Identification of Diatom DNA Barcodes for Biomonitoring of the New Jersey Pine Barrens Aquatic Ecosystems

Abstract

The goal of this project was to investigate the use of DNA metabarcoding for evaluating and monitoring environmental health of waterbodies in the New Jersey Pinelands. Metabarcoding is a technique of taxonomic identification of organisms in environmental samples via analysis of short DNA sequences. We explored metabarcoding of diatom and other protistan assemblages in ephemeral ponds which are increasingly appreciated as valuable ecosystems and targets for environmental conservation. Metabarcoding has proven to be an efficient approach to monitor changes in aquatic biological communities circumventing the need for time and labor-consuming visual identification of organisms. While this approach has many advantages, such as reduced cost and the ability to characterize multiple taxonomic groups simultaneously, it also has some shortcomings. The major limitation of metabarcoding is incompleteness of the taxonomic reference databases that leaves many DNA sequences unassigned to taxa. For example, the reference database suitable for diatom metabarcoding (Diat.barcode) was developed mostly using diatoms from European rivers and therefore, does not have a good coverage of other geographic areas and habitats. Adding new records to this database typically involves culturing and sequencing diatoms, which is often prohibitively expensive. In this project we explored an opportunity to establish diatom barcodes from natural samples with low species diversity to establish correlation between dominant morphospecies and most abundant sequences.