Ted Sommer

The Collapse of Pelagic Fishes in the Upper San Francisco Estuary: El Colapso de los Peces Pelagicos en La Cabecera Del Estuario San Francisco

Abstract Although the pelagic fish community of the upper San Francisco Estuary historically has shown substantial variability, a recent collapse has captured the attention of resource managers, scientists, legislators, and the general public. The ecological and management consequences of the decline are most serious for delta smelt (Hypomesus transpacificus), a threatened species whose narrow range overlaps with large water diversions that supply water to over 25 million people. The decline occurred despite recent moderate hydrology, which typically results in at least modest recruitment, and investments of hundreds of millions of dollars in habitat restoration and environmental water allocations to support native fishes. In response to the pelagic fish collapse, an ambitious multi-hyphen;agency research team has been working since 2005 to evaluate the causes of the decline, which likely include a combination of factors: stock-recruitment effects, a decline in habitat quality, increased mortality rates, ...

California's Yolo bypass: Evidence that flood control can be compatible with fisheries, wetlands, wildlife, and agriculture

Abstract Unlike conventional flood control systems that frequently isolate rivers from ecologically-essential floodplain habitat, Californias Yolo Bypass has been engineered to allow Sacramento Valley floodwaters to inundate a broad floodplain. From a flood control standpoint, the 24,000 ha leveed floodplain has been exceptionally successful based on its ability to convey up to 80% of the flow of the Sacramento River basin during high water events. Agricultural lands and seasonal and permanent wetlands within the bypass provide key habitat for waterfowl migrating through the Pacific Flyway. Our field studies demonstrate that the bypass seasonally supports 42 fish species, 15 of which are native. The floodplain appears to be particularly valuable spawning and rearing habitat for the splittail (Pogonichthys macrolepidotus), a federally-listed cyprinid, and for young chinook salmon (Oncorhynchus tshawytscha), which use the Yolo Bypass as a nursery area. The system may also be an important source to the down...

Habitat Use and Stranding Risk of Juvenile Chinook Salmon on a Seasonal Floodplain

Abstract Although juvenile Chinook salmon Oncorhynchus tshawytscha are known to use a variety of habitats, their use of seasonal floodplains, a highly variable and potentially risky habitat, has not been studied extensively. Particularly unclear is whether a seasonal floodplain is a net “source” or a net “sink” for salmonid production. To help address this issue, we studied salmon habitat use in the Yolo Bypass, a 24,000-ha floodplain of the Sacramento River, California. Juvenile salmon were present in the Yolo Bypass during winter–spring; fish were collected in all regions and substrates of the floodplain in diverse habitats. Experimental releases of tagged hatchery salmon suggest that the fish reared on the floodplain for extended periods (mean = 33 d in 1998, 56 d in 1999, and 30 d in 2000). Floodplain rearing and associated growth are also supported by the significantly larger size of wild salmon at the floodplain outlet than at the inlet during each of the study years. Several lines of evidence sugge...

Factors Affecting Fish Entrainment into Massive Water Diversions in a Tidal Freshwater Estuary: Can Fish Losses be Managed?

Abstract We examined factors affecting fish entrainment at Californias State Water Project and Central Valley Project, two of the largest water diversions in the world. Combined, these diversions from the upper San Francisco Estuary support a large component of the municipal and agricultural infrastructure for California. However, precipitous declines in the abundance of several estuarine fish species, notably the threatened delta smelt Hypomesus transpacificus, have generated major concern about entrainment as a possible cause of the declines. We examined a 13-year data set of export pumping operations and environmental characteristics to determine factors affecting entrainment (as indexed by salvage at fish screens) and the potential for manipulation of these factors to improve conditions for fish. Entrainment of three migratory pelagic species—delta smelt, longfin smelt Spirinchus thaleichthys, and striped bass Morone saxatilis—was primarily determined by the seasonal occurrence of particular life sta...

Otolith Microchemistry Provides Information Complementary to Microsatellite DNA for a Migratory Fish

Abstract We investigated the ability of otolith microchemistry to discriminate natal habitats of the splittail Pogonichthys macrolepidotus, a migratory cyprinid endemic to the San Francisco Estuary, California. Splittails are broadly distributed in the brackish and freshwater portions of the lower estuary and make long-distance upstream migrations during winter to rivers and floodplains for spawning. We found that the ratios of Sr: Ca and 87Sr: 86Sr in the otoliths (ascertained by laser ablation inductively coupled mass spectrometry) of age-0 fish collected from natal habitats significantly varied among four primary spawning rivers. Based on these two constituents, quadratic discriminant function analysis correctly classified 71% of the fish to their natal rivers. Recent work with microsatellite DNA indicates that splittails from these same rivers represent two genetically distinct populations. Thus, integrating data obtained from otolith microchemistry and microsatellite DNA can provide complementary inf...

Importance of Flood Dynamics versus Intrinsic Physical Habitat in Structuring Fish Communities: Evidence from Two Adjacent Engineered Floodplains on the Sacramento River, California

Abstract We examined the factors structuring fish communities at two adjacent engineered floodplain systems on the Sacramento River, California: Yolo and Sutter bypasses. We intensively sampled fishes at each location during January–June 2002 and 2004 by rotary screw trap, collecting a total of 126,635 fish comprised of 29 species. Nonmetric multidimensional scaling indicated that distinct fish communities persisted between the locations during our study, despite nearly identical hydrographs and water temperature regimes. Regression models evaluated with an information-theoretic approach also indicated that location was an important factor explaining the abundances of selected species. Overall, Yolo Bypass had more species and a greater proportion of native species than did Sutter Bypass. Sutter Bypass had a greater proportion of species classified as freshwater, while Yolo Bypass had a greater proportion of species classified as either estuarine or anadromous. We believe these results are related to subs...

