Abstract
The spotted wing drosophila (Drosophila suzukii, Matsumara) is a rapidly spreading global pest of soft and stone fruit production. Due to the similarity of many of its life stages to other cosmopolitan drosophilids, surveillance for this pest is currently bottlenecked by the laborious sorting and morphological identification of large mixed trap catches. DNA metabarcoding presents an alternative high-throughput sequencing (HTS) approach for multi-species identification, which may lend itself ideally to rapid and scalable diagnostics of D. suzukii within unsorted trap samples. In this study, we compared the qualitative (identification accuracy) and quantitative (bias toward each species) performance of four metabarcoding primer pairs on D. suzukii and its close relatives. We then determined the sensitivity of a non-destructive metabarcoding assay (i.e., which retains intact specimens) by spiking whole specimens of target species into mock communities of increasing specimen number, as well as 29 field-sampled communities from a cherry and a stone fruit orchard. Metabarcoding successfully detected D. suzukii and its close relatives Drosophila subpulchrella and Drosophila biarmipes in the spiked communities with an accuracy of 96, 100, and 100% respectively, and identified a further 57 non-target arthropods collected as bycatch by D. suzukii surveillance methods in a field scenario. While the non-destructive DNA extraction retained intact voucher specimens, dropouts of single species and entire technical replicates suggests that these protocols behave more similarly to environmental DNA than homogenized tissue metabarcoding and may require increased technical replication to reliably detect low-abundance taxa. Adoption of high-throughput metabarcoding assays for screening bulk trap samples could enable a substantial increase in the geographic scale and intensity of D. suzukii surveillance, and thus likelihood of detecting a new introduction. Trap designs and surveillance protocols will, however, need to be optimized to adequately preserve specimen DNA for molecular identification.
Highlights
The combined influences of international trade, tourism, and changing climates are increasing the rate at which new insect pests emerge and spread across borders, creating a global burden on food security (Savary et al, 2019)
All taxa within the mock communities were recovered by the four primer combinations, apart from D. biarmipes which was below the 0.01% relative read abundances (RRA) detection threshold for BF1-BR1 (Figure 1A)
Only the D. immigrans and D. hydei false positives were recorded across all primers with > 1% RRA, indicating they may be due to physical cross contamination of a specimen when the mock communities were assembled
Summary
The combined influences of international trade, tourism, and changing climates are increasing the rate at which new insect pests emerge and spread across borders, creating a global burden on food security (Savary et al, 2019). A striking example is the rapid intercontinental spread of Drosophila suzukii, Matsumara (spotted wing drosophila), a significant pest of soft and stone fruits which over the last two decades has expanded from its native range in Southeast Asia (Kanzawa, 1939; Walsh et al, 2011), to Europe, the Americas, and more recently Africa (Cini et al, 2012; Asplen et al, 2015; Boughdad et al, 2021). The pace of this range expansion is attributed to a high fecundity, short generation time, and a broad host range that allows populations to persist throughout the year by alternating between cultivated and wild fruits with different ripening times (Cini et al, 2012). The resulting risk of misidentification and delayed management response has potential to incur considerable costs to individual growers and national economies (Hauser, 2011)
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