The Salmon Ocean Ecology Team at the SWFSC Fisheries Ecology Division originated from the Physiological Ecology Investigation at the Tiburon Laboratory, which was closed in 2000. In that research group, the relationships between physiological functions of fishes and their environment formed the basis for research on a variety of marine and estuarine species, including northern anchovy (Engraulis mordax), starry flounder (Platichthys stellatus), striped bass (Morone saxatilis), and several species of rockfish (Sebastes spp.).
In 1995, the research team initiated studies of juvenile Chinook salmon (Oncorhynchus tshawytscha) as they emigrated through San Francisco Estuary and into the coastal waters of central California. Following seven years of drought in California, and considering the highly industrialized and urbanized shoreline of the estuary, it was hypothesized that transiting the estuary was detrimental to juvenile salmon originating from natal streams and hatcheries in the Central Valley of California. Greater significance was placed on the study because the Evolutionarily Significant Units (ESUs) of Chinook salmon in the Central Valley are in jeopardy. Of the three ESUs, the Sacramento River Winter Run was listed as Endangered by the U.S. Endangered Species Act of 1973 (ESA) in 1994 and the Central Valley Spring Run was listed as Threatened in 1999. The remaining ESU, Central Valley Fall and Late-fall Run, the largest run due in part to substantial hatchery supplementation, was considered a Species of Concern in 2004.
The research design for studies on juvenile salmon followed that of the Physiological Ecology Investigation. Data are collected to determine development in various environmental conditions or habitats. Analyses focus on growth, residence time, feeding ecology, and energy dynamics, and their relationships to natural and anthropogenic environmental variables including temperature, freshwater flow, salinity, dissolved oxygen, and contaminant concentrations.
Since relocating in Santa Cruz, California, research by the Salmon Ecology Team has expanded in scope to include reproductive behavioral ecology, small estuaries on the central California coast, ocean ecology, juvenile survival and migratory patterns, and a captive broodstock program.
Scott Creek, a stream near Santa Cruz inhabited by steelhead (Oncorhynchus mykiss) and the southernmost population of coho salmon (O. kisutch), both listed under ESA, provides an excellent natural laboratory to study life history characteristics and interactions between naturally-spawned and hatchery-produced salmonids. The steelhead population is part of the Central California Coast (CCC) Distinct Population Segment (DPS) and was listed as Threatened in 1997, whereas the coho salmon population, part of the Central California Coast ESU, was listed as Threatened in 1996 but downgraded to Endangered in 2005. A hatchery, the Kingfisher Flat Fish Facility operated by the Monterey Bay Salmon and Trout Project in cooperation with California Department of Fish and Game, on a Scott Creek tributary produces both steelhead and coho for supplementation to natural spawning that has significantly enhanced the persistence of both species in the watershed. We are studying reproduction and early life history of steelhead in the system with emphasis on the extent and consequences of interactions between natural and hatchery produced fish.
Estuaries are considered important nursery and protective habitats for juvenile salmon during the critical phase of development when physiological adaptations are preparing them for life in the ocean. What is known originates primarily from studies in the Pacific Northwest and Alaska. In California, estuarine dynamics differ from those to the north and their influence on juvenile salmon may differ. For example, many are small with large fluctuations of freshwater discharge and are separated from the ocean by sandbar formation during the low flow period of summer and fall. In addition, a variety of environmental conditions exits among the small estuaries. Some are downstream of logging and agriculture, some are urbanized, while others are less impacted by human activities. A comparative study of small estuaries, evaluating the influences of varying environmental conditions on the occurrence, abundance, residence time, growth, smoltification, physiological performance, and feeding of juvenile salmonids is underway. The goal of this study is to determine the variability in juvenile salmon development and usage of differing estuary types and the conditions that are beneficial to year-class strength.
