Northwest Fisheries Science Center

Newportal Blog

A gateway to oceanographic adventures from the Newport Line and beyond

Blog Entries for August 2016

Juvenile Salmon Necropsy

By Cheryl Morgan
Posted on August 31, 2016


The NWFSC and Oregon State University collaborators conducted two ocean juvenile salmon surveys in May and June of 2016. But, once the fish are collected, our work is just beginning! We bring the frozen juveniles back to the lab and organize as many people as possible to help us necropsy the fish. We reexamine the fish to confirm that the species is the same as we thought it was on the boat, get another length, and a weight (picture), and check for any hatchery tags. After that, it’s time to cut the fish open to take a variety of samples that will help us glean a variety of information about each fish.

Measuring and weighing juvenile salmon before they are necropsied.

We take a fin clip from all of the juvenile Chinook and sockeye salmon and steelhead for genetic analysis. Our past research has shown that there are differences in juvenile salmon attributes, such as time of ocean entry, size, growth, and condition among different stocks within the same species.

Juvenile salmon otoliths (ear stones).

We collect otoliths (ear stones) from many of the juvenile salmon collected in the ocean. Fish use otoliths for balance and orientation but researchers can use otoliths to determine the age and migration history of individual fish. Otoliths are calcium carbonate structures that grow along with the fish and a growth ring is formed each day, similar to annual growth rings on a tree. Additionally, trace elements, such as strontium and barium, are deposited in the otolith in proportion to their abundance in the water. Therefore, given naturally occurring differences between waters within the Columbia River and the ocean, our measurements of these elements in the otoliths can tell us when and at what size a juvenile entered marine waters. We can then use this information to better understand what factors influence the growth and survival of juveniles during their early marine residence.

Juvenile coho salmon stomach with rockfish and krill prey.

Stomachs are also removed from the salmon, in order to identify and quantify juvenile salmon trophic habits soon after they enter the ocean. Juvenile Chinook and coho salmon typically eat small fish, krill, and crab larvae.  Early marine growth has been shown to correlate with juvenile survival to adult salmon and our lab has identified that it is not just what they are eating (prey type) but also how much they eat that relates to their early marine condition (thinness or fatness for their size) and survival to adults.

A juvenile salmon infected with larval parasites (Neascus) in the skin.  The black spots are caused by the black pigment melanin, a reaction of the fish to the larval trematodes that are in encysted in the skin. Although it has been reported that these types of parasites could incrase mortality of juvenile shortnose suckers in Oregon, this has not been documented for juvenile salmon.

We also look for parasites on or in the skin of the salmon, as well as in the body cavity or swim bladder once the fish is opened. On the skin we sometimes see parasitic copepods, also known as sea lice. In the skin we can see evidence of larval stages of trematodes, these larval stages are in cysts waiting to be eaten by a predator of the salmon, often a bird or mammal, where they will mature into their adult stage. Inside the fish we can find nematodes (roundworms) of freshwater and marine origin that were acquired when the salmon consumed infected prey.


Tagged: Salmon Survey

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