Marine ecosystem thrives at Alameda Point

Conservation of wildlife isn’t just important at Crab Cove 

Visitors flock to Crab Cove, a State Marine Conservation Area, to learn about and experience the Bay’s sea dwellers. The educational lessons at the Crab Cove Visitor Center are equally relevant throughout the waterway south of the USS Hornet at Alameda Point where even more creatures thrive in relative obscurity.

The area encompasses an interconnected web of vegetation, birds, seals, fish, mollusks, crustaceans and worms. Ghost shrimp, bat rays, leopard sharks, striped crabs, mussels, California sea hares and fish with light-emitting diodes are just a sampling. A 36-foot-wide rock wall, known as a breakwater and built by the Navy in 1945, forms the mile-long southern boundary.

Ghost shrimp at Breakwater Beach, Alameda Point. Red spots on shrimp are baby shrimp. Click on photo to enlarge.
Ghost shrimp at Breakwater Beach, Alameda Point. Red spots on shrimp are baby shrimp. Click on photo to enlarge.

Ghost shrimp are seldom seen, since they spend most of their lives in tunnels constantly digging and filtering the sandy mud for nutrients. But the evidence of their presence is plain to see during low tide at the mudflat west of the Encinal Boat Ramp. Thousands of small mud mounds dotting the landscape have an opening in the center leading down into the shrimp burrow.

Mudflat at Breakwater Beach, Alameda Point, during low tide showing shrimp burrows.
Mudflat at Breakwater Beach, Alameda Point, during low tide showing shrimp burrows.

The shrimps’ perpetual mining and aeration of the mud makes the environment attractive to other species as well, such as the arrow goby. These tiny fish are only a few inches long and almost completely transparent. They share the burrows with the shrimp. At low tide they can be seen darting around in shallow pools of water in the sand. Occasionally least terns dive to grab a goby.

Two arrow gobies at Breakwater Beach, Alameda Point. The gobies take shelter inside of ghost shrimp tunnels and also benefit from the shrimps' feeding activities that release food morsels the fish can eat.
Two arrow gobies at Breakwater Beach, Alameda Point. The gobies take shelter inside of ghost shrimp tunnels and also benefit from the shrimps’ feeding activities that release food morsels the fish can eat.

Lugworm at Breakwater Beach, Alameda PointA neighbor of the shrimp and gobies is the lugworm or sandworm. They, too, are seldom seen, but at low tide their ropey casings of excavated sand and mud are a clear sign of their presence. Another sign of their presence in recent weeks are the almost clear egg sacs. At low tide they look like deflated balloons that washed ashore. But when submersed in water, it becomes apparent that the egg sacs are tethered to the worms’ tunnels. The jelly sac keeps the eggs moist at low tide.

Lugworm egg sacs on Breakwater Beach, Alameda Point.
Lugworm egg sacs on Breakwater Beach, Alameda Point.

Another seldom seen creature is the foot-long California sea hare or sea slug. Their brownish color and slow movement makes them difficult to spot, even when they venture among the rocks near the water surface. During egg-laying season, a clue to their presence is the large bright yellow clumps of eggs deposited on the rocks, which look like angel hair pasta. 

CA sea hare, or sea slug, foraging for food on rocky shoreline next to Bay Trail.
CA sea hare, or sea slug, foraging for food on rocky shoreline next to Bay Trail.

Sea vegetation serves as an anchor for herring eggs. Some eggs are churned up by tides and currents during the prolific herring-spawning season and eaten by birds.

Gull with herring eggs attached to shafts of vegetation it retrieved from just below the water surface in Alameda Point harbor.
Gull with herring eggs attached to shafts of vegetation it retrieved from just below the water surface in Alameda Point harbor.

Algae and vegetation on rocks in the tidal zone serve as food for striped crabs, always busy picking away. But crabs will quickly move under a rock if they spot a visitor with one of their eyes that can be raised up out of the socket.

Striped crab on breakwater at Alameda Point.
Striped crab on breakwater at Alameda Point.

Armies of kelp flies walk – not fly – along the waterline on the beach during warm weather waiting for kelp to wash up so they can lay eggs.

Kelp flies on Breakwater Beach, Alameda Point.
Kelp flies on Breakwater Beach, Alameda Point.

Small fish, such as the jack smelt, provide food for the diving California least terns.  Just about any size fish is prey for the California brown pelicans that hang out by the thousands on the section of breakwater surrounded by water known as Breakwater Island.  Fellow marine birds the double-crested cormorants dive deep, chasing down prey by paddling their webbed feet.  Mussels are a delicacy for gulls, which can often be seen hovering and dropping mussels on rocks and pavement to crack open the shell.

Mussels and barnacles on the breakwater at Breakwater Beach, Alameda Point.
Mussels and barnacles on the breakwater at Breakwater Beach, Alameda Point.

