Background Agricultural runoff recycling systems are manmade aquatic ecosystems of growing significance to global water sustainability, crop health, and production. This study investigated the seasonal dynamics of microbial community in a three-reservoir recycling irrigation system with a stepwise water flow and compared with that of an adjacent runoff-free stream. Runoff water from all production areas was captured in a sedimentation reservoir which overflowed to a transition reservoir then retention reservoir through a culvert. Stream water was pumped to replenish the reservoirs as needed during growing seasons.

Results 6S rDNA PCR clone libraries of quarterly water samples from three reservoirs and one stream were sequenced, and 575 operational taxonomic units (OTUs) were identified and assigned to cyanobacteria, eukaryotic phytoplankton, and other bacteria. When compared to the stream, three reservoirs consistently had low microbial diversity. A distinct seasonal pattern of microbial community structure was observed for each reservoir and the stream. Stream was consistently dominated by other bacteria. Retention reservoir was dominated by cyanobacteria during the summer and fall and eukaryotic phytoplankton during the winter and spring. Sedimentation reservoir was dominated by cyanobacteria beginning in the spring but that dominance was altered when water was pumped from the stream from early spring to fall seasons. Transition reservoir had the greatest shift of microbial community structure, being dominated by other bacteria in the summer, cyanobacteria in the fall, and eukaryotic phytoplankton in the winter and spring. Water temperature and ammonium level were the two most important contributing factors to the seasonality of microbial community in these reservoirs.

Conclusions The three recycling irrigation reservoirs consistently had lower microbial diversity and distinct community structure when compared to the stream. These reservoirs were typically dominated by cyanobacteria during warm seasons and eukaryotic phytoplankton during cool seasons. This seasonal pattern was altered when water was pumped from the stream. The cyanobacteria dominance was associated with rising water temperature and ammonium level. These results highlight the importance of preventing agricultural runoff from entering natural waterways and water resources and provide a useful framework for further investigations into the ecological processes of this emerging ecosystem.