Soilless system design impacts the diversity and composition of microbiota

Abstract Controlled environment agriculture (CEA), including soilless farming systems, is rapidly expanding as a strategy to improve food security and resource efficiency. However, limited information is available on how different soilless farming system designs influence microbial populations relevant to plant health and food safety. This study investigated the effects of soilless growing systems and growing season on aerobic plate counts (APC) and bacterial community composition in nutrient solution and on bok choy ( Brassica rapa subsp. chinensis ) leaves. Five soilless systems, deep water culture (DWC), Kratky (KR), nutrient film technique (NFT), ebb and flow (EF), and drip irrigation (DI), were evaluated across fall and spring growing seasons. Soilless system type significantly influenced APC in nutrient solution, with the DI system consistently exhibiting the highest counts across both seasons. Increased nutrient solution pH was negatively associated with APC, whereas temperature did not significantly affect bacterial concentrations. In contrast, APC on bok choy leaves were not significantly influenced by system type, season, pH, or temperature. Bacterial community composition in nutrient solution was strongly shaped by season, soilless system type, sampling day, and temperature, as determined by 16S rRNA V4 amplicon sequencing. Microbial diversity varied primarily by system type, with limited influence of pH or temperature. Core microbiota analysis identified a small subset of taxa that persisted across systems and seasons, with Acidovorax detected in all samples. We found that soilless system design and seasonal conditions strongly influence microbial load and community structure in nutrient solution, providing a foundation for developing system-specific microbial management strategies. Importance Understanding factors that shape microbial community composition in soilless farming systems is critical for optimizing plant health, system productivity, and food safety. Microbial communities influence nutrient cycling, biofilm formation, and pathogen survival, all of which affect the ecological stability and performance of these systems. By identifying how system design, seasonal variation, and environmental conditions influence shifts in microbial populations, targeted strategies can be developed to promote beneficial microorganisms and mitigate risks associated with pathogens. This knowledge contributes to advancing safe and sustainable soilless farming practices that can meet the growing demand for fresh produce grown in controlled environments.