Understanding prey consu­­mption patterns is critical to understanding the ways in which seabirds cope with a changing ocean. However, characterizing the dietary habitats of seabirds can be challenging. In this study, we investigated the diet of the Marbled Murrelet (Brachyramphus marmoratus) population that lives in waters off California, Oregon, and Washington, USA, using fecal DNA, custom metabarcoding, and high-throughput sequencing. Murrelets were captured at sea by dip-netting at night. Across this region, murrelets consumed highly diverse prey types including 17 fish species and 10 invertebrate species, in accord with previous work indicating the species’ forage on a wide range of prey. Pacific Herring (Clupea pallasii) was the most common prey in Washington and Oregon (frequency of occurrence = 0.84 and 0.69, respectively), replaced by Northern Anchovy (Engraulis mordax) in California (frequency of occurrence = 0.77). In Oregon, where our sample size was sufficient, diet composition differed between the 2017 and 2018 breeding seasons, with an apparent decline in the proportional consumption of energy-dense prey. Common and energy-dense prey were consumed in equal proportions by males and females, perhaps because of foraging in the same habitat. Diet did not vary between breeders and non-breeders. Our study offers the first detailed report on the diet of adult Marbled Murrelets in waters where they are listed as Threatened by the US federal government. This indicates that managing fisheries and conserving spawning habitat for high-occurrence prey species could benefit murrelet populations.

We extracted DNA from the fecal material using QIAamp® DNA Stool Mini Kit and the QIAamp DNA Stool Mini Kit. For all cloacal swabs, we extracted genomic DNA using a QIAamp DNA Investigator Kit following the manufacturer’s protocol for buccal swab extraction. We quantified DNA concentration for all extractions using a qubit fluorometer and high-sensitivity assay. We amplified a fragment of the 16S gene in prey DNA using single primer PCR reactions for four primer sets: 16S (fish, Deagle et al. 2007), SQ16S (cephalopods), Cala16S (copepods and amphipods), and Mala16S (malacostracans).

We used QIIME2 (Bolyen et al. 2019) for all filtering and processing of raw sequence data. We used the R package vegan (Oksanen et al. 2020) to calculate diversity metrics, frequency of occurrence, percent occurrence, and PERMANOVA tests.

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