Next‐generation sequencing technologies for environmental DNA research

Abstract

Since 2005, advances in next‐generation sequencing technologies have revolutionized biological science. The analysis of environmental DNA through the use of specific gene markers such as species‐specific DNA barcodes has been a key application of next‐generation sequencing technologies in ecological and environmental research. Access to parallel, massive amounts of sequencing data, as well as subsequent improvements in read length and throughput of different sequencing platforms, is leading to a better representation of sample diversity at a reasonable cost. New technologies are being developed rapidly and have the potential to dramatically accelerate ecological and environmental research. The fast pace of development and improvements in next‐generation sequencing technologies can reflect on broader and more robust applications in environmental DNA research. Here, we review the advantages and limitations of current next‐generation sequencing technologies in regard to their application for environmental DNA analysis.

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

“…If the database is incomplete, algorithms are used to find the best taxonomic assignment for the query sequences within a certain threshold of sequence dissimilarity (Boyer et al 2016;Rimet et al 2016). Metabarcoding, combined with new high-throughput, next-generation sequencing (NGS) techniques such as Illumina amplicon sequencing, potentially provides a sufficiently high number of sequences compared to cloning and Sanger sequencing, to reveal the community composition adequately (Shokralla et al 2012;Taberlet et al 2012a). Other advantages of NGS-based metabarcoding are the potential for automated sample handling and standardized laboratory protocols that allow for better comparison between different studies (Hajibabaei et al 2011;Thomsen and Willerslev 2015).…”

Molecular genetic tools for environmental monitoring of New Zealand's aquatic habitats, past, present and the future

“…Our preliminary results indicate that it is possible to detect a single Asterias larva when it is spiked into a c. 0.3 mg of sediment or concentrated (2000 organisms per mL) plankton sample using pyrosequencing (Pochon unpublished data). Despite some significant technical challenges associated with these techniques (Shokralla et al 2012), NGS technologies provide unprecedented opportunities for the development of innovative diagnostic tools able to detect multiple species from a variety of life stages in environmental samples, and for the early detection, management and prevention of invasive species worldwide.…”

Large-scale genotyping of highly polymorphic loci by next-generation sequencing: how to overcome the challenges to reliably genotype individuals?

“…This protocol allows reliable genotyping of amplicons with low coverage thanks to the assignation of reads based only on a few bps of the primers instead of the whole sequence and to clustering reads containing sequencing errors such as indels. Given that ampliconbased NGS techniques remain expensive (Glenn, 2011;Shokralla et al, 2012), the proposed protocol contributes to the reduction of the sequencing costs.…”

“…Owing to their wide range of applications, amplicon-based NGS techniques have undergone an extremely fast development (see Shokralla et al (2012) for details on development of NGS technologies) leading to the emergence of several NGS platforms such as 454, Illumina, SOLiD or Ion Torrent. Although these NGS platforms may differ in terms of the number of obtained reads per run, the number of base pairs (bps) per read, the run time or the cost per run (see Glenn, 2011;Shokralla et al, 2012 for reviews of available NGS techniques), all amplicon-based NGS techniques generate multiple reads for a given amplicon and are prone to errors such as artifacts (substitutions and chimeras) during PCR or indels during the sequencing process (Glenn, 2011).…”

“…Although these NGS platforms may differ in terms of the number of obtained reads per run, the number of base pairs (bps) per read, the run time or the cost per run (see Glenn, 2011;Shokralla et al, 2012 for reviews of available NGS techniques), all amplicon-based NGS techniques generate multiple reads for a given amplicon and are prone to errors such as artifacts (substitutions and chimeras) during PCR or indels during the sequencing process (Glenn, 2011). Discerning true alleles versus sequencing errors is thus challenging, especially where several functionally distinct alleles may differ by a single nucleotide (Babik, 2010), and post-processing procedures are then needed.…”