A DNA barcode database of Australia’s freshwater macroinvertebrate fauna

Abstract

Macroinvertebrates are widely used for monitoring freshwater ecosystems. In most monitoring programs, identifications take substantial time and expense. Methods that improve the speed, accuracy and cost-effectiveness of macroinvertebrate identification would benefit such programs. Increasingly, DNA barcodes are being used to provide accurate species-level identifications and have the potential to change how macroinvertebrates are routinely identified. Herein we discuss the need for DNA barcodes of freshwater macroinvertebrates with particular reference to Australia. We examine the use of DNA barcodes for species identification and compare DNA barcoding efforts of macroinvertebrates from Australia with those globally. We consider the role of high-throughput sequencing of DNA barcodes in freshwater bioassessment and its potential use in biosurveillance. Finally, we outline a strategy for developing a comprehensive national DNA barcode database for Australian freshwater macroinvertebrates and present the initial efforts in creating this database.

Comprehensive DNA barcodes for species identification and discovery of cryptic diversity in mayfly larvae from South Korea: Implications for freshwater ecosystem biomonitoring

“…Recently, under advanced technology, efficacy of valid DNA barcode database has been paid more attention for biomonitoring of freshwater macroinvertebrate fauna using metabarcoding (Douglas et al 2012) and environmental DNA (eDNA) analysis based on next-generation sequencing platforms (Hajibabaei et al 2011;Cardoni et al 2015;Carew et al 2017). Our data clearly demonstrate that DNA barcode clustering corresponds well to the morphologically identified species group and could distinguish nearly all species except three species (E. nipponicus, E. strigata, P. japonica) according to the phylogeny-based species criterion.…”

“…Our data clearly demonstrate that DNA barcode clustering corresponds well to the morphologically identified species group and could distinguish nearly all species except three species (E. nipponicus, E. strigata, P. japonica) according to the phylogeny-based species criterion. Recently, under advanced technology, efficacy of valid DNA barcode database has been paid more attention for biomonitoring of freshwater macroinvertebrate fauna using metabarcoding (Douglas et al 2012) and environmental DNA (eDNA) analysis based on next-generation sequencing platforms (Hajibabaei et al 2011;Cardoni et al 2015;Carew et al 2017). Thus, valid barcoding system including diverse taxa as much as possible has become more critical since the feasibility of those barcoding methods is solely based on the known DNA sequences as references.…”

Towards routine DNA metabarcoding of macroinvertebrates using bulk samples for freshwater bioassessment: Effects of debris and storage conditions on the recovery of target taxa

“…Jackson et al, 2014;Sweeney, Battle, Jackson, & Dapkey, 2011). Currently, over a million DNA barcodes are available to identify freshwater macroinvertebrates species through the Barcode of Life-BOLD systems v4 database (http:// v4.bolds ystems.org/) (Carew et al, 2017). Using high-throughput DNA sequencing (HTS) technology, it is now feasible and cost-effective to use species DNA barcodes for routine bioassessment through a process known as DNA metabarcoding (Yu et al, 2012).…”

“…As with any sampling effort, this suggests that a large proportion of the bulk collection should be processed if needing to detect the rarer taxa present in collections. Options to enable greater volumes of bulk samples we were unable to assign all macroinvertebrates to species because of the lack of reference DNA barcodes for freshwater macroinvertebrates, suggesting that more individual DNA barcoding is required to fill gaps in DNA barcode libraries (seeCarew et al, 2017;Weigand et al, 2019). Thus, even with DNA metabarcoding we were only able to identify some macroinvertebrate taxa to courser taxonomic levels.…”

Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring

“…Despite some methodological limitations (presence/absence data, primer bias) (Piñol, Mir, Gomez-Polo, & Agustí, 2014;Elbrecht & Leese, 2015), assessment results are at least comparable if not superior to conventional morphology-based stream monitoring approaches (Elbrecht, Vamos, Meissner, Aroviita, & Leese, 2017;Emilson et al, 2018;Gibson et al, 2015). Some macroinvertebrate reference databases are already fairly comprehensive especially for common taxa (Carew et al, 2017;Curry, Gibson, Shokralla, Hajibabaei, & Baird, 2018).…”