Dissolved Oxygen Depletion in the Stockton Deep Water Ship Channel: Biological and Ecological Effects Conceptual Model

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Secondary Driver: Existence and Accessibility
of Alternative Habitats

Jump down this page to: Steelhead | Chinook Salmon | Delta Smelt | Longfin Smelt | Sacramento Splittail | White Sturgeon | Green Sturgeon | Striped Bass

General Effects

The DWSC may function as different fish habitat depending on the species and life stage of the fish using it. For some fish, the DWSC functions mainly as a migratory pathway to upstream spawning locations. Alternatively, this same area may constitute important rearing habitat for other fish during their journey to the lower Delta. The threshold oxygen concentration at which a species begins to seek alternative habitat relative to the lethal oxygen concentration will depend on the energy costs and tradeoffs among the risk of mortality from low oxygen, risk of mortality from predation, and loss of reproductive and feeding opportunities (Breitburg 2002). Additionally, the presence and accessibility of alternative habitats to the DWSC must be determined in the context of the life history and habitat requirements of each species, as ability to tolerate low DO concentrations varies greatly among life stages and species.

The extent of habitat lost as a result of DO concentration sags in the DWSC will depend on the severity of the low DO concentrations and the physiological tolerances and behaviors of the fish species affected (Breitburg 2002). For certain species, the DWSC functions mainly as a migration corridor through which fish move on their way to upstream spawning grounds. The importance of such a migration pathway to the completion of a speciesí life history is different for individual species. Chinook salmon return to their natal streams and spawn only one time during their lives. If the DWSC became impassable to Chinook salmon, it could prevent spawning of an entire year class of fish. Alternatively, white sturgeon are known to spawn multiple times in one lifespan and often swim long distances in search of suitable habitat. If the DWSC became impassable to sturgeon, it may not be a critical impact on the species. Alternatively for longfin smelt, which live most of their lives throughout brackish to marine waters of the Delta, the DWSC may not be significant to any life stage. In this case, the question of alternative habitats may not apply.

The existence of alternative habitats and the energy costs associated with reaching those habitats are different for each species. For homing species like Chinook salmon and steelhead that require very specific spawning and rearing habitats found in the upper San Joaquin River and its tributaries, alternative habitats may not truly exist if the DWSC is uninhabitable, largely because of the inherent life history requirements of the species. For striped bass, however, a species much more plastic in its homing behavior and more able to tolerate low DO concentrations, alternative spawning habitat readily exists downstream of the DWSC, where the bulk of spawning occurs in most years. Because such alternative habitat is close, striped bass invest less energy to reach it. For other species such as sturgeon, which require a large river system for successful spawning, the energy requirements of a long migration to the Sacramento River are much more costly. The extent of habitat loss in a coastal system such as the Delta is often much greater than just the areas of lethal conditions. Fish will avoid areas of lethal conditions, areas that would require increased energy expenditure for ventilation, and areas where conditions could reduce growth (Breitburg 2002). Breitburg (2002) found that fish avoided oxygen concentrations two to three times higher than the 24-hour and 96-hour LC50 exposure concentrations.

The concept of alternative habitats and their accessibility must also be considered in the context of life stage. Adult and juvenile fish usually have well-developed swimming abilities. For larvae subject to river or tidal currents, such as those of striped bass, avoiding low DO concentrations may not be possible. In this instance, the accessibility of alternative habits becomes moot, even if such habitats exist. When alternative habitats are not accessible or do not exist, unsuitable conditions in the DWSC will have a much greater effect on fish that depend on it for some part of their life history.

Jump to "General Effects" discussion under other Secondary Drivers:
Low DO Tolerance | Occurrence of Sensitive Life Stages | Food Web | Parasites and Pathogens | Toxic Substances | Activity Levels | High Water Temperatures

Species-Specific Effects

Steelhead (Oncorhynchus mykiss)

Hypothesis:

Steelhead adults and juveniles are able to access alternative spawning and rearing habitats in the Sacramento and Mokelumne Rivers.

