SECTION 4.0

ENVIRONMENTAL SETTING, IMPACTS, AND MITIGATION

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PROPOSED PROJECT

4.6    MARINE BIOLOGICAL RESOURCES

The following sections describe the regulatory framework and the biological resources and natural communities occurring within the marine segment of the Project area, and provide an assessment of potential Project impacts. This evaluation of biological resources includes a review of special-status species with the potential to occur in the Project area. The results of this assessment are based upon literature searches and data base queries. The sources of reference data reviewed for this section included the following:

• Antioch North, Honker Bay, Vine Hill, Benicia, Mare Island, Petaluma Point, San Quentin, Richmond, Oakland West, San Leandro, Hunters Point, Point Bonita, and San Francisco North, California, USGS 7.5-minute topographic quadrangles

• California Natural Diversity Database (CNDDB) queries of the Antioch North, Honker Bay, Vine Hill, Benicia, Mare Island, Petaluma Point, San Quentin, Richmond, Oakland West, San Leandro, Hunters Point, Point Bonita, and San Francisco North USGS 7.5 minute quadrangles (California Department of Fish and Game [CDFG], 2005)

• Baylands Ecosystem Species and Community Profiles, Life Histories and Environmental Requirements of Key Plants, Fish, and Wildlife. (San Francisco Bay Area Wetlands Ecosystem Goals Project [Goals Project, 2000])

• U.S. Fish and Wildlife Service Species List for Antioch North, Honker Bay, Vine Hill, Benicia, Mare Island, Petaluma Point, San Quentin, Richmond, Oakland West, San Leandro, Hunters Point, Point Bonita, and San Francisco North, California USGS 7.5 minute quadrangles (U.S. Fish and Wildlife Service[USFWS], 2005a)

• Review of the literature and other published reports relevant to the Project area

This section first describes the general nearshore and tidal habitat types found around the relevant portions of San Francisco Bay, and provides general locations of these habitat types and the species commonly found in them. The open water community of the Bay is described based on the following broad categories:

Benthos (bottom-dwelling organisms)
• Fish

• Birds

• Marine mammals

• Aquatic plants

Species and habitats (e.g., eelgrass beds, etc.) protected under the state and federal endangered species acts and other regulations are also described.

4.6.1    Environmental Setting

The following description of the marine environment covers only the offshore DC and AC cable routes in San Francisco Bay. Biological resources for onshore components of the proposed Project are discussed in Section 4.5, Terrestrial Biological Resources. The biological resources in San Francisco Bay are discussed in the following sections by location and type. For purposes of this section, San Francisco Bay is categorized into two subregions, which are defined as the following:

• North Bay – North of the Richmond Bridge extending to Suisun Bay and the west delta

• Central Bay – Richmond Bridge to the southern most portion of the proposed cable route in San Francisco

4.6.1.1    Marine Habitat Types

Marine habitats around San Francisco Bay include those that fringe the Bay such as Bay flats as well as the open Bay itself. The habitats types around the Bay often blend with one another in transition zones called ecotones. Species found in these areas often occur in more than one habitat type. The habitats and common species associated with those habitat types have the potential to occur within the Project boundaries.

4.6.1.1.1    Bay Flats. Bay flats are sparsely vegetated intertidal areas that occur from approximately mean lower low water (MLLW) to mean tide level (MTL). They provide protection to banks and upland shoreline from wave energy and sediment. Bay flats around San Francisco Bay provide habitat for many types of invertebrates, including diatoms (microscopic algae), polychaetes (marine bristleworms), oligochaetes (earthworms and relatives), amphipods (shrimp-like organisms), isopods (sow bugs and relatives), and crustaceans (shrimps, crabs, barnacles, etc.).

During low tide, Bay flats provide crucial foraging and roosting areas for almost one million shorebirds that utilize the Bay during the spring migration. Shorebirds frequently found on Bay flats in the Bay include western sandpiper (Calidris mauri), least sandpiper (Calidris minutilla), dunlin (Calidris alpina), long- and short-billed dowitcher (Limnodromus griseus, and L. scolopaceus, respectively), long-billed curlews (Numenius americanus), whimbrels (Numenius phaeopus), and American avocet (Recurvirostra americana).

During high tide, Bay flats provide foraging habitat for fish, including longfin smelt (Spirinchus thaleichthys), staghorn sculpin (Leptocottus armatus), starry flounder (Platichthys stellatus), and leopard shark (Triakis semifasciata). One of the few mammals occasionally present on Bay flats is the Pacific harbor seal (Phoca vitulina).

4.6.1.1.2    Open Bay. The Goals Report (Goals Project, 1999) subdivides the open Bay into two habitat subunits: deep Bay/channel and shallow Bay. Deep Bay/channel habitat, which accounts for approximately one-third of the area of San Francisco Bay, is defined as those portions of the Bay deeper than 18 feet below MLLW, including the deepest portions of the Bay and the largest tidal channels. Shallow Bay is defined as that portion of the Bay between MLLW and 18 feet below MLLW. The shallow Bay habitat accounts for two-thirds of the Bay's area (Goals Project, 1999).

Species that use the deep Bay habitat include several species of free-swimming invertebrates such as California Bay shrimp (Crangon fransicorum), and fishes such as brown rockfish (Sebastes auriculatus), halibut (Paralichthys californicus), and sturgeon (Asipenser sp.). This habitat provides important roosting and "loafing" habitat for waterbirds, especially in areas protected from intense wind fetch or wave action. Waterbirds, such as surf scoter (Melanitta perspicillata), scaups (Aythya spp.), brown pelican (Pelecanus occidentalis), and terns (Sterna spp.), and marine mammals, such as harbor seal and California sea lion (Zalophus californianus), can be found utilizing this habitat type. Anadromous fish, such as Chinook salmon, use the deep Bay habitat as a migratory pathway to and from upstream spawning areas.

