DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists

<div><p>DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity. In addition to these uses, DNA barcoding is a powerful tool to empower, engage, and educate students in the scientific method while conducting productive and creative research. The study presented here provides the first assessment of Marine Park (Brooklyn, New York, USA) biodiversity using DNA barcoding. New York City citizen scientists (high school students and their teachers) were trained to identify species using DNA barcoding during a two–week long institute. By performing NCBI GenBank BLAST searches, students taxonomically identified 187 samples (1 fungus, 70 animals and 116 plants) and also published 12 novel DNA barcodes on GenBank. Students also identified 7 ant species and demonstrated the potential of DNA barcoding for identification of this especially diverse group when coupled with traditional taxonomy using morphology. Here we outline how DNA barcoding allows citizen scientists to make preliminary taxonomic identifications and contribute to modern biodiversity research.</p></div

Overview of the twelve novel DNA barcodes generated by the participants of the Urban Barcoding Project Institute at GESC in the summers of 2014 and 2015.

<p>Overview of the twelve novel DNA barcodes generated by the participants of the Urban Barcoding Project Institute at GESC in the summers of 2014 and 2015.</p

List of ant samples, and their corresponding morphological and DNA barcoding identifications.

<p>List of ant samples, and their corresponding morphological and DNA barcoding identifications.</p

The DNA barcoding workflow.

<p>Biochemical protocols at the website <i>DNA Barcoding 101</i> (<a href="http://www.dnabarcoding101.org/" target="_blank">www.dnabarcoding101.org</a>) and bioinformatics tools at <i>DNA Subway</i> (<a href="http://www.dnasubway.org/" target="_blank">www.dnasubway.org</a>) support all parts of the workflow. (A) Participants collected samples and extracted genomic DNA, generated DNA barcodes using PCR, verified the correct size by gel electrophoresis and sent amplicons for automated sequencing. Sequence data was uploaded to the internet-based DNA barcoding bioinformatics pipeline <i>DNA Subway</i>, and participants assembled contigs, compared them to additional sequences and analyzed sequence data for potential export to GenBank. (B) Trace file of a DNA sequence from a local ant sample. (C) DNA reads are paired and manually edited to create consensus sequence. (D) Top BLAST hits for an ant consensus sequence identifying it as <i>Tetramorium caespitum</i>. (E) <i>DNA Subway</i> integrated export function for novel DNA barcodes to GenBank. (F) User-friendly <i>DNA Subway</i> interface. (G) <i>DNA Subway’s</i> “Blue Line” for DNA barcoding and phylogenetics allows for sequence editing, performing a BLAST search, and phylogenetic tree building on an intuitive, open-source platform.</p

Overview of plants identified by this project, organized by taxonomic level.

<p>Of the 116 collected and identified plants the majority were in the Asterales (n = 32; 27.6% of total plants) and Poales (n = 28; 24.1% of total plants) orders, with the highest number of species within each order falling in the Asteraceae (n = 32; 27.6% of total plants) and Poaceae families (n = 28; 24.1%). Taxonomic groups in legends are organized from largest to smallest.</p

Overview of invertebrates identified by this project, organized by taxonomic level.

<p>The vast majority of the animal samples belonged to the phylum Arthropoda (n = 63; 90% of collected animals). Of those 63 samples, most were from the Insecta class (n = 47; 67.1% of collected animals) in the Hymenoptera (n = 30; 42.8% of collected animals) and Diptera (n = 9; 12.8% of collected animals) orders. Taxonomic groups in legends are organized from largest to smallest.</p

Sampling sites for this study.

<p>Samples were obtained at Marine Park (Brooklyn, New York, USA) in two localities: at a restored, more natural habitat (# 1 above) and an unrestored, disturbed habitat (#2 above). The figure was prepared based on data available from the U.S. Geological Survey Department of the Interior (USGS) public domain (USGS-viewer.nationalmap.gov) and edited by Chun-hua Yang, DNALC.</p