Daniel L. Bottom

Return to the River: Scientific Issues in the Restoration of Salmonid Fishes in the Columbia River

Abstract The Columbia River once was one of the most productive river basins for anadromous salmonids on the West Coast of North America; however, its current runs total less than 10% of historic levels. The Independent Scientific Group (ISG) of the Northwest Power Planning Council reviewed regional salmon management actions described in the Columbia River Basin Fish and Wildlife Program and concluded that the current program is unlikely to recover declining salmon and steelhead stocks. Adoption of a salmon life history ecosystem concept as a guiding foundation is needed to recover depressed stocks. Increasing natural ecosystem processes and functions should rebuild salmon populations to more abundant, productive, and stable levels. Elements of a salmon recovery program that increase these normative conditions include restoration of habitat for all life history stages (including migrations), reduction of mortality sources (including harvesters), planning of hydropower mitigation measures in the context of...

Landscape Structure and Scale Constraints on Restoring Estuarine Wetlands for Pacific Coast Juvenile Fishes

Juveniles of many Pacific Northwest coastal fishes and particularly anadromous species, utilise coastal marshes as “nursery” habitats, predicating the assumption that restoration of marsh sites will promote increased fish survival and production. However, species such as anadromous salmonids have evolved life history strategies that to various degrees depend upon the structure and scale of the estuarine landscape rather than habitat sites per se. Examples include: 1) migration of juvenile salmon among interconnected wetlands along estuarine gradient, 2) their access to dendritic tidal channels, and 3) extended residence in tidal freshwater sloughs. Unfortunately, estuarine habitat restoration is seldom designed or implemented with landscape structure and scale in mind, ignoring important landscape attributes and processes such as habitat matrix heterogeneity, dendritic tidal channel complexity, allometric relationships of estuarine sloughs, and disturbance frequency and intensity. In this analysis, we draw on several estuarine wetland mitigation and restoration sites in the Pacific Northwest to explore the effect of estuarine landscape structure and scale on their effectiveness for protecting and rehabilitating coastal fisheries resources. We argue that basing restoration solely on site-specific criteria may be significantly inhibiting our ability to re-establish estuarine support function for fisheries resources. To significantly recover the function of juvenile fish migration and survival in coastal ecosystems, future marsh restoration must be conceptualized, designed, constructed and assessed taking into account estuarine landscape structure and scale.

Species composition, distribution, and invertebrate prey of fish assemblages in the Columbia River Estuary

Abstract The fish community of the Columbia River Estuary was sampled with trawl, beach seine, and purse seine over an 18 month period during 1980–1981. Seasonality of abundance and species richness in the estuary reflect the timing of migrations and the reproductive cycles of marine and anadromous species. Composition of the fish community and dominant species in the Columbia River estuary are similar to many smaller estuaries in the Pacific Northwest. These similarities reflect the influence of the nearshore marine environment on fish community structure throughout the West Coast as well as the wide geographic distribution and considerable physiological tolerance of many dominant euryhaline species. The distribution of fish assemblages within the Columbia River estuary is influenced by large seasonal variation in river discharge and salinity. Within large areas or salinity zones, species assemblages use different habitats and invertebrate prey. The distribution of abundance and the stomach fullness of fishes vary directly with the density of potential prey. We hypothesize that fish production may be limited by dynamic physical processes that control prey availability or the feeding efficiencies of predators in the highly turbid estuary.

Reconstructing Juvenile Chinook Salmon Life History in the Salmon River Estuary, Oregon, Using Otolith Microchemistry and Microstructure

Abstract We quantified the juvenile rearing and migratory patterns of individuals from a population of fall-spawning Chinook salmon Oncorhynchus tshawytscha in Oregons Salmon River estuary using otolith microchemistry and microstructure. The study confirmed the daily periodicity of otolith growth increments in a natural fish population under field conditions and validated fundamental assumptions about increased otolith strontium: calcium values during entry into saline waters. The otolith results indicated that more than 75% of the subyearling Chinook salmon captured near the mouth of the Salmon River had entered the estuary during the summer and that two-thirds of these fish had spent more than a month in the estuary before capture. Unlike in other Oregon coastal estuaries, in which the fingerling-migrant portion of their life histories is dominant, approximately two-thirds of Salmon River Chinook salmon in upper-estuary marshes were early fry (<50-mm) migrants. A much smaller proportion at the river mo...

