Spatial distribution prediction of soil heavy metals based on sparse sampling and multi-source environmental data

Predicting the precise spatial distribution of heavy metals in soil is crucial, especially in the fields of environmental management and remediation. However, achieving accurate spatial predictions of soil heavy metals becomes quite challenging when the number of soil sampling points is relatively limited. To address this challenge, this study proposes a hybrid approach, namely, Light Gradient Boosting Machine plus Ordinary Kriging (LGBK), for predicting the spatial distribution of soil heavy metals. A total of 137 soil samples were collected from the Shengli Coal-mine Base in Inner Mongolia, China, and their heavy metal concentrations were measured. Leveraging environmental covariates and soil heavy metal data, we constructed the predictive model. Experimental results demonstrate that, in comparison to traditional models, LGBK exhibits superior predictive performance. For copper (Cu), zinc (Zn), chromium (Cr), and arsenic (As), the coefficients of determination (R²) from the cross-validation results are 0.65, 0.52, 0.57, and 0.63, respectively. Moreover, the LGBK model excels in capturing intricate spatial features in heavy metal distribution. It accurately forecasts trends in heavy metal distribution that closely align with actual measurements. ENVIRONMENTAL IMPLICATION: This study introduces a novel method, LGBK, for predicting the spatial distribution of soil heavy metals. This method yields higher-precision predictions even with a limited number of sampling points. Furthermore, the study analyzes the spatial distribution characteristics of Cu, Zn, Cr, and As in the grassland coal-mine base, along with the key environmental factors influencing their spatial distribution. This research holds significant importance for the environmental regulation and remediation of heavy metal pollution.

Geospatial prediction of total soil carbon in European agricultural land based on deep learning

Accurate geospatial prediction of soil parameters provides a basis for large-scale digital soil mapping, making efficient use of the expensive and time-consuming process of field soil sampling. To date, few studies have used deep learning for geospatial prediction of soil parameters, but there is evidence that it may provide higher accuracy compared to machine learning methods. To address this research gap, this study proposed a deep neural network (DNN) for geospatial prediction of total soil carbon (TC) in European agricultural land and compared it with the eight most commonly used machine learning methods based on studies indexed in the Web of Science Core Collection. A total of 6209 preprocessed soil samples from the Geochemical mapping of agricultural and grazing land soil (GEMAS) dataset in heterogeneous agricultural areas covering 4,899,602 km2 in Europe were used. Prediction was performed based on 96 environmental covariates from climate and remote sensing sources, with extensive comprehensive hyperparameter tuning for all evaluated methods. DNN outperformed all evaluated machine learning methods (R2 = 0.663, RMSE = 9.595, MAE = 5.565), followed by Quantile Random Forest (QRF) (R2 = 0.635, RMSE = 25.993, MAE = 22.081). The ability of DNN to accurately predict small TC values and thus produce relatively low absolute residuals was a major reason for the higher prediction accuracy compared to machine learning methods. Climate parameters were the main factors in the achieved prediction accuracy, with 23 of the 25 environmental covariates with the highest variable importance being climate or land surface temperature parameters. These results demonstrate the superiority of DNN over machine learning methods for TC prediction, while highlighting the need for more recent soil sampling to assess the impact of climate change on TC content in European agricultural land.

The possibility of spatial mapping of SOC content in olive groves under integrated production using easy-to-obtain ancillary data in a Mediterranean area

Background

Unlike most of Europe, Andalucía in southern Spain as a Mediterranean area still lacks digital maps of SOC content provided by machine learning algorithms. The wide diversity of climate, geology, hydrology, landscape, topography, vegetation, and micro-relief data as easy-to-obtain covariates facilitated the development of digital soil mapping (DSM). The purpose of this research is to model and map the spatial distribution of SOC at three depths, in an area of approximately 10000 km 2 located in Seville and Cordoba Provinces, and to use R programming to compare two machine learning techniques (cubist and random forest) for developing SOC maps at multiple depths.

