SUISUN MARSH FISH STUDY Trends in Fish and Invertebrate Populations of Suisun Marsh January 2011 - December 2011 Annual Report for the California Department of Water Resources Sacramento, California Teejay A. O'Rear and Peter B. Moyle Department of Wildlife, Fish, and Conservation Biology University of California, Davis July 2012 SUMMARY Suisun Marsh, at the geographic center of the San Francisco Estuary, is important habitat for introduced and native fishes. With funding from the California Department of Water Resources (DWR), the University of California, Davis, Suisun Marsh Fish Study has systematically monitored the marsh's fish populations since 1980. The purpose of the study has been to determine the environmental factors affecting fish abundance and distribution within the context of evolving water management. In 2011, we conducted 259 otter trawls and 74 beach seines. Our catches of plankton- feeding macroinvertebrates and fishes were strongly influenced by the interaction of high Delta outflows, low salinities, and the cold winter and spring. The prolonged low salinities severely reduced the population of overbite clams (Potamocorbula amurensis) in the southwest marsh, in addition to delaying the appearance of Black Sea jellyfish (Maeotias marginata) medusae until very late in the year. Species that ultimately benefit from high flows for spawning, due to either increased floodplain inundation [e.g., Sacramento splittail (Pogonichthys macrolepidotus)] or reduced salinities [e.g., white catfish (Ameiurus catus)], recruited to the marsh in high numbers. Additionally, delta smelt (Hypomesus transpacificus) reached their highest abundance in the marsh since 2001, which was likely due to the combination of (1) high flows both reducing entrainment and promoting plankton blooms, (2) colder water during spring creating more favorable spawning conditions, and (3) appropriate temperatures and salinities occurring in the marsh during autumn. Cold temperatures in the first part of the year delayed reproductive development of introduced fishes such as striped bass (Morone saxatilis) and Mississippi silverside (Menidia audens). In the case of striped bass, young-of-year fish arrived in the marsh later than in average years and after mysids, their primary prey, had already declined to low levels; consequently, there was a mismatch in timing between predator and prey. This mismatch probably increased mortality of young striped bass, leading to their reduced abundance in our otter trawls, and forced a greater proportion of these fish inshore, which was reflected in an increase in their numbers in our beach seines. As in 2010, cold temperatures truncated the spawning period and increased mortality of Mississippi silverside, with the effect that they reached their lowest abundance since 1998. The end result was that native species comprised a greater proportion of the macroinvertebrate and fish assemblages in 2011 relative to recent years. We were also able to sample two areas during spring to which we previously have not had access: the upper Cordelia Slough complex and a duck-club ditch. The Cordelia Slough sampling reflected a fish community primarily structured by a salinity gradient, with salt-intolerant species more abundant in reaches influenced by freshwater flows. Sampling in the duck club ditch showed high abundances of small fish, reflecting the high productivity of these habitats. However, the fish assemblages in different parts of the ditch revealed that a water control structure was limiting larger, older fish to just part of the ditch. 2 TABLE OF CONTENTS Introduction………………………………………………………………………………..….….4 Methods………………………………………………………………………………….…….….7 Results and Discussion……………………………………………………………………….....13 Abiotic Conditions...........................................................................................................13 Trends in Invertebrate Abundance and Distribution..................................................17 Trends in Fish Distribution and Abundance.................................................................20 Cordelia Slough Complex................................................................................................37 Tule Red Duck Club........................................................................................................39 Conclusions……………………………………………………………………………………...42 References……………………………………………………………………………………….43 Appendices………………………………………………………………………………………47 3 INTRODUCTION Suisun Marsh is a brackish-water marsh bordering the northern edge of Suisun, Grizzly, and Honker bays in the San Francisco Estuary (Figure 1); it is the largest uninterrupted expanse of estuarine marsh remaining on the western coast of the contiguous United States (Moyle et al. 