A new tool to monitor invertebrates using DNA

Invertebrates make up a large proportion of biodiversity and they have critical roles in the environment. However, their inclusion in biodiversity monitoring and conservation planning has lagged behind larger fauna because collecting and sorting invertebrates using conventional monitoring techniques is often time consuming, expensive, and restricted to experts who can identify invertebrates accurately.

A 2017 study examined at how invertebrates could be monitored using emerging DNA metabarcoding techniques by providing the ability to characterise entire invertebrate communities from a single, easily collected environmental sample. These techniques have the potential to make it easier and more cost-effective for conservation groups to undertake invertebrate community monitoring and to evaluate the performance of restoration projects.

DNA metabarcoding analysis works by extracting DNA from environmental samples such as soil, water, leaves, or bulk invertebrates, and then analysing parts of genes that can act as genetic “barcodes” to identify species whose DNA was present in the sample. Soil, for example, is easily collected and includes lots of DNA molecules of organisms that live in or near it.

It was hypothesised that:

1. For a similar cost, metabarcoding analysis of DNA extracted from bulk invertebrate samples would provide greater taxonomic coverage (breadth of taxa and resolution within taxa) compared with conventional methods of identification
2. Metabarcoding analysis of bulk invertebrate DNA would be able to reproduce patterns of diversity and composition detected by conventional methods, and ecological variation in these patterns between forest interior and forest edge
3. Metabarcoding analysis of DNA extracted from soil would show similar community patterns to the conventional trap samples, therefore indicating that soil is a reservoir of DNA from the broader invertebrate community, potentially negating the need for alternative sampling strategies (i.e. would not need to collect invertebrate samples).

Cape to City

The study looked at Cape to City as an example of a landscape-scale restoration project and aimed to characterise the invertebrate fauna of an isolated, coastal forest fragment at Mohi Bush using both conventional monitoring and DNA metabarcoding methods.

The budget was the same for each method – $20,000 – in order to directly compare the value for money.

Invertebrates were collected at the forest edge, and in the forest interior, using malaise and pitfall traps. Soil samples were collected from the same locations.

The invertebrate samples were first analysed by conventional methods – morphological identifications and assessment of specimen composition. 

DNA metabarcoding was then used to analyse both the invertebrate samples, and the soil samples.

The results of the study support the idea that DNA metabarcoding can be used as a tool to characterize whole invertebrate communities from either bulk invertebrate samples collected using malaise or pitfall traps, or from soil samples. DNA metabarcoding provided broader and more detailed invertebrate biodiversity information than conventional monitoring methods, for the same cost. The soil DNA analysis identified the widest range of invertebrate types.

The main costs of conventional invertebrate monitoring were specimen sorting and morphological identifications, whereas the main costs of DNA metabarcoding methods were molecular laboratory procedures (DNA extraction, PCR, and sequencing library preparation) and bioinformatic processing.

While DNA metabarcoding methods can provide rich information about invertebrate biodiversity, a lack of reference DNA sequences often makes the accurate identification of species difficult, particularly for New Zealand invertebrates. Therefore generation of reference DNA sequences for more invertebrates is needed to make DNA metabarcoding a more useful approach for restoration and monitoring projects.

Watts, C., Dopheide, A., Holdaway, R., Davis, C., Wood, J., Thorburrow, D. and Dickie, I.A. (2019) DNA metabarcoding as a tool for invertebrate community monitoring: a case study comparison with conventional techniques, Austral Entomology, 58: 675-686.

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20 May 2020

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