A Scientific Assessment of Alternatives for Reducing Water Management Effects on Threatened and Endangered Fishes in California's Bay-Delta (2010)

Declines in the listed species must be considered in the context of the many changes that are occurring in the “baseline” factors in the region. While the CVP and SWP pumps kill fish, no scientific study has demonstrated that pumping in the south delta is the most important or the only factor accounting for the delta-smelt population decline. Therefore, the multiple other stressors that are affecting fish in the delta environment as well as in the other environments they occupy during their lives must be considered, as well as their comparative importance with respect to the effects of export pumping. These factors and their impacts, only some of which originate within the delta itself, will be described in greater detail in the committee’s second report. Some are described here to highlight their potential importance and to underscore that a holistic approach to managing the ecology of imperiled fishes in the delta will be required if species declines are to be reversed. The factors described here are not meant to be exhaustive, but are intended to demonstrate that the effects of these factors are numerous and, in some cases, not only potentially very important but also under-characterized. Moreover, while individual relationships with these stress factors are generally weakly understood, the cumulative or interactive effects of these factors with each other and with water exports are virtually unknown and unexplored (Sommer et al., 2007).

It has long been recognized that contaminants are present in the delta, have had impacts on the fishes, and may be increasing (Davis et al., 2003; Edmunds et al., 1999; Linville et al., 2002). Contamination of runoff from agricultural use of pesticides has been documented and has been shown to affect invertebrates and other prey, as well as on some life stages of fish (e.g., Giddings, 2000; Kuivila and Foe, 1995; Weston et al., 2004). Kuivila and Moon (2004) found

that larval and juvenile delta smelt coincide with elevated levels of pesticides in the spring. Pyrethroid insecticide use has increased in recent years. Such insecticides have been found in higher concentrations in runoff, and may be toxic to macroinvertebrates in the sediment (Weston et al., 2004, 2005); it is toxic to the amphipod Hyalella azteca, which is found in the delta (Weston and Lydy, 2010). The use of pyrethroids increased substantially in the recent years during which the decline of pelagic organisms in the delta became a serious concern as compared to earlier decades (Oros and Werner, 2005). Among other identified contaminants that may also have effects are selenium and mercury. Histopathological studies have shown a range of effects, from little to no effect (Foott et al., 2006) to significant evidence of impairment depending on species, timing, and contaminant biomarker.

Nutrients have received recent attention as a potential stress factor for phytoplankton, zooplankton, and fish populations for several reasons. First, research by Wilkerson et al. (2006) and Dugdale et al. (2007) found that phytoplankton (diatom) growth in mesocosm experiments did not occur under in situ ammonium levels, and only increased when ammonium levels were reduced. They interpreted this finding to mean that diatom growth was suppressed under ambient ammonium levels, and only after ammonium concentrations began to be drawn down did diatoms begin to use nitrate, an alternate nitrogen form, and then proliferate.

With respect to nutrient loading effects, declines in phosphate loading may be related to declines in chlorophyll-a throughout the Sacramento-San Joaquin delta (Van Niewenhuyse, 2007). While these results show that chlorophyll-a in the water column declined coincident with the decline in phosphate in 1996, phosphate levels, both inorganic and organic, are not at extremely low concentrations in the water. Nevertheless, the effects of the rapid and substantial change in the ratio of inorganic nitrogen to inorganic phosphate in the system have yet to be adequately explored.

Significant changes in the food web may have affected food abundance and food quality available to delta smelt. From changes in zooplankton to declines in chlorophyll to increases in submerged aquatic vegetation, these changes have

enormous effects on the amount and quality of food potentially available for various fish species (e.g., Bouley and Kimmerer, 2006; Muller-Solger et al., 2006). The benthic community was significantly changed after the overbite clam, Corbula amurense, became dominant in the late 1980s; such changes have effects on food availability that may cascade through the food web to affect the abundance of delta smelt.

In addition to changes in food availability, other changes in the food web have had potentially large impacts on smelt. Since 1999, blooms of the cyano-bacterium Microcystis have increased and are especially common in the central delta when water temperatures exceed 20°C (Lehman et al., 2005). Although delta smelt may not be in the central delta during the period of maximum Microcystis abundance, during dry years the spread of Microcystis extends well into the western delta so that the zone of influence may be greater than previously thought (Lehman et al., 2008). Most recently it has been demonstrated that the Microcystis toxin, microcystin, not only is present in water and in zooplankton, but histopathological studies have shown liver tissue impacts on striped bass and silversides (Lehman et al., 2010).

