Use of a restored Central California floodplain by larvae of native and alien fishes Patrick K Crain* Department of Wildlife, Fish, and Conservation Biology, University of California, 1 Shields Avenue, Davis CA 95616, U.S.A. Keith Whitener The Nature Conservancy, Cosumnes River Preserve, 13501 Franklin Blvd., Galt CA 95632 Peter B. Moyle Department of Wildlife, Fish, and Conservation Biology, University of California, 1 Shields Avenue, Davis CA 95616, U.S.A. 2 Abstract. We sampled larval fish in 1999 and 2001 on a restored floodplain along the lower Cosumnes River, California, from the onset of flooding to when the sites dried up or when larval fish became rare. We collected over 13,000 fish, of which prickly sculpin Cottus asper made up the majority (73%). Eleven species made up 99% of the catch. Three native fishes (prickly sculpin, Sacramento sucker Catostomus occidentalis, and Sacramento splittail Pogonichthys macrolepidotus) and two alien species (common carp Cyprinus carpio and bigscale logperch Percina macrolepida) were associated with higher inundation and associated cool temperatures of early Spring. In contrast, six other alien taxa , sunfish Lepomis spp., largemouth bass Micropterus salmoides, crappie Pomoxis spp. , golden shiner Notemigonus crysoleucas, and inland silverside Menidia beryllina were associated with less inundation and warmer water temperatures. One native species, Sacramento blackfish Orthodon microlepidotus, was also associated with these conditions. Species did not show strong associations with habitat because of different spawning times of adults and expansion and contraction of flood waters. Most species could be found at all sites throughout the flooded areas, although river and floodplain spawning fishes usually dominated sites closest to levee breaches. Highest species richness was consistently found in two sloughs with permanent water, because they both received drainage water from the floodplain and had a complement of resident species. Splittail, an obligate floodplain spawner, was found primarily in association with submerged annual plants. Our results suggest that a natural hydrological cycle in the Spring is important for providing flooding and cool temperatures required by many native larval fishes. Alien fishes are favored if low flows and higher temperatures prevail. Restoration of populations of native fishes that use floodplains for rearing should emphasize early (February-April) flooding followed by rapid draining to prevent alien fishes from becoming abundant. 3 Floodplains are important spawning and nursery habitats for many fishes (Welcomme 1979, Bayley 1995, Sparks 1995). Seasonal spawning and rearing habitat is made available when terrestrial vegetation becomes inundated by flood waters. Floodplains are important nursery habitats because they provide abundant small invertebrates for food (Holland and Huston 1985), sanctuary from unfavorable temperatures and high velocity river currents (Holland 1986), and cover from predators (Paller 1987). Many of the habitats available to fishes change seasonally in relation to the ebb and flow of flood waters, resulting in successional shifts in the use of floodplains by fishes (Winemiller 1989). In California, the importance of floodplain habitats to fishes has not been appreciated until recently, although native fishes are adapted to seasonal inundation of valley flood lands, a major event in pre-water development times (Sommer et al. 2001). Rain and snowmelt occur mainly in winter and spring and native riverine fishes spawn during periods of high flow from February through early May (Marchetti and Moyle 2000, Moyle 2002). Historically, the high flows provided both access to upstream spawning areas and created extensive flooded habitat for rearing. Today dams and diversions have altered the natural flow regimes in most California rivers, with most high flows captured in reservoirs (Moyle 2002). Floodplains have become separated from rivers through channelization and levee construction and heavily developed for agricultural and urban uses (Mount 1995, Rasmussen 1996). The combination of altered flows and reduced habitats has been a major factor in the decline of the native fish fauna of California (Moyle 2002). An additional problem has been the invasion of many alien fishes that are favored by the altered habitats (Moyle 2002). This high degree of habitat loss has greatly enhanced the significance of remnant floodplain habitat (Sommer et al. 2001), such as that found along the lower Cosumnes River in central California. The Cosumnes River is the largest stream 4 flowing into California’s Central Valley without a major dam on its main stem (Florsheim and Mount 2002). Because the Cosumnes River still maintains its natural hydrograph during winter and spring, a major floodplain restoration effort along the lower river has been undertaken by The Nature Conservancy (TNC) and various state and federal agencies (Florsheim and Mount 2002). Levees were breached in five places to allow seasonal flooding of a mosaic of habitat types