The shallow Bay habitat is a feeding area for Pacific herring (Clupea harengus), northern anchovy (Engraulis mordax), bat ray (Myliobatis californica), and jacksmelt (Catherinops californiensis), as well as at least 40 other species of fish, crabs, and shrimp. Pacific herring spawn on hard substrates and eelgrass along the shallow margins of the Central Bay (refer to Figure 4.6-1). Shallow Bay habitat is also a nursery area for juvenile halibut and sanddabs (Citharichthys stigmaeus), leopard shark, shiner perch (Cymatogaster aggregata), herring, and other fishes. Anadromous fish use the shallow Bay area as migratory pathways to and from upstream spawning areas. This habitat is within the depth range of many diving birds and therefore provides important avian foraging habitat. Marine mammals such as harbor seals also forage in this habitat type (refer to Figure 4.6-2). Eelgrass (Zostera marina L.), San Francisco Bay's only rooted seagrass, is present in some areas of this habitat type. Eelgrass is particularly important to many species of fish such as Pacific herring, which deposit eggs on the blades of this plant, and the endangered least tern (Sterna antillarum browni), which can forage on small fishes associated with the eelgrass.

4.6.1.2    Biological Resources

4.6.1.2.1    Benthos. Benthos are bottom-dwelling organisms that generally live non-mobile lifestyles, though some mobile species such as crabs do exist. In the Bay Area, many benthic invertebrates live within sedimentary or soft-bottom habitats, usually within the top 2 to 3 centimeters of the soft sediment. Some benthic invertebrates also live on hard substrates, which are much less common in the Bay compared to sedimentary habitats.

Three major benthic species assemblages (groups of organisms that inhabit a location or locations at a certain time or over a period of time) are present in the Bay Area: fresh-brackish, estuarine, and marine assemblages. Fresh-brackish assemblages are found in the delta, with a transition assemblage extending into Suisun Bay. Estuarine assemblages are prevalent in San Pablo Bay. The Central Bay harbors marine assemblages. Assemblage characteristics, such as species composition and abundance, are affected by many physical factors, including salinity and sediment grain size, or by biological factors such as competition and predation (Thompson et al., 2000). Changes in these factors can influence individual benthic species differently.

Many of the more common benthic species in San Francisco Bay today are accidentally or intentionally introduced species (SFEP, 1992). Most of these non-native species were transported here in ballast water of ships or on the oyster shells brought from the east coast for commercial farming purposes in the late 19th century (Carlton, 1979). Some of these nonindigenous species serve ecological functions similar to those of the native species that they have displaced. Examples of these include the eastern oyster (Crassostrea virginica), the Japanese littleneck clam (Tapes philippinarum), and the soft-shelled clam (Mya arenaria), all of which have supported commercial or sport fisheries. However, other species, such as one of the so-called Asian clam species (Potamocorbula amurensis), have a negative effect on phytoplankton and zooplankton populations and organisms that depend on them. Though P. amurensis may serve as a food source for diving ducks and sturgeon, their high feeding rates can remove much of the phytoplankton from the water column and may have an adverse effect on zooplankton and other organisms that in the food chain that feed on them (SFEP, 1992).

In Suisun Bay and the western part of the delta, the benthos found are mostly fresh-brackish assemblages, with a transition assemblage extending into Suisun Bay. Fresh-brackish water species include oligochaetes, chironomids (midges), soft-shelled clams, so-called Asian clam species in the genus Corbicula, and amphipods (SFEP, 1992; Thompson et al., 2000). Further west into San Pablo Bay, more estuarine conditions exist and intertidal bay flats and marshes are extensive. Here, estuarine assemblages are prevalent. Common benthic species include ribbed mussels (Ischadium demissum), Baltic clams (Macoma balthica), P. amurensis, California hornsnails (Cerithidea californica), yellow shore crabs (Hemigrapsus oregonensis), amphipods, polychaete worms, and Bay mussels (Mytilus spp.).

In the Central Bay marine conditions exist. Benthic species common in these areas consist of clams (including P. amurensis), amphipods such as Monocorophium and Ampelisca, polychaete worms, and Bay mussels (SFEP, 1992).

4.6.1.2.2    Fish. More than 100 species of fish inhabit the San Francisco Bay system. The majority of species are native, but there are also many introduced species. A large portion complete all life stages within the Bay. A smaller portion, anadromous fish, migrate from ocean waters, through the estuary, and into a series of freshwater streams where they spawn. Common fish species found in the Bay are listed in Table 4.6-1, and include northern anchovy, topsmelt (Atherinops affinis), jacksmelt, striped bass, white croaker (Genyonemus lineatus), Pacific herring, and English sole (Parophrys vetulus).

Fish population trends can be determined by analyzing the data resulting from the monitoring efforts of CDFG. An analysis of these data from a monitoring study between 1980 and 1995 suggests a general distribution of fishes in the Bay as follows (Baxter 1999, SFEP 1992):

• North Bay – Fish species typically found in the North Bay include sharks, rays, longfin smelt, staghorn sculpin, starry flounder, topsmelt, arrow goby (Clevelandia ios), yellowfin goby (Acanthogobius flavimanus), stickleback (Gasterosteus sp.), mosquitofish (Gambusia affinis), green sunfish (Lepomis cyanellus), Pacific herring, Chinook salmon (Oncorhynchus tshawytscha), and steelhead (Oncorhynchus mykiss).

• Central Bay – Typical fish species occurring in the Central Bay include Chinook salmon, striped bass (Morone saxatillis), white croaker, Pacific herring, and northern anchovy.

Because of the large number of fish species that could potentially be present, not all are discussed in detail. The more ecologically, commercially, and/or recreationally important species are included in Appendix F. A discussion of fish species with either federal or state protection status is included in Section 4.6.1.3 (Special Status Species).

