents in agricultural soils at the field scale for food security and monitoring long-term changes related to soil health and climate change. In Germany, SOC maps are mostly available with a spatial resolution of 250 m to 1 km2. The nationwide availability of both digital elevation models at various spatial resolutions and multi-temporal satellite imagery enables the derivation of multi-scale terrain attributes and (here: Landsat-based) multi-temporal soil reflectance composites (SRC) as explanatory variables. In the example of a Bavarian test of about 8000 km2, relations between 220 SOC content samples as well as different aggregation levels of the explanatory variables were analyzed for their scale-specific predictive power. The aggregation levels were generated by applying a region-growing segmentation procedure, and the SOC content prediction was realized by the Random Forest algorithm. In doing so, established approaches of (geographic) object-based image analysis (GEOBIA) and machine learning were combined. The modeling results revealed scale-specific differences. Compared to terrain attributes, the use of SRC parameters leads to a significant model improvement at field-related scale levels. The joint use of both terrain attributes and SRC parameters resulted in further model improvements. The best modeling variant is characterized by an accuracy of R2 = 0.84 and RMSE = 1.99.

Ground Observations and Environmental Covariates Integration for Mapping of Soil Salinity: A Machine Learning-Based Approach

Soil salinization is a severe danger to agricultural activity in arid and semi-arid areas, reducing crop production and contributing to land destruction. This investigation aimed to utilize machine learning algorithms to predict spatial soil salinity (dS m−1) by combining environmental covariates derived from remotely sensed (RS) data, a digital elevation model (DEM), and proximal sensing (PS). The study is located in an arid region, southern Iran (52°51′–53°02′E; 28°16′–28°29′N), in which we collected 300 surface soil samples and acquired the spectral data with RS (Sentinel-2) and PS (electromagnetic induction instrument (EMI) and portable X-ray fluorescence (pXRF)). Afterward, we analyzed the data using five machine learning methods as follows: random forest—RF, k-nearest neighbors—kNN, support vector machines—SVM, partial least squares regression—PLSR, artificial neural networks—ANN, and the ensemble of individual models. To estimate the electrical conductivity of the saturated paste extract (ECe), we built three scenarios, including Scenario (1): Synthetic Soil Image (SySI) bands and salinity indices derived from it; Scenario (2): RS data, PS data, topographic attributes, and geology and geomorphology maps; and Scenario (3): the combination of Scenarios (1) and (2). The best prediction accuracy was obtained for the RF model in Scenario (3) (R2 = 0.48 and RMSE = 2.49), followed by Scenario (2) (RF model, R2 = 0.47 and RMSE = 2.50) and Scenario (1) for the SVM model (R2 = 0.26 and RMSE = 2.97). According to ensemble modeling, a combined strategy with the five models exceeded the performance of all the single ones and predicted soil salinity in all scenarios. The results revealed that the ensemble modeling method had higher reliability and more accurate predictive soil salinity than the individual approach. Relative improvement (RI%) showed that the R2 index in the ensemble model improved compared to the most precise prediction for the Scenarios (1), (2), and (3) with 120.95%, 56.82%, and 66.71%, respectively. We applied the best model in each scenario for mapping the soil salinity in the selected area, which indicated that ECe tended to increase from the northwestern to south and southeastern regions. The area with high ECe was located in the regions that mainly had low elevations and playa. The areas with low ECe were located in the higher elevations with steeper slopes and alluvial fans, and thus, relief had great importance. This study provides a precise, cost-effective, and scientific base prediction for decision-making purposes to map soil salinity in arid regions.

