Abstracts

254 - Microbial community characterization at bioremediation
sites using next generation sequencing
Philip Dennis, Ximena Druar, & Peter Dollar
SiREM, Guelph, Ontario, Canada
Kirill Krivushin, Line Lomheim, & Elizabeth Edwards
Department of Chemical Engineering – University of Toronto, Toronto, Ontario, Canada
Next generation sequencing (NGS) is increasingly used to provide detailed microbial
community characterization in public health, medical, wastewater treatment, industrial
fermentation and resource extraction scenarios. The growing affordability of NGS now
makes this technology practical for bioremediation monitoring and performance assessment.
While NGS protocols are robust, the ability to analyze and interpret results in a
meaningful way requires ongoing use and observations at a variety of remediation sites to
better understand the benefits, and limitations, of NGS approaches.
In this study, NGS using a 454 pyrotag platform and primers targeting 16S rRNA genes,
were employed to characterize eubacteria and archaea from five geographically distinct
chlorinated solvent bioremediation sites in Ontario (ON), Oregon (OR), Alaska (AK)
Kansas (KS) and Florida (FL). All sites were bioaugmented and at various stages of remediation
and had varying geochemistry and contaminant profiles. Archived genomic
DNA samples spanning several years were used for the analyses. The resulting sequences
were analyzed using cluster analysis, to compare the microbial communities over time and
between sites and non-metric multidimensional scaling (NMDS) to provide correlations
with geochemical parameters.
NGS returned an average of 8,000 reads per sample, providing detailed microbial community
profiles. Cluster analysis indicated that samples generally grouped together by site
suggesting geographic uniqueness of microbial community structure across these diverse
sites. Based on the number of operational taxonomic units (OTUs) the AK site had the
lowest apparent microbial diversity and the FL site had the highest. Furthermore, cluster
analysis indicated that microbial community at the FL site evolved to become the most
similar to the bioaugmentation culture injected at the site (KB-1) and may indicate that
the FL site was most compatible with bioremediation in general. Observations of OTU
frequency indicated that changes in the abundance of individual microorganisms were significant,
and could be correlated to specific changes in site geochemistry such as oxidation
reduction potential, and metabolic processes such as toxicity, methanogenesis, sulfate reduction
and methanotrophy. It would appear that NGS has great potential to increase our
understanding of microbial communities in bioremediation systems and may find uses in
site monitoring, diagnosis of problematic sites, remediation optimization and monitoring
ecological recovery of aquifers. The technology’s usefulness will undoubtedly increase in
tandem with our ability to meaningfully interpret NGS results.
142 IAH-CNC 2015 WATERLOO CONFERENCE