1986). Most of the marsh area is diked wetlands managed for waterfowl, with the rest of the acreage consisting of tidal sloughs and marsh plain (DWR 2001). The marsh's central location in the San Francisco Estuary makes it an important nursery for salt-tolerant-freshwater, estuarine, and marine fishes. Figure 1. Suisun Marsh and Bay (from Schroeter et al. 2006). In January 1979, DWR contracted with UC Davis to monitor fish populations in Suisun Marsh. Since 1979, monitoring has remained continuous and in compliance with regulatory requirements of (1) the San Francisco Bay Conservation and Development Commission 4-84 (M) Special Condition B, (2) the US Army Corps of Engineers 16223E58B Special Condition 1, and (3) the Revised Suisun Marsh Monitoring Agreement (Agreement Number 4600000634). The study has used two primary methods for sampling fishes: beach seines and otter trawls. Juveniles and adults of all species have been surveyed systematically since 1980; between 1994 and 1999, larval fishes were also surveyed to better understand their ecology in the marsh (Matern and Meng 2001). Other objectives have included (1) evaluating the effects of the Suisun Marsh Salinity Control Gates on fishes (Matern et al. 2002), which began operating in 1988 4 (DWR 2001); (2) examining long-term changes in the Suisun Marsh ecosystem in relation to other changes in the San Francisco Estuary; and (3) enhancing understanding of the life history and ecology of key species in the marsh. Secondary objectives have included supporting research by other investigators through special collections; providing background information for in-depth studies of other aspects of the Suisun Marsh aquatic ecosystem (e.g., studies of jellyfish biology); contributing to the general understanding of estuarine systems through publication of peer-reviewed papers; training undergraduate and graduate students in estuarine studies and fish sampling; and providing a venue for managers and biologists interested in the marsh to experience it firsthand. The project also collected fish for studies on (1) documenting predation on delta smelt by Mississippi silverside and striped bass via DNA techniques, (2) American shad (Alosa sapidissima) life history and distribution using genetic analyses, (3) sexual behavior of tule perch (Hysterocarpus traski), (4) longfin smelt (Spirinchus thaleichthys) ecology through otolith chemistry, (5) food-web structure using stable isotopes, and (6) fatty-acid composition of key zooplankton species. Additionally, the long-term dataset is currently being used to (1) model delta and longfin smelt population dynamics, (2) study trends in near-shore fish assemblages along the San Francisco Estuary's longitudinal axis, (3) inform wetland restoration in the western marsh, and (4) compare the biomass of marsh fishes to those in the bays. Data collected by the study has also been used to inform future management of the San Francisco Estuary for the benefit of native fishes (Moyle et al. 2012a) and to compare fish assemblages along the estuary's salinity gradient (Moyle et al. 2012b). Moyle et al. (1986) evaluated the first five years of data collected by the study and found three groups of species that exhibited seasonal trends in abundance, primarily due to recruitment. The structure of the fish community was relatively constant through time; however, total fish abundance declined over the five years. The decline was partly due to strong cohorts early in the study period, which was followed by both extremely high river flows and drought that resulted in poor recruitment. The authors also found that native fishes tended to be more prevalent in small, shallow sloughs, while introduced species were more prominent in large sloughs. Meng et al. (1994) incorporated eight more years into their study, which revealed that the fish assemblage structure was less constant over the longer time period than the earlier study indicated. Additionally, introduced fishes had become more common in small, shallow sloughs, possibly as a result of drought and high exports allowing increased salinities in the marsh and depressing reproductive success of native fishes. Like Moyle et al. (1986), Meng et al. (1994) found a general decline in total fish abundance (particularly in the native fishes) through time. Matern et al. (2002) found results similar to Meng et al. (1994): fish diversity was highest in small sloughs, and native fish abundances continued to decrease. In recent years, O'Rear and Moyle (2010, 2009, 2008) have bolstered the findings of previous studies and documented changes that appear to be happening in other parts of the estuary. For instance, the timing, variability, and magnitude of Delta outflow continue to be important factors affecting the