Sentinel-2 Recognition of Uncovered and Plastic Covered Agricultural Soil

Medium resolution satellite data, such as Sentinel-2 of the Copernicus programme, offer great new opportunities for the agricultural sector, and provide insights on soil surface characteristics and their management. Soil monitoring requires a high-quality dataset of uncovered and plastic covered agricultural soil. We developed a methodology to identify uncovered soil pixels in agricultural parcels during seedbed preparation and considered the impacts of clouds and shadows, vegetation cover, and artificial covers, such as those of greenhouses and plastic mulch films. We preserved the spatial and temporal integrity of parcels in the process and analysed spectral anomalies and their sources. The approach is based on freely available tools, namely Google Earth Engine and R Programming packages. We tested the methodology on the northern region of Belgium, which is characterised by small, fragmented parcels. We selected a period between mid-April to end-May, when active agricultural management practices leave the soil bare in preparation for the main cropping season. The spectral angle mapper was used to identify soil covered by non-plastic greenhouses or temporary soil covers, such as plastic mulch films. The effect of underlying soil on temporary covers was considered. The retrogressive plastic greenhouse index was used for detecting plastic greenhouses. The result was a high quality dataset of potential bare uncovered agricultural soil that allows further soil surface characterisation. This offered an improved understanding of the use of artificial covers, their spatial distribution, and their corresponding crops during the considered period. Artificial covers occurred most frequently in maize parcels. The approach resulted in precision values exceeding 0.9 for the detection of temporary covers and non-plastic greenhouses and a sensitivity value exceeding 0.95 for non-plastic and plastic greenhouses.

Sentinel-2 and Landsat-8 Multi-Temporal Series to Estimate Topsoil Properties on Croplands

The spatial and temporal monitoring of soil organic carbon (SOC), and other soil properties related to soil erosion, is extremely important, both from the environmental and economic perspectives. Sentinel-2 (S2) and Landsat-8 (L8) time series increase the probability to observe bare soil fields in croplands, and thus, monitor soil properties over large regions. In this regard, this work suggests an automated pixel-based approach to select only pure soil pixels in S2 and L8 time series, and to make a synthetic bare soil image (SBSI). The SBSIs and the soil properties measured in the framework of the European LUCAS survey were used to calibrate SOC, clay, and CaCO3 prediction models. The results highlight a high correlation between laboratory soil spectra and the SBSIs median spectra, especially for the SBSI obtained by a three-year S2 collection, which provides satisfactory results in terms of SOC prediction accuracy (RPD: 1.74). The comparison between S2 and L8 results demonstrated the higher capability of the S2 sensor in terms of SOC prediction accuracy, mainly due to the greater spatial resolution of the bands in the visible region. Whereas, neither S2 nor L8 could accurately predict the clay and CaCO3 content. This is because of the low spectral and spatial resolution of their SWIR bands that prevent the exploitation of the narrow spectral features related to these two soil attributes. The results of this study prove that large S2 time series can estimate and monitor SOC in croplands using an automated pixel-based approach that selects pure soil pixels and retrieves reliable synthetic soil spectra.

Estimation of Soil Organic Carbon Contents in Croplands of Bavaria from SCMaP Soil Reflectance Composites

For food security issues or global climate change, there is a growing need for large-scale knowledge of soil organic carbon (SOC) contents in agricultural soils. To capture and quantify SOC contents at a field scale, Earth Observation (EO) can be a valuable data source for area-wide mapping. The extraction of exposed soils from EO data is challenging due to temporal or permanent vegetation cover, the influence of soil moisture or the condition of the soil surface. Compositing techniques of multitemporal satellite images provide an alternative to retrieve exposed soils and to produce a data source. The repeatable soil composites, containing averaged exposed soil areas over several years, are relatively independent from seasonal soil moisture and surface conditions and provide a new EO-based data source that can be used to estimate SOC contents over large geographical areas with a high spatial resolution. Here, we applied the Soil Composite Mapping Processor (SCMaP) to the Landsat archive between 1984 and 2014 of images covering Bavaria, Germany. Compared to existing SOC modeling approaches based on single scenes, the 30-year SCMaP soil reflectance composite (SRC) with a spatial resolution of 30 m is used. The SRC spectral information is correlated with point soil data using different machine learning algorithms to estimate the SOC contents in cropland topsoils of Bavaria. We developed a pre-processing technique to address the issue of combining point information with EO pixels for the purpose of modeling. We applied different modeling methods often used in EO soil studies to choose the best SOC prediction model. Based on the model accuracies and performances, the Random Forest (RF) showed the best capabilities to predict the SOC contents in Bavaria (R² = 0.67, RMSE = 1.24%, RPD = 1.77, CCC = 0.78). We further validated the model results with an independent dataset. The comparison between the measured and predicted SOC contents showed a mean difference of 0.11% SOC using the best RF model. The SCMaP SRC is a promising approach to predict the spatial SOC distribution over large geographical extents with a high spatial resolution (30 m).

