Microbiome Analysis of Channel Catfish Pond Water Samples

Divya Rose1,2, Caitlin E. Older3, Bradley M. Richardson3, Cyndi Ware1,2, Marsha Lewis1,2, Geoffrey C. Waldbieser3, Lester H. Khoo1,2, Hasan Tekedar4, Andy Perkins5, Larry Hanson4, T. Graham Rosser4, Sujita Balami1,2, Celene Slifka4, David J. Wise2,6 and Matt J. Griffin1,2

 1Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, MS 38776; 2Thad Cochran National Warmwater Aquaculture Center, Delta Research and Extension Center, Mississippi State University, Stoneville, MS 38776; 3Warmwater Aquaculture Research Unit, Agriculture Research Service, U.S. Department of Agriculture, Stoneville, MS 38776; 4Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762; 5Department of Computer Science and Engineering, Mississippi State University, MS; 6Mississippi Agriculture and Forestry Experiment Station, College of Forest Resources, Mississippi State University, MS 38776​

ABSTRACT

Mississippi produces 58% of the farm-raised catfish in the United States, with aquaculture ponds spanning more than 36,000 acres.  Most production is in the Delta region of Western Mississippi. Bacterial infections account for 60% of catfish disease related mortality. Feed restriction and/or antibiotic intervention are the most common responses to bacterial infection. Reports from the Aquatic Research and Diagnostic Laboratory (ARDL) in Stoneville, Mississippi, indicate antibiotic resistance has increased over the past decade. Pond water samples were taken from two adjacent farms ~6 km apart.  These farms employ different management strategies in response to bacterial disease.  Both farms vaccinate their stocks, but Farm A uses medicated feed, while Farm B relies on feed restriction in response to bacterial disease. Fifty-six pond water samples (33 from Farm A and 23 from Farm B) were subjected to Illumina sequencing of the 16S rRNA gene (V4 region) and Nanopore shotgun metagenomics. Relative abundance of bacterial taxa between farms highlighted considerable variability between ponds and farms. While alpha diversity showed variation between medicated and non-medicated ponds, visualization of beta diversity did not suggest differences in the bacterial community structure between these two groups. These results highlight discrepancies in the composition of pond microbiota between farms employing different management strategies. Metagenomics data were used to assemble contigs and identify potential plasmids. The highly diverse nature of the pond water samples yielded large numbers of low-coverage contigs primarily associated with bacterial chromosomes, with low numbers of candidate plasmid contigs. Antibiotic resistance genes were nearly absent; only 22 of the over 7 million sequences obtained from all samples aligned with florfenicol, tetracycline, or sulfonamide resistance gene sequences, despite resistant bacteria being isolated from resident fish. Future research using more targeted methods is needed to better understand the prevalence of antibiotic resistance genes and potential bacterial pathogens in catfish ponds.