Influence of system type and management practices on bacterial and fungal community structure in hydroponic systems: insights from commercial facilities in Ohio.

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. Few studies have evaluated the occurrence of bacteria in the root zone and nutrient solution of hydroponically grown crops, however fungal communities have not been deeply described. This research aimed to characterize the diversity and structure of bacterial and fungal communities in commercial hydroponic systems, as well as to determine how system design and management practices drive microbial variation. Leaves, roots, growth media and nutrient solution samples were collected from commercial facilities in Ohio with different system designs (NFT, DWC, Ebb & flow, and Vertical Drip), and analyzed using amplicon metagenomics of ribosomal markers (16S rRNA and ITS1). Analysis of community composition revealed that bacterial and fungal community structure differed across habitats (leaves, roots, growth media, and nutrient solution). Factors such as system type, plant age, nutrient solution parameters (pH, EC, and temperature), and environmental factors (humidity) significantly influenced microbial community variation in hydroponics. Furthermore, this work identified members of the bacterial genera Flavobacterium , Sphingobium , Pseudomonas and Rhizobium , and fungal genera Olpidium , Golovinomyces and Plectosphaerella as the most abundant and prevalent in the sampled hydroponic systems. This research enhances our understanding of microbial communities associated with hydroponics and provides valuable insights for developing strategies to manage hydroponic systems to improve agricultural crop production.