Optimised scat collection protocols for dietary <scp>DNA</scp> metabarcoding in vertebrates

McInnes, Julie C.; Alderman, Rachael; Deagle, Bruce E.; Lea, Mary‐Anne; Raymond, Ben; Jarman, Simon

doi:10.1111/2041-210x.12677

Cited by 101 publications

(138 citation statements)

References 46 publications

(101 reference statements)

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“…Two different DNA markers were amplified. The first used a metazoan primer set that is highly conserved and amplifies a region of the nuclear small subunit ribosomal DNA (rDNA) 18S gene (McInnes et al, 2017a, Table 2). For this marker the taxonomic resolution is relatively low; however, it recovers DNA from all animal lineages and provides a broad view of the diet.…”

Section: Dna Metabarcodingmentioning

confidence: 99%

“…Universal metazoan markers are useful dietary markers as they amplify DNA from all eukaryotes, which enables all possible prey groups to be identified. However, they also amplify nonfood DNA such as plant, parasite, and consumer DNA (McInnes et al, 2017a). A consumer blocking primer can increase the detection of food DNA (Vestheim and Jarman, 2008), but was not used in this study as they may inadvertently block similar groups such as other vertebrates like fish (Piñol et al, 2015).…”

Section: Amplification Successmentioning

confidence: 99%

“…In addition, many samples collected during incubation had little food DNA due to birds fasting. Subsequent to the data collection for this study, optimized scat collection protocols for DNA dietary metabarcoding have been developed that will hopefully improve the amount of DNA detected in future studies allowing diet data to be collected during all breeding stages (McInnes et al, 2017a).…”

Section: Amplification Successmentioning

confidence: 99%

“…Although the method cannot be used to identify prey size and meal mass, it does give an indication of species occurrence in the diet. Samples can also be collected during all breeding stages (McInnes et al, 2017a) and the technique is non-invasive and requires minimal field time compared to conventional diet sampling, increasing the options for simultaneous sampling across broad spatial scales (Jarman et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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DNA Metabarcoding as a Marine Conservation and Management Tool: A Circumpolar Examination of Fishery Discards in the Diet of Threatened Albatrosses

et al. 2017

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Almost all of the world's fisheries overlap spatially and temporally with foraging seabirds, with impacts that range from food supplementation (through scavenging behind vessels), to resource competition and incidental mortality. The nature and extent of interactions between seabirds and fisheries vary, as does the level and efficacy of management and mitigation. Seabird dietary studies provide information on prey diversity and often identify species that are also caught in fisheries, providing evidence of linkages which can be used to improve ecosystem based management of fisheries. However, species identification of fish can be difficult with conventional dietary techniques. The black-browed albatross (Thalassarche melanophris) has a circumpolar distribution and has suffered major population declines due primarily to incidental mortality in fisheries. We use DNA metabarcoding of black-browed albatross scats to investigate their fish prey during the breeding season at six sites across their range, over two seasons. We identify the spatial and temporal diversity of fish in their diets and overlaps with fisheries operating in adjacent waters. Across all sites, 51 fish species from 33 families were identified, with 23 species contributing >10% of the proportion of samples or sequences at any site. There was extensive geographic variation but little inter-annual variability in fish species consumed. Several fish species that are not easily accessible to albatross, but are commercially harvested or by-caught, were detected in the albatross diet during the breeding season. This was particularly evident at the Falkland Islands and Iles Kerguelen where higher fishery catch amounts (or discard amounts where known) corresponded to higher occurrence of these species in diet samples. This study indicates ongoing McInnes et al. Fishery Discards in Albatross Diets interactions with fisheries through consumption of fishery discards, increasing the risk of seabird mortality. Breeding success was higher at sites where fisheries discards were detected in the diet, highlighting the need to minimize discarding to reduce impacts on the ecosystem. DNA metabarcoding provides a valuable non-invasive tool for assessing the fish prey of seabirds across broad geographic ranges. This provides an avenue for fishery resource managers to assess compliance of fisheries with discard policies and the level of interaction with scavenging seabirds.

