Assessing Freshwater Microbiomes from Different Storage Sources in the Caribbean Using DNA Metabarcoding

Abstract

Next-generation sequencing (NGS) and the technique of DNA metabarcoding have provided more efficient and comprehensive options for testing water quality compared to traditional methods. Recent studies have shown the efficacy of DNA metabarcoding in characterizing the bacterial microbiomes of varied sources of drinking water, including rivers, reservoirs, wells, tanks, and lakes. We asked whether DNA metabarcoding could be used to characterize the microbiome of different private sources of stored freshwater on the Caribbean Island nation of Antigua and Barbuda. Two replicate water samples were obtained from three different private residential sources in Antigua: a well, an above-ground tank, and a cistern. The bacterial microbiomes of different freshwater sources were assessed using 16S rRNA metabarcoding. We measured both alpha diversity (species diversity within a sample) and beta diversity (species diversity across samples) and conducted a taxonomic analysis. We also looked for the presence of potentially pathogenic species. Major differences were found in the microbiome composition and relative abundances depending on the water source. A lower alpha diversity was observed in the cistern sample compared to the others, and distinct differences in the microbiome composition and relative abundance were noted between the samples. Notably, pathogenic species, or genera known to harbor such species, were detected in all the samples. We conclude that DNA metabarcoding can provide an effective and comprehensive assessment of drinking water quality and has the potential to identify pathogenic species overlooked using traditional methods. This method also shows promise for tracing the source of disease outbreaks due to waterborne microorganisms. This is the first study from small island countries in the Caribbean where metabarcoding has been applied for assessing freshwater water quality.