Long-Read Metagenomics Reveals Microbial Taxonomic and Functional Disruptions After Fumigation in Florida Potato Soils
Soil fumigation and phosphorus (P) fertilization are widely used in potato production systems to secure yield, yet their combined effects on soil microbial function and nutrient-use efficiency remain poorly understood. We conducted a field experiment integrating long-read metagenomics with agronomic measurements across four key time points, from pre-fumigation to tuberization, under five P fertilizer rates in sandy soils of Northeast Florida. Fumigation with 1,3-dichloropropene was associated with significant shifts in bacterial and fungal communities. Those shifts were followed by an incomplete recovery observed 62 days after fumigation. Fumigation was also associated with an increase in bacterial alpha diversity, primarily by suppressing dominant, ecologically important taxa such as Bradyrhizobium. Metagenomic analysis showed that fumigation was significantly associated with the depletion of gene sets involved in nitrogen acquisition, colonization, competitive exclusion, and phytohormone production, while increasing traits associated with plant cell wall degradation, indicating a restructuring of plant-microbe interactions. Genes used as indicators of soil health also shifted, with arylsulfatase declining and beta-glucosidase increasing, reflecting altered nutrient-cycling potential. Despite increasing soil P availability, higher P fertilization did not enhance yield, P uptake, or P use efficiency, indicating that fumigation was associated with disruption of microbial nutrient-cycling functions affecting the crop's ability to convert fertilizer inputs into productive growth. Instead, the yield response showed diminishing returns at higher P rates. Overall, our results suggest that fumigation was associated with shifts in soil microbial communities and in the biological pathways underlying fertilizer efficiency, highlighting a trade-off between pest control and sustainable nutrient management in intensive potato systems.