Influence of System Type and Management Practices on Bacterial and Fungal Community Structure in Hydroponic Systems: Insights from Commercial Facilities in Ohio

Abstract

Hydroponics is a method of growing plants using a nutrient-enriched solution in a controlled environment. Unlike soil-based systems, where soil acts as the primary source of microbial inoculum, hydroponic systems rely on the nutrient solution composition and controlled environment conditions to influence microbial growth, survival, and dynamics. Various studies have evaluated the occurrence of bacteria in the root zone and nutrient solution of hydroponically grown crops; however, bacterial and fungal communities have not been deeply described across commercial system types and hydroponic environments. This research aimed to characterize the diversity and structure of bacterial and fungal communities in commercial hydroponic facilities and to determine how system design and management practices drive microbial variation. Lettuce leaves, roots, growth media, and nutrient solution were collected from facilities in Ohio with different system designs (nutrient film technique, deep water culture, ebb and flow, and vertical drip) and analyzed using amplicon sequencing of ribosomal markers (16S rRNA and ITS1). The analysis revealed that bacterial and fungal community structures differed across habitats (leaves, roots, growth media, and nutrient solution). Factors such as system type, plant age, nutrient solution parameters (pH, electrical conductivity, and temperature), and facility humidity significantly contributed to the observed community variation. This work identified bacterial genera Flavobacterium, Sphingobium, Pseudomonas, and Rhizobium and fungal genera Olpidium, Golovinomyces, and Plectosphaerella as the most abundant and prevalent in the sampled hydroponic facilities. This research enhances our understanding of microbial communities associated with commercial hydroponics and provides insights for developing strategies to manage hydroponics to improve crop production.

Antonino Malacrinò

Assistant Professor

I’m a molecular ecologist interested in host-microorganism interaction.