Pilot project: Evaluation of DNA-based metabarcoding of microeukaryotic assemblages for water-quality monitoring in New Jersey rivers and streams: Final Report

Abstract

The goal of this pilot project was to explore the DNA metabarcoding approach to biological assessment of New Jersey wadeable streams. We used methodology previously recommended to characterize the whole eukaryotic community by Illumina Mi-Seq sequencing of the V9 fragment of 18S rDNA gene following the Earth Microbiome Project protocol. In order to compare the outcome of molecular characterization of stream biofilms community with traditional microscopy-based assessment, we also enumerated diatoms in the same samples. To evaluate the response of biofilm communities to impairment we sampled 14 sites along a disturbance gradient. To estimate variability of the results obtained by both methods, we analyzed three field replicate samples per sampling site and two lab replicates per sample, which were two separate DNA extractions.