Microbial Resilience Modulates Community Structure in Flooded Rice Soils

Flooded rice cultivation, contributing 75% to global rice production, significantly influences soil redox potential, altering element speciation, pH, and nutrient availability. Despite its agricultural importance, concerns arise regarding extensive water usage and potential soil property alterations. Brazil, a major rice producer, experiences varied soil conditions during seasons, impacting microbial communities and crop production. This study aimed to understand microbial composition changes in low and high-carbon-content soils during successive draining and flooding cycles. Soil samples from rice cultivation areas in Rio Grande do Sul, Brazil, underwent 11 cycles of flooding and draining. DNA extracted after each cycle underwent next-generation sequencing of the 16S rRNA gene. Despite significant differences in physical and chemical attributes between soils, including organic matter, pH, and nutrient levels, similarities in microbial dynamics were observed. Both soils showed decreased bacterial richness initially, recovering in the third cycle, highlighting microbial adaptability to environmental stress. Beta diversity analysis revealed four microbial community states, suggesting a trend toward stabilization over successive cycles. Phylum-level shifts, like decreased Acidobacteria and increased Proteobacteria and Chloroflexi, indicated microbial community adaptation to environmental changes. Genus-level analyses emphasized specific taxonomic responses, with certain genera recovering after initial decreases, showcasing microbial adaptability. Functional predictions showed increased nitrification in drained cycles and a surge in fermenters after the sixth cycle, signifying dynamic metabolic responses to changing conditions. The observed stabilization in microbial communities, regardless of soil carbon content, suggests resilience to cyclic disturbances. This study enhances our understanding of microbial responses to flooding and draining cycles, offering valuable insights for sustainable rice cultivation practices and soil management.