First insight into the environmental microbial communities associated with potentially pathogenic strains in pond cultured tilapia (Oreochromis niloticus) at various growth stages based on 16S, 18S, and ITS2 rRNA gene amplicons sequencing

Abstract

The tilapias have become one of the most essential and commercial freshwater aquatic products of China. Here, 16S, 18S, and ITS2 rRNA genes were used through high-throughput sequencing (HTS) to investigate the microbiome from sixteen pond-cultured environments of tilapia (Oreochromis niloticus) at the larvae, juvenile, rearing, and harvesting growth stages (n = 4). A total of 8,659,384 high-quality counts and 272,854 OTUs were obtained. Overall, the larvae group comparatively had more taxa of microbes and a higher community richness index than those in the juvenile, rearing, and harvesting groups. The most dominant phyla included cyanobacteria (35.7%) of 16S rRNA gene, Opisthokonta (28.5%) of 18S rRNA gene, and Chlorophyta (59.5%) of ITS2 rRNA gene. There were 585 bacteria, 395 micro-eukaryotic, and 29 fungi (eukaryotes) shared at the genus level. Annotation analyses showed that the most abundant bacterium, micro-eukaryotes, and fungi were Cylindrospermopsis (13%), Cryptomonas (30%), and Nectriaceae (27%), respectively. Besides, 113 significant KEGG pathway annotations were identified, and the most significant proportion was metabolism (52.4%). The relative abundance revealed that the larvae group had higher pathogenic potential and oxidative stress tolerant among nine investigated bacterial phenotypes. Moreover, 12 guild types were identified as the guilds of animal and plant pathogen origin. Importantly, our results demonstrated that the environmental factors of stocking density, temperature, pH, transparency, and dissolved oxygen have significant impacts on the distribution and abundance of eight identified potential pathogens. These results indicated that water quality management should be prioritized in all growth stages of tilapias. Altogether, this is the first robust study to elucidate the detailed characteristics of microbiota in different growth stages of pond cultured tilapias environments. Our results will provide necessary data for environmental regulation, disease prevention and control, and healthy breeding of tilapias.