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In order to ensure the sustainability of production from agricultural lands, the degradation processes surrounding the fertile land environment must be monitored. Human-induced risk and status of soil degradation (SD) were assessed in the Northern-Eastern part of the Nile delta using trend analyses for years 2013 to 2023. SD hotspot areas were identified using time-series analysis of satellite-derived indices as a small fraction of the difference between the observed indices and the geostatistical analyses projected from the soil data. The method operated on the assumption that the negative trend of photosynthetic capacity of plants is an indicator of SD independently of climate variability. Combinations of soil, water, and vegetation’s indices were integrated to achieve the goals of the study. Thirteen soil profiles were dug in the hotspots areas. The soil was affected by salinity and alkalinity risks ranging from slight to strong, while compaction and waterlogging ranged from slight to moderate. According to the GIS-model results, 30% of the soils were subject to slight degradation threats, 50% were subject to strong risks, and 20% were subject to moderate risks. The primary human-caused sources of SD are excessive irrigation, poor conservation practices, improper utilisation of heavy machines, and insufficient drainage. Electrical conductivity (EC), exchangeable soil percentage (ESP), bulk density (BD), and water table depth were the main causes of SD in the area. Generally, chemical degradation risks were low, while physical risks were very high in the area. Trend analyses of remote sensing indices (RSI) proved to be effective and accurate tools to monitor environmental dynamic changes. Principal components analyses were used to compare and prioritise among the used RSI. RSI pixel-wise residual trend indicated SD areas were related to soil data. The spatial and temporal trends of the indices in the region followed the patterns of drought, salinity, soil moisture, and the difficulties in separating the impacts of drought and submerged on SD on vegetation photosynthetic capacity. Therefore, future studies of land degradation and desertification should proceed using indices as a factor predictor of SD analysis.