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Bay Biodiversity

We graduated from seining to trawling on the 4th day of Week 00. Scarlett Arbuckle steered our boat along Newport Bay first to eelgrass beds and then to sandflats to see what we could catch using a trawl net. A trawl net is funnel-shaped. The wide-open mouth is lined with floats along the upper edge and weighted along the bottom edge with a linked chain. Otter boards on either side of the wide-mouth opening are connected to the net by hand ropes. The otter boards are kept apart by water tension when dragged by the boat and thus keep the net open while it trawls the bay floor. The end of the net that is flaked out into the water is loosely tied off and quickly released when the catch is pulled onto the boat.

Photo - Otter boards on either side of the trawl net. Kevin is loosely tying the end of the net in preparation for flaking.

Trawling was a three-person job. On a three count, two people thrust the otter boards into the water while simultaneously the third individual tossed the right-side rope over the boat’s motor to avoid tangling the propeller.

We pulled a lot of sea lettuce and eelgrass from the net before it was light enough to heave on deck.

Photo - Sea lettuce removal from the trawl net. 

We measured shiner and striped surf perch, Pacific staghorn sculpin, English sole, Dungeness crab, and pipefish.

Photo - English sole,  Parophrys vetulus

Photo - Pipefish,  Syngnathus leptorhynchus

After an exciting morning of trawling, we met Mary Markland for a librarian-led discussion of effective research techniques and database use through Oregon State University’s library webpages. Our day finished with a more in-depth discussion of how to approach a mentor and term project expectation.

We packed a lot of learning into four days. I learned how complex fisheries and management can be; how all stakeholders including private landowners, commercial fisherman, researchers, scientists, law enforcement, educators and more must be included in the discussion of coastal ecology restoration and protection for effective management to succeed.

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Restoring Marshlands and Estuary Function - Salmon River Estuary

Near Cascade Head the Salmon River estuary delivers anadromous salmon into the Pacific Ocean and tidal marshlands provide habitat to birds, elk, and beavers. The open and connected bottomlands were once disconnected, polluted, and functionally impaired. But, because of the efforts of local scientists like Kami Ellingson, hydrologist, and Kim Jones, fisheries biologist, the Salmon River estuary has undergone a remarkable transformation. 

Kim talked about studying fish otoliths to determine age and duration in fresh and saltwater. Otolith rings are created daily and in fresh water are comprised of calcium carbonate. When an anadromous fish transitions to a saltwater environment, the otolith develops from strontium. Thus, scientists can tell when an anadromous fish entered an estuary or the ocean and the duration of their stay in either fresh or salt water.

Kami described some of the hydrological obstacles to restoration her team faced such as sinking pastureland, leaky septic systems, and private landowner buy-in. She also talked about the portfolio effect which focuses on increasing biocomplexity to improve biodiversity, morphology and life history. I was struck by how many times Kami mentioned that she loves the estuary and the work she does. Even though she moved away from coastal Oregon at one point in her life, she is continuously drawn back to the incredible Pacific Northwest and her restored estuary. 

Kim took us down into the estuary during low tide to seine.

Photo - Seine and measuring tray. We used the cooler and buckets to hold fish in estuary water during our survey.

We had a great time learning to seine eelgrass. We caught Pacific staghorn sculpin (Leptocottus armatus), fluffy sculpin (Oligocottus snyderi), shiner surf perch (Cymatogaster aggregata), and juvenile Chinook salmon (Oncorhynchus tshawytscha). We measured the fish and recorded species and count.

Photo - Striped surf perch measured in millimeters.

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Fisheries: Important and Complex

Day two started with some mentor talk with our instructor Scarlett Arbuckle and a visit from Itchung Cheung, Education Coordinator at Hatfield Marine Science Center (HMSC). Itchung enthusiastically declared that HMSC is student-focused and everyone is eager to help us succeed.

