Change in microbial population in farm ponds and irrigation distribution systems throughout two crop production seasons in Georgia Coastal Plains

Studies on the distribution of microbial populations within irrigation lines are limited. We evaluated the ecology, diversity, and composition of the microbial communities present in different irrigation distribution systems in the Georgia Coastal Plains during the 2023 (May-November) and 2024 (March-October) growing seasons. DNA samples (n = 499) were collected using HiCap swabs from irrigation systems (drip systems or center pivots) in six fresh produce commercial farms and sequenced for taxonomy determination. Oxford Nanopore Technologies’ 16S microbiome sequencing kit was used, followed by bioinformatics analysis using Sepia. Water samples (n = 57) from irrigation sources or from the drip line were tested for physicochemical properties, total coliforms, and generic E. coli. Overall, there was a wide diversity of microbial populations with Exiguobacterium, Thiobacillus, Pseudomonas, Aeromonas, and Bacillus abundant in most farms throughout the two sampling years. No significant differences between alpha diversity indices were observed across the farms (p > 0.05), and an increase in microbial diversity at the end of the drip line was observed compared to the beginning. Regardless of the sampling year, all diversity indices were significantly different by month (p < 0.001). Bray-Curtis’ beta diversity metric resulted in no significant clusters across the farm and some seasonal variation. Water quality and microbial composition across water samples revealed significant fluctuations. This work provides the first comprehensive evaluation of microbial communities within active produce farm irrigation systems, capturing their natural dynamics across seasons, water sources, and management practices.