Spawning and Rearing of Splittail in a Model Floodplain Wetland

Abstract The splittail Pogonichthys macrolepidotus, which has been listed as threatened by the U.S. government, does not produce strong year-classes unless it has access to the floodplain habitat of the San Francisco estuary and its tributaries. In this small-scale, single-year study, we tested the hypothesis that managed inundation of a floodplain can be used to support splittail reproduction in dry years, when this habitat type is not readily available. Adult splittails were captured on their 2001 upstream spawning migration and transferred to a 0.1-ha model floodplain wetland. Our results suggest that adults will successfully spawn if they are provided access to floodplain habitat in dry years. In snorkel surveys, progeny showed a significant association with the lower portion of the water column. Young splittails (15-20 mm fork length (FL)) concentrated in edge habitat near an inflow during the day but at night moved into deeper-water habitats, including open water and habitats with submerged vegetati...

The influence of floodplain habitat on the quantity and quality of riverine phytoplankton carbon produced during the flood season in San Francisco Estuary

Primary productivity, community respiration, chlorophyll a concentration, phytoplankton species composition, and environmental factors were compared in the Yolo Bypass floodplain and adjacent Sacramento River in order to determine if passage of Sacramento River through floodplain habitat enhanced the quantity and quality of phytoplankton carbon available to the aquatic food web and how primary productivity and phytoplankton species composition in these habitats were affected by environmental conditions during the flood season. Greater net primary productivity of Sacramento River water in the floodplain than the main river channel was associated with more frequent autotrophy and a higher P:R ratio, chlorophyll a concentration, and phytoplankton growth efficiency (αB). Total irradiance and water temperature in the euphotic zone were positively correlated with net primary productivity in winter and early spring but negatively correlated with net primary productivity in the late spring and early summer in the floodplain. In contrast, net primary productivity was correlated with chlorophyll a concentration and streamflow in the Sacramento River. The flood pulse cycle was important for floodplain production because it facilitated the accumulation of chlorophyll a and wide diameter diatom and green algal cells during the drain phase. High chlorophyll a concentration and diatom and green algal biomass enabled the floodplain to export 14–37% of the combined floodplain plus river load of total, diatom and green algal biomass and wide diameter cells to the estuary downstream, even though it had only 3% of the river streamflow. The study suggested the quantity and quality of riverine phytoplankton biomass available to the aquatic food web could be enhanced by passing river water through a floodplain during the flood season.

Effects of high temperatures on threatened estuarine fishes during periods of extreme drought.

ABSTRACT Climate change and associated increases in water temperatures may impact physiological performance in ectotherms and exacerbate endangered species declines. We used an integrative approach to assess the impact of elevated water temperature on two fishes of immediate conservation concern in a large estuary system, the threatened longfin smelt (Spirinchus thaleichthys) and endangered delta smelt (Hypomesus transpacificus). Abundances have reached record lows in California, USA, and these populations are at imminent risk of extirpation. California is currently impacted by a severe drought, resulting in high water temperatures, conditions that will become more common as a result of climate change. We exposed fish to environmentally relevant temperatures (14°C and 20°C) and used RNA sequencing to examine the transcriptome-wide responses to elevated water temperature in both species. Consistent with having a lower temperature tolerance, longfin smelt exhibited a pronounced cellular stress response, with an upregulation of heat shock proteins, after exposure to 20°C that was not observed in delta smelt. We detected an increase in metabolic rate in delta smelt at 20°C and increased expression of genes involved in metabolic processes and protein synthesis, patterns not observed in longfin smelt. Through examination of responses across multiple levels of biological organization, and by linking these responses to habitat distributions in the wild, we demonstrate that longfin smelt may be more susceptible than delta smelt to increases in temperatures, and they have little room to tolerate future warming in California. Understanding the species-specific physiological responses of sensitive species to environmental stressors is crucial for conservation efforts and managing aquatic systems globally. Highlighted Article: An integrative approach to assess the impact of elevated water temperature on fishes of immediate conservation concern highlights the vulnerability of longfin smelt relative to delta smelt.

Just add water: sources of chironomid drift in a large river floodplain

Although seasonal floodplains represent one of the most dynamic and productive of aquatic ecosystems, the sources of this productivity are poorly understood. We examined composition and sources of chironomid drift in the Yolo Bypass, the primary floodplain of the Sacramento River. We found that invertebrate drift during winter floodplain inundation is dominated by a single species, the newly identified chironomid Hydrobaenus saetheri (Diptera: Chironomidae). In order to determine sources of chironomids in the Yolo Bypass, invertebrates were sampled from several potential sources prior to and during initial floodplain inundation. Rehydration of dried floodplain sediments from several locations showed that H. saetheri dominated insect emergence from this colonization pathway. By contrast, H. saetheri was not a substantial component of inundated floodplain ponds or of tributary inputs to the floodplain. We conclude that the initial pulse of invertebrate abundance in Yolo Bypass floodwaters is dominated by chironomid emergence from sediments in multiple regions of the floodplain.