Assessment of Stream Health with DNA Metabarcoding

Following on from last week’s press release ‘How Clean are Finnish Rivers?’, Vasco Elbrecht et al. have produced a video to explain the methods in ‘Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring‘.

In this video, the authors explore the potential of DNA metabarcoding to access stream health using macroinvertebrates. They compared DNA and morphology-based identification of bulk monitoring samples from 18 Finnish stream ecosystems. DNA-based methods show higher taxonomic resolution and similar assessment results as currently used morphology-based methods. Their study shows that the tested DNA-based methods integrate well with current approaches, but further optimisation and validation of DNA metabarcoding methods is encouraged.

This video is based on the article ‘Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring‘ by Elbrecht et al.

 

Building Universal PCR Primers for Aquatic Ecosystem Assessments

Post provided by Vasco Elbrecht

Many things can negatively affect stream ecosystems – water abstraction, eutrophication and fine sediment influx are just a few. However, only intact freshwater ecosystems can sustainably deliver the ecosystem services – such as particle filtration, food biomass production and the supply of drinking water – that we rely on. Because of this, stream management and restoration has often been in the focus of environmental legislation world-wide. Macrozoobenthic communities are often key biological components of stream ecosystems. As many taxa within these communities are sensitive to negative stressors introduced by humans, they’re ideal for assessing the quality of water.

Unfortunately, most macrozoobenthic taxa – such as stone-, may-, and caddisflies as well as most other invertebrates – are often found in juvenile larval life stages in these ecosystems, so they’re often difficult to identify based on morphology. With the DNA based metabarcoding method though, almost all taxa in a stream can be reliably identified up to species level using a standardised gene fragment. One key component of this strategy is the development of universal markers, which allow detection of the diverse macrozoobenthic groups.

Our new R package PrimerMiner provides a framework for obtaining sequence data from available reference databases and identifying suitable primer binding sites for marker amplification. The package makes this process quicker and easier. In the following pictures, we summarise the key steps of DNA metabarcoding.

To find out more about PrimerMiner, read our Methods in Ecology and Evolution article ‘PrimerMiner: an r package for development and in silico validation of DNA metabarcoding primers’. Like all Applications articles, this paper is freely available to everyone.