Drivers of Organic Carbon Stocks in Different LULC History and Along Soil Depth for a 30 Years Image Time Series

Soil organic carbon (SOC) stocks are a remarkable property for soil and environmental monitoring. The understanding of their dynamics in crop soils must go forward. The objective of this study was to determine the impact of temporal environmental controlling factors obtained by satellite images over the SOC stocks along soil depth, using machine learning algorithms. The work was carried out in São Paulo state (Brazil) in an area of 2577 km2. We obtained a dataset of boreholes with soil analyses from topsoil to subsoil (0–100 cm). Additionally, remote sensing covariates (30 years of land use history, vegetation indexes), soil properties (i.e., clay, sand, mineralogy), soil types (classification), geology, climate and relief information were used. All covariates were confronted with SOC stocks contents, to identify their impact. Afterwards, the abilities of the predictive models were tested by splitting soil samples into two random groups (70 for training and 30% for model testing). We observed that the mean values of SOC stocks decreased by increasing the depth in all land use and land cover (LULC) historical classes. The results indicated that the random forest with recursive features elimination (RFE) was an accurate technique for predicting SOC stocks and finding controlling factors. We also found that the soil properties (especially clay and CEC), terrain attributes, geology, bioclimatic parameters and land use history were the most critical factors in controlling the SOC stocks in all LULC history and soil depths. We concluded that random forest coupled with RFE could be a functional approach to detect, map and monitor SOC stocks using environmental and remote sensing data.

Mapping soil organic carbon stocks and trends with satellite-driven high resolution maps over South Africa

Estimation and monitoring of soil organic carbon (SOC) stocks is important for maintaining soil productivity and meeting climate change mitigation targets. Current global SOC maps do not provide enough detail for landscape-scale decision making, and do not allow for tracking carbon sequestration or loss over time. Using an optical satellite-driven machine learning workflow, we mapped SOC stocks (topsoil; 0 to 30 cm) under natural vegetation (86% of land area) over South Africa at 30 m spatial resolution between 1984 and 2019. We estimate a total topsoil SOC stock of 5.6 Pg C with a median SOC density of 6 kg C m^-2 (IQR: interquartile range 2.9 kg C m^-2). Over 35 years, predicted SOC underwent a net increase of 0.3% (relative to long-term mean) with the greatest net increases (1.7%) and decreases (-0.6%) occurring in the Grassland and Nama Karoo biomes, respectively. At the landscape scale, SOC changes of up to 25% were evident in some locations, as evidenced from fence-line contrasts, and were likely due to local management effects (e.g. woody encroachment associated with increased SOC and overgrazing associated with decreased SOC). Our SOC mapping approach exhibited lower uncertainty (R² = 0.64; RMSE = 2.5 kg C m^-2) and less bias compared to previous low-resolution (250-1000 m) national SOC mapping efforts (average R² = 0.24; RMSE = 3.7 kg C m^-2). Our trend map remains an estimate, pending repeated measures of soil samples in the same location (time-series); a global priority for tracking SOC changes. While high resolution SOC maps can inform land management decisions aimed at climate mitigation (natural climate solutions), potential increases in SOC are likely limited by local climate and soils. It is also important that climate mitigation efforts such as planting trees balance trade-offs between carbon, biodiversity and overall ecosystem function.

African soil properties and nutrients mapped at 30 m spatial resolution using two-scale ensemble machine learning

