Exploring the impact of agricultural practices, temperature, and CO2 on potato health and soil microbiome biodiversity

Abstract

Agriculture plays an important role in global food security, but significant challenges, including climate change and land degradation, threaten crop productivity and soil health. Potato (Solanum tuberosum L.) is one of the most important non-grain food crops worldwide. However, production of the crop faces major obstacles due to changing climatic conditions, particularly because of its sensitivity to heat stress. In addition, intensive agricultural practices have led to soil degradation, further reducing crop yields and negatively influencing soil ecosystem functioning. Central to these challenges is the soil microbiome, which plays a vital role in nutrient cycling, disease suppression, and plant resilience against environmental stressors. However, climate change and intensive agricultural practices lead to disruptions in soil microbial communities, posing a threat to soil biodiversity, agroecosystem stability, and long-term crop productivity. This study aimed to explore the complex interactions between climate change factors (elevated temperature and carbon dioxide (CO2) levels), agricultural practices, and the soil microbiome within potato production systems in South Africa. The effect of elevated temperature and CO2 was observed on microbial taxonomic shifts in the potato soil microbiome. Two growth chamber trials were conducted using four temperature-CO2 treatment combinations reflecting projected climatic conditions for South Africa. While alpha diversity remained stable under elevated temperature and CO2 conditions, significant shifts in beta diversity indicated changes in microbial community composition with CO2 as a primary driver. Notably, elevated temperature favoured thermo-tolerant taxa such as Gemmatimonadota and Bacillota, whereas elevated CO2 favoured genera such as Saccharomonospora and Flavobacterium, known for their roles in nutrient cycling and plant growth promotion. A mini-plot trial was conducted to evaluate the effect of different agricultural practices, namely chemical pest control, integrated pest management (IPM), and organic farming, on potato yield, tuber blemish diseases, soil chemistry, and soil microbial diversity. The IPM and organic treatments significantly increased tuber yield compared to the chemical treatment, particularly in the first season. Soil pH and potassium levels increased under the IPM and organic treatments. Soil microbiome analysis revealed that the IPM and organic treatments promoted higher bacterial diversity, whereas the chemical treatment promoted fungal diversity. When comparing the effects of climate change and agricultural practices, climate-induced shifts in microbial community composition emerged as more pronounced compared to shifts caused by agricultural practices. Elevated CO2 levels were identified as a primary driver of microbial communities, indicating that climate change had a stronger influence on the soil microbiome dynamics than the short-term changes induced by agricultural management practices. However, sustainable agricultural practices may be a potential mitigation strategy for climate change by enhancing soil microbial diversity and promoting ecosystem resilience. Notably, beneficial taxa associated with nutrient cycling and disease suppression were enriched under the IPM and organic treatments, suggesting these practices could be a potential buffer against the negative impacts of climate change.