Dr Francesco Martoni1,2, Dr Lea Rako1, Professor Brendan Rodoni1,2, Dr Mark Blacket1,2
1Agriculture Victoria, AgriBio Centre, Bundoora, Australia, 2La Trobe University, School of Applied Systems Biology, Bundoora, Australia
Biography:
Dr Francesco Martoni is a Senior Research Scientist for Agriculture Victoria, based at the AgriBio Centre. Francesco has more than 10 years research experience developing and optimising molecular methods to study insects and their associated microflora. During the past 8 years, Francesco has focused on developing and optimising workflows for high throughput metabarcoding of insects, bacteria and fungi for diagnostics and surveillance, including from environmental DNA analysis. Francesco’s main interest focuses on exploring the “biodiversity behind the pests”, using metabarcoding to dive deep in the ecological networks linking both pests and beneficial insects to the surrounding environment.
Abstract:
Long-term surveillance of native and exotic arthropod pests in Australia is often labour-intensive and costly, relying on the manual screening of large numbers of trap samples and morphological identification by highly skilled taxonomists. Molecular approaches, particularly quantitative PCR and high-throughput sequencing (HTS) metabarcoding, have become increasingly important for providing rapid and accurate species-level identifications. When combined with trapping technologies capable of collecting large volumes of airborne or ground-dwelling insects, HTS can greatly enhance pest surveillance and on-farm decision-making. However, metabarcoding detections may be questioned when corresponding morphological evidence of the target species cannot be confirmed.
Here, we present multiple case studies demonstrating that arthropod metabarcoding of insect trap samples can include a significant environmental DNA (eDNA) component, providing valuable surveillance and species-detection information even when intact specimens are absent or cannot be recovered. We investigated cases in which DNA from target taxa was detected despite a lack of morphological evidence for their presence. Although these detections originated from physical insect samples, we show that eDNA contributed substantially to the sequence data, including DNA derived from predator-prey interactions, faecal material, and traces of shed exoskeletal tissue.
Our findings highlight that eDNA is already an important contributor to HTS-based arthropod metabarcoding, despite often going unrecognised. Understanding this contribution expands the potential applications of eDNA metabarcoding for biosecurity surveillance, pest monitoring, and biodiversity assessment.