Soil property and class maps for the continent of Africa were so far only available at very generalised scales, with many countries not mapped at all. Thanks to an increasing quantity and availability of soil samples collected at field point locations by various government and/or NGO funded projects, it is now possible to produce detailed pan-African maps of soil nutrients, including micro-nutrients at fine spatial resolutions. In this paper we describe production of a 30 m resolution Soil Information System of the African continent using, to date, the most comprehensive compilation of soil samples ([Formula: see text]) and Earth Observation data. We produced predictions for soil pH, organic carbon (C) and total nitrogen (N), total carbon, effective Cation Exchange Capacity (eCEC), extractable-phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sulfur (S), sodium (Na), iron (Fe), zinc (Zn)-silt, clay and sand, stone content, bulk density and depth to bedrock, at three depths (0, 20 and 50 cm) and using 2-scale 3D Ensemble Machine Learning framework implemented in the mlr (Machine Learning in R) package. As covariate layers we used 250 m resolution (MODIS, PROBA-V and SM2RAIN products), and 30 m resolution (Sentinel-2, Landsat and DTM derivatives) images. Our fivefold spatial Cross-Validation results showed varying accuracy levels ranging from the best performing soil pH (CCC = 0.900) to more poorly predictable extractable phosphorus (CCC = 0.654) and sulphur (CCC = 0.708) and depth to bedrock. Sentinel-2 bands SWIR (B11, B12), NIR (B09, B8A), Landsat SWIR bands, and vertical depth derived from 30 m resolution DTM, were the overall most important 30 m resolution covariates. Climatic data images-SM2RAIN, bioclimatic variables and MODIS Land Surface Temperature-however, remained as the overall most important variables for predicting soil chemical variables at continental scale. This publicly available 30-m Soil Information System of Africa aims at supporting numerous applications, including soil and fertilizer policies and investments, agronomic advice to close yield gaps, environmental programs, or targeting of nutrition interventions.

An Analysis of Bare Soil Occurrence in Arable Croplands for Remote Sensing Topsoil Applications

A better comprehension of soil properties and processes permits a progress in agricultural management effectiveness, together with a diminution of environmental damage and more beneficial use of resources. This research investigated the usage of multispectral (Sentinel-2 MSI) satellite data at the farm/regional level, for the identification of agronomic bare soil presence, utilizing bands of the spectral range from visible to shortwave infrared. The research purpose was to assess the frequency of cloud-free bare soil time-series images available during the year in typical agricultural areas, needed for the development of digital soil mapping (DSM) approaches for agricultural applications, using hyperspectral satellite missions such as current PRISMA and the planned EnMAP or CHIME. The research exploited the Google Earth Engine platform, by processing all available cloud-free Sentinel-2 images throughout a time span of four years. Two main results were obtained: (i) bare soil frequency, indicating where and when a pixel (or an agricultural field) was detected as bare surface in three representative agricultural areas of Italy, and (ii) a temporal sensitivity analysis, providing the acquisition frequency of useful bare soil images applicable for the retrieval of soil variables of interest. It was shown that, in order to provide for an effective agricultural soil monitoring capability, a revisit frequency in the range of five to seven days is required, which is less than the planned specifications e.g., of PRISMA or CHIME hyperspectral missions, but could be addressed by combining data from the two sensors.

Terrain Analysis in Google Earth Engine: A Method Adapted for High-Performance Global-Scale Analysis

Terrain analysis is an important tool for modeling environmental systems. Aiming to use the cloud-based computing capabilities of Google Earth Engine (GEE), we customized an algorithm for calculating terrain attributes, such as slope, aspect, and curvatures, for different resolution and geographical extents. The calculation method is based on geometry and elevation values estimated within a 3 × 3 spheroidal window, and it does not rely on projected elevation data. Thus, partial derivatives of terrain are calculated considering the great circle distances of reference nodes of the topographic surface. The algorithm was developed using the JavaScript programming interface of the online code editor of GEE and can be loaded as a custom package. The algorithm also provides an additional feature for making the visualization of terrain maps with a dynamic legend scale, which is useful for mapping different extents: from local to global. We compared the consistency of the proposed method with an available but limited terrain analysis tool of GEE, which resulted in a correlation of 0.89 and 0.96 for aspect and slope over a near-global scale, respectively. In addition to this, we compared the slope, aspect, horizontal, and vertical curvature of a reference site (Mount Ararat) to their equivalent attributes estimated on the System for Automated Geospatial Analysis (SAGA), which achieved a correlation between 0.96 and 0.98. The visual correspondence of TAGEE and SAGA confirms its potential for terrain analysis. The proposed algorithm can be useful for making terrain analysis scalable and adapted to customized needs, benefiting from the high-performance interface of GEE.