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Section: Dna Metabarcodingmentioning

confidence: 99%

Section: Amplification Successmentioning

confidence: 99%

Section: Amplification Successmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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DNA Metabarcoding as a Marine Conservation and Management Tool: A Circumpolar Examination of Fishery Discards in the Diet of Threatened Albatrosses

et al. 2017

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“…As fungi contained in the intestinal tract of seabirds, Blastocladiomycota, Chytridiomycota, Entomophthoromycotina, Ascomycota, Mucoromycotina,andBasidiomycota have been detected [58,59]. Nebela spp., Alveolata, Stramenopila, Rhizaria, Amoebozoa, Excavata, Choanoflagellatea, Glaucophyta, Cryptophyceae, Chlorophyceae, Trebouxiophyceae, Ulvophyceae, Prasinophyceae, and Mamiellophyceae have been detected as protozoa contained in the intestinal tract of seabirds.…”

Section: Protozoa and Fungi In Migratory Birdsmentioning

confidence: 99%

Public Health Implications of Intestinal Microbiota in Migratory Birds

Kenzaka¹,

Tani²

2018

Metagenomics for Gut Microbes

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Understanding the transboundary movement of microorganisms is a significant public health issue. It is possible that large amounts of various bacteria existing on the earth's surface are spreading across borders through migratory birds, but their identities and rates of migration have yet to be elucidated. Although modern bacteriology has advanced based on culture technology, many environmental bacteria may be in a "viable but nonculturable" state. To date, various novel culture-independent detection methods have been developed, including next-generation sequencing (NGS) technology that enables high-throughput sequencing and in-depth gene analysis independent of culture. By using NGS to comprehensively analyze the intestinal microbiota of migratory birds, research on bacterial and viral communities traveling over long distances has entered a new era, providing a new insight for the analysis of the livestock industry, agriculture, and human health risks. Here, we describe the current state and future outcomes of studying intestinal microbiota associated with migratory birds.

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Assessment of the diet of the critically endangered northern hairy‐nosed wombat (Lasiorhinus krefftii) using DNA metabarcoding

Casey,

Old,

Stannard

2023

Ecology and Evolution

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Invasive buffel grass (Cenchrus ciliaris) is considered a threat to the critically endangered northern hairy‐nosed wombat (Lasiorhinus krefftii; NHW). Buffel grass outcompetes native grasses, reducing availability of native food items for NHW, and causes more intense fires due to the large volumes of dead matter it produces. Previous studies suggested buffel grass was increasing in the diet; however, the diet of the NHW has not been reassessed for over two decades and was limited to Epping Forest National Park, with the population at Richard Underwood Nature Refuge having never been assessed. The recently released 2022 Recovery Action Plan for the species outlined objectives to assist its conservation and recommended the impact of buffel grass on the species' diet be investigated. This study aimed to determine: (1) which plant species are being consumed by the NHW; (2) the differences in the diet between sites; (3) differences between seasons; and (4) the abundance of buffel grass in the diet. The diet was assessed using DNA metabarcoding of scat samples collected from both sites from winter 2020 to spring 2021. Site and season significantly affected the diet of the NHW. Buffel grass dominated the diet and has increased in the diet since past assessments. The findings of this study will support population and habitat management of the critically endangered NHW. Enhanced knowledge of dietary items consumed at both sites will also assist efforts to locate additional sites suitable for translocation.

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Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates

Cited by 101 publications

References 46 publications

DNA Metabarcoding as a Marine Conservation and Management Tool: A Circumpolar Examination of Fishery Discards in the Diet of Threatened Albatrosses

DNA Metabarcoding as a Marine Conservation and Management Tool: A Circumpolar Examination of Fishery Discards in the Diet of Threatened Albatrosses

Public Health Implications of Intestinal Microbiota in Migratory Birds

Assessment of the diet of the critically endangered northern hairy‐nosed wombat (Lasiorhinus krefftii) using DNA metabarcoding

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