Metabarcoding and applied ecology with hyperdiverse organisms: Recommendations for biological control research

Abstract

Metabarcoding is revolutionizing fundamental research in ecology by enabling large‐scale detection of species and producing data that are rich with community context. However, the benefits of metabarcoding have yet to be fully realized in fields of applied ecology, especially those such as classical biological control (CBC) research that involve hyperdiverse taxa. Here, we discuss some of the opportunities that metabarcoding provides CBC and solutions to the main methodological challenges that have limited the integration of metabarcoding in existing CBC workflows. We focus on insect parasitoids, which are popular and effective biological control agents (BCAs) of invasive species and agricultural pests. Accurately identifying native, invasive and BCA species is paramount, since misidentification can undermine control efforts and lead to large negative socio‐economic impacts. Unfortunately, most existing publicly accessible genetic databases cannot be used to reliably identify parasitoid species, thereby limiting the accuracy of metabarcoding in CBC research. To address this issue, we argue for the establishment of authoritative genetic databases that link metabarcoding data to taxonomically identified specimens. We further suggest using multiple genetic markers to reduce primer bias and increase taxonomic resolution. We also provide suggestions for biological control‐specific metabarcoding workflows intended to track the long‐term effectiveness of introduced BCAs. Finally, we use the example of an invasive pest, Drosophila suzukii, in a reflective “what if” thought experiment to explore the potential power of community metabarcoding in CBC.

Insights into Ecological & Evolutionary Processes via community metabarcoding

“…While the available diet is impacted for both trophic levels, the negative effects of urbanisation are stronger for predators than herbivores, likely due to their increased requirement for larger, unfragmented habitat. The approach can also be used to address applied questions of biological control interactions as reviewed in Lue et al (2022) who showed that it can allow not only identification of biological control interactions but also evidence of hyperparasitism or multiparasitism, which can disrupt biological control by introduced agents.…”

“…The importance of a reference collection is highlighted by Lue et al. (2022) who describe the importance of a vetted and curated reference library for biological control studies. Likewise, Lu et al.…”

“…Thus, rather than diminishing any role of natural history museums in such approaches, the vast data that have been generated through molecular profiling approaches have increasingly highlighted the fundamental importance of barcodes from reliably identified species and populations (Valdivia-Carrillo et al, 2021). The importance of a reference collection is highlighted by Lue et al (2022) who describe the importance of a vetted and curated reference library for biological control studies. Likewise, Lu et al (2022) emphasise the limitations of inference without a reference database, and introduce a fungal rRNA operon database (FRODO) with 1116 sequences linked to taxonomically identified species.…”

“…The approach can also be used to address applied questions of biological control interactions as reviewed in Lue et al. (2022) who showed that it can allow not only identification of biological control interactions but also evidence of hyperparasitism or multiparasitism, which can disrupt biological control by introduced agents.…”

Insights into Ecological & Evolutionary Processes via Community Metabarcoding

“…Thus, rather than diminishing any role of natural history museums in such approaches, the vast data that have been generated through molecular profiling approaches have increasingly highlighted the fundamental importance of barcodes from reliably identified species and populations (Valdivia-Carrillo, Rocha-Olivares, Reyes-Bonilla, Dominguez-Contreras, & Munguia-Vega, 2021). The importance of a reference collection is highlighted by Lue et al (2022) which describes the importance of a vetted and curated reference library for biological control studies. Likewise, Lu et al (2022) emphasize the limitations of inference without a reference database, and introduce a fungal rRNA operon database (FRODO) with 1116 linked to taxonomically identified species.…”