1. How does this driver operate?

Steelhead adults and juveniles migrating through the lower San Joaquin River and Delta may encounter DO concentrations lower than the regulatory minimum in the DWSC during their upstream and downstream migrations. Alternative migration routes for adults include the Sacramento River and Mokelumne River. Use of these rivers as an alternative habitat by adults originating from tributaries in the lower San Joaquin River would result in straying but may permit successful spawning. Steelhead smolts migrating downstream through the lower San Joaquin River are likely to follow the dominant flow path to the estuary and ocean (Fried et al. 1978 in Meehan 1991) and therefore are not likely to use alternative migration routes once they have reached the ship channel.

2. Are there critical thresholds associated with this driver?

Hicks (2000) summarized the literature on salmonid avoidance and found that salmonids generally avoided DO concentrations of 5 mg/L and below in both field and laboratory studies. Hallock et al. (1970) found evidence that adult Chinook salmon delayed migration in the lower San Joaquin River until DO concentrations increased to 5 mg/L. Adult steelhead may respond similarly to low DO concentrations.

3. How important is this driver?

The importance of this driver for migrating adult or juvenile steelhead is low because the majority of fish migrate during periods when DO concentrations are frequently above the regulatory minimum.

4. How well is this driver understood?

Empirical evidence of the response of adult and juvenile steelhead to low DO concentrations in the DWSC is lacking. A summary of field and laboratory studies indicates that salmonids avoid DO concentrations of 5 mg/L and lower (Hicks 2000).

Jump to "Steelhead" discussion under other Secondary Drivers:
Low DO Tolerance | Occurrence of Sensitive Life Stages | Food Web | Parasites and Pathogens | Toxic Substances | Activity Levels | High Water Temperatures

Chinook Salmon (Oncorhynchus tshawytscha)

Hypothesis 1:

San Joaquin River Chinook salmon adults are able to access alternative spawning habitats in non-natal rivers such as the Sacramento and Mokelumne Rivers.

Hypothesis 2:

San Joaquin River Chinook salmon smolts are able to migrate downstream through alternative pathways, avoiding the DWSC.

1. How does this driver operate?

Chinook salmon adults may encounter low DO concentrations below the regulatory minimum in the DWSC during their upstream migration to spawning tributaries in the San Joaquin River. Adults may respond to low DO concentrations in the DWSC by altering their migration path and straying to other rivers for spawning.

Chinook salmon smolts may encounter DO concentrations below the regulatory minimum in the DWSC during their downstream migration to the ocean. Smolts may respond to low DO concentrations in the DWSC by altering their migration path and straying to other parts of the Delta to reach the ocean.

2. Are there critical thresholds associated with this driver?

Hallock et al. (1970) found evidence that Chinook salmon delayed migration up the San Joaquin River until DO concentrations in the DWSC increased to 5 mg/L. In the Willamette River, a water temperature of 22.4°C and a minimum DO concentration of 3.3 mg/L caused spring-run Chinook salmon to stop migrating (Alabaster 1988 in McCullough 1999). In a laboratory experiment performed by Whitmore et al. (1960 in Karna 2003), Chinook salmon selected areas of DO concentrations of 9 mg/L or higher over concentrations of 1.5 mg/L. Moderate selection over DO concentrations of 3.5 mg/L was observed, and selection over 4.5 and 6.0 mg/L was detected in some cases.

Flows and export rates in the Delta also may affect the degree of straying. Mesick (2001) found evidence of increased straying of adult Chinook salmon into the Sacramento River and Mokelumne River when water exports in the south Delta exceeded San Joaquin River flows by 300% over a 10-day period in October.

Low DO concentration was not considered a factor in Chinook salmon smolt outmigration patterns through the Delta. Flow was used in determining the travel time from various places in the Delta to the ocean. Increased flows entering the Delta from the San Joaquin River at Vernalis were thought to decrease travel times through the Delta and increase speed toward the ocean. However, this is not true. The main factor determining travel time through the Delta was the size of the smolt. The larger the fish, the shorter the travel time through the Delta (Baker and Morhardt 2001, 173Ė175).

