DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

Abstract

Morphology-based profiling of benthic communities has been extensively applied to aquatic ecosystems’ health assessment. However, it remains a low-throughput, and sometimes ambiguous, procedure. Despite DNA metabarcoding has been applied to marine benthos, a comprehensive approach providing species-level identifications for estuarine macrobenthos is still lacking. Here we report a combination of experimental and field studies to assess the aptitude of COI metabarcoding to provide robust species-level identifications for high-throughput monitoring of estuarine macrobenthos. To investigate the ability of metabarcoding to detect all species present in bulk DNA extracts, we contrived three phylogenetically diverse communities, and applied four different primer pairs to generate PCR products within the COI barcode region. Between 78–83% of the species in the contrived communities were recovered through HTS. Subsequently, we compared morphology and metabarcoding-based approaches to determine the species composition from four distinct estuarine sites. Our results indicate that species richness would be considerably underestimated if only morphological methods were used: globally 27 species identified through morphology versus 61 detected by metabarcoding. Although further refinement is required to improve efficiency and output of this approach, here we show the great aptitude of COI metabarcoding to provide high quality and auditable species identifications in estuarine macrobenthos monitoring.

Assessing the impact of the threatened crucian carp (Carassius carassius) on pond invertebrate diversity - a comparison of conventional and molecular tools

“…Metabarcoding offers a rapid, high-resolution, cost-effective approach to biodiversity assessment, where entire communities can be identified using High-Throughput Sequencing (HTS) in conjunction with community DNA from bulk tissue samples (DNA metabarcoding), or environmental DNA (eDNA) from environmental samples (eDNA metabarcoding), such as soil or water (Deiner et al, 2017;Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, 2012). DNA metabarcoding of aquatic invertebrate samples has proven relatively successful, with applications in biomonitoring (Andújar et al, 2017;Elbrecht, Vamos, Meissner, Aroviita, & Leese, 2017a;Emilson et al, 2017;Lobo, Shokralla, Costa, Hajibabaei, & Costa, 2017). Use of eDNA metabarcoding for invertebrate assessment in freshwater rivers (Blackman et al, 2017;Carew, Kellar, Pettigrove, & Hoffmann, 2018;Deiner, Fronhofer, Mächler, Walser, & Altermatt, 2016;Klymus, Marshall, & Stepien, 2017;Leese et al, 2020), streams (Macher et al, 2018), and lakes (Klymus et al, 2017) is also gaining traction, but there are currently few published studies that have used metabarcoding for small lake or pond invertebrates (Beentjes, Speksnijder, Schilthuizen, Hoogeveen, & van der Hoorn, 2019).…”

“…2) DNA and eDNA metabarcoding would enable species resolution data for problematic taxa that cannot be morphotaxonomically identified to species-level using standard keys (e.g. Blackman et al, 2017;Elbrecht et al, 2017a;Lobo et al, 2017;Nichols et al, 2020); and 3) alpha diversity would be lower in ponds with crucian carp due to direct predation or altered habitat quality (e.g. Lemmens et al, 2013;Maceda-Veiga, López, & Green, 2017;Schilling et al, 2009a;Wood et al, 2001), but beta diversity would be enhanced due to community heterogeneity induced by crucian carp presence in the pond network (e.g.…”

Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring – the need for calibration experiments

“…(1) Bulk DNA metabarcoding of macroinvertebrates has proven successful in several studies so far (Hajibabaei et al 2012;Yu et al 2012;Ji et al 2013;Gibson et al 2014Gibson et al , 2015Elbrecht et al 2017a;Emilson et al 2017;Lobo et al 2017) and is even applicable to bioassessment in freshwater and marine environments alike (Aylagas et al 2014(Aylagas et al , 2018Elbrecht et al 2017a). However, the most obvious technical challenges with bulk sample analysis are processing speed (i.e.…”

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

“…Both primer combinations have been previously found to perform better across metazoan phylogenetic diversity than the mICOIintF reverse complement with LCO1490 (and its degenerate versions dgLCO1490 and jgLCO1490) (Leray et al 2013). A primer pair targeting exactly this same region, but using instead LoboR1 (Lobo et al 2013(Lobo et al , 2017 has been shown to produce similar or higher taxa recovery (e.g. Haenel et al 2017, Ip et al 2019, Chang et al 2020, but it has not been tested yet in NIS-focused studies.…”