The strangest fish to appear in the channel is the plainfin midshipman. It can create its own light in the deep waters it inhabits during most of the year. Their skin is laced with hundreds of bioluminescent photophores that can help it attract prey, as well as emitting light that matches surrounding water to make it difficult for predators to see.

Cormorant holding plainfin midshipman that it retrieved by diving in the Alameda Point Channel. Dotted lines on underbelly of fish are light-emitting photophores. These fish lay eggs among shoreline rocks and their young are capable of breathing air during low tide before maturing and swimming away. Due to lack of research, it is unknown whether plainfin midshipman lay eggs at Alameda Point. Other smaller and easier to swallow plainfin midshipman were caught by this cormorant.
Cormorant holding plainfin midshipman that it retrieved by diving in the Alameda Point Channel. Dotted lines on underbelly of fish are light-emitting photophores. These fish lay eggs among shoreline rocks and their young are capable of breathing air during low tide before maturing and swimming away. Due to lack of research, it is unknown whether plainfin midshipman lay eggs at Alameda Point. Other smaller and easier to swallow plainfin midshipman were caught by this cormorant.

The leopard shark with its large leopard-like brown markings can grow to seven feet in length but is harmless to humans. These fish forage for food in the shallow intertidal zone going after crabs, shrimp, worms, other fish and fish eggs.

Leopard shark next to breakwater at Alameda Point.
Leopard shark next to breakwater at Alameda Point.

A gracefully beautiful fish and a regular at Alameda Point is the bat ray, which feeds along the bottom but can occasionally be seen swimming just below the surface.

Bat ray near Bay Trail at Alameda Point.
Bat ray near Bay Trail at Alameda Point.

A moon jellyfish was recently spotted in Alameda Point waters, drifting along near the surface.

Moon jellyfish drifting at the gap in the breakwater at Alameda Point.
Moon jellyfish drifting at the gap in the breakwater at Alameda Point.

Harbor seals, representing marine mammals, round out the marine life roster. Alameda Point hosts the only harbor seal haul-out in the East Bay between Yerba Buena Island and Fremont.

Harbor seals at Alameda Point at sunrise.
Harbor seals at Alameda Point at sunrise.

Originally published in the Alameda Sun.

More photos of Alameda Point marine life, with map

Ghost shrimp with eggs at Breakwater Beach, Alameda Point.
Ghost shrimp with eggs at Breakwater Beach, Alameda Point.
Red objects on ghost shrimp are baby ghost shrimp, at Breakwater Beach, Alameda Point.
Red objects on ghost shrimp are baby ghost shrimp, at Breakwater Beach, Alameda Point.
CA sea hare, or sea slug, foraging along rocky shoreline next to Bay Trail at Alameda Point.
CA sea hare, or sea slug, foraging along rocky shoreline next to Bay Trail at Alameda Point.
CA sea hare (rear view) with yellow strands of eggs recently deposited on the breakwater.
CA sea hare (rear view) with yellow strands of eggs recently deposited on the breakwater.
Closeup showing individual CA sea hare eggs at Alameda Point.
Closeup showing individual CA sea hare eggs at Alameda Point.
School of anchovies at shoreline next to Bay Trail.
School of anchovies at shoreline next to Bay Trail.
Tube worm on Breakwater Beach, Alameda Point.
Tube worm on Breakwater Beach, Alameda Point.
Jack smelt caught by fisherman at Alameda Point breakwater to use as bait.
Jack smelt caught by fisherman at Alameda Point breakwater to use as bait.
Two striped crabs eating vegetation on the breakwater at Alameda Point.
Two striped crabs eating vegetation on the breakwater at Alameda Point.

Alameda Point waterway

Navy adds a wetland and grassland

The Navy’s cleanup program has not only removed toxic substances from below ground, it has dramatically improved some of the above ground environment by creating new native grassland and wetlands. January rains filled the Navy’s new seasonal wetland on the northwest shoreline corner of Alameda Point and fostered growth of newly planted native grass seed on the surrounding soil.

New Site 1 wetland on January 13, 2016, with San Francisco in background. Rows in soil with emerging growth were created during sowing of seeds. Navy photo.
New Site 1 wetland on January 13, 2016, with San Francisco in background. Rows in soil with emerging growth were created during sowing of seeds. Navy photo.

The 2.25-acre wetland lies within an approximately 37-acre shoreline cleanup area known as Site 1 at the confluence of the Oakland Estuary and San Francisco Bay. It is where the Navy buried its waste between 1943 and 1956. Most of the waste pits were covered by pavement in the mid-1950s when a new runway was added.

The approved plan for leaving the waste in place was completed in 2015 after 17 years of study by state and federal regulatory agencies. None of the studies showed any toxic leaching from the waste material into Bay waters after sitting below the water table for more than 50 years. Hence, the plan to further isolate the waste with a soil cover mirrors the remedy used at other underground dumps.

