Measuring the state of aquatic environments using eDNA—upscaling spatial resolution of biotic indices

Abstract

Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they are strongly affected by anthropogenic activities. As many of these taxa are highly sensitive to environmental change, they offer a particularly good early warning system for human-induced change, thus leading to their intense monitoring. In aquatic ecosystems there is a plethora of biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported for freshwater taxa alone. Ultimately, monitoring of aquatic macroinvertebrates is used to calculate ecological indices describing the state of aquatic systems. Many of the methods and indices used are not only hard to compare, but especially difficult to scale in time and space. Novel DNA-based approaches to measure the state and change of aquatic environments now offer unprecedented opportunities, also for possible integration towards commonly applicable indices. Here, we first give a perspective on DNA-based approaches in the monitoring of aquatic organisms, with a focus on aquatic insects, and how to move beyond traditional point-based biotic indices. Second, we demonstrate a proof-of-concept for spatially upscaling ecological indices based on environmental DNA, demonstrating how integration of these novel molecular approaches with hydrological models allows an accurate evaluation at the catchment scale. This article is part of the theme issue ‘Towards a toolkit for global insect biodiversity monitoring’.

eDITH: An R‐package to spatially project eDNA‐based biodiversity across river networks with minimal prior information

“…Firstly, it is generalizable across any taxonomic group. Secondly, it upscales the understanding of species occurrences and derived biodiversity or ecological indices from a point-based distribution to a space-filling projection (Blackman et al, 2024).…”

“…, and are thus subject to intense monitoring including biodiversity and ecological indices assessments(Blackman et al, 2024). Novel eDNA-based approaches, especially when coupled with hydrology-based models, offer unprecedented opportunities to advance freshwater biodiversity assessments.…”

Towards a toolkit for global insect biodiversity monitoring

“…[ 23 ], who proposed that short pieces of standardized marker genes could serve as reliable keys to species identification. The rapid advance of sequencing techniques has revolutionized this field: sequencing platforms have become more efficient and more affordable, allowing not only the screening of large samples [ 28 , 29 ] but also efficient species discovery [ 30 ]. As a particularly exciting development, DNA barcodes can not only identify the species identity of insects themselves, but also reveal more of their Eltonian niches [ 31 ], including the plant species the pollen they carry belongs to [ 32 ], and their microbiomes, as shown by Łukasik & Kolasa [ 33 ].…”

“…[ 29 ] and Blackman et al . [ 28 ] demonstrate how the resulting data can be used for efficient landscape-level predictions of species distributions, community structure and the state of the environment. In an exciting outlook, Meier et al .…”

Environmental DNA: The next chapter

“…However, as eDNA is inherently a different form of sampling (e.g. represents both different taxonomic information and at a different spatial scale to traditional point-based biomonitoring), it should be integrated into existing monitoring schemes as such (Blackman et al, 2024), and not used to distinguish 'true' signals by comparing it to traditional methods. Environmental DNA allows monitoring efforts to be upscaled; spatially and temporally (Altermatt et al, 2020), to integrate cryptic or elusive species, to detect multiple organismal groups that are targeted with specific primers and to incorporate new indicator groups, for example, previously overlooked taxa or novel bioindicators (see Pereira-da-Conceicoa et al, 2021;Sagova-Mareckova et al, 2021).…”