Nucleic acid based microbiome profiling provides better resolution for faecal contamination tracking in estuaries than traditional plate count approaches Metagenome

Traditional plate counts for assessing water quality are limited in their ability to identify contaminant sources or presence of pathogens. More informative methods are required for defining the risk of gastro-pathogens and identifying mitigation strategies. In this study, seawater samples were tested for faecal contamination simultaneously by plate counts and 16S rRNA gene next generation sequencing (NGS). Two different pore filter sizes used to collect bacteria were compared; 0.22 micrometre (typically used in Aquatic Microbial Ecology studies) and 0.45 micrometer (routinely used in plate count protocols), revealing no significant effect (p > 0.05) in alpha or beta diversity on the relative abundance of dominant phyla. Microbiome profile comparisons were carried out based on parameters known to correlate to elevated levels of faecal contamination: i.e., E. coli abundances, rainfall and river flow. NGS-based microbiome analysis provided an accurate representation of community changes associated with known faecal contamination and a wider range of potential indicator organisms to detect contamination and potentially the source. Culturing on the E. coli selective media CM1046 enhanced the detection of foodborne pathogens and faecal related genera, suggesting potential for downstream sequencing capabilities. This downstream step (combination of culturing followed by 16S rRNA sequencing) provided a deeper identification of key taxa that could be targeted for microbial source tracking (MST). Thus, 16S rRNA sequencing could be incorporated into water quality assessments to identify the usefulness of downstream applications such as MST and pathogen subtyping.