Please use this identifier to cite or link to this item: https://doi.org/10.1371/journal.pone.0161841
Title: Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents
Authors: Paula D.P.
Linard B.
Crampton-Platt A.
Srivathsan A. 
Timmermans M.J.T.N.
Sujii E.R.
Pires C.S.S.
Souza L.M.
Andow D.A.
Vogler A.P.
Keywords: agroecosystem
aphid
Brazil
Coccinellidae
earwig
filtration
gastrointestinal tract
genetic susceptibility
genus
identity
intraguild predation
microbiome
nonhuman
parasitoid
predator
reference database
species
uncertainty
animal
beetle
chemistry
DNA sequence
food chain
insect
physiology
procedures
stomach juice
Animals
Beetles
Food Chain
Gastrointestinal Contents
Insects
Sequence Analysis, DNA
Issue Date: 2016
Citation: Paula D.P., Linard B., Crampton-Platt A., Srivathsan A., Timmermans M.J.T.N., Sujii E.R., Pires C.S.S., Souza L.M., Andow D.A., Vogler A.P. (2016). Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents. PLoS ONE 11 (9) : e0161841. ScholarBank@NUS Repository. https://doi.org/10.1371/journal.pone.0161841
Rights: Attribution 4.0 International
Abstract: Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challenge has been to achieve simultaneously high taxonomic breadth and resolution. General and practical methods are still needed, preferably independent of PCR amplification of barcodes, to recover a broader range of interactions. Here we applied shotgun-sequencing of the DNA from arthropod predator gut contents, extracted from four common coccinellid and dermapteran predators co-occurring in an agroecosystem in Brazil. By matching unassembled reads against six DNA reference databases obtained from public databases and newly assembled mitogenomes, and filtering for high overlap length and identity, we identified prey and other foreign DNA in the predator guts. Good taxonomic breadth and resolution was achieved (93% of prey identified to species or genus), but with low recovery of matching reads. Two to nine trophic interactions were found for these predators, some of which were only inferred by the presence of parasitoids and components of the microbiome known to be associated with aphid prey. Intraguild predation was also found, including among closely related ladybird species. Uncertainty arises from the lack of comprehensive reference databases and reliance on low numbers of matching reads accentuating the risk of false positives.We discuss caveats and some future prospects that could improve the use of direct DNA shotgunsequencing to characterize arthropod trophic networks. © 2016 Paula et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Source Title: PLoS ONE
URI: https://scholarbank.nus.edu.sg/handle/10635/161552
ISSN: 19326203
DOI: 10.1371/journal.pone.0161841
Rights: Attribution 4.0 International
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