Metatranscriptomic characterization of active microbial communities in strawberry hydroponic drainage effluent

Hydroponic cultivation systems improve water and nutrient use efficiency; however, little is known about the active microbial communities inhabiting hydroponic drainage effluent. This study employed metatranscriptomic sequencing to characterize active microbial communities present in drainage effluent collected from strawberry cultivation beds within a commercial recirculating hydroponic system. Drainage effluent samples were collected during the spring and winter cultivation periods and subjected to RNA-based metatranscriptomic analysis. Following quality filtering, de novo assembly, and taxonomic classification, bacterial, fungal, and viral-associated transcripts were analyzed to characterize active microbial communities within the drainage environment. Metatranscriptomic sequencing generated 65.2 million and 53.2 million paired-end reads from the spring and winter samples, respectively. Taxonomic classification revealed distinct microbial profiles between the two analyzed drainage samples. Bacterial transcripts represented the dominant classified component in both samples. The spring sample exhibited a relatively diverse bacterial community composed of multiple taxa, whereas the winter sample was strongly dominated by Serratia marcescens and Serratia proteamaculans. Fungal community composition also differed between samples, with a greater representation of yeast-associated fungi in the winter sample. Viral-associated transcripts were detected in both samples and were primarily represented by bacteriophage-related sequences. A large proportion of transcripts remained unclassified, particularly in the spring sample, highlighting the limited representation of hydroponic drainage microorganisms in current reference databases. Although the study was limited to a single commercial production site, the findings should be interpreted as site-specific observations rather than representative characteristics of strawberry hydroponic systems in general. Nevertheless, the study provides an initial metatranscriptomic characterization of active microbial communities inhabiting strawberry hydroponic drainage effluent under commercial cultivation conditions and establishes a baseline dataset for further comparative investigations involving multiple hydroponic production systems. These findings provide baseline information on active microbial and viral assemblages associated with hydroponic drainage effluent and demonstrate the utility of metatranscriptomics for characterizing microbial communities in recirculating cultivation systems.