Federally Managed Fish Species. Under the Magnuson-Stevens Fisheries Conservation and Management Act, the Pacific Fisheries Management Council (PFMC) is responsible for managing commercial fisheries resources along the coasts of Washington, Oregon, and California. Managed species are covered under three fisheries management plans:

• Coastal Pelagic Fishery Management Plan (includes species such as sardines and anchovy)

• Pacific Groundfish Fishery Management Plan (includes species groups such as flatfish and rockfish)

• Pacific Salmon Fishery Management Plan (includes Chinook and other salmon)

Most of the federally managed species in these plans are not found in San Francisco Bay. Federally managed species found in the Bay are listed in Table 4.6-2.

4.6.1.2.3    Birds. San Francisco Bay provides diverse habitat for many species of waterfowl and shorebirds. Open water, Bay flats, and tidal marsh are just some of these habitats.

TABLE 4.6-1
COMMON SAN FRANCISCO BAY FISH SPECIES,
CALIFORNIA DEPARTMENT OF FISH AND GAME SAMPLING¹

¹  Source: California Department of Fish and Game, Bay-Delta Monitoring Project, unpublished data. Species lists also reported in Baxter et al., 1999.

TABLE 4.6-2
FEDERALLY MANAGED FISH SPECIES OCCURRING IN THE BAY

Roughly 120 species from 16 avian families occur in the Bay. Of these birds, approximately two-thirds are represented by three families: Anatidae (waterfowl), Laridae (gulls and terns), and Scolopacidae (sandpipers and phalaropes).

The Bay serves as an important staging and wintering ground on the Pacific Flyway for numerous species of waterbirds. The Pacific Flyway is a bird migration corridor along the Pacific Coast that stretches as far north as northern Canada and Alaska, and as far south as the southern tip of South America (SFEP, 1992). In the Bay, the greatest waterbird abundance and species diversity is seen in winter, as birds migrate along the flyway. Each year, nearly one million waterfowl and more than one million shorebirds pass through this area. San Francisco Bay is also recognized as a site of hemispheric importance for shorebirds by the Western Hemisphere Shorebird Reserve Network (2005) (a site is designated of hemispheric importance if it is utilized by at least 500,000 shorebirds annually). Between 1988 and 1995, the Bay supported 24 to 96 percent of the key species of shorebirds surveyed along the Pacific Flyway. No other site within the Pacific Flyway supported more than 16 to 32 percent of these species (Page et al., 1999). Tidal Bay flats in particular offer important habitat and a migratory staging area for shorebirds.

The most predominant birds in the open Bay are diving ducks, including scaup, scoter, and canvasback. A comprehensive survey and analysis of waterbirds in the Bay was conducted between 1988 and 1990 (Accurso, 1992). During this time, diving ducks consisted of up to 75 percent of the Bay's waterfowl, depending on the month. Greater and lesser scaup were the most abundant species, accounting for nearly 47 percent of all species. Surf scoter was the second most abundant species making up about 20 percent of all waterfowl in the Bay. Canvasback, another diving bird, accounted for 7 percent of all waterfowl species in the Bay (Accurso, 1992). Similar results were obtained in more recent mid-winter surveys from 1998 to 2000 where scaup comprise about 43 percent of all waterfowl in the entire Bay and 67 percent of waterfowl in the Central Bay open water. Scoters, the second most abundant waterfowl in the Bay, accounted for 29 percent of total waterfowl in the Central Bay (USFWS, 2005b).

Tidal flats are a primary foraging habitat for shorebirds within the Bay. The North Bay supports approximately 20 percent of shorebirds in San Francisco Bay, while the South Bay (south of the proposed Project cable route) supports the majority of shorebirds due to the extensive tidal flats and salt ponds present there (SFEP, 1992). Western sandpipers and dunlins comprise the majority of shorebirds in the Bay, but also occurring in large numbers are dowitchers, marbled godwits, willets, and American avocets.

4.6.1.2.4    Marine Mammals. The waters off California support an abundance and diversity of marine mammals, primarily because of the numerous upwelling centers that stimulate primary production, the central location between arctic and subtropical areas, and the diversity of habitats (Harvey, 1998). Some species migrate through the area on their way to summer feeding or winter breeding areas; others reside in the area year-round. San Francisco Bay, like many estuaries, serves as a nursery for some species of marine mammals (e.g., harbor seals), provides protected waters for resting ashore and in the water (e.g., California sea lions and harbor seals), and is used as a foraging area (e.g., harbor seals and, occasionally, gray whales).

Several marine mammal species can be found in San Francisco Bay including the harbor seal (Phoca vitulina), California sea lion (Zalophus californianus), and more recently, the gray whale (Eschrichtius robustus). Characteristics of these species are included in Appendix F.

Harbor seals are the most common and abundant marine mammal in the Bay and are the only marine mammals that are permanent residents in the Bay. All harbor seals use resting areas (called haul-out sites) that are free from frequent disturbance and near channels or open water. Habitats used as haul-out sites include tidal rocks, mudflats, sandbars, and sandy beaches (Zeiner et al., 1990). These haul-out sites are critical habitats for harbor seals and are used consistently from year to year. Haul-out sites in the Project area are shown on
Figure 4.6-2.

Other marine mammal species that have been seen very rarely in the Bay include the humpback whale (Megaptera novaeangliae), harbor porpoise (Phocoena phocoena), northern elephant seal (Mirounga angustirostris), Steller sea lion (Eumetopius jubatus), northern fur seal (Callorhinus ursinus), and the southern sea otter (Enhydra lutris). The species occur frequently off the California coast and occasionally enter the Bay either mistakenly, or while searching for food.

