Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents.
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 shotgun-sequencing to characterize arthropod trophic networks.
Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Brasília, Brazil.|Department of Life Sciences, Natural History Museum, Cromwell Rd, London, United Kingdom.
Débora P
DP
Paula
Department of Life Sciences, Natural History Museum, Cromwell Rd, London, United Kingdom.
Benjamin
B
Linard
Department of Life Sciences, Natural History Museum, Cromwell Rd, London, United Kingdom.|Department of Genetics, Evolution and Environment, Faculty of Life Sciences, University College London, Gower Street, London, United Kingdom.
Alex
A
Crampton-Platt
Department of Life Sciences, Natural History Museum, Cromwell Rd, London, United Kingdom.|Department of Biological Sciences, National University of Singapore, Singapore, Singapore.|Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, United Kingdom.
Amrita
A
Srivathsan
Department of Life Sciences, Natural History Museum, Cromwell Rd, London, United Kingdom.|Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, United Kingdom.|Department of Natural Sciences, Hendon Campus, Middlesex University, The Burroughs, London, United Kingdom.
Martijn J T N
MJ
Timmermans
Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Brasília, Brazil.
Edison R
ER
Sujii
Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Brasília, Brazil.
Carmen S S
CS
Pires
Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Brasília, Brazil.
Lucas M
LM
Souza
Department of Entomology, University of Minnesota, St. Paul, Minnesota, United States of America.
David A
DA
Andow
Department of Life Sciences, Natural History Museum, Cromwell Rd, London, United Kingdom.|Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, United Kingdom.
Alfried P
AP
Vogler
D000818:Animals; D001517:Coleoptera / Q000502:physiology*; D020387:Food Chain; D005766:Gastrointestinal Contents / Q000737:chemistry*; D007313:Insecta / Q000502:physiology*; D017422:Sequence Analysis, DNA / Q000379:methods*