The genus Aeromonas comprises more than 60 recognized species that include many important fish pathogens such as the causative agents of furunculosis and motile Aeromonas septicemia (MAS). Although MAS is typically considered a secondary infection, a new virulent A. hydrophila (vAh) strain has been causing devastating losses to the catfish industry in Alabama since 2009. The objective of this study was to characterize the spatiotemporal distribution of Aeromonas sp. and, specifically, vAh in a commercial catfish farm in western Alabama. We sampled biofilm, sediment, and water from three ponds during four consecutive months during the growing season. Total aerobic counts were between 8.8 × 10 5 and 1.5 × 10 6 CFU/mL but were significantly higher in biofilm and sediment than in water throughout the sampling period. Total Aeromonas counts in water samples significantly increased in all three ponds after the month of August and ranged from 7.8 × 10 3 to 4.9 × 10 4 CFU/mL. A similar trend was observed in biofilm and sediment samples for which total Aeromonas counts increased in samples taken in late summer to early fall. Over time, the concentration of Aeromonas in water samples decreased by one order of magnitude, while there was a significant increase in sediments as temperature dropped. The virulent vAh was detected in 35.4% of biofilm samples and 22.9% of sediment samples, suggesting that both environments serve as the major reservoir for this pathogen. Future monitoring efforts should focus on targeting sediment and biofilms since samples of these appear to naturally enrich for the presence of vAh and other Aeromonas species.

The objective of this study was to characterize the gut and skin microbiomes of three common freshwater fishes including two important sport fishes, Largemouth Bass Micropterus salmoides and Bluegill Lepomis macrochirus as well as the distantly-related Spotted Gar Lepisosteus oculatus. Skin and gut samples were collected in August and November 2014, and May 2015. All samples were sequenced as paired-end reads of the 16S rRNA gene via the Illumina MiSeq platform. More than 5M reads were analyzed representing 4,130 and 2,744 OTUs from gut and skin samples, respectively. Approximately 51.84% of the total OTUs were shared between the skin and gut bacterial communities. Good's coverage was higher than 98% in all samples. Spotted Gar exhibited the most diverse skin microbiome, while Largemouth Bass was the least diverse species in terms of both the skin and gut microbiome compositions. The highest diversity in the gut microbiome was observed in Bluegill; however, the bacterial communities of Spotted Gar were the most variable across seasons. Seasonal changes in bacterial community structures were also observed. For both the skin and the gut microbiomes, sampling date was found to exert a stronger influence on microbial composition than the species itself; however, season had a lesser impact on the gut microbiome than in the skin indicating the gut microbiomes are more stable. This study provides baseline data on the bacterial symbiont communities of three iconic freshwater fish species in North America. Our data could be used in future studies to identify environmental stressors that result unbalanced microbiomes and loss of homeostasis.