Investigation into the bacterial diversity of sediment samples obtained from Berg River, Western Cape, South Africa

Abstract

This study used conventional culturing and 16S rRNA metagenomics analyses to assess the diversity of bacterial communities in sediment samples obtained from the Berg River, Western Cape, South Africa. Samples were collected from six points: a residential and recreational area, an industrial area, an informal residential settlement, a point next to a wastewater treatment plant (WWTP), a pumping station, and a residential and agricultural farming area along the river. High bacterial counts recorded on general selective and differential culture media signify substantial microbial contamination along the sampling sites. The most prevalent bacterial phyla detected (through metagenomics analyses) along the sampling sites were Proteobacteria (61%), Planctomycetes (9.5%), Firmicutes (7.8%), Bacteroidetes (5%), Acidobacteria (4.6%), and Actinobacteria (4.6%). Some members of the identified predominant bacterial phyla, genera, and classes are important public health bacteria that have been implicated in human diseases and outbreaks, while some others are metal or hydrocarbon tolerant, indicating possible significant environmental pollution. Notable human pathogenic genera such as Bacillus, Clostridium, Shigella, Legionella, Mycobacterium, and Pseudomonas were identified in varying percentages at five of the six sampling areas. Fecal contamination was particularly rife at all residential areas, with the informal housing area being the most notably polluted. Diverse functional pathways were predicted for identified bacteria, such as those associated with different chronic and infectious human diseases as well as those related to hydrocarbon and metal remediation. The point next to a WWTP contained vastly diverse groups of bacterial contaminants as well as the most abundant pathway identities and titles.