3. How important is this driver?

This may be an important driver because of the potential for overlap in the timing of upstream migration of adult Chinook salmon and the occurrence of low DO concentrations in the DWSC. The ability of adults to access other rivers may permit successful spawning but would reduce the number of adults that spawn in the San Joaquin River system. Avoidance or prolonged delays in migration also could adversely affect spawning success by increasing energy expenditures and reducing the amount of energy available for gonad development and spawning.

This driver may not be important for smolts because during their main outmigration period (January through May) flows are high and DO concentrations are generally more than 5 mg/L.

4. How well is this driver understood?

The relative importance of low DO as a causal factor for migration delays or increased straying is uncertain because of the potential role of other factors such as high water temperatures and export-outflow ratios in the lower San Joaquin River and Delta.

Jump to "Chinook Salmon" discussion under other Secondary Drivers:
Low DO Tolerance | Occurrence of Sensitive Life Stages | Food Web | Parasites and Pathogens | Toxic Substances | Activity Levels | High Water Temperatures

Delta Smelt (Hypomesus transpacificus)

Hypothesis:

Delta smelt that encounter a low-DO plume in the DWSC cannot access most of the alternative spawning habitats in the Delta because their small size and short lifespan limit their ability to swim long distances or spend large amounts of time in search of alternative spawning habitats.

1. How does this driver operate?

The availability of habitat upstream of the DWSC and the extent to which Delta smelt use such habitat are unknown.

The accessibility of alternative habitats is also unknown but is probably low. The ability of delta smelt to swim away from low DO concentrations is partially a function of their swimming ability. Delta smelt display a wide variety of swimming abilities in laboratory tests (Swanson et al. 1998); their small adult size restricts their maximum swimming speed and endurance and limits their ability to swim long distances quickly. Delta smelt are believed to use tidal fluctuations to move (or maintain position) geographically (Aasen 1999; Bennett et al. 2002). Still, it is unlikely that, after encountering a low-DO plume in the DWSC, delta smelt could swim across the Delta to alternative habitats in the northern Delta or southern Sacramento River.

2. Are there critical thresholds associated with this driver?

N/A

3. How important is this driver?

The importance of available alternative habitats to delta smelt is not known because:

  • the fraction of the population that encounters low DO concentrations in the DWSC is not known and
  • the ability of delta smelt to access alternative habitats after encountering low DO concentrations in the DWSC is not known. In addition, the relative value of these alternative habitats compared with those available in and upstream of the DWSC is not known.

4. How well is this driver understood?

Little is known about the ability of delta smelt to detect low DO concentrations and swim or use tides to move away from such concentrations. The accessibility of alternative habitats to delta smelt migrating from the edge of a low-DO plume in the DWSC is unknown.

Jump to "Delta Smelt" discussion under other Secondary Drivers:
Low DO Tolerance | Occurrence of Sensitive Life Stages | Food Web | Parasites and Pathogens | Toxic Substances | Activity Levels | High Water Temperatures

Longfin Smelt (Spirinchus thaleichthys)


Hypothesis:

Longfin smelt that encounter a low-DO plume in the DWSC cannot access most of the alternative spawning habitats in the Delta because their small size and short lifespan limit their ability to swim long distances or spend large amounts of time in search of alternative spawning habitats.

1. How does this driver operate?

In the Delta, longfin smelt spend most of their life cycle in deep, cold, brackish-to-marine waters of the Delta and nearshore environments (Moyle 2002; Rosenfield and Baxter in prep.). They are capable of living their entire life cycle in fresh water, as demonstrated by landlocked populations. These fish are believed to spawn in fresh or slightly brackish water in the Delta. Catches of gravid adults and larval longfin smelt indicate that the primary spawning locations for these fish are in or near the Suisun Bay channel, the Sacramento River channel near Rio Vista, and (at least historically) Suisun Marsh (Wang 1991; Moyle 2002; Rosenfield and Baxter in prep.). These areas serve as viable alternatives to the DWSC habitat for longfin smelt.

