Metabarcoding avian diets at airports: implications for birdstrike hazard management planning

Abstract

BackgroundWildlife collisions with aircraft cost the airline industry billions of dollars per annum and represent a public safety risk. Clearly, adapting aerodrome habitats to become less attractive to hazardous wildlife will reduce the incidence of collisions. Formulating effective habitat management strategies relies on accurate species identification of high-risk species. This can be successfully achieved for all strikes either through morphology and/or DNA-based identifications. Beyond species identification, dietary analysis of birdstrike gut contents can provide valuable intelligence for airport hazard management practices in regards to what food is attracting which species to aerodromes. Here, we present birdstrike identification and dietary data from Perth Airport, Western Australia, an aerodrome that saw approximately 140,000 aircraft movements in 2012. Next-generation high throughput DNA sequencing was employed to investigate 77 carcasses from 16 bird species collected over a 12-month period. Five DNA markers, which broadly characterize vertebrates, invertebrates and plants, were used to target three animal mitochondrial genes (12S rRNA, 16S rRNA, and COI) and a plastid gene (trnL) from DNA extracted from birdstrike carcass gastrointestinal tracts.ResultsOver 151,000 DNA sequences were generated, filtered and analyzed by a fusion-tag amplicon sequencing approach. Across the 77 carcasses, the most commonly identified vertebrate was Mus musculus (house mouse). Acrididae (grasshoppers) was the most common invertebrate family identified, and Poaceae (grasses) the most commonly identified plant family. The DNA-based dietary data has the potential to provide some key insights into feeding ecologies within and around the aerodrome.ConclusionsThe data generated here, together with the methodological approach, will greatly assist in the development of hazard management plans and, in combination with existing observational studies, provide an improved way to monitor the effectiveness of mitigation strategies (for example, netting of water, grass type, insecticides and so on) at aerodromes. It is hoped that with the insights provided by dietary data, airports will be able to allocate financial resources to the areas that will achieve the best outcomes for birdstrike reduction.

Advancing the integration of multi‐marker metabarcoding data in dietary analysis of trophic generalists

“…Second, our study confirmed the value of using multiple markers, but suggests that previous studies based on a mix of nonoverlapping specific markers each targeting a particular dietary component (e.g., Coghlan et al, ; Groom et al, ; Robeson et al, ; Sullins et al, ) may not be sufficient to overcome marker biases and thus provide a reliable diet composition. This is because markers considered universal for a given taxonomic clade may still have considerable variations in affinity across taxa within that clade, and thus may not amplify some important items in the diet (Aizpurua et al, ; Alberdi et al, , ; Bowser et al, ; Clarke et al, ; Kaunisto et al, ; Piñol et al, ).…”

“…One problem that has attracted much attention is the selection of molecular markers, because primer specificity and biases can greatly affect the results of dietary studies (Alberdi et al, ; Taberlet et al, ). In general, studies build on previous knowledge of the diet of one or more species of interest, or of ecologically similar species, to select a primer that amplifies DNA from the main food items expected to be consumed (Alberdi et al, ; Coghlan et al, ). For instance, the studies of Soininen et al () and Valentini et al () used primers amplifying a fragment of the chloroplast trn L intron to analyse the diet of a number of herbivore species.…”

The microbiome of New World vultures

“…Amplification of potentially contaminating human DNA was reduced by the addition of blocker oligos during PCR. Although these primers have been successfully used in other dietary DNA studies [6][7][8] , we detected mammalian amplicons in only four (8%) of the vulture hindgut samples (all turkey vultures). In contrast, mammalian DNA was readily amplified from most facial swabs (B90%), representing nine mammalian families (Bovidae, Canidae, Cervidae, Didelphidae, Equidae, Leporidae, Mephitidae, Procyonidae, Suidae).…”

DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

“…(c) Relative numbers of species from different habitats, whose diet was assessed through barcoding techniques. Some species were studied more than once, in a total of 261 different wild species, two unidentified (pipit, Coghlan et al, ; and Bison sp., Willerslev et al, ), seven domesticated taxa, two studies focused on humans, and one taxa described only by a superior taxonomic rank (i.e., Muridade; Shirako et al, )…”