Aggregate size matters: The impact of soil aggregation on microbial community assembly and suppression of tomato Ralstonia disease

Abstract

Agricultural food production must increase by at least 70% to feed our growing population, but the heavy use of chemical fertilizers has caused issues like land degradation, biodiversity loss, and soil health problems. A potential solution is bio-organic fertilizers that improve soil quality through the soil microbiome. However, the link between soil structure and microbiome remains unclear. Soil structure depends on soil aggregation, which creates various micro-environments for soil microbes. These aggregates also isolate microbial communities, affecting their activities. Understanding this interplay can aid in agricultural production and disease control. This research explores the impact of fertilizer amendments on microbial communities and their role in disease control. We focus on soil aggregate heterogeneity and its effect on microbial assembly and disease suppression against Ralstonia solanacearum, using tomato wilt disease as a model. In Chapter 2, we found that soil aggregate size influences the balance between stochastic and deterministic processes in bacterial community assembly. Homogenous selection dominates all size classes, but its importance varies, indicating different micro-environments within soil aggregates. Dispersal limitation occurs among size classes, confirming that soil aggregates are isolated microhabitats. Chapter 3 links these assembly differences with disease suppression. Different size classes suggest distinct potential pathogen-inhibitors, emphasizing the need to study microbial interactions within soil aggregates. Microaggregates are the primary habitat of R. solanacearum, and bio-organic amendments improve their resistance to pathogen invasion. Chapter 4 explores how tomato growth stages affect bacterial communities in different soil aggregates and disease levels. We found that soil aggregation influences bacterial community succession during tomato growth. Potential pathogen inhibitors are more abundant in macroaggregates, indicating their role in disease resistance. Chapter 5 reveals how bio-organic amendments reduce pathogen abundance in microaggregates, leading to reduced disease incidence. This research highlights the importance of fine-scale soil aggregate heterogeneity in microbial ecology and its role in disease suppression through soil amendments.