Using next-gen sequencing techniques to categorize microbiome communities within catfish production ponds

Authors: TUTTLE, JAMES - Auburn University; BRUCE, TIMOTHY - Auburn University; ROY, LUKE - Auburn University; ABDELRAHMAN, HISHAM - Auburn University; Garcia, Julio; Beck, Benjamin; KELLY, ANITA - Auburn University

Submitted to: Annual Eastern Fish Health Workshop
Publication Type: Abstract Only
Publication Acceptance Date: 2/27/2024
Publication Date: 3/4/2025
Citation: Tuttle, J.T., Bruce, T.J., Roy, L.A., Abdelrahman, H.A., Garcia, J.C., Beck, B.H., Kelly, A.M. 2025. Using next-gen sequencing techniques to categorize microbiome communities within catfish production ponds [ABSTRACT]. 47th Annual AFS Eastern Fish Health Workshop. Gulfport, Mississippi. March 4-8, 2024

Interpretive Summary:

Technical Abstract: Next generation sequencing techniques such as 16s amplicon sequencing have allowed for more specific categorizations of microbial communities within digestive systems of aquatic organisms and more recently within the biofilms and surrounding environments of aquaculture systems. Very few microbiome studies have been conducted on extensive aquaculture systems like those used primarily in the commercial catfish industry. The western Alabama region containing a majority of channel (Ictalurus punctatus) and hybrid catfish (' channel catfish × ' blue catfish I. furcatus) production ponds is described as having soil conditions suitable for efficient catfish production, however long-term issues including sedimentation and persistent or recurring bacterial diseases can render ponds less than ideal. A better understanding of microbial populations within catfish production ponds may yield more favorable future management strategies, identification or pathogenic bacteria, and assessment of overall pond health. Microbiomes of commercial catfish ponds were assessed by collecting six cylindrical soil cores (15 cm height, 5 cm diameter) form 21 production ponds both prior to and after renovation. Soil cores were separated by depth (0-5 cm, 5-10 cm, and 10-15 cm) and combined, resulting in three total composite samples per pond. Additionally, the top layer sediments from 36 in-production ponds were collected to create 36 composite samples. Next, 1 g of soil and sediment samples were submerged in 1X DNA/RNA Shield and sent to Zymo Research Corp. for 16s Amplicon Sequencing. Once the raw sequence reads were obtained from all samples, each read was subjected to a bioinformatics pipeline that filtered, trimmed, and mapped via a USEARCH and VSEARCH software to later determine Alpha and Beta diversity metrics. Chao1 species richness indices across all samples ranged from 320-2258. The most prevalent phyla among in-production ponds accounted for 25.13, 24.37, and 18.95 % of all bacterial sequences (Figure 1). An unweighted unifrac PCoA of soil core samples revealed no differences between microbial communities either by depth (P = 0.3299), or between renovation status (P = 0.4456). Continued and further investigation into production pond microbiomes will improve our understanding of what influences microbial dynamics in extensive catfish aquaculture ponds