Oblivious to what is going on below, the sea otter rolls once more in the kelp, cracks open a sea urchin, and slurps up the jellied innards. From beneath, human divers, using non-bubbling closed-circuit scuba gear, float in wait. They hold a large trap. At the right moment, they spring. Meal interrupted, engulfed safely in a net, this otter has become the latest study recruit.

“We come up from underneath, like a killer whale or a great white,” said Jim Bodkin, a marine biologist with the U.S. Geological Survey. “When they’re disturbed, their response is to dive down into the water. We then draw the traps close, like drawing a purse string, and they’re caught.”

Hauling the sea otter into a small boat, the divers deliver her to “Dr. Mike.” Aboard the main expedition boat, the otter will be placed on an examining table to be prodded, measured, injected and extracted from.

This scene played out dozens of times this summer, and nearly 300 times over the past three years, as part of the massive USGS Pacific Nearshore Project. The team of scientists is studying the nearshore environment in a new way: using otters as an indicator.

The environment near the shore is a complicated, difficult-to-understand region. It is influenced by a combination of natural and man-made factors, from both the land and the sea. Beyond giving a home to sea otters, the nearshore region supports fisheries, human recreation and many other species. And the otters may be able to provide researchers with a view of the nearshore they haven’t been able to get with other methods.

Scientists began to notice a change in sea otters about a decade ago. Throughout the otters’ range, population growth rates — which had been as high as 20 percent annually — began to stall or decline. Some areas, such as California, are faring worse than others. Currently no one knows what is behind the change, or the regional differences. If members of the USGS project can uncover the causes, we will better understand how to protect the coast.

The project called on a small army of fisheries biologists, geneticists, GIS specialists and Murray, head vet at the Monterey Bay Aquarium, in Monterey, Calif. The researchers finished collecting field data for the three-year study in August, after sampling at nine field sites, along the coasts of Alaska, British Columbia, Washington and California.

The data set they have gathered is unprecedented: samples and measurements from hundreds of otters, collected throughout their range. To assess otter health, Murray and his assistants completed a battery of tests. About 10 minutes after an injection of painkillers and sedatives (fentanyl and midazolam, drugs also used on humans), each otter was weighed and measured. Murray took measurements of the girth, paws, teeth, tail, total length and — in males — the length of the baculum, a bone in the penis.

The animals were swabbed, whiskers taken and blood drawn. To age the animal, Murray extracted a tooth, a little-used upper premolar. Following the last step, Murray gave the animals another injection (naltrexone), to reverse the sedative’s effects. In a few minutes the otters were awake and ready for release.

“The relatively small females were often the animals most difficult to handle,” said Murray. “Spitfires! They just wanted to kick your butt. Fortunately, no one was bit.”

The blood samples will tell researchers if the otter is anemic, low in electrolytes, and if its liver and kidneys are healthy. Geneticists will analyze the blood to see which genes each otter’s body has turned, an indication of what diseases and environmental contaminants it is fighting. Portions of blood will be frozen and archived for future researchers. If years from now a biologist wants sea otter blood dating from 2011 in British Columbia, it will be available.

The sea otter whiskers are reserved for the University of Wyoming’s Stable Isotope Facility. Scientists there slice whiskers into half-millimeter disks and, by evaluating their chemical composition, can detect what the otters were primarily preying upon when that whisker section grew. Otter researchers suspect the animals change their diet seasonally, as prey become more or less abundant or nutritious.

Beyond the otters, two species of fish — specifically the bones in their ears — are helping the team’s investigation. Fish ear bone expert Vanessa von Biela, from the USGS Alaska Science Center, worked with the expedition studying otoliths, which have annual growth rings, like trees. The rings reveal differences in a fish’s year-to-year growth rate, and are another way to document ocean productivity.

For von Biela, catching her study subjects was less perilous than the sea otter grabs. She and her team primarily caught fish by hook and line, fishing as much as 12 hours a day, for two species: black rockfish, or Sebastes melanops, and kelp greenling, or Hexagrammos decagrammus.

Because rockfish feed primarily on phytoplankton, and the greenlings eat mostly kelp, each fish will indicate the productivity of different food webs, stretching back as much as 40 years, depending on the fish’s age. Cross-indexing these measurements with estimates of productivity from satellite data, which go back about 15 years, may start to fill in some blanks.

Growth indicates a fish’s overall health and, in females, how many eggs they will lay. “We’d like to know what makes a good, versus a poor, production year,” said von Biela. “What is the perfect set of conditions? There are theories, but it is not very clear-cut.”

When published, Bodkin expects the project’s findings will be useful for the state and regional agencies that manage the nearshore habitat.

Note: The USGS Pacific Nearshore Project involved partners from 18 institutions and organizations. Project members blogged extensively from the field, read their accounts or see more images from the field.

Video: Alaska Science Center/USGS. Images: 1) At top, Mike Murray, Monterey Bay Aquarium; Right: Jim Bodkin, USGS; Front: Kim Kloecker, USGS. Credit: USGS. 2) At bottom, divers prepare to enter the water in pursuit of a sea otter, a hand-held compass helps orient the crew to the animal’s position. Credit: Keith Miles/USGS.