Analysis of bacterial diversity in pond water through the addition of microalgae Nannochloropsis sp and two Porphyridium spp using NGS (New Generation Sequencing)

Abstract

Research of disease management in shrimp culture by the use of microalgae have been carried out in the RICAFE since 2016. Later, in 2020, trial application of whole-cell microalgae for treating vibriosis in shrimp grow-out pond was done using microalgae Nannochloropsis sp. and Porphyridium spp. There are three treatments of microalgae applied in this study, namely Nannochloropsis sp, Porphyridium sp, and P. aerugineum, and one Control treatment (without the addition of microalgae). In this research, 12 brackishwater ponds of 25 × 10 m2 at water depth of 80 cm were each stocked with 8 pcs of PL16 tiger shrimp/m2. Sampling for NGS analysis was done at the end of study by taking three liters of pond water then filtered using a vacuum pump and 0.2 µm Whatmann filter. Furthermore, genomic DNA extraction from the pond water samples was carried out using the ZymoBIOMICS DNA Mini Kit. The sequencing analysis was carried out by the 1st Base Singapore Laboratory. The results showed that the use of Nannochloropsis sp resulted in higher diversity of bacteria than other treatments. The treatment with the highest number of bacteria species was found in the use of Porphyridium sp and the lowest was found in Control. The most common bacterial phylum found in all treatments except Control was Proteobacteria, followed by Actinobacteria, and Cyanobacteria. The results of this study indicated that microalgae administration provides better microbial diversity compared to control.