Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

Abstract

Conventional morphology-based identification is commonly used for routine assessment of freshwater ecosystems. However, cost and time efficient techniques such as high-throughput sequencing (HTS) based approaches may resolve the constraints encountered in conducting morphology-based surveys. Here, we characterized stream macroinvertebrate species diversity and community composition via metabarcoding and morphological analysis from environmental samples collected from the Shigenobu River Basin in Ehime Prefecture, Japan. We compared diversity metrics and assessed both approaches' ability to evaluate the relationship between macroinvertebrate community and environmental variables. In total, we morphologically identified 45 taxa (3 families, six subfamilies, 31 genera, and five species) from 8,276 collected individuals from ten study sites. We detected 44 species by metabarcoding, with 35 species collapsed into 11 groups matching the morphologically identified taxa. A significant positive correlation between logged depth (number of HTS reads) and abundance of morphological taxa was observed, which implied that quantitative data can be used for subsequent analyses. Relatively higher estimates of alpha diversity were calculated from the metabarcoding data in comparison to morphology-based data. However, beta diversity estimates between metabarcoding and morphology data based on both incidence and abundance-based matrices were correlated proving that community differences between sampling sites were preserved in the molecular data.Also, both models were significant, but metabarcoding data (93%) explained a relatively higher percentage of variation in the relationship between community composition and the environmental variables than morphological data (91%). Overall, we present both the feasibility and limitations of HTS-driven estimations of taxonomic richness, community composition, and diversity metrics, and that metabarcoding was proven comparable and more sensitive against morphology-based analysis for stream macroinvertebrate biodiversity assessment and environmental monitoring.

Lake-depth related pattern of genetic and morphological diatom diversity in boreal Lake Bolshoe Toko, Eastern Siberia

“…The overall taxonomic composition obtained from genetic and morphological data reveals a distinct intra-lake diatom distribution pattern in the investigated localities of the large and heterogenous Lake Bolshoe Toko. Both approaches largely overlap in beta diversity estimations, whereas we find large differences in the taxonomic assignment and richness of identified taxa, similar to that reported in studies on stream invertebrates [57] or seagrass communities [58]. In our data, the families Fragilariacaea and Aulacoseiraceae are abundant and rich according to both approaches, but the genetic dataset does not uncover the abundance and diversity within the family Stephanodiscaceae and Achnanthaceae.…”

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring

“…Previous studies have shown the great potential of metabarcoding for biotic assessments in various contexts, including Malaise trap surveys (Morinière et al, ), biosurveillance of invasive and pest species (Ashfaq & Hebert, ; L. A. Hardulak et al in prep), macrozoobenthos sampling for assessing water and stream health (Elbrecht & Leese, ; Serrana, Miyake, Gamboa, & Watanabe, ), faeces analyses for dietary inference (De Barba et al, ; Hawlitschek, Fernández‐González, Balmori‐de la Puente, & Castresana, ), species identification for forensic entomology (Chimeno et al, ) and for soil biology (Oliverio, Gan, Wickings, & Fierer, ). This approach combines the advantages of DNA barcoding, namely the capacity to identify any life stage, body fragment or even trace DNA in the environment, with the ability of high‐throughput sequencers to analyse millions of DNA fragments and thousands of specimens at a time.…”

Macroinvertebrate community diversity and habitat quality relationships along a large river from targeted eDNA metabarcode assays

“…Biodiversity assessment and ecosystem monitoring require accurate measures of community composition to address environmental comparisons and identify negative anthropogenic impacts (Hillebrand et al, 2018;US Environmental Protection Agency, 2011). In aquatic systems, macroinvertebrates commonly comprise a focal group for biomonitoring, due to their high diversity and range of responses to environmental conditions (Menezes, Baird, & Soares, 2010;Resh, Norris, & Barbour, 1995). However, current biomonitoring methods often have coarse taxonomic resolution leading to false negatives for rare or cryptic macroinvertebrate taxa (Haase et al, 2006;Pfrender et al, 2010) and frequently miss important differences between closely related species (Macher et al, 2016).…”