Cook Inlet Seabird and Forage Fish Study

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A massive die-off of Common Murres was documented in the Gulf of Alaska (GOA) during the fall and winter of 2015-2016 in association with a record-breaking marine heat wave in the GOA.

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Common Murres in their colony in Cook Inlet, Alaska. Adult touching bill to chick.

Common Murres in their colony in Cook Inlet, Alaska.
(Credit: Sarah Schoen, USGS, Alaska Science Center. Public domain.)

Starvation from lack of food was identified as the most likely cause of the die-off, and so we reexamined forage fish in lower Cook Inlet, where earlier (1995-1999) work established a baseline for populations of forage fish and seabirds in the region. We assessed the recent status of forage fish and seabirds in lower Cook Inlet with hydro-acoustic and trawl surveys for fish, and strip transects for seabirds, during summer, 2016-2018. We concurrently monitored populations, productivity, diets and physiology of seabirds at two colonies (Gull and Chisik islands) in lower Cook Inlet. Seabird population changes are linked to climate cycles, likely through the effect of climate on fluctuating prey resources. Consequently, management of seabird populations- or the mitigation of effects from offshore oil development, drilling and shipping- necessitates long-term information on seabird population status and trends, and on the prey base upon which those populations depend. We conducted surveys to update our knowledge of seabird demography and forage fish communities in lower Cook Inlet. This will further establish the range of natural variability in bird and fish population parameters in relation to environmental factors, and will provide an updated baseline on ecosystem condition in advance of new oil and gas leasing in Cook Inlet.

Scientist holding a herring dip net of forage fish in Cook Inlet, Alaska

Brian Robinson holding a herring dip net of forage fish in Cook Inlet, Alaska.
(Credit: Sarah Schoen, USGS, Alaska Science Center. Public domain.)

Project overview: In this study, we focused on assessing the prey base around seabird colonies in lower Cook Inlet, but we also gathered some fundamental demographic data on seabirds at the colonies. We compare our findings to USGS-led studies that were conducted in lower Cook Inlet during 1995-1999 to assess the recovery of seabird populations following the 1989 Exxon Valdez oil spill. The original project was designed to measure the foraging and population responses of six seabird species to fluctuating forage fish densities around seabird colonies in lower Cook Inlet. These studies included at-sea surveys for forage fish (hydroacoustics, trawling, seining and associated oceanographic measurements) while measuring aspects of seabird breeding biology (egg and chick production, chick growth, population status and trends) and foraging behavior (diets, feeding rates, foraging time) at the three colonies. Detailed data were collected on Common murres (COMU) and Black-legged kittiwakes (BLKI), the most commonly monitored species in Alaska. The breeding biology and population trends of seabirds differed markedly between colonies relative to persistent geographic differences in forage fish abundance which were in turn related to persistent oceanographic structuring of habitat in lower Cook Inlet.

  1. Assess the abundance, distribution and species composition of forage fish in marine waters adjacent to Chisik and Gull island seabird colonies in lower Cook Inlet.
  2. Census populations of COMU and BLKI at Chisik and Gull island colonies in lower Cook Inlet.
  3.  Obtain an index of COMU and BLKI reproductive success from brief colony visits and/or video camera recordings.  
  4. Examine COMU and BLKI diets and relate them to available prey base  
  5. Compare findings for fish and seabirds in 2016-2018 with results of studies conducted in 1995-1999, and relate observations to long-term changes in the ocean environment.


Two scientists capturing Black-legged Kittiwakes for physiology study in Cook Inlet, Alaska

Brielle Heflin and Brian Robinson capturing Black-legged Kittiwakes at the base of the colony in Cook Inlet, Alaska. These birds were used in adult physiology studies.
(Credit: Mayumi Arimitsu, USGS, Alaska Science Center. Public domain.)

Methods: To facilitate comparisons with data from prior studies, similar protocols for measuring food availability and seabird population biology are employed.

Acoustic-trawl surveys: We conduct acoustic-trawl surveys for forage fish in Lower Cook Inlet, effort is focused around two seabird colony sites: Gull and Chisik islands. Transects were established previously in both “nearshore” and “offshore” habitats. Biomass in the water column is estimated using a split beam dual frequency echosounder system (SIMRAD® EK60) operating at 38 (12° beam width) and 120 (7° beam width) kHz frequencies. To ground-truth the echosounder hydroacoustic backscatter we deploy a modified-herring trawl to confirm species and length frequency and collect samples for measures of body condition and age structure, and to detect changes in overall community structure relative to habitat.

