Bacterial features in tilapia (Oreochromis niloticus) and environments in a goose-tilapia polyculture model

The polyculture model embracing poultry-fish farming is a conventional and crucial culture model of tilapia (Oreochromis niloticus) universally. Though, recent doubts are raised that there is a possibility that some pathogens may spread from poultry to fish in this model. To evaluate such risks, we performed bacterial 16S rRNA gene sequencing on the MiSeq Illumina platform for characterization of bacterial compositions and diversities of tilapia animals and environments, including tilapia gills (TG), goose feces (GF), pond water (PW), and bottom sediment (BS) in a tilapia-goose culture model. Our results showed an average of 22 phyla with 169 genera, 27 phyla with 176 genera, and 38 phyla with 206 genera, were identified in TG, GF, and PW, respectively. The highest bacterial diversity was found in BS with 60 phyla with 205 genera (Shannon index 6.64). At the phylum level, bacteria composition in TG, BS, and PW were more stable than that in GF per time with an abundance of Firmicutes, Proteobacteria, Bacteroidetes, and Cyanobacteria. At the genus level, no common pathogenic bacteria have been found in both GF and TG. However, it is noteworthy that some pathogenic bacteria such as Fusobacterium, Acinetobacter, Clostridium, and Campylobacter have been identified in GF. Several beneficial bacteria such as Lactobacillus, Geobacillus, and Bacillus were abundant in TG, compared with that of pathogenic bacteria, including Pseudomonas and Streptococcus. Most of the identified bacteria in BS were anaerobes, such as Dechloromonas, Anaeromyxobacter, and Geobacter which mainly participates in bioremediation. The β-diversity analysis also revealed the bacterial compositions had less similarity between different sources of samples. Above all, the present study gives an insight into bacterial characteristics in the polyculture model. No direct proof supports the pathogenic bacteria were transported from goose to tilapia.