Using patterns in prey DNA digestion rates to quantify predator diets

Invasive European green crab (Carcinus maenas) predation in a Washington State estuary revealed with DNA metabarcoding

Predation by invasive species can threaten local ecosystems and economies. The European green crab (Carcinus maenas), one of the most widespread marine invasive species, is an effective predator associated with clam and crab population declines outside of its native range. In the U.S. Pacific Northwest, green crab has recently increased in abundance and expanded its distribution, generating concern for estuarine ecosystems and associated aquaculture production. However, regionally-specific information on the trophic impacts of invasive green crab is very limited. We compared the stomach contents of green crabs collected on clam aquaculture beds versus intertidal sloughs in Willapa Bay, Washington, to provide the first in-depth description of European green crab diet at a particularly crucial time for regional management. We first identified putative prey items using DNA metabarcoding of stomach content samples. We compared diet composition across sites using prey presence/absence and an index of species-specific relative abundance. For eight prey species, we also calibrated metabarcoding data to quantitatively compare DNA abundance between prey taxa, and to describe an 'average' green crab diet at an intertidal slough versus a clam aquaculture bed. From the stomach contents of 61 green crabs, we identified 54 unique taxa belonging to nine phyla. The stomach contents of crabs collected from clam aquaculture beds were significantly different from the stomach contents of crabs collected at intertidal sloughs. Across all sites, arthropods were the most frequently detected prey, with the native hairy shore crab (Hemigrapsus oregonensis) the single most common prey item. Of the eight species calibrated with a quantitative model, two ecologically-important native species-the sand shrimp (Crangon franciscorum) and the Pacific staghorn sculpin (Leptocottus armatus)-had the highest average DNA abundance when detected in a stomach content sample. In addition to providing timely information on green crab diet, our research demonstrates the novel application of a recently developed model for more quantitative DNA metabarcoding. This represents another step in the ongoing evolution of DNA-based diet analysis towards producing the quantitative data necessary for modeling invasive species impacts.

Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding

Diet analysis is a vital tool for understanding trophic interactions and is frequently used to inform conservation and management. Molecular approaches can identify diet items that are impossible to distinguish using more traditional visual-based methods. Yet, our understanding of how different variables, such as predator species or prey ration size, influence molecular diet analysis is still incomplete. Here, we conducted a large feeding trial to assess the impact that ration size, predator species, and temperature had on digestion rates estimated with visual identification, qPCR, and metabarcoding. Our trial was conducted by feeding two rations of Chinook salmon (Oncorhynchus tshawytscha) to two piscivorous fish species (largemouth bass [Micropterus salmoides] and channel catfish [Ictalurus punctatus]) held at two different temperatures (15.5 and 18.5°C) and sacrificed at regular intervals up to 120 h from the time of ingestion to quantify the prey contents remaining in the digestive tract. We found that ration size, temperature, and predator species all influenced digestion rate, with some indication that ration size had the largest influence. DNA-based analyses were able to identify salmon smolt prey in predator gut samples for much longer than visual analysis (~12 h for visual analysis vs. ~72 h for molecular analyses). Our study provides evidence that modelling the persistence of prey DNA in predator guts for molecular diet analyses may be feasible using a small set of controlling variables for many fish systems.

High variation in handling times confers 35-year stability to predator feeding rates despite community change

Historical resurveys of ecological communities are important for placing the structure of modern ecosystems in context. Rarely, however, are snapshot surveys alone sufficient for providing direct insight into the rates of the ecological processes underlying community functioning, either now or in the past. In this study, I used a statistically reasoned observational approach to estimate the feeding rates of a New Zealand intertidal predator, Haustrum haustorium, using diet surveys performed at several sites by Robert Paine in 1968-1969 and by me in 2004. Comparisons between time periods reveal a remarkable consistency in the predator's prey-specific feeding rates, which contrasts with the changes I observed in prey abundances, the predator's body-size distribution, and the prey's proportional contributions to the predator's apparent diet. Although these and additional changes in the predator's per-capita attack rates seem to show adaptive changes in its prey preferences, they do not. Rather, feeding-rate stability is an inherently statistical consequence of the predator's high among-prey variation in handling times which determine the length of time that feeding events will remain detectable to observers performing diet surveys. Though understudied, similarly high among-prey variation in handling (or digestion) times is evident in many predator species throughout the animal kingdom. The resultant disconnect between a predator's apparent diet and its actual feeding rates suggests that much of the temporal, biogeographic, and seemingly context-dependent variation that is often perceived in community structure, predator diets, and food-web topology may be of less functional consequence than assumed. Qualitative changes in ecological pattern need not represent qualitative changes in ecological process.

Using patterns in prey DNA digestion rates to quantify predator diets

Dietary metabarcoding-the process of taxonomic identification of food species from DNA in consumer guts or faeces-has been rapidly adopted by ecologists to gain insights into biocontrol, invasive species and the structure of food webs. However, an outstanding issue with metabarcoding is the semi-quantitative nature of the data it provides: because metabarcoding is likely to produce false negatives for some prey more often than for other prey, we cannot infer relative frequencies of prey in the diet. To correct for this, we can adjust detected prey frequencies using DNA detectability half-lives unique to each predator-prey combination. Because the feeding experiments required to deduce these half-lives are time- and resource-intensive, our ability to weight the frequency of observations using their detectability has thus far been limited to systems with just a few prey. Here, we present a meta-analysis of 24 spider prey DNA half-lives and show that these half-lives are predictable given predator and prey mass, predator family, digestion temperature and DNA amplicon length. We further provide a new technique for weighting observations with half-lives, which allows not just for the ranking of prey in the diet, but reveals the proportion of the diet each prey comprises. Lastly, we apply this method to published dietary metabarcoding data to calculate half-lives and proportion of the predator's diet for 35 prey families, demonstrating that this technique can generate improved understanding of diets in real, diverse systems.