Marine Predator Surveys: During hydroacoustic transects we also conduct marine bird and mammal surveys following strip transect protocols developed by Gould & Forsell (1989) (modified for working in coastal areas). Two observers count and identify all marine birds and mammals out to 150 meters on both sides and forward of the ship. These surveys are used to determine predator density relative to prey availability.

Habitat Sampling:

Scientist lowering CTD equipment into the water

Mayumi Arimitsu lowering the CTD equipment into the water.
(Public domain.)

Zooplankton: At each fishing station we sample small zooplankton using a 3 meters long plankton net with 333 µ mesh, a flowmeter is used to estimate volume filtered through the net. Sample contents are preserved and later identified in the lab to species (or lowest possible taxon) and developmental stage. Biomass by volume (mg m-3) is calculated for each species by multiplying the weights by the count per sample for each stage by species, summing the weights of all stages for each species, and dividing by the volume filtered.

Oceanography and Nutrients: We use a CTD (SeaBird SBE19plusV2) equipped with a fluorometer, beam transmissometer, photosynthetically active radiometer, optical backscatter and dissolved oxygen sensors. CTD profiles are conducted to within 5 meters of the seafloor, or to a maximum depth of 300 meters. Water samples are collected at the surface, 10 meters, and near the bottom with a watersampler (SeaBird SBE 55). Water for nutrient samples are frozen in the field, and later analyzed for inorganic nutrient concentrations, including nitrate, nitrite, ammonium, silicate, and phosphate. Chlorophyll a samples from the surface and 10 meters depths were filtered onto 25 mm GFF papers, placed in a cryovial and frozen in the field and were later extracted in acetone and concentrations are measured.

Population Monitoring:

Population plots: We relocated and surveyed COMU and BLKI population plots at Chisik and Gull islands between mid-incubation and early chick fledging. Species were counted from high resolution images, and for BLKI we also marked all well-developed nests (those with new nesting material and nest bowls). Bird counts on plots on a given day were summed to give a single count for each species per day. Each count-day was treated as a replicate and averaged to estimate a mean population count for the season.

Phenology and predation: To monitor phenology, effects of predators on colonies, and breeding productivity, we analyze camera footage from each colony. Time-lapse cameras are deployed on Duck and Gull islands to monitor COMU. The cameras recorded a photo every 20 seconds during daylight hours throughout the approximate breeding season for murres in both years.

To monitor BLKI, we analyze footage collected by a live, solar powered, remote-controlled video camera owned by the Pratt Museum in Homer, Alaska, and mounted on nearby Gull Island. The camera was programmed to rotate and scan various plots twice daily, and recorded five minutes of video at each plot.

Productivity: To estimate productivity of murres, we review time-lapse camera footage at Duck and Gull Islands. Camera footage allows us to determine when eggs are laid, and we calculate breeding success by dividing the number of chicks that fledged (those who survived for >15 days) by the number of eggs that are laid. We also calculate an estimate of the proportion of birds that were breeding compared to the assumed breeding population.

A bucket of the trawl catch of forage fish

Catch of forage fish from a trawl in Cook Inlet, Alaska. Trawling was part of an assessment of abundance, distribution and species composition of forage fish in marine waters in lower Cook Inlet.
​​​​​​​(Credit: Mayumi Arimitsu, USGS, Alaska Science Center. Public domain.)

Diet: Murres bring single fish to their chicks, held in line with the bill and with the tail outwards, leaving about half of the fish visible. To assess COMU chick diets we use photos (both high-speed digital cameras with telephoto lenses and time-lapse camera data at nesting sites) to capture images of prey during breeding, and then identify prey items to the lowest possible taxonomic level.

To assess kittiwake diet composition, we collect regurgitations from adults during the breeding period. Adult kittiwakes store partially digested food for their chicks, when disturbed they readily regurgitate the contents We target breeding adult kittiwakes at their nests using noose poles. These samples are collected at random from accessible nests. Samples will be analyzed for composition and proportional biomass later in the lab. Additionally, we used photos of kittiwakes with fish in their bill for diet identification.

Adult physiology: To assess the physiology of adult BLKI and COMU we measure body mass with spring scales, head-plus-bill, culmen, and tarsus length with vernier calipers, and relaxed standard wing using a ruler. On COMU, we also measure culmen depth with calipers and assessed coloration of 1° coverts to assess age based on plumage. Scaled mass to body size as an index of body condition, dividing mass by the wing length.