Community Metabarcodes for Biodiversity Assessments

Annette Govindarajan, Biology

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2015 OLI Funded Project

Abstract

Identification of organisms is a fundamental aspect of biological and ecological research: accurate identifications are required for biodiversity assessments, to identify anthropogenic community changes, geographic range shifts, and ecosystem management.  Species identification is extremely challenging and time-consuming, and is often the bottleneck in research programs.  Ecological patterns are species – specific, but organisms are often lumped in higher taxonomic categories, and this impedes our understanding of ecological processes.  Traditionally, species identification for invertebrates involves detailed analysis of morphological features, and experts are necessary to corroborate identifications made by non-specialists.  This process is laborintensive and can be inaccurate, especially for cryptic life stages like larvae.  Genetic species identification has facilitated biodiversity assessments.  Typically, DNA is extracted from individuals, and a diagnostic DNA marker is amplified and sequenced with traditional “Sanger” technology.  Individuals within a species share similar or identical marker sequences, while different species have divergent sequences.  However, barcoding still requires significant handling time and associated cost to process multiple samples.  Genetic barcoding of entire biological communities (“metabarcoding”) using next-generation sequencing technology is potentially vastly more informative and cost effective than Sanger barcoding of individual specimens.  Metabarcode samples typically yield hundreds of thousands to millions of barcode sequences and potentially provide community snapshots.  However, the use of metabarcoding for addressing ecological problems is in its infancy, and methodological issues need to be resolved to interpret the sequencing results.

Here, I propose to evaluate several aspects of metabarcode protocols to facilitate its application to marine metazoan (animal) biodiversity assessments.  I will compare biodiversity assessments based on metabarcoding and morphological/Sanger barcoding identifications, and will evaluate sampling strategy (concentrated vs.  whole-water environmental DNA sampling), within-sample replication, and barcode marker choice.  Because metabarcoding is likely to be especially useful for assessing small life stages like larvae, the assessments will be conducted on samples where invertebrate larvae (including those from exploited species) are likely to be present.  However, the metabarcoding results will yield DNA sequences from all organisms whose DNA is amplified, including zooplankton, phytoplankton, and microbes, and thus our results will likely stimulate new research directions.  This study will be one of the first comparative assessments in marine systems and so have high impact on future applications.  The proposed work aligns with OLI themes of ocean biodiversity and advancing the study of marine organisms and biological processes with new approaches.