A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes

Pinol, J., San Andrés, V., Clare, E. L., Mir, G. and Symondson, W. O. C. ORCID: https://orcid.org/0000-0002-3343-4679 2014. A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes. Molecular Ecology Resources 14 (1) , pp. 18-26. 10.1111/1755-0998.12156

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Abstract

Predicting whether a predator is capable of affecting the dynamics of a prey species in the field implies the analysis of the complete diet of the predator, not simply rates of predation on a target taxon. Here, we employed the Ion Torrent next-generation sequencing technology to investigate the diet of a generalist arthropod predator. A complete dietary analysis requires the use of general primers, but these will also amplify the predator unless suppressed using a blocking probe. However, blocking probes can potentially block other species, particularly if they are phylogenetically close. Here, we aimed to demonstrate that enough prey sequence could be obtained without blocking probes. In communities with many predators, this approach obviates the need to design and test numerous blocking primers, thus making analysis of complex community food webs a viable proposition. We applied this approach to the analysis of predation by the linyphiid spider Oedothorax fuscus in an arable field. We obtained over two million raw reads. After discarding the low-quality and predator reads, the libraries still contained over 61 000 prey reads (3% of the raw reads; 6% of reads passing quality control). The libraries were rich in Collembola, Lepidoptera, Diptera and Nematoda. They also contained sequences derived from several spider species and from horticultural pests (aphids). Oedothorax fuscus is common in UK cereal fields, and the results showed that it is exploiting a wide range of prey. Next-generation sequencing using general primers but without blocking probes provided ample sequences for analysis of the prey range of this spider and proved to be a simple and inexpensive approach.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Biosciences
Subjects:	Q Science > QH Natural history > QH301 Biology Q Science > QL Zoology
Uncontrolled Keywords:	crop ecology; gut content analysis; linyphiid spiders; predator-prey interactions
Additional Information:	Pdf uploaded in accordance with publisher's policy at http://www.sherpa.ac.uk/romeo/issn/1755-098X/ (accessed 29/03/2016)
Publisher:	Wiley
ISSN:	1755-098X
Date of First Compliant Deposit:	30 March 2016
Date of Acceptance:	20 July 2013
Last Modified:	06 Dec 2024 18:15
URI:	https://orca.cardiff.ac.uk/id/eprint/52924

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