The Marine Mammal Protection Act (MMPA) of 1972 protects all marine mammals, with additional laws, including the Federal Endangered Species Act of 1973 (FESA), and the California Endangered Species Act of 1984 (CESA), protecting certain species because their populations are at very low levels (e.g., sea otter).

4.6.1.2.5    Aquatic Plants. Substrate in much of the Bay consists of soft mud, making it difficult for many macroalgal species to colonize. Some types can initially attach to a hard substrate such as a small rock or piece of shell, and, as they become larger, move with the small attachment (Josselyn and West, 1985). Common Bay species include the green algae Enteromorpha clathrata, E. intestinalis, U. lactuca, and Cladophora sericea and the aquatic plant eelgrass (Zostera marina).

Eelgrass (Zostera marina). Eelgrass is a native marine vascular plant indigenous to the soft-bottom bays and estuaries of the Northern Hemisphere. The species is found from middle Baja California and the Sea of Cortez to northern Alaska along the west coast of North America and is common in healthy shallow bays and estuaries. Eelgrass serves as a food source for a number of invertebrates, fish, and some migratory birds. It also provides habitat for many commercially and recreationally important finfish and shellfish species. Pacific herring regularly spawn on eelgrass leaves, and juvenile salmonid and smelt often spend extensive amounts of time within eelgrass habitats prior to heading for the open ocean (Wyllie-Echeverria and Rutten, 1989).

Distribution of eelgrass in the Bay is limited by sediment in the water (turbidity) and the depth to which light can penetrate at levels high enough to sustain eelgrass growth. In San Francisco Bay, eelgrass is limited to depths of about 10 feet or less along the shoreline. Locations of eelgrass beds are shown on Figure 4.6-2.

Eelgrass is protected under the Clean Water Act of 1972 (as amended), Section 404(b) (1) "Guidelines for Specification of Disposal Sites for Dredged or Fill Material," Subpart E, "Potential Impacts on Special Aquatic Sites."

4.6.1.3    Special-status Species

Special-status plant and animal species are those that are recognized as rare and vulnerable to habitat loss or population decline. A list of special-status plant and animal species reported to occur within or in the vicinity of the project area was compiled using data in the CNDDB and consultation with the CDFG and USFWS (CDFG, 2005; USFWS, 2005a). These species and their potential to be impacted by the Project activities are summarized in a table included in Appendix F of this EIR. The table indicates each species' potential to occur in suitable habitat that is located in the immediate vicinity of the Project. Of the special-status plants and animals listed in the table, three fish species with federal and/or state listing have a medium or higher potential to occur within portions of the Project area. The "Potential for Impact" determination in this table is made based on locations of known occurrences of the species, the presence of preferred habitats and the potential for project activities to affect a species or associated habitats. The marine species occurring in the Project area with the potential to be affected include the fish species discussed in the following sections.

4.6.1.3.1    Delta Smelt. The delta smelt (Hypomesus transpacificus) is a federal- and state-listed threatened species. It is endemic to Suisun Bay upstream of San Francisco Bay through the delta estuary in Contra Costa, Sacramento, San Joaquin, Solano, and Yolo counties. It is a euryhaline (capable of tolerating a wide range of water salinity) species, but for a large part of its life span it is associated with the freshwater edge of the mixing zone (saltwater-freshwater interface). In the San Francisco Bay Area, the mixing zone has been estimated, during a normal water runoff year, to be in the Carquinez Strait during April and to move upstream to approximately Chipps Island in eastern Suisun Bay in August.

During spawning activities, the smelt prefers freshwater habitats. Delta smelt begin a diffuse, gradual migration to upstream spawning areas in September or October (Moyle, 2002). Delta smelt spawn from February to July in side channels and sloughs in the upper delta and in the Sacramento River north of Rio Vista (Moyle, 2002). In addition, spawning has been documented in the lower San Joaquin River, Georgiana, Barker, Lindsey, Cache, Prospect, Beaver, Hog, and Sycamore sloughs; and in sloughs of the Suisun Marsh, including Montezuma Slough and potentially Suisun Slough (Goals Project, 2000; Moyle, 2002). Adhesive, demersal eggs attach on submerged and inshore plants, primarily in sandy and hard-bottom substrates (Wang, 1986). Newly hatched larvae drift downstream to the freshwater/saltwater interface in nearshore and channel areas. Downstream distribution of adult and juvenile delta smelt appears to be generally limited to western Suisun Bay, although populations do occur in San Pablo Bay and the Napa River (Goals Project, 2000). The delta smelt is generally a pelagic species, filter feeding within the open waters of the San Francisco Bay estuary system (Wang, 1986).

Breeding habitat for the delta smelt is designated as federally-listed threatened critical habitat. Their critical habitat is defined as "…all water and submerged lands below ordinary high water and the entire water column bounded by and contained in Suisun Bay (including the contiguous Grizzly and Honker Bays); the length of Montezuma Slough; and the existing contiguous waters contained within the Delta, as defined by section 12220, of the State of California's Water Code of 1969 (a complex of bays, dead-end sloughs, channels typically less than 4 meters deep, marshlands, etc.)."

4.6.1.3.2    Central Valley Steelhead. The National Marine Fisheries Service (NMFS) classifies and lists steelhead as an Evolutionarily Significant Unit (ESU). "To be considered an ESU, a population or group of populations must: 1) be substantially reproductively isolated from other populations; and 2) contribute substantially to the ecological or genetic diversity of the biological species" (Myers et al., 1998). Factors used in determining ESUs include spatial, temporal, and genetic isolation, maturation rates, and other life history traits.