The delta is a substantially altered ecosystem, and that applies to the fish species present as well. Some environmental changes likely enhance the spread of nonnative species (for example warm, irregularly flowing water around dams or diversions can favor warm-water species) (FWS, 2008, p. 147), as can the presence of riprap to support banks (Michny and Hampton, 1984). Thus, the spread of nonnative species may be, at least in part, an effect of other ecosystem changes. Once nonnative species become established, they further alter the ecosystem. Some species, such as American shad (Alosa sapidissima) and striped bass (Morone saxatilis), native to the Atlantic and Gulf coasts of North America, have been present in the delta region since the late 19^th century (Lampman, 1946; Moyle, 2002). Striped bass (along with the native Sacramento pikeminnow, Ptychocheilus grandis) have been implicated as predators on juvenile Chinook salmon, especially when they congregate below the Red Bluff Diversion Dam (Tucker et al., 2003) and other structures; at the Suisun Marsh Salinity Control Gates they were the dominant predator on juvenile Chinook salmon (Edwards et al., 1996; Tillman et al., 1996). Other introductions are more recent, and some might be more threatening to native species. For example, the silverside, Menidia beryllina, is becoming more widespread in the delta and

likely preys on juvenile delta smelt (Moyle, 2002) or competes for similar copepod prey (Bennett and Moyle, 1996). Largemouth bass (Micropterus salmoides) and many other members of its family (Centrarchidae), along with various species of catfish (family Siluridae), native to the Mississippi and Atlantic drainages, also are increasing, while the lone member of the centrarchid family that was native to the region, the Sacramento perch (Archoplites interruptus), no longer occurs in the delta (Moyle, 2002). All the above species include fish in their diets to a greater or lesser degree, including various life stages of delta smelt at times. In addition, other species, such as common carp (Cyprinus carpio) and threadfin shad (Dorosoma petenense), are not significant piscivores, but likely compete with delta smelt for food or otherwise affect their environment. Finally, the wakasagi (Hypomesus nipponensis), an introduced Japanese smelt very similar to the delta smelt, is becoming increasingly widespread in the delta. It interbreeds and competes with the delta smelt and might prey on it, and its presence in the delta complicates the assessment of delta smelt populations and salvage because it is so similar to the delta smelt that it is not easy to distinguish between the two species (Moyle, 2002). Delta smelt have co-existed with many of these alien fishes for more than 100 years before the recent declines, and so the decline of smelt cannot be attributed entirely to their presence, but some species have increased recently and their effects on smelt and salmonids—including on the potential for smelt populations to recover—have not been well studied.

Clark (1929) estimated that 80 percent of the original spawning habitat available to Chinook salmon in California’s Central Valley had been made unavailable by blockages, mainly dams, by 1928. A similar loss of habitat has occurred for Central Valley steelhead as well (Lindley et al., 2006). Dams, diversion points, gates, and screens also affect green sturgeon. Ocean conditions vary, and in general they fluctuate between periods of relatively high productivity for salmon and lower productivity (Hare et al., 1999; Mantua and Hare, 2002). Lindley et al. (2009) concluded that ocean conditions have recently been poor for salmon, although there has been a long-term, steady deterioration in freshwater and estuarine environments as well. Sport and commercial fishing for salmon, sturgeon, and steelhead has been tightly regulated both at sea and in freshwater, and in 2008, there was a complete closure of the commercial and recreational fishery for Chinook salmon (NMFS, 2009, p. 145). However, Chi-

nook salmon make very long oceanic migrations and their bycatch in other fisheries cannot be totally eliminated (NRC, 2005). Hatchery operations have been controversial, but it is almost impossible to operate hatcheries without adverse genetic and even ecological effects on salmon (NRC, 2004b; NMFS, 2009, p. 143) or steelhead (NMFS, 2009, p. 143).

Histopathological studies have revealed a range of diseases of potential concern in the delta. For example, parasites have been found in threadfin shad gills, but not at a high enough infection rate to be of alarm, but evidence from endrocrine disruption analyses shows some degree of intersex delta smelt males, having immature oocytes in the testes (Anderson et al., 2003). Other investigators have found myxosporean infections in yellowfin goby in Suisun Marsh (Baxa et al., In Progress). These and other measures suggest that parasitic infections, viral infections, or other infections are affecting fish, and that interactions with other stressors, such as contaminants, may be having increasing effects on fish.

Climate change could have severe negative consequences for the listed fishes. There are at least three reasons why this is of concern. First, the recent meteorological trend has runoff from the Sierra Nevada shifting from spring to winter as more precipitation falls as rain rather than snow, and as snowmelt occurs earlier and faster because of warming, increasing the likelihood and frequency of winter floods and altered hydrographs, and thus changes in the salinity of delta water (Knowles and Cayan, 2002, 2004; Roos, 1987, 1991). Alteration of precipitation type and timing of runoff may affect patterns in reproduction of the smelt and migration of salmon and sturgeon (Moyle, 2002). Additionally, effects of sea-level rise will increase salinity intrusion further upstream, again impacting fish distributions that rely on salinity gradients to define habitat; their habitat will be reduced. Lastly, as climate warms, so too does the water. This will impact fish distributions in several ways. Temperature is a cue for many biological processes, so many stages of the life cycle are likely to be affected. Moreover, warmer water will mean proportionately more days in which the temperature is in the lethal range, ~25^oC (Swanson et al., 2000). The effects of these climate consequences are less suitable habitat for delta smelt in future

years as well as threats to the migration of anadromous species like salmon and sturgeon.

Based on the evidence summarized above, the committee agreed that the adverse effects of all the other stressors on the listed fishes are potentially large. Time did not permit full exploration of this issue in this intense first phase of the committee’s study. The committee will explore this issue more thoroughly in its second report.