Methods

Environmental covariates used in this research include nine derivatives from digital elevation models (DEM), three climatic variables and finally eighteen remotely-sensed spectral data (band ratios calculated by the acquired Landsat-8 OLI and Sentinel-2A MSI in July 2019). In total, 300 soil samples from 100 points were taken (0-25 cm). The purpose of this research is to model and map the spatial distribution of SOC, in an area with approximately 10000 km2 located in Seville and Cordoba Provinces, and to compare two machine learning techniques (cubist and random forest) by R programming.

Results

The findings showed that the novel approach for integrating the indices using Landsat-8 OLI and Sentinel-2A MSI satellite data had a better result.

Conclusions

Finally, we obtained evidence that the resolution of satellite images is more important in modelling and digital mapping.

Drone images afford more detections of marine wildlife than real-time observers during simultaneous large-scale surveys

There are many advantages to transitioning from conducting marine wildlife surveys via human observers onboard light-aircraft, to capturing aerial imagery using drones. However, it is important to maintain the validity of long-term data series whilst transitioning from observer to imagery surveys. We need to understand how the detection rates of target species in images compare to those collected from observers in piloted aircraft, and the factors influencing detection rates from each platform. We conducted trial ScanEagle drone surveys of dugongs in Shark Bay, Western Australia, covering the full extent of the drone's range (∼100 km), concurrently with observer surveys, with the drone flying above or just behind the piloted aircraft. We aimed to test the assumption that drone imagery could provide comparable detection rates of dugongs to human observers when influenced by same environmental conditions. Overall, the dugong sighting rate (i.e., count of individual dugongs) was 1.3 (95% CI [0.98-1.84]) times higher from the drone images than from the observers. The group sighting rate was similar for the two platforms, however the group sizes detected within the drone images were significantly larger than those recorded by the observers, which explained the overall difference in sighting rates. Cloud cover appeared to be the only covariate affecting the two platforms differently; the incidence of cloud cover resulted in smaller group sizes being detected by both platforms, but the observer group sizes dropped much more dramatically (by 71% (95% CI [31-88]) compared to no cloud) than the group sizes detected in the drone images (14% (95% CI [-28-57])). Water visibility and the Beaufort sea state also affected dugong counts and group sizes, but in the same way for both platforms. This is the first direct simultaneous comparison between sightings from observers in piloted aircraft and a drone and demonstrates the potential for drone surveys over a large spatial-scale.

Multi-environment Genomic Selection in Rice Elite Breeding Lines

BACKGROUND

Assessing the performance of elite lines in target environments is essential for breeding programs to select the most relevant genotypes. One of the main complexities in this task resides in accounting for the genotype by environment interactions. Genomic prediction models that integrate information from multi-environment trials and environmental covariates can be efficient tools in this context. The objective of this study was to assess the predictive ability of different genomic prediction models to optimize the use of multi-environment information. We used 111 elite breeding lines representing the diversity of the international rice research institute breeding program for irrigated ecosystems. The lines were evaluated for three traits (days to flowering, plant height, and grain yield) in 15 environments in Asia and Africa and genotyped with 882 SNP markers. We evaluated the efficiency of genomic prediction to predict untested environments using seven multi-environment models and three cross-validation scenarios.

RESULTS

The elite lines were found to belong to the indica group and more specifically the indica-1B subgroup which gathered improved material originating from the Green Revolution. Phenotypic correlations between environments were high for days to flowering and plant height (33% and 54% of pairwise correlation greater than 0.5) but low for grain yield (lower than 0.2 in most cases). Clustering analyses based on environmental covariates separated Asia's and Africa's environments into different clusters or subclusters. The predictive abilities ranged from 0.06 to 0.79 for days to flowering, 0.25-0.88 for plant height, and - 0.29-0.62 for grain yield. We found that models integrating genotype-by-environment interaction effects did not perform significantly better than models integrating only main effects (genotypes and environment or environmental covariates). The different cross-validation scenarios showed that, in most cases, the use of all available environments gave better results than a subset.

CONCLUSION

Multi-environment genomic prediction models with main effects were sufficient for accurate phenotypic prediction of elite lines in targeted environments. These results will help refine the testing strategy to update the genomic prediction models to improve predictive ability.