The Central Valley steelhead ESU (Oncorhynchus mykiss) is federally listed as threatened and a state species of special concern. This ESU occurs in the Sacramento and San Joaquin rivers and their tributaries. Steelhead migrate from fresh water to the ocean and return to spawn in fresh water. Steelhead spend most of their adult life in the open ocean. The Central Valley steelhead ESU migrate upstream through the Carquinez Strait from the ocean between August and May to spawn in freshwater streams. Spawning occurs between December and April, with most spawning activity occurring between January and March. Steelhead remain in freshwater for one to four years before they out-migrate through the Strait into the open ocean during spring and early summer (Goals Project, 2000). The population, based on Red Bluff Diversion Dam counts, hatchery counts, and past natural spawning escapement estimates for some tributaries, was estimated to be no greater than 10,000 adult fish (McEwan and Jackson, 1996).

4.6.1.3.3    Chinook Salmon. Chinook salmon (Oncorhynchus tshawytscha) historically ranged from the Ventura River in California to Point Hope, Alaska. The general life history of the anadromous Chinook salmon includes both fresh water and oceanic phases of development. Incubation of the eggs, hatching, and emergence occur in freshwater, followed by migration to the ocean. Once in the ocean the fish mature and return to freshwater habitats to spawn. Adult chinook migrate through San Francisco Bay on their way to upstream spawning grounds as part of four distinct "runs": winter, spring, fall, and late-fall, defined by the timing of the adult spawning migration.

The NMFS classifies and lists salmon by ESU. Three Chinook salmon ESUs are known to occur in the study area, and they all receive some federal protection.

• Central Valley Fall/Late Fall-Run ESU is a candidate for federal listing. This ESU spawns in the Sacramento and San Joaquin river basins. This ESU may enter fresh water anytime between August and March, with spawning occurring between October and March (Goals Project, 2000). Juveniles may emigrate from freshwater between November and May.

• Sacramento River Winter-Run ESU is designated as a federal- and state-listed endangered species. The ESU spawns in the Upper Sacramento River below Keswick Dam. This ESU typically enters fresh water between January and May, with spawning occurring May through July. Juvenile emigration occurs during February and March (Goals Project, 2000). Critical habitat for the Central Valley Winter Run ESU includes the Sacramento River from Keswick Dam downstream to Chipps Island in the Sacramento – San Joaquin Delta and from Chipps Island west to the Benicia Bridge.

• Central Valley Spring-Run ESU is designated as a federal- and state-listed threatened species. The ESU spawns in the Sacramento River basin. This ESU typically enters fresh water between April and June, with spawning occurring between August and October (Goals Project, 2000). Juvenile out-migration typically occurs between October and December.

4.6.2    Regulatory Setting

The regulatory setting for marine resources is presented below. Additional regulations pertaining to marine resources are also summarized in Section 4.5, Terrestrial Biological Resources.

4.6.2.1    Federal

4.6.2.1.1    Federal Endangered Species Act (FESA) (16 USC 1531-1544). The federal endangered species act is described in Section 4.5.2.1.1.

4.6.2.1.2    Section 404/10 Jurisdiction (33 USC 1251-1376). Under Section 404 of the Clean Water Act, the U.S. Army Corps of Engineers (USACE) regulates the disposal of dredged and fill materials into "waters of the U.S.," which include intrastate lakes, rivers, streams (including intermittent streams), bay flats, sandflats, wetlands, sloughs, prairie potholes, wet meadows, playa lakes, or natural ponds, and wetlands adjacent to any water of the U.S. (CFR 33 Part 328). In areas subject to tidal influence, Section 404 jurisdiction extends to the high tide line.

The USACE also regulates navigable waters under Section 10 of the Rivers and Harbors Act. Navigable waters are defined as "those waters of the United States that are subject to the ebb and flow of the tide shoreward to the mean high water mark and/or are presently used, or have been used in the past, or may be susceptible to use to transport interstate or foreign commerce" (33 CFR Part 322.2).

In San Francisco Bay, waters of the U.S. include open waters of the Bay, seasonal and tidal wetlands, and intertidal habitats. Any dredge or fill activities required as a part of Project implementation and/or operation would require a permit from the USACE.

4.6.2.1.3    Estuary Protection Act (16 United States Code [USC] 1221-1226). This act requires the Secretary of the Interior to review all project plans and reports for land and water resource development affecting estuaries and to make recommendations for conservation, protection, and enhancement.

4.6.2.1.4    Magnuson-Stevens Fisheries Act (16 USC 1801-1882). The Amended Magnuson-Stevens Fishery Conservation and Management Act, also known as the Sustainable Fisheries Act (Public Law 104-297), requires all federal agencies to consult with the Secretary of Commerce on activities, or proposed activities authorized, funded, or undertaken by that agency that may adversely affect Essential Fish Habitat (EFH) (Office of Habitat Conservation, 1999). The EFH provisions of the Sustainable Fisheries Act are designed to protect fisheries habitat from being lost due to disturbance and degradation.

4.6.2.1.5    Marine Mammal Protection Act (16 USC 1361-1421h). Under the MMPA of 1972 (16 USC 1371), it is unlawful to take or import marine mammals and marine mammal products. Under Section 101(a)(5)(D), an incidental harassment permit may be issued for activities other than commercial fishing which may impact small numbers of marine mammals. An incidental harassment permit covers activities that extend for periods of not more than 1 year and that will have a negligible impact on the impacted species.

4.6.2.1.6    Executive Order 13112: Invasive Species. In 1999, Executive Order 13112 was issued to prevent the introduction of invasive species and provide for their control. Under this order, the federal government may "not authorize, fund, or carry out actions that it believes are likely to cause or promote the introduction or spread of invasive species in the United States or elsewhere unless, pursuant to guidelines that it has prescribed, the agency has determined and made public its determination that the benefits of such actions clearly outweigh the potential harm caused by invasive species; and that all feasible and prudent measures to minimize risk of harm will be taken in conjunction with the actions."

