DNA metabarcoding as a tool for invertebrate community monitoring: a case study comparison with conventional techniques

Abstract

When conserving native biodiversity, it is particularly important to consider invertebrates, a diverse and functionally important component of biodiversity. However, their inclusion in monitoring and conservation planning has lagged behind larger fauna because collecting, sorting and identifying invertebrates using conventional monitoring techniques is often expensive, time consuming and restricted by expertise in diagnostics. Emerging DNA metabarcoding techniques could potentially revolutionise monitoring of invertebrates by providing the ability to characterise entire communities from a single, easily collected environmental sample. We aimed to characterise the invertebrate fauna of an isolated, coastal forest fragment in New Zealand using the same level of financial investment for conventional invertebrate monitoring (pitfall and malaise traps) and a DNA metabarcoding approach applied to two alternative sample types (conventional invertebrate samples and soil samples). The bulk invertebrate and soil DNA metabarcoding methods were able to reproduce ecological patterns observed in the beetle community detected using conventional sampling. The soil DNA metabarcoding method detected a different beetle community and a more diverse array of invertebrate taxa than conventional sampling techniques. DNA metabarcoding offers conservation managers a practical, cost-effective technique for characterising whole invertebrate communities. However, increasing the taxonomic coverage of reference sequence databases (particularly for New Zealand invertebrates) through DNA barcoding efforts should be the focus of future research as it would improve the utility of metabarcoding methods for invertebrate monitoring, which would complement conventional techniques.

Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches

“…However, the minimal overlap between our soil and Malaise trap samples may simply reflect that insect communities found in different biological substrates in the same habitat or location differ significantly in composition (Koziol et al, ). For instance, in a study somewhat similar to ours, Watts et al () found big differences in the communities retrieved in soil samples and aboveground traps, although in their case the crawling organisms were retrieved in the aboveground traps, whereas they were primarily found in the soil samples (leaf litter fraction) in our study.…”

“…COI primers with lower degeneracy can be useful with eDNA samples, picking up fewer nontarget taxa than degenerate primers while still recovering a good portion of the invertebrate diversity, but they are still likely to result in lower coverage of the target taxon than in bulk samples (e.g. Watts et al, 2019). Our results…”

“…COI primers with lower degeneracy can be useful with eDNA samples, picking up fewer nontarget taxa than degenerate primers while still recovering a good portion of the invertebrate diversity, but they are still likely to result in lower coverage of the target taxon than in bulk samples (e.g. Watts et al, ). Our results show that the 16S primers chosen work well for analysis of insect community composition in eDNA samples, since the primer‐binding site is more conserved than for COI, but the lower degeneracy prevents off‐target amplification.…”

“…Even when less degenerate primers are used, like those for 18S, DNA amplified from nondesired organisms can still form half of the sequencing output (Yang et al, 2014). Studies comparing the results of metabarcoding of eDNA and trap samples have been scarce, and have mainly focused on freshwater samples (Deiner, Fronhofer, Mächler, Walser, & Altermatt, 2016;Macher et al, 2018), or soil (Horton et al, 2017;Watts et al, 2019). To our knowledge, only one study has combined both types of samples with an ecological aim, rather than a methodological one (Yang et al, 2014).…”

Are insects and other invertebrates in decline in Australia?

“…Other novel approaches to monitoring include deploying automated 'biodiversity weather stations' of the type envisaged in Germany to routinely monitor the diversity and abundance of invertebrates (Vogel 2017), the use of higher taxa (e.g. Family-level) as surrogates for species-level identification to monitor changes in invertebrate assemblages (Driessen and Kirkpatrick 2019) and DNA metabarcoding techniques for characterising and monitoring whole invertebrate communities (Watts et al 2019).…”