AquaSens: exploring the use of 16S rRNA next-generation sequencing to determine bacterial composition of various water matrices

Abstract

Access to clean water, one of the United Nation’s Sustainable Development Goals, is challenged by an increase in the presence of emerging microbial and other contaminants due to urbanization, among other factors. Traditionally, the presence of indicator microorganisms is determined using culturing methods. However, these classical methods cannot be used to determine the identities of ‘unknown’ bacteria and is limited to isolating the culturable state of microorganisms. Thus with culturing, the identities of many bacteria, particularly novel or non-culturable, may remain unknown. The use of a DNA-based method, 16S rRNA next-generation sequencing (NGS), can assist with determining the identities of bacterial populations in a water sample. The objective of this 16S rRNA NGS study was to investigate the bacterial community composition and diversity in a range of water sources. Water samples comprising of potable, surface, ground, marine, aquaculture, rain, wetland and swimming bath water matrices were subjected to 16S rRNA NGS using the Illumina 16S rRNA Metagenomics analysis pipeline. Operational taxonomic units were analysed and the identities of bacterial genera determined. In this study, genera of Acinetobacter, Mycobacterium, Pseudomonas, Legionella, Burkholderia, Yersinia, Staphylococcus and Vibrio were spread across the water matrices. Alpha (within sample) and beta (between samples) diversities for each bacterial community within the tested samples were also determined.