Additionally, federal agencies must consult with the Invasive Species Council, consistent with the Invasive Species Management Plan.

4.6.2.2    State

4.6.2.2.1    California Endangered Species Act (CESA) (California Fish and Game Code 2050‑2116). The California Endangered Species Act is discussed in Section 4.5.2.2.

4.6.2.3    Local

No local regulations apply to marine biology.

4.6.3    Environmental Impacts

The following section describes the potential impacts that the Project would have on the biological environment. The discussion focuses on the offshore cable route. Impacts to biological resources for the onshore components of the Project are discussed in Section 4.5, Terrestrial Biological Resources.

Impacts are categorized as construction-related or operations-related impacts and are further organized by impact type, since a particular type of impact may affect more than one species or habitat type (e.g., overall Bay habitat, benthic environment, fish, marine mammals, etc.). This analysis addresses the potential for impacts and, where applicable, the mitigation measures that can be adopted to avoid or minimize these effects.

4.6.3.1    Thresholds of Significance

California Environmental Quality Act (CEQA) Guidelines Section 15206 specifies that a project shall be deemed to be of statewide, regional, or area-wide significance if it would substantially affect sensitive wildlife habitats including, but not limited to, riparian lands, wetlands, bays, estuaries, marshes, and habitats for rare and endangered species as defined by State Fish and Game Code Section 903.

The following thresholds of significance are based on the CEQA Guidelines (Appendix G), and resource agency concerns. Impacts would be considered significant if they would:

• Substantially affect threatened, endangered species, or protected species

• Alter or diminish critical habitat or a special aquatic site, including eelgrass beds, mudflats, and wetlands

• Cause substantial spread of invasive nonnative plants or wildlife

• Interfere substantially with the movement of resident or migratory fish or wildlife species

• Cause substantial or sustained impact to spawning habitat of commercially important species (e.g., Pacific herring)

The proposed offshore cable route was selected to avoid shipping channels, anchorages, dredge disposal areas, other known obstacles as well as known sensitive biological resources. For example, as depicted on Figure 4.6-2, eelgrass beds and known harbor seal haul-out sites have been specifically avoided in developing the cable route to avoid impacts to these sensitive areas.

4.6.3.2    Construction-related Impacts

Offshore cable installation is expected to require approximately 4 to 5 months to complete and would take place 24 hours a day, seven days a week. Cable installation from the Carquinez Strait eastward is planned (to the extent possible) to take place between June 1 and November 30, a period of time that NMFS suggests that sensitive life stages of ESA-listed salmonids (Chinook and steelhead) are not likely to be present within the San Francisco Bay region.

4.6.3.2.1    Installation Vessel Operation. Installation from San Francisco to the Carquinez Straits would likely be accomplished by cable ship. This ship would operate much like any other large merchant ship in the Bay, subject to state and federal regulations regarding pollutant discharges. No significant impacts to marine life are expected from the operation of the Cable Ship (C/S) Giulio Verne (or comparable vessel).

From approximately the Carquinez Straits to Pittsburg installation would likely be done from a cable installation barge. This barge would be moored to deployed anchors. Disturbance to the benthos at the anchor sites would result. This disturbance would be temporary and minor at these locations. No significant impacts are expected from the deployed anchors.

4.6.3.2.2    Introduction of Non-native Species from Ballast Water. The C/S Giulio Verne ship would travel from elsewhere to San Francisco Bay, with the cable for installation in the Bay. Since this ship would come from a foreign port, there is the potential that non-native species could be introduced to the Bay. Larval forms of non-native species can be carried in the ballast water of ships, and if ballast water is released in the Bay, larvae can be introduced into the Bay ecosystem. The benthic clam P. amurensis is an example of an introduced non-native species. The U.S. Coast Guard currently has mandatory regulations in effect that require ships carrying ballast water to have a ballast water management and reporting program in place and, without jeopardizing the safety of the crew, exchange ballast water with mid-ocean water or use an approved form of ballast water treatment, prior to releasing any ballast water within a U.S. port. Since the Giulio Verne would be transiting carrying a full load of cable, it is unlikely ballast water would be needed. No impact is expected.

4.6.3.2.3    Cable Installation Using the Hydroplow or Equivalent Technology. The Hydroplow (or other equivalent cable-laying technology whose sediment disturbances are similar to those of the Hydroplow) works by fluidizing the seabed material in a narrow path, at a predetermined depth, without displacing the majority of the material, and minimizing the suspension of sediment in the surrounding water. In this case, the Hydroplow would cut a trench approximately 1 foot wide and would lay the cable at a typical target burial depth of approximately 3 to 6 feet, with the potential for local burial to greater depths if required. The actual burial depth would be determined by the marine survey and Risk Analysis to be conducted, and Insurance Company requirements. The Hydroplow straddles the cable, creates a trench below the cable, and guides the cable into the trench. The trench then partially collapses after the passage of the burial machine and the remaining part of the trench is generally filled by natural sediment deposition. The operation would move along the route at approximately 1 to 2 miles per day, so time of construction disturbance in any given area would be limited.

Potential impacts from the Hydroplow or equivalent technology would include temporary disturbance of the seabed at the trench site and a localized increase in turbidity due to suspended sediment in the water column from the fluidization of the seabed, which would not be considered significant impacts. No long-term or permanent impacts from cable installation are expected.

4.6.3.2.4    Impacts to Mobile Animals. Mobile animals, such as fish, crustaceans, and marine mammals, may be temporarily displaced in the immediate vicinity of the operation by cable installation equipment or by exposure to short-term changes in suspended sediments and turbidity. The temporary displacement would primarily be limited to demersal (bottom dwelling) fish species. Species that primarily inhabit the mid-and upper water column, such as anchovies and salmon, are expected to continue using the water column, though these might avoid a small portion of the active cable installation area. Fish migration routes, such as through the Carquinez Strait, would not be blocked by the installation activities. Pelagic larval and egg life stages with limited mobility would be carried through the active installation area with minimal exposure to the operations. The effects of these temporary disturbances are considered adverse, but less than significant.

