Biodiversity assessments in the 21st century: the potential of insect traps to complement environmental samples for estimating eukaryotic and prokaryotic diversity using high-throughput DNA metabarcoding

Abstract

The rapid loss of biodiversity, coupled with difficulties in species identification, call for innovative approaches to assess biodiversity. Insects make up a substantial proportion of extant diversity and play fundamental roles in any given ecosystem. To complement morphological species identification, new techniques such as metabarcoding make it possible to quantify insect diversity and insect–ecosystem interactions through DNA sequencing. Here we examine the potential of bulk insect samples (i.e., containing many non-sorted specimens) to assess prokaryote and eukaryote biodiversity and to complement the taxonomic coverage of soil samples. We sampled 25 sites on three continents and in various ecosystems, collecting insects with SLAM traps (Brazil) and Malaise traps (South Africa and Sweden). We then compared our diversity estimates with the results obtained with biodiversity data from soil samples from the same localities. We found a largely different taxonomic composition between the soil and insect samples, testifying to the potential of bulk insect samples to complement soil samples. Finally, we found that non-destructive DNA extraction protocols, which preserve insect specimens for morphological studies, constitute a promising choice for cost-effective biodiversity assessments. We propose that the sampling and sequencing of insect samples should become a standard complement for biodiversity studies based on environmental DNA.

Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol

“…Moreover, it would have been very difficult or even impossible to avoid the amplification of such biota in highly diverse insect samples using universal primers (Smith et al, ). Although the primer pair used in this study was designed to amplify a wide array of metazoans (Leray et al, ), recent studies showed that these primers are also capable to amplify fungi DNA (Leray & Knowlton, ; Ritter, Häggqvist, et al, ) and, thus, not so surprisingly, fungi OTUs were also found in our samples. However, the high number of OTUs assigned to fungi species and the discrepancies between the number of fungi OTUs obtained in the different biomes may have been caused by the cascade effects of three factors: (a) the logistics in transporting the samples from the sampling areas to the laboratory; (b) the long period of time between the field collection of insect samples and the processing of preservative ethanol samples; and (c) the storage conditions (i.e., room temperature) in which the samples were preserved during this period of time.…”

“…Although a number of DNA extraction approaches are available for environmental samples such as soil (Dopheide, Xie, Buckley, Drummond, & Newcom, ), feces (Rytkönen et al, ), and water (Brannock & Halanych, ), little attention has been given to preservative ethanol. Excepting, Shokralla et al () that successfully amplified COI fragments from a single Lepidoptera larva directly from a preservative medium containing 95% ethanol but also mescal solution, followed by first generation sequencing (but see Ritter, Häggqvist, et al, for a recent method). We have tried Shokralla et al () method on our samples preserved just in 95% ethanol, but the present methods showed higher DNA and PCR yields at least for the majority of our environmental samples preserved in 95% ethanol.…”

“…Moreover, it would have been very difficult or even impossible to avoid the amplification of such biota in highly diverse insect samples using universal primers (Smith et al, 2012). Although the primer pair used in this study was designed to amplify a wide array of metazoans (Leray et al, 2013), recent studies showed that these primers are also capable to amplify fungi DNA (Leray & Knowlton, 2015;Ritter, Häggqvist, et al, 2019b) and, thus, not so surprisingly, fungi OTUs were also found in our samples. However, the high number of OTUs assigned to fungi species and the discrepancies between the number of fungi OTUs obtained in the different biomes in the laboratory, as shown for water samples (Taberlet et al, 2018).…”

“…(Borror, Triplehorn, & Johnson, 1989), and thus, it is very difficult to find their DNA in water and soil samples. Alternatively, insect DNA has been metabarcoded from tissue samples and/or whole specimens obtained from traps that are highly effective for many flying insects, although in some cases, it leads to sample destruction and thus loss of vouchers for species identification (e.g., Gibson et al, 2014;Ji et al, 2013;Matos-Maraví et al, 2018;Ritter, Häggqvist, et al, 2019b).…”

Trends in DNA barcoding and metabarcoding

“…A second notable trend is towards increasingly holistic approaches to biodiversity analysis, jointly considering multiple kingdoms and scales of biodiversity. In this issue, Ritter et al (2019) explore a multi-faceted approach to high-throughput bioinventory, focused more on capturing total biodiversity rather than on abundance data. They advocate for a combined sampling scheme, consisting of soil samples and insect trapping (such as through Malaise traps), followed by eDNA metabarcoding the soil biota as well as metabarcoding of DNA extracted from the bulk insect samples using a non-destructive protocol.…”