NOAA's Response and Restoration Blog

An inside look at the science of cleaning up and fixing the mess of marine pollution


NOAA Scientist Helps Make Mapping Vital Seagrass Habitat Easier and More Accurate

Shoal grass seagrass on a sandy ocean floor.

Seagrass beds serve as important habitat for a variety of marine life, and understanding their growth patterns better can help fisheries management and restoration efforts. (NOAA)

Amy Uhrin was sensing a challenge ahead of her. As a NOAA scientist working on her PhD, she was studying the way seagrasses grow in different patterns along the coast, and she knew that these underwater plants don’t always create lush, unbroken lawns beneath the water’s surface.

Where she was working, off the North Carolina coast near the Outer Banks, things like the churning motion of waves and the speed of tides can cause seagrass beds to grow in patchy formations. Clusters of bigger patches of seagrass here, some clusters of smaller patches over there. Round patches here, elongated patches over there.

Uhrin wanted to be able to look at aerial images showing large swaths of seagrass habitat and measure how much was actually seagrass, rather than bare sand on the bottom of the estuary. Unfortunately, traditional methods for doing this were tedious and tended to produce rather rough estimates. These involved viewing high-resolution aerial photographs, taken from fixed-wing planes, on a computer monitor and having a person digitally draw lines around the approximate edges of seagrass beds.

While that can be fairly accurate for continuous seagrass beds, it becomes more problematic for areas with lots of small patches of seagrass included inside a single boundary. For the patchy seagrass beds Uhrin was interested in, these visual methods tended to overestimate the actual area of seagrass by 70% to more than 1,500%. There had to be a better way.

Seeing the Light

Patches of seagrass beds of different sizes visible from the air.

Due to local environmental conditions, some coastal areas are more likely to produce patchy patterns in seagrass, rather than large beds with continuous cover. (NOAA)

At the time, Uhrin was taking a class on remote sensing technology, which uses airborne—or, in the case of satellites, space-borne—sensors to gather information about the Earth’s surface (including information about oil spills). She knew that the imagery gathered from satellites (i.e. Landsat) is usually not at a fine enough resolution to view the details of the seagrass beds she was studying. Each pixel on Landsat images is 30 meters by 30 meters, while the aerial photography gathered from low-flying planes often delivered resolution of less than a meter (a little over three feet).

Uhrin wondered if she could apply to the aerial photographs some of the semi-automated classification tools from imagery visualization and analysis programs which are typically used with satellite imagery. She decided to give it a try.

First, she obtained aerial photographs taken of six sites in the shallow coastal waters of North Carolina’s Albemarle-Pamlico Estuary System. Using a GIS program, she drew boundaries (called “polygons”) around groups of seagrass patches to the best of her ability but in the usual fashion, which includes a lot of unvegetated seabed interspersed among seagrass patches.

Six aerial photographs of seagrass habitat off the North Carolina coast, with yellow boundary lines drawn around general areas of seagrass habitat.

Aerial photographs show varying patterns of seagrass growth at six study sites off the North Carolina coast. The yellow line shows the digitally drawn boundaries around seagrass and how much of that area is unvegetated for patchy seagrass habitat. (North Carolina Department of Transportation)

Next, Uhrin isolated those polygons of seagrass beds and deleted everything else in each image except the polygon. This created a smaller, easier-to-scan area for the imagery visualization program to analyze. Then, she “trained” the program to recognize what was seagrass vs. sand, based on spectral information available in the aerial photographs.

Though limited compared to what is available from satellite sensors, aerial photographs contain red, blue, and green wavelengths of light in the visible spectrum. Because plants absorb red and blue light and reflect green light (giving them their characteristic green appearance), Uhrin could train the computer program to classify as seagrass the patches where green light was reflected.

Classify in the Sky

Amy Uhrin stands in shallow water documenting data about seagrass inside a square frame of PVC pipe.

NOAA scientist Amy Uhrin found a more accurate and efficient approach to measuring how much area was actually seagrass, rather than bare sand, in aerial images of coastal North Carolina. (NOAA)

To Uhrin’s excitement, the technique worked well, allowing her to accurately identify and map smaller patches of seagrass and export those maps to another computer program where she could precisely measure the distance between patches and determine the size, number, and orientation of seagrass patches in a given area.