Community structure, distribution, and standing stock of benthos, epibenthos, and plankton in the Columbia River Estuary

Abstract Secondary producers were sampled in the Columbia River estuary during the 1980–81 Columbia River Data Development Program (CREDDP) studies. Benthic infaunal macroinvertebrates were sampled in all estuarine zones and habitats with a grab sampler during a single estuary-wide survey. Epibenthic macro- and meiofauna were sampled monthly with epibenthic pump and sled, beach seine, and trawl in tidal flat, slope, and channel bottom habitats throughout the estuary. Zooplankton and larval fish were sampled monthly with oblique zooplankton net tows in the main channel. The distribution of secondary consumers coincided with division of the estuary into three salinity zones and siz habitat types, where the principal physical and biological processes that influenced the distribution and assemblage structure of secondary consumers were: (1) river discharge; (2) river discharge and tidal flow interaction which created circulation and salinity patterns and turbidity maximum characteristics; and (3) benthic processes, such as sediment type and transport and geomorphology. Standing stocks of benthic infauna were highest in protected tidal flat habitats and were comparatively depressed in the Estuarine Mixing Zone of the estuary. Standing stocks of epibenthic and zooplanktonic organisms, in contrast, were concentrated within the Estuarine Mixing Zone.

The contribution of estuary-resident life histories to the return of adult Oncorhynchus kisutch

This study evaluated estuarine habitat use, life-history composition, growth and survival of four successive broods of coho salmon Oncoryhnchus kisutch in Salmon River, Oregon, U.S.A. Subyearling and yearling O. kisutch used restored and natural estuarine wetlands, particularly in the spring and winter. Stream-reared yearling smolts spent an average of 2 weeks in the estuary growing rapidly before entering the ocean. Emergent fry also entered the estuary in the spring, and some resided in a tidal marsh throughout the summer, even as salinities increased to >20. A significant portion of the summer stream-resident population of juvenile O. kisutch migrated out of the catchment in the autumn and winter and used estuary wetlands and adjacent streams as alternative winter-rearing habitats until the spring when they entered the ocean as yearling smolts. Passive integrated transponder (PIT) tag returns and juvenile life-history reconstructions from otoliths of returning adults revealed that four juvenile life-history types contributed to the adult population. Estuarine-associated life-history strategies accounted for 20-35% of the adults returning to spawn in the four brood years, indicating that a sizable proportion of the total O. kisutch production is ignored by conventional estimates based on stream habitat capacity. Juvenile O. kisutch responses to the reconnection of previously unavailable estuarine habitats have led to greater life-history diversity in the population and reflect greater phenotypic plasticity of the species in the U.S. Pacific Northwest than previously recognized.

Tidal movements and residency of subyearling Chinook salmon (Oncorhynchus tshawytscha) in an Oregon salt marsh channel.

A novel application of full-duplex passive integrated transponder (PIT) tag technology was used to investigate movements of individual subyearling Chinook salmon (Oncorhynchus tshawytscha; fork length ‡ 60 mm) into and out of tidally flooded salt marsh habitat in the Salmon River estuary, Oregon, USA. PIT interrogation was effective, with mean tag detection ‡ 92%. Salmon movement peaked late during both flood and ebb tide periods, indicating that salmon did not drift passively. Most movements were in the direction of tidal currents, but 20% of individuals entered the channel against the ebbing tide. Individuals occupied the intertidal channel for a median 4.9 h and as long as 8.9 h per tidal cycle, and few were detected moving when water depth was <0.4 m. Some individuals used the channel on multiple successive tidal cycles, and others entered intermittently over periods of up to 109 days. Using an individual-based approach, we character- ized diversity of juvenile Chinook salmon behavior within a marsh channel, providing insight into the value of such habi- tats for conservation and restoration of salmon populations. Resume´ : Une utilisation inedite de la technologie des transpondeurs passifs integresatransmission bidirectionnelle simul- tanee( etiquettes PIT) a servi a etudier les deplacements de saumons chinook (Oncorhynchus tshawytscha; longueur a la

