Microbial diversity and community structure of microalgae (Nannochloropsis oculata) and rotifer (Brachionus plicatilis) in aquaculture by 16S rRNA amplicon-based sequencing

Live cultures, including Nannochloropsis oculata and Brachionus plicatilis, are essential in aquaculture due to its economic and nutritional value for commercial fish species. Pathogens and probiotics can be introduced to aquaculture systems by live feed, with variations in abundance influenced by environmental physicochemical parameters. To investigate this, amplicon sequencing of the V3-V4 region of the 16S rRNA was conducted using Illumina MiSeq to elucidate bacterial abundances and their variations in response to changes in physicochemical parameters in live feed cultures. Results revealed that pathogens like, Tenacibaculum, predominantly found in rotifer cultures, was inhibited under dissolved oxygen levels of 6.87–8.19 mg/L and pH levels of 8.63–9.23. Winogradskyella, mainly present on day 1 of the microalgae culture, thrived under these same conditions. Potential probiotics were also analyzed. Phaeodactylibacter, primarily found on day 1 of microalgae cultures, was favored by dissolved oxygen levels of 7.11–7.68 mg/L and pH levels of 8.63–9.23 but was inhibited by nitrite levels of 0.46–0.5 mg/L. Overall, dissolved oxygen was the key parameter modulating microbial diversity. This study shows that optimizing environmental parameters can enhance culture health by promoting probiotics and reducing harmful bacteria.