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Utilizing RNA for Metabarcoding Benthic Marine Communities: Can Environmental RNA Change the Future of Community Diversity Assessments?
  • +2
  • Marissa Giroux,
  • Jay Reichman,
  • Troy Langknecht,
  • Robert Burgess,
  • Kay Ho
Marissa Giroux
ORISE c/o U.S. EPA ORD/CEMM

Corresponding Author:[email protected]

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Jay Reichman
US Environmental Protection Agency Center for Public Health and Environmental Assessment Pacific Ecological Systems Division
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Troy Langknecht
ORISE c/o U.S. EPA ORD/CEMM
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Robert Burgess
US Environmental Protection Agency Office of Research and Development Atlantic Coastal Environmental Sciences Division
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Kay Ho
US Environmental Protection Agency Office of Research and Development Atlantic Coastal Environmental Sciences Division
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Abstract

Microfauna and meiofauna organisms are often overlooked in traditional diversity assessments due to their small size and difficulty to morphologically identify. Metabarcoding is an emerging method for the rapid identification of organisms. Environmental DNA (eDNA) is often used as a template for metabarcoding, but legacy DNA is problematically detected from organisms no longer in the environment during sampling. Environmental RNA (eRNA) can also be collected and sequenced using the same pipeline as eDNA metabarcoding, but it is only produced by living organisms. The aim of this study was to determine the differences in detected community composition and diversity between eRNA and eDNA templates for downstream metabarcoding. Seven field-collected mesocosms from the Narrow River Estuary in Narragansett, RI (USA) were held in a flow-through seawater laboratory for 14 days to ensure no residual DNA contamination from non-living organisms. RNA and DNA were co-extracted from the top layer of sediment, libraries were prepared for two loci (18S V4 region and Cytochrome c Oxidase subunit 1) and sequenced using an Illumina MiSeq. Results show a higher number of unique sequences detected from eRNA in both the 18S and COI markers and higher α-diversity compared to eDNA. Significant differences between eRNA and eDNA for all β-diversity metrics were also detected. This study is the first to demonstrate community differences detected with eRNA compared to eDNA from a dynamic estuarine system under controlled laboratory conditions and start to illustrate the broad applications of eRNA as a tool for assessing benthic community diversity.