The ability of longfin smelt to detect, and move away from, low DO concentrations has not been studied. Similarly, no studies of longfin smelt swimming abilities have been published, although, given their preference for deep, fast-flowing channel environments, they are expected to have better swimming abilities than their distant cousins, delta smelt (Hypomesus transpacificus). Like delta smelt, longfin smelt are believed to use tidal fluctuations to move (or maintain position) geographically (Bennett et al. 2002). Longfin smelt are semelparous spawners; thus, individuals that are delayed in reaching suitable spawning habitat (e.g., by migrating away from a low-DO plume in search of suitable habitat) may not reproduce at all.

2. Are there critical thresholds associated with this driver?

N/A

3. How important is this driver?

The importance of accessible alternative habitats to longfin smelt is not known because (a) the fraction of the population that encounters low DO concentrations in the DWSC is not known, and (b) the ability of longfin smelt to access these alternative habitats after encountering low DO concentrations is not known. In addition, the relative value of these alternative habitats compared with that available in and upstream of the DWSC is not known.

4. How well is this driver understood?

Little is known about the ability of longfin smelt to detect low DO concentrations and swim or use tides to move away from such conditions. The accessibility of alternative habitats to longfin smelt migrating from the edge of a low-DO plume in the DWSC is unknown. The effect of delays in spawning that may be experienced while searching for alternative habitats is also not well understood.

Jump to "Longfin Smelt" discussion under other Secondary Drivers:
Low DO Tolerance | Occurrence of Sensitive Life Stages | Food Web | Parasites and Pathogens Toxic Substances | Activity Levels | High Water Temperatures

Sacramento Splittail (Pogonichthys macrolepidotus)

Hypothesis:

Sacramento splittail that encounter low DO concentrations in the DWSC during spawning migrations will not be able to access alternative habitats in the same spawning season.

1. How does this driver operate?

Sacramento splittail spawning and rearing requirements and locations have received much study in recent years (sources in Sommer et al. unpublished; Moyle et al. 2004). Alternatives to the spawning and rearing habitats located above the DWSC are available elsewhere in the Delta, notably in the Yolo and Sutter Bypasses and the Cosumnes River floodplain.

The accessibility of these alternative habitats to Sacramento splittail migrating from the edge of a low-DO plume in the DWSC and the relative value of these alternative habitats compared with those available upstream of the DWSC are unknown. The long lifespan of Sacramento splittail (up to 10 years, with an average of approximately 5 years) (U.S. Fish and Wildlife Service 1996; Moyle et al. 2004) and their opportunistic spawning habits may enable them to forgo spawning in a particular year, thereby reducing the adverse effects of low DO concentrations, which may block spawning migrations during periods of individual years but not every day of every year.

The ability of Sacramento splittail to detect and move away from low DO concentrations has not been studied. These fish are strong swimmers (as measured by the highest flow in which they can hold their position) (Young and Cech 1996). Swimming ability increases with body size but decreases with acclimation temperature. Therefore, it is unclear whether upstream-migrating adult Sacramento splittail (swimming in relatively cold water) are better able to avoid low DO concentrations than are downstream-migrating juveniles (which swim downstream in warmer late-spring and summer flows). Little is known about the ability of Sacramento splittail to detect and move away from low DO concentrations into alternative habitats.

2. Are there critical thresholds associated with this driver?

N/A

3. How important is this driver?

The importance of available alternative habitats to Sacramento splittail is not known because:

  • the fraction of the population that encounters low DO concentrations in the DWSC is not known and
  • the ability of Sacramento splittail to access these alternative habitats after encountering low DO concentrations is not known.