Machine learning based estimation of field-scale daily, high resolution, multi-depth soil moisture for the Western and Midwestern United States

Background

High-resolution soil moisture estimates are critical for planning water management and assessing environmental quality. In-situ measurements alone are too costly to support the spatial and temporal resolutions needed for water management. Recent efforts have combined calibration data with machine learning algorithms to fill the gap where high resolution moisture estimates are lacking at the field scale. This study aimed to provide calibrated soil moisture models and methodology for generating gridded estimates of soil moisture at multiple depths, according to user-defined temporal periods, spatial resolution and extent.

Methods

We applied nearly one million national library soil moisture records from over 100 sites, spanning the U.S. Midwest and West, to build Quantile Random Forest (QRF) calibration models. The QRF models were built on covariates including soil moisture estimates from North American Land Data Assimilation System (NLDAS), soil properties, climate variables, digital elevation models, and remote sensing-derived indices. We also explored an alternative approach that adopted a regionalized calibration dataset for the Western U.S. The broad-scale QRF models were independently validated according to sampling depths, land cover type, and observation period. We then explored the model performance improved with local samples used for spiking. Finally, the QRF models were applied to estimate soil moisture at the field scale where evaluation was carried out to check estimated temporal and spatial patterns.

Results

The broad-scale QRF model showed moderate performance (R² = 0.53, RMSE = 0.078 m³/m³) when data points from all depth layers (up to 100 cm) were considered for an independent validation. Elevation, NLDAS-derived moisture, soil properties, and sampling depth were ranked as the most important covariates. The best model performance was observed for forest and pasture sites (R² > 0.5; RMSE < 0.09 m³/m³), followed by grassland and cropland (R² > 0.4; RMSE < 0.11 m³/m³). Model performance decreased with sampling depths and was slightly lower during the winter months. Spiking the national QRF model with local samples improved model performance by reducing the RMSE to less than 0.05 m³/m³ for grassland sites. At the field scale, model estimates illustrated more accurate temporal trends for surface than subsurface soil layers. Model estimated spatial patterns need to be further improved and validated with management data.

Conclusions

The model accuracy for top 0-20 cm soil depth (R² > 0.5, RMSE < 0.08 m³/m³) showed promise for adopting the methodology for soil moisture monitoring. The success of spiking the national model with local samples showed the need to collect multi-year high frequency (e.g., hourly) sensor-based field measurements to improve estimates of soil moisture for a longer time period. Future work should improve model performance for deeper depths with additional hydraulic properties and use of locally-selected calibration datasets.

The impact of modelling choices on modelling outcomes: a spatio-temporal study of the association between COVID-19 spread and environmental conditions in Catalonia (Spain)

The choices that researchers make while conducting a statistical analysis usually have a notable impact on the results. This fact has become evident in the ongoing research of the association between the environment and the evolution of the coronavirus disease 2019 (COVID-19) pandemic, in light of the hundreds of contradictory studies that have already been published on this issue in just a few months. In this paper, a COVID-19 dataset containing the number of daily cases registered in the regions of Catalonia (Spain) since the start of the pandemic to the end of August 2020 is analysed using statistical models of diverse levels of complexity. Specifically, the possible effect of several environmental variables (solar exposure, mean temperature, and wind speed) on the number of cases is assessed. Thus, the first objective of the paper is to show how the choice of a certain type of statistical model to conduct the analysis can have a severe impact on the associations that are inferred between the covariates and the response variable. Secondly, it is shown how the use of spatio-temporal models accounting for the nature of the data allows understanding the evolution of the pandemic in space and time. The results suggest that even though the models fitted to the data correctly capture the evolution of COVID-19 in space and time, determining whether there is an association between the spread of the pandemic and certain environmental conditions is complex, as it is severely affected by the choice of the model.

Modeling arsenic content in Brazilian soils: What is relevant?