Ocean Ecology Studies
Of California's 13 salmonid ESUs and DPSs, ten are listed by the ESA and one is a candidate for listing. Although freshwater habitat loss and degradation contribute to population declines, it is becoming apparent that ocean conditions play a major role in the interannual variability of salmon populations, especially during the first months after exiting freshwater. Climatic and oceanographic forcing, ranging from interdecadal ocean oscillations to more regional effects such as El Niño and La Niña, affect environmental conditions and marine productivity that influence salmon growth and survival. Effective management of salmonid stocks and their ecosystems requires greater knowledge of juvenile salmonids during marine residence. The need for basic biological data and the influences of environmental factors on survival and health have been identified as high priority research needs by the Pacific Fishery Management Council as well as the scientific community. To address these needs, we are conducting research on the ocean ecology of juvenile salmon off California. The goal is to determine interannual variability of juvenile salmon physiology and the influences of biotic and abiotic environmental factors through assessment of abundance, distribution, movement patterns, growth, feeding, and energy status.
Survival and Migratory Patterns of Juvenile Salmonids
Tracking migration, movement patterns, and survival of juvenile salmonids in the Central Valley has been a difficult task, producing fragmentary and often confusing results. Recent advances in acoustic tagging and tracking technology, most notably the reduction in tag size and increase in battery life of the tags, provide an opportunity to gather accurate, high-resolution, information on the movement patterns and survival of juvenile salmonids. This information is critical to determining the timing and duration of migration through the Central Valley and San Francisco Estuary, which sections of the migration corridor appear to be used for holding and rearing, and most importantly, which sections produce significant mortality.
Starting in 2007, a project funded by the CALFED Science Program and in collaboration with Peter Klimley of the University of California, Davis will acquire movement and survival data of salmonids through the Central Valley and San Francisco Estuary. Chinook salmon and steelhead, two salmonid species with different life history strategies will be followed. We will place acoustic receivers in the Sacramento River and San Francisco Estuary to monitor passage of acoustically tagged fish past key reference points related to human activities and watershed morphology. Within the estuary, several agencies, including the U.S. Army Corps of Engineers, the Port of Oakland, and the Bay Planning Coalition will collaborate with this project by placing additional receivers in areas of interest to their organizations’ missions. Juvenile steelhead and late-fall run Chinook salmon from Coleman National Fish Hatchery will be implanted with acoustic tags yearly during the winters of 2007, 2008, and 2009 and released over a month’s time in Battle Creek and the upper Sacramento River. Time of passage data retrieved from the receivers will be used to reconstruct and model rates of movement and survival through system segments. The results will be correlated with water projects, hydrologic data (e.g., temperature, flow), and land use patterns to determine their relationships to survival and movement patterns.
Captive Broodstock Studies
The Salmon Ecology Team maintains a captive broodstock of Central California Coast ESU coho salmon starting with progeny from the 2002 broodyear. Populations of coho salmon (O. kisutch) are declining throughout their range on the West Coast. Of seven Evolutionarily Significant Units (ESU), one is listed as Endangered, three are listed as Threatened, and one as a Species of Concern by the ESA. Populations at the southern margin of the Central California Coast ESU (most southerly coho salmon ESU) are considered to be at high risk of extinction and were recently downgraded from Threatened to Endangered (2005). All coastal streams south of the Golden Gate have lost their natural runs of coho except Scott and Waddell Creeks in Santa Cruz County. The populations in Waddell and Scott Creeks would be in even greater jeopardy without supplementation from artificial propagation. The Monterey Bay Salmon and Trout Project maintains a cooperative hatchery, the Kingfisher Flat Fish Facility with the California Department of Fish and Game (CDFG) on Big Creek, a tributary of Scott Creek. Since the mid-1970s, Scott and Waddell Creeks have been stocked with progeny of coho salmon trapped in Scott Creek and spawned at the hatchery. In recent years, the collection of broodstock has become increasingly difficult due to poor returning year-classes. The causes are not known but are probably related to poor ocean survival and premature flushing of juveniles from streams by recent large storms. To ensure the continuation and recovery of coho salmon populations at the southernmost margin of their distribution, we are developing a captive broodstock program to provide gametes to the Kingfisher Flat Fish Facility, which will preserve and increase the genetic diversity of southern coho salmon populations. Another benefit of the program will be to increase our knowledge and understanding of the physiological and ecological requirements and genetic structure of southern coho by using progeny from the broodstock.