Kirsten Bowser

Sequencing a seabird food chain

MSc CandidateKirsten Bowser (photographed by R. Holberton)
Department/Faculty: Biology
University of New Brunswick

Supervisors: Tony Diamond and Jason Addison
Committee: Myriam Barbeau and Rick Cunjak

Brief Abstract of Research:

To understand how an ecosystem functions, we look to the food web, which is a collection of interconnected food chains.  Information learned from diet studies provide the building blocks for our knowledge of food chains and the quality of the data affects our ability to accurately understand how and why changes within ecosystems occur.

Traditional methods of studying diet rely on the visual identification of prey.   One common technique of learning about seabird diet is through feeding observations, where prey being delivered by adult birds to chicks is identified visually.  The widely accepted method of determining diet used for fish is identifying the remains of prey within stomach contents.  Any techniques used however, suffers from inherent bias.

Developed in 2005, next generation DNA sequencing is a molecular tool gaining popularity among ecologists.  This technique has been particularly useful for investigating diet and community composition, since DNA from many species can be sequenced at the same time.

I am interested in using next generation DNA sequencing as a way to critically evaluate the diets of two components in a known food chain.

Known food chainSimplified Machias Seal Island puffin-herring food chain.

Atlantic puffins (Fratercul arctica) are a seabird species whose (chick) diet is known from over 15 years of feeding observation data from Machias Seal Island, New Brunswick.  Adults feed remotely at sea and subsequently their diet has not been directly studied.  Juvenile Atlantic herring (Clupea harengus) have typically dominated the diet of puffin chicks and this species is known to play a pivotal role in the Gulf of Maine ecosystem. The diet of juvenile herring is known from a handful of stomach content analysis studies from 1930s to the 1980s

Atlantic puffin delivering prey to a chick during a feeding observationObjective

I am interested in learning how DNA-based diet studies might enhance our current understanding of the puffin-herring food chain. I aim to answer the following questions:

Do feeding observations provide accurate diet information?
Do Atlantic puffin chicks and adults have similar diets?
Do stomach content analyses provide accurate diet information?


To test the known puffin-herring food chain I am using Roche 454 massively parallel sequencing technology with universal primers and multiplex identifiers. I will compare the prey identification abilities of two gene regions (16S and CO1) and will examine the effect of blocking primers on prey detection capacity. The diet of puffin adults and chicks will be determined by identifying the DNA sequences of the prey within fecal samples. The DNA sequences within herring stomach contents will be used to determine herring diet. Juvenile Atlantic herring dropped by a provisioning adult puffin in the colony and collected for DNA amplification of stomach contents.


This project will refine our knowledge of the puffin-herring food chain and highlight the value of DNA-based diet determination. Learning how puffins are linked to the base of the food chain through their major prey herring will give context for potential bottom-up effects that may affect these seabirds. On a larger scale, knowledge of this important fish species juvenile diet is a significant contribution in constructing an accurate food web for the Gulf of Maine.

Diet studies provide the fundamental predator-prey interactions that allow us to construct food chains and subsequently, food webs. As necessary tools for understanding ecosystem functioning, food webs should be accurate and current. The occasional critical evaluation of how we study diet and how we construct food chains is a necessary step to ensure that the inferences we make about ecosystem functioning are true.