Arsenic accumulation in the environment poses ecological and human health risks. A greater knowledge about soil total As content variability and its main drivers is strategic for maintaining soil security, helping public policies and environmental surveys. Considering the poor history of As studies in Brazil at the country's geographical scale, this work aimed to generate predictive models of topsoil As content using machine learning (ML) algorithms based on several environmental covariables representing soil forming factors, ranking their importance as explanatory covariables and for feeding group analysis. An unprecedented databank based on laboratory analyses (including rare earth elements), proximal and remote sensing, geographical information system operations, and pedological information were surveyed. The median soil As content ranged from 0.14 to 41.1 mg kg^-1 in reference soils, and 0.28 to 58.3 mg kg^-1 in agricultural soils. Recursive Feature Elimination Random Forest outperformed other ML algorithms, ranking as most important environmental covariables: temperature, soil organic carbon (SOC), clay, sand, and TiO₂. Four natural groups were statistically suggested (As content ± standard error in mg kg^-1): G1) with coarser texture, lower SOC, higher temperatures, and the lowest TiO₂ contents, has the lowest As content (2.24 ± 0.50), accomplishing different environmental conditions; G2) organic soils located in floodplains, medium TiO₂ and temperature, whose As content (3.78 ± 2.05) is slightly higher than G1, but lower than G3 and G4; G3) medium contents of As (7.14 ± 1.30), texture, SOC, TiO₂, and temperature, representing the largest number of points widespread throughout Brazil; G4) the largest contents of As (11.97 ± 1.62), SOC, and TiO₂, and the lowest sand content, with points located mainly across Southeastern Brazil with milder temperature. In the absence of soil As content, a common scenario in Brazil and in many Latin American countries, such natural groups could work as environmental indicators.

A high-resolution map of soil pH in China made by hybrid modelling of sparse soil data and environmental covariates and its implications for pollution

The soil's pH is the single most important indicator of the soil's quality, whether for agriculture, pollution control or environmental health and ecosystem functioning. Well documented data on soil pH are sparse for the whole of China - data for only 4700 soil profiles were available from China's Second National Soil Inventory. By combining those data, standardized for the topsoil (0-20 cm), with 17 environmental covariates at a fine resolution (3 arc-second or 90 m) we have predicted the soil's pH at that resolution, that is at more than 10⁹ points. We did so by parallel computing over tiles, each 100 km × 100 km, with two machine learning techniques, namely Random Forest and XGBoost. The predictions for the tiles were then merged into a single map of soil pH for the whole of China. The quality of the predictions were assessed by cross-validation. The root mean squared error (RMSE) was an acceptable 0.71 pH units per point, and Lin's Concordance Correlation Coefficient was 0.84. The hybrid model revealed that climate (mean annual precipitation and mean annual temperature) and soil type were the main factors determining the soil's pH. The pH map showed acid soil mainly in southern and north-eastern China, and alkaline soil dominant in northern and western China. This map can provide a benchmark against which to evaluate the impacts of changes in land use and climate on the soil's pH, and it can guide advisors and agencies who make decisions on remediation and prevention of soil acidification, salinization and pollution by heavy metals, for which we provide examples for cadmium and mercury.

Modelling environmental drivers of black band disease outbreaks in populations of foliose corals in the genus Montipora

Seawater temperature anomalies associated with warming climate have been linked to increases in coral disease outbreaks that have contributed to coral reef declines globally. However, little is known about how seasonal scale variations in environmental factors influence disease dynamics at the level of individual coral colonies. In this study, we applied a multi-state Markov model (MSM) to investigate the dynamics of black band disease (BBD) developing from apparently healthy corals and/or a precursor-stage, termed ‘cyanobacterial patches’ (CP), in relation to seasonal variation in light and seawater temperature at two reef sites around Pelorus Island in the central sector of the Great Barrier Reef. The model predicted that the proportion of colonies transitioning from BBD to Healthy states within three months was approximately 57%, but 5.6% of BBD cases resulted in whole colony mortality. According to our modelling, healthy coral colonies were more susceptible to BBD during summer months when light levels were at their maxima and seawater temperatures were either rising or at their maxima. In contrast, CP mostly occurred during spring, when both light and seawater temperatures were rising. This suggests that environmental drivers for healthy coral colonies transitioning into a CP state are different from those driving transitions into BBD. Our model predicts that (1) the transition from healthy to CP state is best explained by increasing light, (2) the transition between Healthy to BBD occurs more frequently from early to late summer, (3) 20% of CP infected corals developed BBD, although light and temperature appeared to have limited impact on this state transition, and (4) the number of transitions from Healthy to BBD differed significantly between the two study sites, potentially reflecting differences in localised wave action regimes.