Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?

Abstract

DNA barcoding of faeces or stomach contents is an emerging approach for dietary analysis. We pyrosequenced mtDNA 16S markers amplified from faeces of captive little penguins (Eudyptula minor) to examine if recovered sequences reflect the proportions of species consumed. We also analysed wild little penguin faeces collected from 100 nests in southeast Australia. In the captive study, pilchards were the primary fish fed to the penguins and DNA sequences from pilchard were the most common sequences recovered. Sequences of three other fish fed in constant mass proportions (45:35:20) were all detected, but proportions of sequences (60:6:34) were considerably different than mass proportions in the diet. Correction factors based on relative mtDNA density in the fish did not improve diet estimates. Consistency between replicate samples suggests that the observed bias resulted from differences in prey digestibility. Detection of DNA from fish consumed before the penguins were brought into captivity indicates that a DNA signal in faeces can persist for at least 4 days after ingestion. In the wild-collected faeces, 24 distinct fish and 1 squid were identified; anchovy, barracouta and pilchard accounted for over 80% of these sequences. Our results highlight that DNA sequences recovered in dietary barcoding studies can provide semi-quantitative information on diet composition, but these data should be given wide confidence intervals.

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

“…In sooty albatross (Phoebetria fusca), the mean retention rate of prey ranged from 11 to 15 h, however some prey was still detected up to 50 h after eating (Jackson, 1992). In little penguins (Eudyptula minor) prey could be detected for up to 4 days using DNA metabarcoding (Deagle et al, 2010). The retention time is also likely to vary depending on whether the food is consumed for self-feeding or regurgitated to the chick partially digested.…”

“…Clusters were based on dissimilarity indices calculated with the Manhattan method, and hierarchical clustering was constructed using the average agglomeration method (note low sample sizes during January 2014 and 2015). As food DNA may persist in scats for several days (Deagle et al, 2010), there may be some carry-over of prey caught in the previous month if samples were collected early in the month, which was the case in January of both years.…”

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

“…Prey species of comparable size, physiology and behaviour are therefore likely to be predated in relation to their distribution and abundance. Direct quantification of prey consumption using amplicon numbers is not recommended because of potential differences in digestibility, individual size and amounts of mitochondrial DNA per gram of tissues from different prey species (Deagle et al, 2010). A few studies have shown that the proportion of prey species' DNA retrieved from predator faecal samples and amplified by qPCR can be somewhat representative of the proportion of biomass eaten (Deagle & Tollit, 2007;Bowles et al, 2011).…”

Molecular tools reveal diets of insectivorous birds from predator fecal matter

“…Studies with Australian fur seals (Deagle et al 2009), little penguins (Deagle et al 2010;Murray et al 2011) and bats (Bohmann et al 2011) have proven that such technology can successfully be applied to predator fecal matter for dietary analysis. Besides sequencing methodology, recent studies have expanded upon prey identification techniques to compare predator diet breadth and composition over time and across different habitats Razgour et al 2011).…”