including rice paddies, oak woodland, willow and cottonwood riparian forest, grasslands, marshlands, and sloughs. We initiated a study in February 1999 to study use of the restored floodplain habitat by larval native and alien fishes. The goals of our study were to (1) compare fish use of different habitats within the floodplain, (2) assess temporal trends in abundance of native and alien species, and (3) characterize the environment in relation to use by larval fish. Special attention was paid to the use of floodplain habitat by native fishes including Sacramento splittail Pogonichthys macrolepidotus for spawning and rearing because it is listed as a federal threatened species (Moyle 2002) and is a floodplain-dependent species (Sommer et al. 1997, 2001, 2002). Study Site The Cosumnes River Preserve (CRP) is located in south Sacramento County bordering the Cosumnes River. It is a large (5,261 hectares) mosaic of floodplain and surrounding uplands (Florsheim and Mount 2002). The preserve has some of the best remaining examples of Central Valley freshwater wetlands, cottonwood-willow riparian corridors, and valley oak riparian forests. The preserve also contains managed farmlands and diked waterfowl ponds, together with annual grasslands interspersed with vernal pools. The CRP is located just upstream (0.5 km) of the confluence of the Cosumnes River and the Mokelumne River (Figure 1). The preserve encompasses three major tidally influenced freshwater sloughs, Middle Slough, 5 Tihuechemne Slough, and Wood Duck Slough. During high flows a large portion of the overland flow exits through Middle Slough into the North Delta (upper San Francisco Estuary). Wood Duck Slough penetrates the middle of the floodplain area and also acts as a conveyor of overland flow during periods of high inundation. Tiechumne Slough sits in between Wood Duck Slough and Middle Slough. It is very similar to Wood Duck Slough in that it bisects the floodplain and conveys overland flow during high flow events. It was not used as a sampling site because access to it was very difficult during high flooding. The extent of flooding is highly variable from year to (Figure 2). In 1999 the river was connected to the floodplain for 135 days and in 2001 for 88 days (Wendy Trowbridge, University of California, Davis unpublished data). Five sampling sites were chosen on the basis of representativeness of habitats and accessibility during flood events (Figure 1): (1) Middle Slough; (2) Wood Duck Slough; (3 and 4) two flood plain sites near levee breaches; and (5) the Cosumnes River adjacent to the floodplain. Another site, only sampled in 1999, was in a ditch that ran perpendicular between the floodplain sites and acted as a catch basin when floodplain waters receded. Methods Field methods. Sampling was conducted in 1999 and 2001 and began with the onset of flooding and terminated when the site dried up or larval fish became rare in samples. In 1999 samples were collected on a weekly basis with Middle Slough and the river site collection beginning on February 9 and ending the end of July (24 weeks). Wood Duck Slough sampling started on February 23 and extended through July (22 weeks). The floodplain site opposite the upper breaches was sampled from February 23 through May 11 (11 weeks). The ditch site was started on March 16 and extended through June 22 (14 weeks). The floodplain site opposite the lower breaches was begun on March 9 and extended through May 25 (12 weeks). In 2001 all 6 sites were started on February 20 except the lower breach floodplain site, which was started on March 1. All sampling was terminated on July 5 (20-21 weeks). At each site light traps were used following the design of Kissick (1993) with the following modifications (Marchetti and Moyle 2000): the openings leading into the traps had 5-mm wide slots on each side, the traps were equipped with extra foam to allow them to float, and the light source used was a waterproof flashlight (2 cell, D size). For each sample date in both years, a single light trap was placed out in each site at least one hour after sunset. Traps were placed out in succession so that each trap could be picked up after 60 minutes of illumination. At each site surface water temperature, pH (1999 only), and conductivity (µS) were measured using a Hanna HI991300 portable meter. Water clarity was measured during daylight hours prior to sampling to the nearest cm using a 10 cm secchi disk. The presence or absence of velocity was determined using a small dip net; any ballooning represented the presence of current. River discharge data were obtained from the USGS gage at Michigan Bar, approximately 58 km upstream. Depth was measured to the nearest centimeter. Percentages of different substrates (silt, mud, clay, sand, gravel, and cobble) and of bottom covered with different types of vegetation (annual plants, trees, woody debris, aquatic macrophytes, emergent macrophytes, and filamentous algae) were estimated in a 1 meter circle surrounding the light trap. Samples were preserved in a 5% solution of buffered formalin.