“This now allows you to calculate how much of the polygon is actually seagrass vegetation,” said Uhrin, “which is good for fisheries management.” The young of many commercially important species, such as blue crabs, clams, and flounder, live in seagrass beds and actively use the plants. Young scallops, for example, cling to the blades of seagrass before sliding off and burrowing into the sediment as adults.

In addition, being able to better characterize the patterns of seagrass habitat could come in handy during coastal restoration planning and assessment. Due to local environmental conditions, some areas are more likely to produce patchy patterns in seagrass. As a result, efforts to restore seagrass habitat should aim for restoring not just cover but also the original spatial arrangement of the beds.

And, as Uhrin noted, having this information can “help address seagrass resilience in future climate change scenarios and altered hurricane regimes, as patchy seagrass areas are known to be more susceptible to storms than continuous meadows.”

The results of this study, which was done in concert with a colleague at the University of Wisconsin-Madison, have been published in the journal Estuarine, Coastal and Shelf Science.

Leave a comment

Watch Art Explain What Kind of Habitat Young Salmon Need to Thrive

Illustration from video of two salmon swimming by tree roots.What do young salmon need to grow into the kind of big, healthy adult salmon enjoyed by people as well as bears, seals, and other wildlife? A recent collaboration between NOAA Fisheries and the Pacific Northwest College of Arts makes the answer come to life in a beautiful animation by artists Beryl Allee and John Summerson.

Watch the intersection of art and science as we follow young salmon happily swimming through the cool, shallow waters along a shore. We see the bits of wood, tangled tree roots, and scattered rocks that provide these fish with both insects to eat and protection from predators.

But what happens when a home or business shows up along the water’s edge? How do people remake the shoreline? What kind of environment does this create for those same little salmon?

NOAA partnered with the Pacific Northwest College of Arts to create this moving and educational tool to raise awareness among waterfront landowners and the general public about how the decisions we make affect endangered salmon. In particular, NOAA wanted to address the practice of “armoring,” or using physical structures such as rocks and concrete to protect shorelines from coastal erosion. As we can see in the animation, armored shorelines do not make for happy, healthy young salmon.

Illustration from animation of a sad fish and an armored shoreline.

However, alternatives to armoring shorelines with hard materials are emerging. They include using plants and organic materials to stabilize the shores while also preserving or creating the kind of habitat young salmon need.

Creating better habitat for fish is often the goal of NOAA’s Damage Assessment, Remediation, and Restoration Program (DARRP). When we determine that fish were harmed after an oil spill or hazardous chemical release, we, with the help of a range of partners and the public, identify and implement restoration projects to make up for this harm.

Take a look at a few examples in which we built better habitat for salmon:

Beaver Creek, Oregon

A tanker truck carrying gasoline overturned on scenic Highway 26 through central Oregon in 1999, spilling 5,000 gallons of gasoline into Beaver Butte Creek and impacting steelhead trout and Chinook salmon. Working with the Confederated Tribes of the Warm Springs Reservation of Oregon and other partners, we have helped implement five restoration projects. They range from adding large wood to stream banks to provide fish habitat to installing two beaver dam–mimicking structures to improve water quality.

White River, Washington

In 2006 a system failure sent 18,000 gallons of diesel into creeks and wetlands important to endangered Chinook salmon around Washington’s White River. To improve and expand habitat for these salmon, NOAA and our partners removed roadfill and added large pieces of wood (“logjams”) along the edges of the nearby Greenwater River. This restoration project will help slow and redirect the river’s straight, fast-moving currents, creating deep pools for salmon to feed and hide from predators and allowing some of the river water to overflow into slower, shallower tributaries perfect for spawning salmon.

Adak, Alaska

On the remote island of Adak in Alaska’s Aleutian Islands, a tanker overfilled an underground storage tank in 2010. This resulted in up to 142,800 gallons of diesel eventually flowing into the nearby salmon stream, Helmet Creek. Pink salmon and Dolly Varden trout were particularly affected. In 2013 NOAA and our partners restored fish passage to the creek, improved habitat and water quality, made stream flow and channel improvements, and removed at least a dozen 55-gallon drums from the creek bed and banks.

You can also watch a video to learn how NOAA is restoring recreationally and commercially important fish through a variety of projects in the northeast United States.

