Adaptation of Agriculture Systems to Metal(loid) and Climate Change Stressors

Abstract

The accumulation and mobility of essential and harmful metal(loid)s in agroecosystems greatly influence crop yields, nutritional quality and the stability of soil prokaryotic communities. Agricultural management, particularly through fertilization, represents a major source of metal(loid)s in agriculture soils. However, its long-term effects on metal(loid) mobility and bioavailability under realistic field conditions remain poorly understood. Climate change further complicates these dynamics by altering biogeochemical processes, which govern metal(loid) mobilization in soil and crop physiology, raising critical concerns about potential impacts on nutritional quality. Additional uncertainty arises from the methodological approaches used in climate incubation studies, which often compare present-day soils under current and projected climate conditions. In reality, future soils will already have been shaped by long-term exposure to those climates. This raises a critical question: do incubations using today’s soils provide valid predictions of future biogeochemical responses? This thesis investigates how agricultural management and climate change jointly shape the mobility, accumulation, and biological effects of essential and harmful metal(loid)s in agroecosystems. It aims to: i) assess metal(loid) transfer from soil to crops under different long-term fertilization regimes, including the use of 87Sr/86Sr isotopes as potential tracers for fertilizer-derived metal(loid)s; ii) evaluate the resistance and resilience of soil prokaryotic communities to metal stress across long-term fertilization histories; iii) determine how future climate conditions affect metal(loid) accumulation in crops; iv) assess the extent to which organic farming practices mandated under EU regulations mitigate climate-induced shifts in metal(loid) accumulation and crop productivity; v) evaluate whether climate incubation experiments using present-day soils provide accurate predictions of future biogeochemical responses. This study focuses on both essential (Fe, Zn, Mg, Mn, V) and harmful (Cd, As, Pb) metal(loid)s. To address the research objectives, it integrates long-term field trials, greenhouse climate simulations, and laboratory microcosm incubations with interdisciplinary approaches spanning soil chemistry, crop metal(loid) uptake, and prokaryotic ecology. This thesis demonstrates that agricultural management is a major factor shaping metal(loid) fate in soils and crops. Long-term mineral fertilization significantly increased Cd and As concentrations in wheat grains, with Cd content up by 70% compared with crops harvested from unfertilized control soils. This treatment also reduced the resistance and resilience of soil prokaryotic communities to additional inputs of Cd, Zn, and Pb, impairing prokaryote-mediated nutrient cycling. In contrast, organic fertilization with manure lowered Cd and As accumulation in wheat grains and supported stable prokaryotic communities under further metal stress. Combined mineral–organic treatments buffered negative effects of mineral fertilization on both grain nutritional quality and soil prokaryotic community stability. The 87Sr/86Sr ratios in wheat grains corresponded with those of the fertilizers used, validating their use as tracers for identifying fertilizer sources. In a separate field experiment, EU-certified organic farming reduced the accumulation of both essential Fe and Zn, as well as harmful Cd and As in wheat and barley grains by up to 24%, resulting in mixed effects on grain nutritional quality. This thesis shows that climate change alters metal(loid) dynamics in soils and crops, with outcomes that vary by environmental and experimental context. In a greenhouse experiment simulating future conditions with a substantial 3.4°C increase in atmospheric temperature, a 290 ppmv rise in CO2 concentration, and a 2-percentage-point decrease in soil moisture, spinach accumulated up to 54% more Cd, while Zn, Mg, and Mn responses were crop variety and soil type specific. These effects were linked to shifts in soil carbon composition and prokaryotic communities that particularly increased Cd mobility in soil. In contrast, a long-term field experiment was conducted under milder future conditions, including a +0.55°C increase in mean annual temperature, a 10% increase in spring and autumn precipitation, and a 20% decrease in summer precipitation. These smaller changes had no significant effects on Fe, Zn, Cd, or As concentrations in wheat and barley grains. However, organic farming did buffer climate-induced yield losses in wheat under this scenario. Climate incubation experiments using present-day soils without prior climate adaptation generally captured the direction of future biogeochemical responses, supporting their validity. Yet, without climate adaptation, the extent and timing of these responses may be misestimated due to inherited geochemical and microbial traits. This thesis demonstrated that metal(loid) dynamics in agroecosystems, and their subsequent effects on crop nutritional quality and soil prokaryotic stability, are governed by complex interactions among soil, crop, and prokaryotic processes. These interactions can be intensified under more severe climate conditions, particularly for harmful elements like Cd and As. Agricultural management might play a dual role in this challenge. While intensive conventional farming with mineral fertilization increases metal(loid) stress on agroecosystems, organic approaches offer promising mitigation strategies. As coupled climate change and metal(loid) contamination increasingly transform global croplands, science-based approaches to managing soil–crop–prokaryote systems will be critical for securing food safety, soil fertility and agroecosystem sustainability.