Research and analysis

Exploring the potential of DNA techniques to monitor macroinvertebrate communities and invasive species in rivers

Published 18 February 2020

1. Chief Scientist’s Group research summary

This project explored the potential for using DNA techniques to track and monitor small animals in rivers. The project was part of a wider programme of research by UK regulatory and conservation agencies to develop DNA-based methods for environmental monitoring.

1.1 What did the project set out to achieve?

This project tested whether macroinvertebrate communities and individual invasive non-native species (INNS) could be reliably detected in rivers using their DNA and if this approach was more sensitive than kick sampling

Macroinvertebrates are small animals such as mussels, insects and dragonflies, and they are commonly used to assess the ecological quality of rivers as part of routine monitoring. The standard method involves disturbing river sediment by kicking it (‘kick sample’) and collecting all the macroinvertebrates (the macroinvertebrate community) in a net. The macroinvertebrates are then identified and counted by eye using a microscope. This can be time-consuming and costly, and requires skilled people to do it.

In addition to looking at the general macro-invertebrate community, the Environment Agency also monitors:

• quagga mussels (Dreissena rostriformis bugensis)
• zebra mussels (Dreissena polymorpha)
• killer shrimp (Dikerogammarus villosus)
• demon shrimp (Dikerogammarus haemobaphes)

Detection can be by sight and trapping techniques that are costly and difficult to do, or by kick sampling which is not particularly effective if the INNS are only present in low numbers as is often the case.

Although it is possible to use DNA taken from the macroinvertebrates themselves (often referred to as bulk DNA), this has the drawback of being destructive. An alternative is to use environmental DNA (eDNA) – traces of DNA such as skin cell and faeces left behind by the animals in the water or sediment. This is non-destructive and it is not necessary to see the animal to detect it.

1.2 What methods were tested?

The first method tested used a modern DNA sequencing technology called next generation sequencing (NGS) and unique pieces of DNA known as DNA barcodes. When NGS is used to identify many barcodes in a sample, the approach is called metabarcoding. This technique enables rapid identification of multiple macroinvertebrates (the whole community) simultaneously. Many samples can be analysed at once and so it is potentially quicker, less labour-intensive and cheaper than using kick samples.

Four sample types were analysed and their macroinvertebrate communities compared from 44 sites across UK rivers. The sample types were:

• a kick sample (analysed using microscopy)
• DNA bulk samples (mashed up animals from the kick sample)
• water eDNA
• sediment eDNA

The second method tested analysed eDNA from river water samples using a technique called quantitative polymerase chain reaction (qPCR) to detect individual INNS. qPCR is a kind of DNA photocopier. It can increase very tiny amounts of DNA found in the environment to detectable levels, as well as measuring how much DNA is in a sample. This approach is used if precision is required and there is a need to identify a specific species from the environment. It is reported to be more sensitive than metabarcoding, but only information on the species of interest is obtained.

The sensitivity of qPCR designed to detect the 4 invasive mussels and shrimps were tested in the laboratory and in rivers with known populations. The efficiency of detection was also compared with traditional kick samples.

1.3 How well did the DNA techniques perform?

Macroinvertebrate communities detected from bulk DNA, eDNA from water and sediment, and from traditional kick samples were all significantly different from each other.

More macroinvertebrates were detected using traditional kick samples. However, metabarcoding did detect many different types of organisms in addition to macroinvertebrates.

Many of these are not visible with the naked eye, but could provide important ecological information. The project also demonstrated that there is enormous power in metabarcoding for the detection of rare or unexpected species, as it detected a new non-native species of shrimp not previously found in UK rivers, Gammarus fossarum (Blackman et al. 2017).

Before testing the ability of the qPCR method to detect INNS in rivers with known populations (Blackman et al. 2018a), rigorous laboratory testing was carried out to ensure each method only detected the target INNS. All 4 INNS were successfully detected in laboratory experiments, but success was higher for the mussel species than the shrimp species. In river experiments, the 2 mussel species and demon shrimp were detected at all the sites where the species were known to be present, and eDNA consistently outperformed traditional kick sampling for species detection, particularly at low numbers. However, killer shrimp eDNA was only detected at 1 out of 5 sites where the species was confirmed by kick sampling.

1.4 What are the next steps?

This work has demonstrated that DNA metabarcoding (from bulk DNA or eDNA) cannot directly replace existing kick sample monitoring as it provides different information, irrespective of sample type. Metabarcoding approaches have also demonstrated their potential for species discovery.

To take advantage of the cost-effective, non-destructive approach offered by eDNA metabarcoding, and if it is to feature in macroinvertebrates assessments, it will be necessary to rethink how all the information generated by DNA – and not just that from macroinvertebrates – can be incorporated into ecological assessments to understand the ecological response to environmental change.

This study has highlighted the huge potential of sampling eDNA from water for INNS detection. It is more sensitive than kick sampling. Early detection of INNS when they are in low numbers is critical for timely and cost-effective management responses such as containment or removal. The quagga mussel method is in the final stages of validation prior to being deployed as a monitoring tool. The other INNS methods require further refinement to improve their sensitivity, particularly the method for killer shrimp.

1.5 Publishing details

This summary relates to information from project SC140030, reported in detail in the following output(s):

BLACKMAN, R.C., 2017. Environmental DNA: from detection of priority invasive species to monitoring entire macroinvertebrate communities in freshwater ecosystems. PhD thesis, University of Hull. Available from: https://hydra.hull.ac.uk/resources/hull:16527 [Accessed 17 December 2018].

BLACKMAN, R.C., CONSTABLE, D., HAHN, C., SHEARD, A.M., DURKOTA, J., HÄNFLING, B. AND LAWSON-HANDLEY, L., 2017. Detection of a new non-native freshwater species by DNA metabarcoding of environmental samples – first record of Gammarus fossarum in the UK. Aquatic Invasions, 12 (2), 177-189.

BLACKMAN, R.C., BENUCCI, M., DONNELLY, R., HÄNFLING, B., HARPER, L.R., KIMBELL, H., SELLERS, G.S., SHEARD, A.M., WATSON, H.V. AND LAWSON-HANDLEY L., 2018a. Targeting the invaders – targeted detection of four priority freshwater invasive species using environmental DNA. PeerJ Preprints 6:e27284v1.

BLACKMAN, R.C., HÄNFLING, B. AND LAWSON-HANDLEY, L., 2018b. The use of environmental DNA as an early warning tool in the detection of new freshwater invasive non-native species. CAB Reviews, 13, 010, 1-15.

February 2020

Project manager:

Kerry Walsh, Research, Analysis and Evaluation

Research Contractor:

PhD Supervisor: Lori Lawson-Handley PhD Student: Rosetta Blackman

The Evolutionary Biology Group,
School of Biological, Biomedical and Environmental Sciences,
University of Hull,
Kingston-upon-Hull,
HU6 7RX.

This project was funded by the Environment Agency’s Research, Analysis and Evaluation group, which provides scientific knowledge, tools and techniques to enable us to protect and manage the environment as effectively as possible.

Enquiries: research@environment-agency.gov.uk

© Environment Agency