Leave a comment

When Oil Spills, School Kids Take Note

The impacts of an oil spill can be varied: closed beaches, dead fish, oiled birds and wildlife—just to name a few. But the impacts can also be emotional, often drawing out of people feelings like anger, sadness, frustration, or an eagerness to help. Those of us at NOAA who work to minimize the impacts of oil spills on America’s water, coasts, plants, and animals are not immune to these impacts either. But we are glad to know that people care.

Here a few examples of letters written by school kids after they learned about oil spills in Alaska and California—and how these spills affected them.

On April 13, 1989, second grader Kelli Middlestead of the Franklin School in Burlingame, Calif., let her feelings be known after hearing about the Exxon Valdez oil spill in Prince William Sound, Alaska. She addressed her letter, illustrated with her beloved sea otters, to Walter Stieglitz, Alaskan Regional Director of the U.S. Fish and Wildlife Service. (Hat tip to the National Archive’s excellent Tumblr.)

In November of 2007, middle school students on a science camp field trip to a San Francisco beach were upset instead to find oil on the water, beach, and even the birds. Days earlier, the cargo ship Cosco Busan had crashed into the San Francisco-Oakland Bay Bridge and spilled 53,000 gallons of thick fuel oil into the marine waters nearby.

An example of the thoughtfully crafted thank you cards sent to oil spill responders by seventh graders in California after the 2007 Cosco Busan oil spill.

An example of the thoughtfully crafted thank you cards sent to oil spill responders by seventh graders in California after the 2007 Cosco Busan oil spill.

While they were saddened by the events, the seventh grade students from Old Orchard Middle School in Campbell, Calif., decided to help by writing hand-written and illustrated thank you cards to the people cleaning up the oil spill. According to a press release about their efforts [PDF]:

“Everyone started pitching in and we came up with the idea to write cards,” said seventh grade student Erin.

“We felt helpless that we couldn’t go and help the animals or clean up the beach,” said Alex, another seventh grader from Old Orchard School. “We saw birds staggering and people trying to catch them.”

“These cards did a lot for the morale of our cleanup crew,” said Barry McFarland of the response company O’Brien’s Group, which worked to clean up the spill at Muir Beach and received the students’ cards. “Some of our crew were actually moved to tears.”

You can read more of the thank you notes from the concerned students [PDF].

Leave a comment

With Restoration, Will Willamette River Lampreys Rebound for Northwest Tribes?

This is a post by Office of Response Restoration’s Robert Neely and Restoration Center’s Lauren Senkyr.

It’s mid-summer, and something amazing is happening at Willamette Falls, a pounding cascade of water about 30 minutes from downtown Portland, Oregon. People are balancing on mossy, wet boulders tucked among the falls, reaching into its waters to harvest Pacific lamprey by hand.

A tribal member holds two lampreys in his hands.

Confederated Tribes of Grand Ronde Tribal member Torey Wakeland displays some lamprey that were harvested at Willamette Falls on Monday, July 18, 2011. (Photo courtesy of Ron Karten.)

After pouring over the falls, the Willamette River rolls on for nearly 30 miles before joining the Columbia River.

Prior to the construction of dams throughout the Columbia River basin, which includes the Willamette River and its tributaries, native Americans harvested lampreys in many other locations in much the same way they do now at Willamette Falls: by braving the cascading water and slippery rocks to grab wriggling lamprey by hand or with dip nets.

Northwest tribes have relied on the lamprey for food, medicinal, and ceremonial purposes for generations, since long before the first European explorers and fur traders became aware of these falls. But virtually all of the tribes’ historic collection spots are gone now, either because they are submerged under dam-impounded waters or because lampreys are absent, their upstream journey blocked by dams. Willamette Falls is the last place in the Columbia basin where tribes can collect lampreys as their ancestors did.

So it’s not surprising that the tribes are concerned about the Willamette River lamprey and the rest of the Columbia basin lamprey population. In fact, lamprey numbers have declined steadily since at least the 1960s.  According to a 2012 U.S. Fish and Wildlife Service fact sheet [PDF], likely threats to lampreys include habitat loss associated with passage barriers, dredging, and stream and floodplain degradation; river flow alterations; predation by non-native species; poor water quality; changing ocean conditions; and exposure to toxic substances.

