Phylogenetic profiling of bacterial populations in perna perna L. before and during red tide in Algoa Bay, Eastern Cape Province, South Africa

Abstract

Shellfish has been known to harbour bacterial agents of marine origin which cause diseases to individuals who consume raw and lightly cooked molluscs. Some populations of Perna perna L. were collected from Algoa Bay in Port Elizabeth, Eastern Cape of South Africa before and during red tide over a period of one month. Samples were dissected, homogenized and their DNA was extracted. A fragment of the bacterial 16S rRNA amplified by PCR with universal primers was visualized on agarose gel electrophoresis. The expected amplicon size (586 bp) from each DNA was further purified using ZymocleanTM Gel DNA recovery kit. The ultra-pure DNA was sequenced in ABI 3500 XL genetic analysers using ABI V3.1 Big Dye kit. The chromatoGrams were converted into text format using Chromas software and blasted on NCBI. The FASTA sequences of each of the bacteria were aligned using Clustal Omega. The evolutionary history was inferred using Neighbour-Joining method and the phylogenetic tree was constructed using MEGA 6 program. Twenty eight bacterial strains were identified in 90% Perna perna collected before red tide, of which 25 strains belong to the Phylum Actinobacteria. They were Gram-positive bacteria and members of the genera Citricoccus, Micrococcus, Zhihengliuella, Arthrobacter, Kocuria, Nesterenkonia, Streptomyces, Saccharothrix, Lechevalieria, Saccharothrix and Rhodococcus, while the remaining three strains belong to Phylum Spirochaetes, genus Spirochaeta and were all Gram-negative. Only few bacteria strains were identified in 10% Perna perna collected during red tide; of which four strains belong to Phylum Proteobacteria, genera Paracoccus and Cohaesibacter, and were all Gram-negative. While Phylum Actinobacteria belonging to the genus Kocuria was detected in the molluscs, Phylum Spirochaetes was equally detected, with the former being Gram positive and the latter Gram-negative bacteria. This study reveals that Perna perna species are potential reservoirs of various bacterial pathogens with associated health threats posed on their consumers. Also, some of these bacterial species are capable of carrying out bioremediation.