4.6.3.2.5    Impacts to Benthic Organisms. Sessile benthic organisms in the path of the Hydroplow or equivalent technology would be impacted as the Hydroplow moves through an area, potentially resulting in the loss or displacement of most if not all of the organisms in the immediate path of the Hydroplow. Some organisms immediately adjacent to the installation may be also be lost due to smothering or burial from sediments resuspended in the water column during the installation. Following sediment disturbing activities, disturbed areas are usually recolonized quickly by benthic organisms (Newell et al., 1998). The species that recolonize first are usually characterized by rapid growth and reproduction rates. Marine benthic invertebrates often colonize disturbed sedimentary habitats via pelagic larvae that settle from the water column. Crustaceans, such as amphipods that are abundant in the Bay, brood young to much more advanced stages than pelagic larvae, releasing what are essentially miniature adults into the sediment, and can rapidly colonize adjacent disturbed areas. Studies have indicated that even relatively large areas disturbed by dredging activities are usually recolonized within 1 month to 1 year, with original levels of biomass and abundance developing within a few months to between 1 and 3 years (MMS, 1999; Newell et al., 1998). Areas disturbed by the proposed Project may be expected to begin to develop benthic assemblages shortly after the Hydroplow moves through a given area, and could be mostly recovered in terms of biomass and abundance a few months to a year later.

Because of the small area disturbed by the installation process, and the rapid recovery and recolonization by benthic organisms, this disturbance to bottom habitat is considered adverse, but less than significant.

4.6.3.2.6    Dredging. There are two locations in USACE dredged shipping channels (MP 52.4 – 52.5 and 55.9 – 56.0) where dredging would be required to bury the cable at a depth adequate to ensure that potential future dredging of the channel would not encounter the cable (refer to Map A.2-1, Sheet 10 of 10 in Appendix A). It would be necessary to dredge approximately 38,000 cubic yards at each location. The dredged area would be approximately 400 feet long by 30 feet wide at the bottom of the channel, dredged to a depth of approximately 15 – 20 feet. Dredging would be done before cable laying began. This dredging applies only to the offshore AC/DC cable route associated with the proposed Standard Oil site in Pittsburg.

Dredging is the process of excavating and relocating sediment. Sediment may be injected into the water column at the site of the dredging operation. Impacts from dredging would include the disturbance of the seabed at the trench site and near-field effects of potential sediment deposition from the dredging activity with effects similar to those described above for the Hydroplow or equivalent technology cable installation operation. This may result in the loss of benthic organisms located in the dredge path and potential smothering of nearby organisms. As described above, adult and juvenile fish and crustaceans temporarily move away from this type of disturbance (Wilber and Clarke, 2001; Berry et. al. 2003) and recovery of the benthos in disturbed areas is rapid. Temporary impacts would include increase in the amount of suspended sediment in the water column from the dredging activity. The dredging would occur in areas located within shipping channels which are currently dredged on a periodic basis and disturbance from this operation is considered adverse, but less than significant.

4.6.3.2.7    Horizontal Directional Drilling in the Bay. Horizontal directional drilling (HDD) would be used at each end (San Francisco and Pittsburg) of the cable installation to transition between the onshore portion of the installation and the Bay bottom. The operation would be mainly land-based, drilling a hole for cable installation from the land to an exit some distance offshore. The directional drilling avoids direct disturbance to nearshore habitat. Bottom habitat disturbance would be limited to the area surrounding the exit hole in the Bay. This type of drilling uses a chemically inert bentonite clay drilling fluid. Standard practices which would minimize the impact for drilling fluid spills include careful monitoring of the drilling fluid volume and development and implementation of a drilling fluid loss response plan. Refer to Section 4.4, Water Resources and Quality for more information. Typically, if bentonite drilling fluid is spilled into saltwater, it flocculates or aggregates into small lumps. The bentonite-water solution has a higher specific gravity than salt or freshwater alone. Consequently, it has a tendency to settle to the Bay bottom, thereby decreasing the complexity of any needed cleanup operations. Potential impacts to fish species at the two directional drill sites are considered adverse, but less than significant and would potentially include temporary localized displacement of fish due to disturbance during drilling.

4.6.3.2.8    Impact from Use of Protective Mattresses. At several locations the cable would either cross existing cable or pipelines, or pass through rocky substrate. Because trenching machines cannot be used in these locations, protective concrete mattresses or comparable materials would be used to provide cable cover. Where an existing cable or pipeline is exposed, protective mattresses would be placed on the Bay floor on top of the existing pipe or cable before the cable is laid in order to provide a physical separation between the utility to be crossed and the Project cable bundle.

Placement of protective mattresses would bury the benthic community beneath the mattress. New communities would be expected to recolonize over time. However, the type of organisms recolonizing over the mattresses may differ from the original benthic community if portions of the original substrate were soft sediment. In general, however, protective mattresses would only be used in areas where the substrate already consists of hard bottom (and sometimes at existing utility crossings) and the communities recolonizing the new hard bottom created by the mattresses would be expected to be similar to what had occurred previously. This impact is considered adverse, but less than significant.

4.6.3.3    Operations-related Impacts

4.6.3.3.1    Electromagnetic Fields. Operation of the proposed Project would involve transmission of current through both the HVDC and HVAC cable systems between the PG&E Pittsburg substation and the Pittsburg Standard Oil Converter Station site. In this proposed design, external electric fields for both HVDC and HVAC submarine cable systems are practically absent due to their shielded design. The electric field is confined within the insulation. The cable shields (metallic sheath and armor) are directly grounded at both ends. Continuous grounding along the entire length of the cable is achieved due to direct contact with water. Therefore, the cable would be at zero potential with respect to the surrounding earth.

