Bacterial Community Structure of Aquaculture and Non-Aquaculture Sediments of Taal Lake (Philippines) using PCR-DGGE of 16S rDNA

Abstract

Background and Objective: Microorganisms, including bacteria, serve as major players in various processes affecting both the quality of aquatic sediment as well as the fate of pollutants released into such matrix. In this study, we evaluated the similarity in bacterial community structure between sediments collected from aquaculture and non-aquaculture sites of a tropical lake. Describing and comparing the bacterial community present in each site may provide clues on the impact of aquaculture practices on aquatic ecosystems.

Methodology: Microbial DNA was extracted using PowerSoil® DNA Isolation Kit for all sediment samples. DNA isolates were used as template in the analysis of the hypervariable region of 16S rDNA through nested polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE). Excised representative 16S rDNA DGGE bands were sequenced and identified through BLAST analysis.

Results: Based on the generated mean Dice similarity coefficient of 57.77%, the bacterial community structure between aquaculture and non-aquaculture sediments was highly similar but certain taxa were found unique for each site. Bacteria belonging to Proteobacteria and Firmicutes dominated the aquaculture sediments while Proteobacteria, Firmicutes, and Chloroflexi dominated the non-aquaculture sediments. Certain physicochemical parameters operating in the two sites may have influenced the shift in representative microbes. Shewanella baltica and Trichococcus sp. were found only in aquaculture sediment owing to their ability to tolerate quantities of ammonia and high organic matter from their environment.

Conclusions: This study describes the applicability of 16S rDNA PCR-DGGE as a culture-independent technique for describing and comparing the similarity between bacterial communities in sediment. Based on the generated similarity index, the bacterial community between aquaculture and non-aquaculture sediments of Taal Lake was highly similar but interestingly, harbored unique bacterial populations as seen in the DGGE profiles. The shift in dominant taxa and unique representatives per site may have been influenced by certain differences between each site's physico-chemical parameters.