Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing.

Ian King,Shadi Shokralla,Colin Curry,Donald J. Baird,Joel F. Gibson,Wendy A. Monk,Mehrdad Hajibabaei

doi:10.1371/journal.pone.0138432

Abstract

Biodiversity metrics are critical for assessment and monitoring of ecosystems threatened by anthropogenic stressors. Existing sorting and identification methods are too expensive and labour-intensive to be scaled up to meet management needs. Alternately, a high-throughput DNA sequencing approach could be used to determine biodiversity metrics from bulk environmental samples collected as part of a large-scale biomonitoring program. Here we show that both morphological and DNA sequence-based analyses are suitable for recovery of individual taxonomic richness, estimation of proportional abundance, and calculation of biodiversity metrics using a set of 24 benthic samples collected in the Peace-Athabasca Delta region of Canada. The high-throughput sequencing approach was able to recover all metrics with a higher degree of taxonomic resolution than morphological analysis. The reduced cost and increased capacity of DNA sequence-based approaches will finally allow environmental monitoring programs to operate at the geographical and temporal scale required by industrial and regulatory end-users.

Highlights

Many ecological studies rely on measuring biodiversity within each sample, between sampling locations, and at the regional scale
Samples were collected using a standard Canadian Aquatic Biomonitoring Network (CABIN) pond net with a sterile 400μm mesh net and attached collecting cup attached to a pole
The added taxonomic resolution supplied by High-throughput sequencing (HTS) methods provides increased resolution of alpha, beta, and gamma biodiversity metrics

Summary

Introduction

Many ecological studies rely on measuring biodiversity within each sample (alpha biodiversity), between sampling locations (beta diversity), and at the regional scale (gamma diversity). Incidence- and abundance-based metrics like taxon richness, taxon evenness, sample dissimilarity, and assemblage variation can all be derived from direct measures of biodiversity within environmental samples. The temporal and spatial drivers of ecosystems can be explored [1,2,3]. Maintenance of baseline alpha, beta, and/or gamma diversity corresponds with increased ecosystem functionality and provision of ecosystem services [4]. In order to determine the impact of anthropogenic and natural stressors on aquatic ecosystems, it is first necessary to establish baseline biodiversity metrics for communities in a variety of PLOS ONE | DOI:10.1371/journal.pone.0138432. In order to determine the impact of anthropogenic and natural stressors on aquatic ecosystems, it is first necessary to establish baseline biodiversity metrics for communities in a variety of PLOS ONE | DOI:10.1371/journal.pone.0138432 October 21, 2015

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Results

Conclusion