A long-term study of microbial and environmental dynamics in an intensely impacted aquaculture ecosystem

Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. As a result of the extremely high density (biomass) of fish reared in the fish ponds, these ecosystems face a constant input of nutrients from fish-feed and excrements. All of these may strongly affect the microbiome of the water. In this research, over the course of three years, we studied the microbiome of two fishponds and an operational Reservoir that is connected to the fishponds and recycles their water. We hypothesized that the massive anthropogenic influences in terms of fish husbandry practices would strongly affect the microbiome structures of the ponds and the operational Reservoir. Clear seasonal dynamics in water properties and microbiome structure were observed in the Reservoir, which contains water throughout the entire year, with repeated cyanobacterial blooms during the spring and summer months. Analysis of the total microbiome of the fishponds and the Reservoir for the three-year period revealed, in contrast to our hypothesis, a significant influence of environmental parameters, mostly water temperature, and the effect of phytoplankton communities in the water (represented by pigment concentration). The fish biomass was found to be a significant explanatory variable when the microbiome of each of the fishponds were analyzed separately. These results emphasize the importance of environmental factors in structuring microbial populations, even in a strongly anthropogenically impacted ecosystem.