Willamette River lamprey may be particularly vulnerable when it comes to toxic substances. Paddle the river as it flows north from the falls and you will eventually pass by downtown Portland. It is about here that you enter the Portland Harbor Superfund site, an 11-mile stretch of river with numerous patches of contaminated sediments from more than 100 years of industrial and urban uses. Juvenile lampreys, called ammocoetes, must pass through this portion of river on their seaward migration, just as adult lampreys do as they return upriver to spawn. But it is the ammocoetes that are most likely to be at risk from pollutants buried in the riverbed.

Pacific lamprey

Pacific lamprey. (Photo courtesy of Oregon Department of Fish and Wildlife)

Lampreys are an anadromous species, which means they spawn in freshwater, spend their adulthood in the ocean, and return to freshwater to reproduce. In this respect they are similar to salmon, but lamprey life cycles are more complex. After hatching from their eggs, ammocoetes drift downstream to areas with slow-moving water and silty, sandy sediments. Here they burrow into the sediments and filter-feed for up to seven years before emerging to continue their journey to the sea. It is during this time that they may be particularly vulnerable as they eat contaminated foods and are directly exposed to pollutants for long periods.

Ammocoetes are known to use the stretch of the Willamette River encompassed by the Superfund site, and lamprey tissue samples collected from within the site show higher levels of contaminants than those collected from cleaner sediments upstream of Portland Harbor. It is not clear how ammocoetes in Portland Harbor are affected by contamination, but at least one analysis suggests exposure to contaminated sediment from Portland Harbor may adversely affect their behavior.

So what is being done? The Environmental Protection Agency (EPA) has been working with its partners and a group of companies called the Lower Willamette Group to assess risks to human health and the environment and to determine how best to clean up the river. EPA’s efforts are ultimately aimed at removing the threats posed by contaminated sediments.

NOAA is one of eight members on a trustee council that is working to understand how contaminants may have impacted natural resources. The council is also planning habitat restoration projects to make up for those impacts.  (The other members of the council include five tribes–Grand Ronde, Siletz, Umatilla, Warm Springs, and Nez Perce–and the state and federal fish and wildlife agencies.)

In addition to the lamprey, the council is planning restoration projects to benefit other types of fish and wildlife, like osprey, bald eagles, mink, and salmon. The council is focusing on these species because evidence suggests they may have been most impacted by contaminants and because they represent species guilds that are important in the lower Willamette River and similar Pacific Northwest ecosystems.

Tribal member displays cooler with harvest of lamprey.

Michael Wilson, Confederated Tribes of Grand Ronde Tribal member and the Tribe’s Natural Resources Department manager, shows the lamprey that were harvested by NRD staff at Willamette Falls on Friday, July 29, 2011. (Photo courtesy of Rebecca McCoun.)

This summer, the council wants to hear what the public thinks about restoration in Portland Harbor. A plan that lays out restoration options to benefit lampreys and other species that use the lower Willamette River, Multnomah Channel, and parts of the Columbia River close to the Superfund site has just been released. The council wants to hear from tribal members; people who fish on the river; folks who like to bike, jog, or picnic along the river; and others who care about the health of fish, wildlife and other natural resources in the Superfund site.

The plan includes a list of 44 potential restoration projects, including activities like removing culverts to improve access to upstream habitats, creating off-channel areas with clean water and sediment where fish can rest during migration, and “daylighting” cold, clean streams that currently run through pipes in the heavily built-up and industrial section of the river. For the next couple of months, the council is hosting meetings, presenting at neighborhood associations, and attending community events around Portland to let people know about their work and gather comments on the plan.

To see a copy of the draft plan and a schedule of meetings and comment deadlines, visit And for a little lamprey fun, take a look at the U.S. Fish and Wildlife Service’s lamprey activity book [PDF].

Robert NeelyRobert Neely is an environmental scientist with the National Oceanic and Atmospheric Administration’s Office of Response and Restoration.  He has experience in ocean and coastal management, brownfields revitalization, Ecological Risk Assessment, and Natural Resource Damage Assessment. He started with NOAA in 1998 and has worked for the agency in Charleston, S.C.; Washington, D.C.; New Bedford, Mass.; and Seattle, Wash., where he lives with his wife and daughter. He’s been working with his co-trustees at Portland Harbor since 2005.

Lauren SenkyrLauren Senkyr is a Habitat Restoration Specialist with NOAA’s Restoration Center.  Based out of Portland, Ore., she works on restoration planning and community outreach for the Portland Harbor Superfund site as well as other habitat restoration efforts throughout the state of Oregon.