4. How well is this driver understood?

Sacramento splittail are bottom-dwelling fish that are expected to have encountered low DO concentrations during their evolutionary history. They display increased agitation when exposed to low DO concentrations, indicating that they may detect and swim away from unfavorable DO concentrations (Young and Cech 1996). Their ability to locate alternative spawning habitats within the time constraints imposed by their seasonal spawning requirements is not known. Similarly, the ability of emigrating juveniles (those moving from spawning areas to more brackish parts of the Delta) to delay their downstream migration in order to avoid low DO concentrations in the DWSC is not known.

Jump to "Sacramento Splittail" discussion under other Secondary Drivers:
Low DO Tolerance | Occurrence of Sensitive Life Stages | Food Web | Parasites and Pathogens | Toxic Substances | Activity Levels | High Water Temperatures

White Sturgeon (Acipenser transmontanus)

Hypothesis:

White sturgeon that encounter low DO in the DWSC can access alternative spawning habitats because their swimming abilities and iteroparous spawning behavior (i.e., they can spawn several times during their lifespan) allow them to swim long distances and take significant amounts of time (including, skipping spawning seasons) as they search for alternative spawning habitats.

1. How does this driver operate?

White sturgeon are believed to spawn in areas of deep, fast-flowing water, over gravel or cobble bottoms. The DWSC is on the southeastern edge of the speciesí range and the Central Valley populationís current range; most of the Central Valley populationís spawning occurs in the Sacramento River (Moyle 2002). Thus, alternative habitats do exist when and if low DO in the DWSC restricts white sturgeon use of this area. These large fish are powerful swimmers and could easily move away from low DO concentrations if these conditions triggered such a response. Whether exposure to low DO concentrations actually causes white sturgeon to orient toward higher DO concentrations is unknown.

White sturgeon are iteroparous spawners (i.e., they can spawn several times during their life), and only a small fraction of the adult population spawns in any given year (Moyle 2002). In addition, these fish are very long-lived (with recent recorded ages over 60 years) (Moyle 2002). As a result, if white sturgeon are delayed during their spawning migration (up the San Joaquin, for example) and cannot locate alternative spawning habitats (e.g., the Sacramento River), they are capable of delaying reproduction until a future spawning season. There is some cost to such delays as these fish would be exposed to additional mortality risks before they had another opportunity to spawn.

2. Are there critical thresholds associated with this driver?

N/A

3. How important is this driver?

The importance of available alternative habitats to white sturgeon is not known because (a) the fraction of the population that encounters low DO concentrations in the DWSC is not known, and (b) the ability of white sturgeon to access these alternative habitats after encountering low DO concentrations is not known. In addition, the relative value of these alternative habitats compared with that available in and upstream of the DWSC is not known.

4. How well is this driver understood?

White sturgeon (and sturgeon in general) show pronounced physiological and behavioral responses to low DO concentrations. They are bottom-dwelling fish that presumably are adapted to hypoxic conditions that often occur naturally in benthic environments. Thus, sturgeon can probably detect and orient away from low DO concentrations. Their ability to locate alternative spawning habitats within the time constraints imposed by their seasonal spawning requirements is not known.

Jump to "White Sturgeon" discussion under other Secondary Drivers:
Low DO Tolerance | Occurrence of Sensitive Life Stages | Food Web | Parasites and Pathogens | Toxic Substances | Activity Levels | High Water Temperatures

Green Sturgeon (Acipenser medirostris)

Although little species-specific information is available for green sturgeon, it is likely that information for white sturgeon is generally applicable to green sturgeon.

Jump to "Green Sturgeon" discussion under other Secondary Drivers:
Low DO Tolerance | Occurrence of Sensitive Life Stages | Food Web | Parasites and Pathogens | Toxic Substances | Activity Levels | High Water Temperatures

Striped Bass (Morone saxatilis)

Hypothesis:

The timing and frequency of low DO concentrations (5 mg/L or less) in the DWSC do not prevent adult striped bass from reaching suitable spawning locations in upstream areas of the San Joaquin River and tributaries, such as the Merced, Tuolumne, and Stanislaus Rivers.

