The early diet of catfish fry consists primarily of zooplankton. Therefore, the zooplankton-associated microbiome represents some of the first microbes catfish come into contact with. These microbes may be an important contributor to establishing the catfish gut microbiome and subsequent health and production outcomes. In the present study, the bacterial communities associated with four zooplankton taxa commonly observed in catfish ponds (Ceriodaphnia spp., ostracods, calanoid copepods, and cyclopoid copepods) were characterized. Additionally, different quantities of organisms were evaluated to determine appropriate methods for future studies.
Zooplankton samples were obtained from a single hybrid (Ictalurus punctatus × I. furcatus) catfish pond in Stoneville, MS, via water sampling with a 80 µm mesh Wisconsin-style net. The sample was filtered through a glass-microfibre disc filter. Then individual zooplankton were sorted taxonomically into culture plates containing deionized water. Zooplankton from each taxonomic plate were filtered again and rinsed with nuclease-free water. Individual zooplankton were then aliquoted into microtubes containing a RNA stabilization buffer in quantities of 5, 10, and 20 organisms per tube, for a total of 12 samples (3 quantities each of 4 taxa). DNA was extracted from the samples, subjected to amplification of the 16S rRNA gene using primers 27F and 1492R, and sequenced on an Oxford Nanopore Technologies GridION. Reads were quality-filtered, mapped to the Greengenes2 database with minimap2, and taxonomic classifications made with a lowest common ancestor approach. Diversity metrics, statistical analyses, and plotting were completed using R.
Ten organisms was the lowest quantity tested which provided sufficient DNA yield for all taxa. Although composition of communities varied among the different quantities within each zooplankton taxa, composition was more different among zooplankton taxa. Communities were primarily composed of species from the phyla Proteobacteria and Bacteroidota. Proteobacteria was the only phyla with at least 30% relative abundance in almost all Ceriodaphnia spp., calanoid copepod, and cyclopoid copepod samples. Ostracods had high relative abundances of Proteobacteria as well (34-44%), but with substantial proportions of Bacteroidota (29-40%). Ostracods had the richest communities, containing an average of 1523 bacterial species, compared to averages between 532 and 974 for the other taxa. These results provide valuable information for guiding additional studies of the microbiome associated with zooplankton in catfish aquaculture ponds. Additionally, the presented data represent the first characterization of the bacterial communities associated with this critical food source for catfish fry.