We made our way to an Oregon Department of Fish and Wildlife (ODFW) office and met with Scott M. and Kelsey Adkisson. Scott and Kelsey work with Oregon Marine Reserves to study areas along the Oregon coast designated for protection. Kelsey works in communications and provided an enlightening overview of five marine reserves off Oregon’s coast: Cape Falcon, Cascade Head, Otter Rock, Cape Perpetua, and Redfish Rocks. These marine reserve areas are closed to disturbance activities like offshore energy development. Kelsey pointed out that protecting these areas increase biodiversity, create buffering, and serve as living laboratories. I also learned that offshore means three miles from the coast. Offshore areas are managed by ODFW. Fisheries in waters beyond the three-mile marker are managed by the federal government.

Kelsey also discussed the importance of research and monitoring of protected marine reserve areas. Survey methods used by ODFW include hook and line (volunteers fish with hook and line off boats and the catch is inventoried), scuba (people observe and survey via scuba diving), video landing (tripods are planted with go-pros attached), and ROV (remotely operated vehicle – ODFW’s Sea Cow). Kelsey said the goal of research and monitoring is to understand changes over time. Scott showed us how research data is captured using the Sea Cow and how it is analyzed using software packages like R.

We left Scott and Kelsey to meet Marcie at Oregon Oyster Farm in Yaquina Bay.

Photo - Marcie shows us Pacific oysters. From right to left, Marcie, Scarlett Arbuckle, Kevin Schaffer, Matthew VanBemmel, Chris Derrikson.

Marcie is customer service oriented. She believes in growing a quality product and making lasting connections with customer. She is also invested in her staff and describes their relationships are close-knit and familial.

We learned the history of Oregon Oyster Farm and how juvenile oysters no bigger than a grain of sand attach to discarded oyster shells to form spats. The spats are placed over rafts distributed along 600 acres of Yaquina bay to grow and later be harvested. Oregon Oyster Farm grows species such as Crassostrea gigas, commonly Pacific Oyster and Kumamoto oysters or Crassostrea sikamea.

We ate some truly delectable oysters and said goodbye to Marcie.

We were lucky enough to get a second visit with Paul Englemeyer this time to talk about wetland restoration. Paul talked about restoration efforts in Beaver Creek near Waldport and how important wetlands are because of services they provide such as carbon sequestration, pollution removal, and production of food and habitat. Estuarine restoration is another way to restore natural marshlands and flood pulsing which dramatically improves the health of the watershed.

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Forest Fragmentation, Habitat Conservation, and Fisheries Management

The first day of Coastal Ecology and Resource Management Week 00 started with introductions followed by a van ride to Cape Perpetua located in Siuslaw National Forest along the Oregon coast. Cape Perpetua is managed by the US Forest Service and offers habitat to many bird species and other wildlife.  We met with Paul Englemeyer who works as Central Coast Preserve Manager for The Wetlands Conservancy and as the Ten Mile Sanctuary Manager for the Audubon Society of Portland. We were also joined at Cape Perpetua by Chris Mayes who serves as a fisheries biologist for the US Forest Service in Siuslaw National Forest.

Photo - Cape Perpetua, Lincoln County, Oregon

Paul cited numerous issues facing coastal ecology and resource management including forest fragmentation, poor water quality, and habitat degradation. Scientific research has provided an abundance of information in recent decades which has helped identify anthropogenic activities greatly impacting coastal ecosystems. An example of such research is water quality testing showing changes of water quality over time in local waterways. Paul displayed a map illustrating all rivers with known water quality issues in Oregon and informed us that water quality is determined using 13 parameters such as temperature, BOD, coliform bacteria, and pH. The Clean Water Act’s section 303(d) helps local agencies determine water quality impairment and identify possible restoration solutions.

Other obstacles to conservation and restoration of coastal landscapes include forest fragmentation, inadequate riparian zones, and extractive activities such timber harvesting and mineral mining. Paul and Chris discussed the impacts of inadequate riparian areas on fish habitat and water quality. Paul also showed us a map of roads that have been decommissioned to restore connections between fragmented forest and riparian areas.

