Non-destructive insect metabarcoding for surveillance and biosecurity in citrus orchards: recording the good, the bad and the psyllids

Background

The Australian citrus industry remains one of the few in the world to be unaffected by the African and the Asian citrus psyllids, Trioza erytreae Del Guercio and Diaphorina citri Kuwayama, respectively, and the diseases their vectored bacteria can cause. Surveillance, early detection, and strict quarantine measures are therefore fundamental to safeguard Australian citrus. However, long-term targeted surveillance for exotic citrus pests can be a time-consuming and expensive activity, often relying on manually screening large numbers of trap samples and morphological identification of specimens, which requires a high level of taxonomic knowledge.

Methods

Here we evaluated the use of non-destructive insect metabarcoding for exotic pest surveillance in citrus orchards. We conducted an 11-week field trial, between the months of December and February, at a horticultural research farm (SuniTAFE Smart Farm) in the Northwest of Victoria, Australia, and processed more than 250 samples collected from three types of invertebrate traps across four sites.

Results

The whole-community metabarcoding data enabled comparisons between different trapping methods, demonstrated the spatial variation of insect diversity across the same orchard, and highlighted how comprehensive assessment of insect biodiversity requires use of multiple complimentary trapping methods. In addition to revealing the diversity of native psyllid species in citrus orchards, the non-targeted metabarcoding approach identified a diversity of other pest and beneficial insects and arachnids within the trap bycatch, and recorded the presence of the triozid Casuarinicola cf warrigalensis for the first time in Victoria. Ultimately, this work highlights how a non-targeted surveillance approach for insect monitoring coupled with non-destructive DNA metabarcoding can provide accurate and high-throughput species identification for biosecurity and biodiversity monitoring.

Development of a cost-effective, morphology-preserving method for DNA isolation from bulk invertebrate trap catches: Tephritid fruit flies as an exemplar

Insect identification and preservation of voucher specimens is integral to pest diagnostic and surveillance activities; yet bulk-trapped insects are a diagnostic challenge due to high catch numbers and the susceptibility of samples to environmental damage. Many insect trap catches rely on examination of morphological characters for species identifications, which is a time consuming and highly skilled task, hence there is a need for more efficient molecular approaches. Many bulk DNA extraction methods require destructive sampling of specimens, resulting in damaged, or fully destroyed, voucher specimens. We developed an inexpensive, rapid, bulk DNA isolation method that preserves specimens as pinned vouchers to a standard that allows for post-extraction morphological examination and inclusion in insect reference collections. Our protocol was validated using a group of insects that are time-consuming to identify when trapped in large numbers-the dacine fruit flies (Diptera: Tephritidae: Dacinae). In developing our method, we evaluated existing protocols against the following criteria: effect on morphology; suitability for large trap catches; cost; ease of handling; and application to downstream molecular diagnostic analyses such as real-time PCR and metabarcoding. We found that the optimum method for rapid isolation of DNA extraction was immersing flies in a NaOH:TE buffer at 75°C for 10 minutes, without the need for proteinase K or detergents. This HotSOAK method produced sufficient high-quality DNA whilst preserving morphological characters suitable for species-level identification with up to 20,000 flies in a sample. The lysates performed well in down-stream analyses such as loop-mediated isothermal amplification (LAMP) and real-time PCR applications, while for metabarcoding PCR the lysate required an additional column purification step. Development of this method is a key step required for upscaling our capacity to accurately detect insects captured in bulk traps, whether for biodiversity, biosecurity, or pest management objectives.

Using DNA metabarcoding to assess insect diversity in citrus orchards

Background

DNA metabarcoding is rapidly emerging as a cost-effective approach for large-scale biodiversity assessment and pest monitoring. The current study employed metabarcoding to assess insect diversity in citrus orchards in Ganzhou City, Jiangxi, China in both 2018 and 2019. Insects were sampled using Malaise traps deployed in three citrus orchards producing a total of 43 pooled monthly samples.

Methods

The Malaise trap samples were sequenced following DNA metabarcoding workflow. Generated sequences were curated and analyzed using two cloud databases and analytical platforms, the barcode of life data system (BOLD) and multiplex barcode research and visualization environment (mBRAVE).

Results

These platforms assigned the sequences to 2,141 barcode index numbers (BINs), a species proxy. Most (63%) of the BINs were shared among the three sampling sites while BIN sharing between any two sites did not exceed 71%. Shannon diversity index (H') showed a similar pattern of BIN assortment at the three sampling sites. Beta diversity analysis by Jaccard similarity coefficient (J) and Bray-Curtis distance matrix (BC) revealed a high level of BIN similarity among the three sites (J = 0.67-0.68; BC = 0.19-0.20). Comparison of BIN records against all those on BOLD made it possible to identify 40% of the BINs to a species, 57% to a genus, 97% to a family and 99% to an order. BINs which received a species match on BOLD were placed in one of four categories based on this assignment: pest, parasitoid, predator, or pollinator. As this study provides the first baseline data on insect biodiversity in Chinese citrus plantations, it is a valuable resource for research in a broad range of areas such as pest management and monitoring beneficial insects in citrus gardens.