Microbial community dynamics of surface water in British Columbia, Canada

Abstract

AbstractTraditional methods for monitoring the microbiological quality of water focus on the detection of fecal indicator bacteria such asEscherichia coli, often tested as a weekly grab sample. To understand the stability ofE.coliconcentrations over time, we evaluated three approaches to measuringE. colilevels in water: microbial culture using Colilert, quantitative PCR foruidAand next-generation sequencing of the 16S rRNA gene. Two watersheds, one impacted by agricultural and the other by urban activities, were repeatedly sampled over a simultaneous ten-hour period during each of the four seasons. Based on 16S rRNA gene deep sequencing, each watershed showed different microbial community profiles. The bacterial microbiomes varied with season, but less so within each 10-hour sampling period.Enterobacteriaceaecomprised only a small fraction (<1%) of the total community. The qPCR assay detected significantly higher quantities ofE. colicompared to the Colilert assay and there was also variability in the Colilert measurements compared to Health Canada’s recommendations for recreational water quality. From the 16S data, other bacteria such asPrevotellaandBacteroidesshowed promise as alternative indicators of fecal contamination. A better understanding of temporal changes in watershed microbiomes will be important in assessing the utility of current biomarkers of fecal contamination, determining the best timing for sample collection, as well as searching for additional microbial indicators of the health of a watershed.