The HVDC and MVDC cables proposed to be buried in the floor of the Bay and for short onshore sections in San Francisco and Pittsburg would develop low-intensity, static magnetic fields approximately equal to the earth's natural magnetic fields. The magnetic fields of the main and return cables would be substantially cancelled due to the fact that the two cables would be bundled closely together. The current flowing in the two cables would be equal, but flow in opposite directions. As a result, the total magnetic field on the Bay floor would be within or near background levels.

Because electrosensitive Elasmobranch fishes (sharks, skates, and rays) can detect the earth's magnetic field and the weak electrical fields produced by biological organisms, they have the potential to detect and respond to the weak electromagnetic fields produced by submarine cables (Gill and Taylor, 2001). A study performed by Gill and Taylor (2001) indicated that the lesser spotted dogfish (Scyliorhinus canicula), a benthic shark, was attracted to electric fields as small as 0.1 micro volt per centimeter (µV/cm), but avoided electric fields at
10 µV/cm.

Model simulations of cable with metallic shielding indicate that the cable does not generate an electric field directly. However, a magnetic field is generated in the local environment. This in turn can generate an induced electric field close to the cable within the range detectable by electrosensitive fish (CMACS, 2003). Burial of the cable does not shield the magnetic field. However the strongest electric and magnetic fields occur within millimeters of the cable (CMACS, 2003). Burying the cable or covering it with protective mattresses provides a physical barrier and keeps organisms at a distance.

Whitehead (2002) conducted field measurements of the electrical characteristics of coastal waters of the Cook Strait (New Zealand) in the immediate vicinity of the Transpower Te Hikowhenua HVDC Cable System. A second element of the study was to document the presence of sharks and rays in the vicinity of the submarine cable to determine the potential effects of the cable system on distribution of these species. The study concluded that the operational multi-cable system did not disturb the general ecology and behavior of sharks and rays in the waters surrounding the system. The Basslink Project was laid between Victoria and Tasmania, in Australia and is similar to the proposed Trans Bay Cable Project. Studies cited in the Basslink Project environmental report (Basslink, 2002) conclude that impacts from magnetic fields from existing buried HVDC cable systems had no significant impacts on marine invertebrates, or fish, including electrosensitive species such as sharks, skates, and rays.

The shielding is designed so that the cable shall emit no electric field. The cable would be buried to a target depth of 1 to 2 meters (3 to 6 feet) below the Bay floor, which would provide an additional physical barrier and distance between organisms and any field produced. Effects from the potential EMF fields produced by the submarine cable are considered potentially adverse, but less than significant.

4.6.3.3.2    Heat Generation Cable During Cable Operation. Operation of the HVDC transmission cable would produce heating of the cable. The temperature at the surface of the cable is expected to operate at about 40°C. The external temperature drop in the area surrounding the cable is logarithmic, and the temperature in the sediments would dissipate rapidly with distance from the cable bundle. Appendix F includes an analysis of potential heating of the Bay sediment overlying the cable. This analysis shows that for the DC cable, heating in the top 20 centimeters of sediment would be minimal, with no temperature increase near the surface, increasing to approximately 0.5°C above ambient at a depth of 20 centimeters (Appendix F). The top 10 to 20 centimeters of sediment is usually considered the zone where most benthic organisms reside. This small increase in sediment temperature is not expected to significantly impact benthic communities in the sediments overlying the cable. The temperature of the cable bundle buried to 1 meter in the seabed would not influence overlying Bay water temperature.

Appendix F also provides calculations for potential warming of concrete pillows, in areas where those need to be used to armor the cable. The calculations show that heating of the surface of the concrete pillows would be less than 1°C over the ambient temperature and no warming of Bay water would occur.

Marine growths around similar HVDC cables have been studied. Boffa Miskell Partners (1998) examined the marine growths that developed near submarine HDVC cables in Cook Strait, New Zealand. The cables were found to be colonized with the same species that occurred in nearby areas. No enhancement of growth over the cables was recorded, though it had been thought that the slight temperature increases associated with the cables might have encouraged growth.

The HVAC line would operate at a higher temperature than the HVDC cable. As discussed in Appendix F, sediment temperature in the area of the HVAC cable would average less than 1°C above ambient in the top 10 centimeters and would be as much as 3°C above ambient at 20 centimeters (Appendix F). The temperature increase would occur over a small area above the cable, a strip of approximately 1 meter in width or less. Ambient water temperatures for the Bay range from about 11°C to 17°C and surficial sediment temperatures are assumed to be roughly the same. The slight increase in temperature would not approach upper tolerable temperatures for benthic organisms which, according to the literature, range from about 25°C to 35°C depending on the species (Stantec Consulting Ltd., 2003). The slight increase in temperature of the surficial sediments may cause either an increase or decrease in the abundance of benthic organisms or may result in a slight change in the species composition in the sediments overlying the HVAC cable. As discussed, temperature changes would be limited to the immediate vicinity of the cable (an area of approximately 1 meter or less). Changes to the benthos, if any, from sediment warming due to operation of the HVAC cable are expected to be adverse, but less than significant. The HVAC cable would not cause warming of Bay water due to the large mass of moving water overlying the cable.

4.6.3.3.3    Maintenance Activities. The transmission cable is not expected to require scheduled maintenance over the anticipated 40-year life of the Project. The bundled cable would be monitored by computer and inspected periodically for any signs that would indicate external damage. If damage to the cable occurs, that section would be removed and a new, spare piece of the original cable would be spliced into the existing cable. Impacts from the repair would be similar to those of original construction, though over a much smaller area. Impacts from cable repair are considered adverse, but less than significant.

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