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A collection of 46 Vibrio harveyi strains were isolated from Epinephelus spp., Lutjanus erythopterus , and other maricultured fish in coastal areas of Hainan Province and Guangdong Province, China, between 2011 and 2013. Eighteen strains were determined to be pathogenic via artificial infection of healthy Epinephelus coioides at 10 7 colony-forming units (CFU) mL − 1 . Mortality occurred within 2 to 6 h after injection. Genotypic assays of the 46 strains by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) revealed a similar genotype profile, referred to as the ERIC-1 profile, for all 18 pathogenic strains. This finding indicates that pathogenic V. harveyi strains in south China have similar genetic backgrounds and might be representative pathogenic strains of this region. All 46 strains were screened for the presence of virulence genes typical of V. harveyi , of zoonotic Vibrio species such as V. cholerae , V. parahaemolyticus , and V. vulnificus and of the aquatic pathogen V. anguillarum . Virulence genes were amplified by PCR using specific primers, and five typical virulence genes of the Harveyi clade, luxR , toxRvh , chiA , serine protease and vhh , were detected in all pathogenic isolates. Non-pathogenic strains carried only 1 to 4 of these genes, indicating that these five genes might be the main virulence genes of ERIC-1 strains. Strain-specific PCR primers were designed based on the sequences of distinct ERIC-PCR bands for the 18 pathogenic strains. Species-specific primers exhibited high specificity and sensitivity. This study demonstrates that bacteria that are highly important to mariculture could be specifically detected using ERIC-PCR fingerprint-based amplification. [ABSTRACT FROM AUTHOR]

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. • The first study to report the characteristics of environmental microbiota in Oreochromis niloticus. • The larvae group had the largest number of microbial communities. • The most influential factor was stocking density as determined by using redundancy analysis. • Eight identified potential pathogen were affected by different environmental factors. [ABSTRACT FROM AUTHOR]