Paul mentioned at least two species affected by forest fragmentation and poor water quality. He mentioned the intracoastal murrelet which is considered a globally or internationally significant species. Murrelets are  protected by Important Bird Area (IBA) conservation efforts which include marine areas where birds often dive up to 250 feet to prey on forage fish such as sardines. Scientists are learning the importance of IBAs which Paul demonstrated using a map of breeding origins of seabirds foraging in the California current system off the coast of Oregon.

Systems such as Baja to the Bering Sea (B2B) and Large Marine Ecosystems (LME) are areas of conservation focus. Programs such as Tagging of Pacific Predators (TOPP) enable scientists to monitor migratory patterns of certain aquatic organisms. Marine protected areas provide scientists the opportunity to study fish such as rockfish which were not well understood. Now we know rockfish have relatively long lifespans and managing fisheries to promote older rockfish result in greater reproductive success via egg volume. Older rockfish can produce around 1.7 million offspring at a time or more.

We moseyed on from Cape Perpetua to Tenmile Creek Sanctuary where we ate lunch and discussed restoration efforts to bolster fish and bird habitat along the creek and adjacent riparian areas. Chris regaled us with historical details of how the US Forest Service used to deal with fallen trees then considered unwanted debris in waterways. Today, we know that naturally occurring fallen logs or large wood debris (LWDs) especially with the root base still intact provide excellent habitat for fish by creating deeper colder pools with slower water flow. Before restoration begins, watershed assessments are completed to gain a thorough understanding of hydrologic regimes, geomorphology, native and invasive plant and wildlife species, and human impact on the area.

Photo - Tenmile Creek Sanctuary. From back left to right: Chris Derrickson, Chris Mayes, Scarlett Arbuckle, Matthew VanBemmel, Paul Englemeyer.

Chris explained the paradigm shift the US Forest Service has undergone and how that influences current practices. US Forest Service efforts now focus on restoring old growth, reducing timber harvesting, decommissioning roads to connect forested areas and coastal regions. Ideally, there should be less than two miles of road per one square mile of forest, yet there are more than 2,500 miles of road in Siuslaw National Forest equating to almost three miles of road per square mile. 

We took a brief hike along a forest trail in Tenmile Creek Sanctuary where Paul pointed out areas of active restoration evidenced by young trees planted deliberately to provide canopy and bird habitat. He also pointed out where tree thinning had been performed to promote new growth and discussed how tree thinning rather than complete removal is often the best option. We said goodbye to Paul and Chris Mayes and headed down to the fishing docks in Newport. 

We met Katie Jacobson at OSU Extension Services along the bay in Newport, Oregon. Katie works with marine fisheries in Lincoln County and does a great deal of public outreach. She is also involved with NOAA’s Sea Grant, available to all coastal and Great Lakes regions in the US, which promotes research, education, community development, fisheries engagement and more in an effort to encourage responsible use and management of oceans. 

Katie administered a pop-quiz on local fisheries which I failed miserably but it helped me recognize my knowledge deficiency and the complexity of fisheries and fisheries management. I did not win Sea Grant swag from my pop-quiz endeavors! 

Another important concept Katie imparted during our discussion is the difference between outreach and engagement. Outreach is simply a way to disseminate information with no expectation of reciprocal dialogue. Whereas engagement is outreach with the goal of generating dialogue and using feedback to thoughtfully change or adjust a program or project. Katie’s work with fisheries and other stakeholders moves beyond outreach to engagement. 

Katie took us down to the commercial fishing docks where she educated us on fishing vessels including gear such as crab pots, shrimp nets, lamprey traps, and Video Electronic Monitoring (VEMs). We ended day one with a discussion of catch limits, choke species such as canary rockfish, and enforcement often provided by state troopers. We learned that there are about 500 to 600 licensed fishing vessels in Oregon and likely another 600 that operate unlicensed.