Evaluating nanopore sequencing for microbial community characterization in catfish pond water

In the United States, catfish are primarily farmed in earthen ponds, resulting an aquatic environment influenced both by management practices and natural ecological processes. Profiling pond water microbiota can be useful for understanding what conditions may lead to microbial communities associated with production issues could inform practices. The aim of this study was identify appropriate methods bacterial community profiling nanopore sequencing 16S rRNA gene. To end, two forward primers, reverse three different polymerase chain reaction (PCR) cycle numbers were tested on a mock consisting aquaculture-relevant bacteria. optimized protocol applied samples obtained from experimental ponds sampled May, June, August, September 2020. Applying these allowed identification 1488 genera, within four dominating phyla: Actinobacteriota, Bacteroidota, Cyanobacteria, Firmicutes. High variation observed between individual sampling timepoints; only 18 genera found relative abundances ≥1% all at least one point. Despite variation, consistent results observed. Samples month had highest number June lowest. Overall, data demonstrated represent distinct microcosms composed unique communities, although effect secondary influence composition.