The Navy will be responsible in perpetuity if anything fails, just as with other Superfund cleanup sites at Alameda Point.

The Navy was required to create the new wetland as a mitigation measure for covering existing wetland with some of the soil cover. The secondary objective was to provide increased native plant and wildlife habitat along San Francisco Bay.

This mitigation requirement means that marginal wetlands that appeared by happenstance from runway drainage have now been replaced by a high quality engineered wetland. The new wetland holds a much larger volume of water and is situated to capture runoff from the soil cover. It is also engineered at a lower elevation than the wetlands it replaces, thereby increasing water retention and allowing for recharging as sea level rises. There is no waste material located below the new wetland.

After removing old pavement and sculpting the site, the wetland substrate was created using imported clean fill material and topsoil.  The soil was then amended with gypsum and potassium sulfate to facilitate growth of wetland plant species.

Learning a bitter lesson from a failed attempt in 2014 to grow native grasses by blowing seeds from a truck onto the soil at the nearby Site 2 cleanup area, the Navy used a different method at both sites. Known as drill seeding, the method involves cutting into the soil with a disc machine and simultaneously depositing seeds. It is followed up with a mulch cover.

Site 1 wetland in late 2015 after seeding and covering with green-colored hydromulch. Tree sections were added for birds to perch on. Navy photo.
Site 1 wetland in late 2015 after seeding and covering with green-colored hydromulch. Tree sections were added for birds to perch on. Navy photo.

Thirteen grass species were planted on the lower zone of the new wetland where longer-term saturation will occur. Another seven species were planted on the upper zone. The seeded area was then covered with mulch. The soil cover over the former dump received another eight species of native grass seed. The palette includes such grasses as chairmaker’s bulrush, seaside heliotrope, Baltic rush, white yarrow, and coyote brush, all of which produce flowers.

The Site 1 grassland and wetland is on land slated to be transferred to the city at no cost and to become part of a 147-acre regional park. Plans call for additional wild grassland and wetlands.

Site 1 soil cover after green-colored mulch was applied in 2015. Green coloring has since disappeared. Navy photo.
Site 1 soil cover after green-colored mulch was applied in 2015. Green coloring has since disappeared. Navy photo.

The Navy’s new wetland sits directly atop the original narrow landmass extending into the Bay that carried train cars to a ferry terminal at the site. Completed in 1859, this strip was called the Alameda Mole.

The Navy’s grassland and wetland work at Site 1 and Site 2 on the old airfield is the only ecological habitat creation, other than the placement of sand on the 9.6-acre least tern nesting site, since military operations ended in April of 1997.

Published in the Alameda Sun.

Additional photos and complete list of native grasses planted on Site 1.

Wetland with soil amendments added. Navy photo.
Wetland with soil amendments added. Navy photo.
Wetland after placing wood features and mulch. Navy photo.
Wetland after placing wood features and mulch. Navy photo.
Native grass seeds loaded into disc planter. Navy photo.
Native grass seeds loaded into disc planter. Navy photo.

Site 1 vegetation plant list 

Zone A (Wetland Mitigation Area) (lower)

  • Salicornia virginica – NC (pickleweed)
  • Juncus effuses (common bog rush)
  • Eleocharis macrostachya (pale spikerush)
  • Frankenia salina (alkali heath)
  • Schoenoplectus americanus (chairmaker’s bulrush)
  • Beckmannia syzigachne-NC (slough grass)
  • Bolboshoenus maritimus (alkali bulrush)
  • Heliotroppium curassavicum (seaside heliotrope)
  • Grindelia stricta (coastal gum plant)
  • Cressa truxillensis (spreading alkaliweed)
  • Juncus balticus (Baltic rush)
  • Hordeum depressum (dwarf barley)
  • Cyperus eragrostis (tall flatsedge)

Zone B (Wetland Mitigation Area) (upper)

  • Artemisia pycnocephala (coastal sagewort)
  • Achillea millefolium, White (white yarrow)
  • Festuca rubra Molate (creeping red fescue)
  • Elymus triticoides (beardless wild rye)
  • Hordeum brachyantherum (California meadow barley)
  • Distichlis spicata (salt grass)
  • Carexpraegracilis (clustered field sedge)

Greater WIC (Waste Isolation Cover)

  • Achillea millefolium, White (white yarrow)
  • Baccharis pilularis (coyote brush)
  • Bromus carinatus, Sonoma (California brome grass)
  • Elymus glaucus, Berkeley (blue wildrye)
  • Lupinus nanus (sky lupine)
  • Distichlis spicata (salt grass)
  • Trifolium ciliatum, Inoc (foothill clover)
  • Vulpia microstachys (small fescue)