Pyrosequencing of prey DNA in faeces of carnivorous land snails to facilitate ecological restoration and relocation programmes

Abstract

Identifying and understanding predator diets is of high importance in biological conservation. This is particularly true for the introduction, establishment and maintenance of predator populations in newly created or modified ecological communities, such as translocation sites or restored habitats. Conservation status of predators may not permit captive feeding trials or intrusive gut-content methods, so non-intrusive diet assessment is required, such as faecal analysis. However, prey such as earthworms leave no morphological clues suitable for accurately discriminating between species consumed through visual faecal analysis. This study uses non-intrusive molecular methods on earthworm DNA extracted from the faeces of the carnivorous land snail Powelliphanta patrickensis to identify its earthworm diet and any seasonal trends. Data from 454-pyrosequencing revealed earthworm DNA in all samples (n = 60). Sequences were compared to a DNA library created from published and unpublished studies of New Zealand's endemic earthworms and online databases. Unidentified earthworm sequences were clustered into molecular operational taxonomic units (MOTUs). Twenty-six MOTUs were identified, 17 of which matched the library, whereas nine did not. Similarity indices indicate that there were seasonal differences (P < 0.05) in the earthworm communities represented in the summer and the winter diets. This study highlights the importance of utilising the vast body of data generated by pyrosequencing to investigate potential temporal diet shifts in protected species. The method described here is widely applicable to a wide range of predatory species of conservation interest and can further inform habitat restoration and relocation programmes to optimize the long-term survival of the target species.

Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats

“…DNA mixtures of known proportions of different prey species), may be necessary to account for technical biases . Therefore, the relative contribution of each predated species to the diet is typically estimated by comparing the occurrence of each prey species in the faeces of several individuals of a given predator population (Bowser et al, 2013;Waterhouse et al, 2014).…”

Disentangling higher trophic level interactions in the cabbage aphid food web using high-throughput DNA sequencing

“…Chimeric sequences, PCR artefacts and missing information on the databases could all lead to low percentage identity, therefore, for MOTUs with percentage identity below the 98% threshold, only those that stricly produced more than five reads in at least one sample and were detected in at least two samples were considered robust and retained in the food web analysis , Waterhouse et al 2014. The retained MOTUs are assumed to represent species that are absent from the Genbank and BOLD databases.…”

Blood, sweat and tears: non-invasive vs. non-disruptive DNA sampling for experimental biology

“…Additionally, the test subject may be required to be alive 166 for further testing, or return to their natural habitat. If further tests involve capturing 167 an animal for a laboratory experiment or for translocation (Waterhouse et al 2014), 168 then the effects of capturing and holding the organisms for DNA sampling are of less 169 concern as individuals will need to be captured for these experiments anyway. 170 However, the potentially stressful effects of capture and manipulation should not be 171 further exacerbated by DNA sampling methods.…”