1. How does this driver operate?

Although striped bass are known to occur in the San Joaquin River and tributaries upstream of the DWSC, most spawning has been reported to occur in the lowest portions of the San Joaquin River between Antioch and Venice Island (Turner and Chadwick 1972; Stevens et al. 1985; California Department of Fish and Game 2005); spawning may occur farther upstream in the San Joaquin River when flows are high enough to dilute saline agricultural return waters (Turner and Chadwick 1972; Moyle 2002; California Department of Fish and Game 2005). The Merced, Tuolumne, and Stanislaus Rivers may support successful spawning, particularly during wet years when river flows are sufficient to transport larvae to estuarine nursery habitat (Moyle 2002).

During years when flows are too low to adequately dilute lower San Joaquin River flows, adult striped bass likely use other spawning habitats. They may also use alternative spawning habitats when DO concentrations in the DWSC fall low enough to block adult migrations to the upper San Joaquin River. Under these conditions, striped bass that may have otherwise spawned upstream of the DWSC may spawn lower in the San Joaquin River. Evidence from the Sacramento River indicates that striped bass exhibit at least moderate homing behavior to their natal rivers in California (Chadwick 1967). Genetic evidence suggests striped bass in eastern systems exhibit homing behavior (Wirgin et al. 1997; Bulak et al. 2004) but that sufficient numbers of fish may stray to homogenize genetic differences across nearby systems (Sidell et al. 1980). Given a tendency to home to natal rivers, striped bass would be expected to still attempt to spawn in the San Joaquin River. It is not known whether and to what extent low DO concentrations might increase straying rates to other rivers, such as the Mokelumne and Sacramento Rivers.

Migrating adults have some flexibility in selecting alternative habitats when encountering poor habitat conditions. However, larval striped bass have little ability to avoid poor conditions because of their need to reach productive estuarine habitat and their limited swimming ability. For striped bass eggs and larvae originating from spawning upstream of the DWSC, low DO concentrations in the DWSC could result in high mortality of eggs and larvae during their downstream dispersal to estuarine rearing areas. Juveniles that encounter low DO concentrations in the DWSC may be better able to avoid these waters until conditions improve. Whether conditions above the DWSC are adequate to substitute for typical estuarine rearing habitats found downstream of the DWSC is unknown.

2. Are there critical thresholds associated with this driver?

The availability of alternative habitats may be closely related to the magnitude of freshwater flows. Recent studies suggest striped bass migrate through the DWSC on their way to spawning grounds only during wet years, when river flows are high enough to dilute saline agricultural return waters in the San Joaquin River (Turner and Chadwick 1972; Moyle 2002; California Department of Fish and Game 2005). In drier years, striped bass may avoid the lower San Joaquin River and seek out other rivers for spawning. The minimum flows needed to attract striped bass to spawning locations above the DWSC or other rivers are unknown. Although striped bass are known to frequent tributaries such as the Stanislaus, Merced, and Tuolumne Rivers, the required flows necessary to support successful spawning in these streams are unknown.

3. How important is this driver?

This driver could be important but its impact is unknown because the relative contribution of striped bass spawning upstream of the DWSC to overall population levels is unknown. The potential for population-level effects is determined by the numbers of adults spawning upstream of the DWSC, the numbers of larvae and juveniles exposed to low DO concentrations in the DWSC, and the ability of adults to use alternative spawning habitats.

4. How well is this driver understood?

This driver is not well understood because little information is available to describe the conditions under which striped bass successfully migrate through and spawn above the DWSC. Additionally, little is known about the distribution and abundance of striped bass in the San Joaquin River and its tributaries above the DWSC. Long-term monitoring data collected by DFG do indicate that several sizes of striped bass use the DWSC, at least seasonally. Thus, there is evidence of the occurrence of striped bass in the DWSC but sparse data to evaluate the importance of low DO concentrations or alternative habitats in determining spawning and recruitment success.

Jump to "Striped Bass" discussion under other Secondary Drivers:
Low DO Tolerance | Occurrence of Sensitive Life Stages | Food Web | Parasites and Pathogens | Toxic Substances | Activity Levels | High Water Temperatures