How can eDNA contribute in riverine macroinvertebrate assessment? A metabarcoding approach in the Nalón River (Asturias, Northern Spain)

Abstract

Background: Bioassessment of rivers is a fundamental method to determine surface water quality. One of the groups most commonly employed as bioindicators of aquatic ecosystems are benthic macroinvertebrates. Their conventional assessment is based on morphological identification and entails several limitations, such as being time-consuming and requires trained experts for taxonomic identification. The use of genetic tools to solve these limitations offers an alternative way to evaluate rivers status. The use of environmental DNA (eDNA) metabarcoding has increased in recent years for different purposes, but its use in water quality evaluation is yet to be tested. Here, morphological and eDNA based inventories of macroinvertebrates were compared from the same seven sampling sites in the Upper Nalón River Basin (Asturias, Spain). Materials & Methods:High-Throughput Sequencing (HTS) of the cytochrome oxidase subunit 1 (COI) gene was carried out on DNA from water samples using an Ion Torrent platform. Biotic water quality indices were calculated from morphological and molecular data and compared with independent physico-chemical habitat assessment to validate eDNA based approach.Results: Highly positive and significant correlation was found between eDNA metabarcoding and morphological methods (Morphological and eDNA indices, r = 0.798, 5 degrees of freedom d.f., P = 0.031;) and a highly significant negative correlation was found between molecular and habitat quality indices (Stress score & eDNA, ρ = -0.878 and P = 0.009; Stress score & Visual, ρ = -0.949 and P = 0.0002). Discussion:The similarity of results from the two approaches and the correlation of eDNA metabarcoding data with the habitat quality indices, suggest that eDNA performs as well as conventional methods for calculating biotic indices in this system, positioning eDNA metabarcoding of macroinvertebrate communities to transform how river bioassessment can be achieved.

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

“…However, our META alpha diversities displayed a strong correlation with ICI scores, suggesting that eDNA META can be used to produce a comparable biotic index. In accordance, other studies found high correspondence between biotic indices inferred from META and MORPH approaches (Fernández et al, 2019;Lejzerowicz et al, 2015;Pawlowski et al, 2018).…”

“…META of environmental (e)DNA in water samples (i.e., genetic material from urine, waste, mucus, or sloughed cells) from aquatic habitats can be used to detect multiple taxa, elucidating much or most of an ecosystem's biodiversity (Cristescu, 2014;Fernández, Rodríguez-Martínez, Martínez, Garcia-Vazquez, & Ardura, 2019;Shokralla, Spall, Gibson, & Hajibabaei, 2012).…”

Peer Review #2 of "Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment (v0.2)"

“…That is because agricultural and urban land use increase in the lower area in our study area, so the larger the stream order, the higher the TN concentration (Table S1). Previous studies reported that eDNA can distinguish geographical changes in communities in river systems for various fauna (fungi: Matsuoka et al, 2019;macroinvertebrates: Hajibabaei et al, 2019b;Fernández et al, 2019). Similarly, the present study showed that the community differences revealed by eDNA analysis were related to the site characteristics by water quality rather than by geographical location.…”

“…Although the biological indices obtained from eDNA vs. the traditional method were only compared in terms of TN concentration in the present study, new environmental indicators can be developed using eDNA data by comparison with more chemical pollution indicators such as biochemical oxygen demand and chemical oxygen demand. While our manuscript was under review, a study that detected macroinvertebrate eDNA and applied this to the environmental status assessment of a river was reported (Fernández et al, 2019). In that report, the environmental assessment score from the IBMWP index was calculated based on the presence/absence of indicator macroinvertebrates at family-level identification.…”

DNA barcoding revels first records of three rare coleopteran genera in Northern lakes of Egypt.

“…Insect researches added huge knowledge to understand the bionomics, genetic development, and evolution. Insects are a powerful indicator of water quality (Junqueira et al, 2000) and one of the most relevant indexes to assess them is already being adapted to use molecular tools and metabarcoding (Fernández et al, 2019). Aquatic beetles are an essential part of the biological system, they are powerful indicators of water quality.…”