Distribution, Size, and Origin of Juvenile Chinook Salmon in Shallow-Water Habitats of the Lower Columbia River and Estuary, 2002–2007

Abstract We monitored fish assemblages monthly at estuarine and tidal freshwater sites in the lower Columbia River and estuary from January 2002 through September 2007 in order to identify specific salmon stocks and migration stages that may benefit from habitat restoration initiatives. We report landscape-scale and seasonal variation in abundance, size, hatchery production (based on adipose fin clips), and genetic stock of origin of juvenile Chinook salmon Oncorhynchus tshawytscha. From fish implanted with coded wire tags (CWTs), we also determined the sites of release and inferred migration patterns. Chinook salmon were found in diverse life history stages and forms, including fry migrants, fingerlings, and (fewer) yearlings. Abundance increased in February and decreased in August, but salmon were present in all months each year. Spatial gradients in abundance and size were strong, with fewer but larger fish in brackish than in tidal freshwater zones. Overall, 30% of the Chinook salmon measured were fry (≤60 mm) that were likely naturally produced fish. These occurred at higher mean monthly proportions in tidal freshwater than in estuarine zones. In contrast, most larger fish were probably raised in hatcheries. Genetic stock assessment revealed that the majority of the Chinook salmon analyzed were from fall-run stock groups originating in the lower Columbia River, with 15% originating from other stock groups. Of these minority contributors, about 6% were identified as upper Columbia River summer-fall-run Chinook salmon while seven other stock groups accounted for the remainder, including 3% from transplants originating in southern Oregons Rogue River. Recaptures of tagged fish revealed maximum migration times of 143 d for subyearlings and 52 d for yearlings, and both CWT and genetic data indicated that fall Chinook salmon from coastal rivers occasionally entered the estuary. These data demonstrated a widespread temporal and spatial distribution of subyearling Chinook salmon in shallow-water habitats of the lower Columbia River and estuary.

Genetic Identification of Chinook Salmon in the Columbia River Estuary: Stock-Specific Distributions of Juveniles in Shallow Tidal Freshwater Habitats

AbstractExtensive efforts are underway to restore and conserve nearshore shallow water habitats in the Columbia River estuary with the intent of increasing the estuarys capacity to provide food, refuge, and other crucial ecosystem functions for juvenile salmon. Juvenile Chinook Salmon Oncorhynchus tshawytscha, including those from the five Evolutionarily Significant Units listed as threatened or endangered under the U.S. Endangered Species Act, are particularly expected to benefit from the habitat improvements. However, information on the temporal and spatial estuarine distributions of juveniles from specific populations or stocks is lacking and impedes restoration planning for at-risk salmon. We conducted a series of surveys to sample juvenile Chinook Salmon occupying shallow-water habitats with sandy beaches in six hydrogeomorphic reaches across the tidal freshwater portion of the estuary and also at one long-term reference site near the estuary mouth. Sites were sampled bimonthly over 26 months during...

Correspondence between Scale Morphometrics and Scale and Otolith Chemistry for Interpreting Juvenile Salmon Life Histories

AbstractFish scales have long been used to reconstruct fine-scale habitat transitions such as the movement of juvenile fish from freshwater, estuary, and ocean environments. Despite the importance of life history information to fisheries management and conservation, few studies have validated that scale morphology accurately describes fish movement between these habitats. Therefore, we tested the accuracy of using scale morphometric criteria to identify the movement of juvenile Chinook Salmon Oncorhynchus tshawytscha from freshwater to marine portions of the Columbia River estuary by comparing scale morphometric classification, scale chemistry, and otolith chemistry. Nearly one-half of all fish collected in the saline portion of the estuary and approximately one-quarter in the freshwater portion exhibited morphometric patterns (i.e., scale checks and intermediate growth) often associated with periods of estuary rearing. Depending upon the criteria used to define scale checks, otolith chemical results indi...