Coastal upwelling supplies oxygen-depleted water to the Columbia River estuary

Low dissolved oxygen (DO) is a common feature of many estuarine and shallow-water environments, and is often attributed to anthropogenic nutrient enrichment from terrestrial-fluvial pathways. However, recent events in the U.S. Pacific Northwest have highlighted that wind-forced upwelling can cause naturally occurring low DO water to move onto the continental shelf, leading to mortalities of benthic fish and invertebrates. Coastal estuaries in the Pacific Northwest are strongly linked to ocean forcings, and here we report observations on the spatial and temporal patterns of oxygen concentration in the Columbia River estuary. Hydrographic measurements were made from transect (spatial survey) or anchor station (temporal survey) deployments over a variety of wind stresses and tidal states during the upwelling seasons of 2006 through 2008. During this period, biologically stressful levels of dissolved oxygen were observed to enter the Columbia River estuary from oceanic sources, with minimum values close to the hypoxic threshold of 2.0 mg L(-1). Riverine water was consistently normoxic. Upwelling wind stress controlled the timing and magnitude of low DO events, while tidal-modulated estuarine circulation patterns influenced the spatial extent and duration of exposure to low DO water. Strong upwelling during neap tides produced the largest impact on the estuary. The observed oxygen concentrations likely had deleterious behavioral and physiological consequences for migrating juvenile salmon and benthic crabs. Based on a wind-forced supply mechanism, low DO events are probably common to the Columbia River and other regional estuaries and if conditions on the shelf deteriorate further, as observations and models predict, Pacific Northwest estuarine habitats could experience a decrease in environmental quality.     

Comparison between some epigean and hypogean populations of Asellus aquaticus (Crustacea: Isopoda: Asellidae)

Samples for benthic meiofauna were collected in the vicinity of a salmon aquaculture farm in Bliss Harbour, Bay of Fundy, Canada in early August 1990. Simultaneously, samples for water content, organic carbon, organic nitrogen were collected, and redox potential and benthic oxygen consumption were measured. Meiobenthic size-spectra of biomass and respiration (calculated using allometric equations) were examined at three locations along a gradient of sediment organic enrichment radiating from the farm. Neither biomass nor respiration size-spectra were significantly different between locations despite a decrease in taxon diversity with increasing sediment organic enrichment. Small nematodes were the single largest contributor to respiration and usually to biomass at all locations, particularly at the most organically enriched location directly under the salmon farm. Calculated meiofauna respiration accounted for a greater proportion of total benthic community respiration in organically enriched sediments than in less enriched sediments.     

Functions of restored wetlands for juvenile salmon in an industrialized estuary

The Duwamish estuary is an industrialized waterway located in Seattle, WA, USA. Despite a history of habitat loss, naturally produced juvenile Chinook salmon use the estuary. In addition to experiencing degraded habitat in the estuary, wild salmon growth may be affected by competition with more than three million hatchery fish released yearly into the river. Restoring habitat to benefit salmon in the Duwamish River is a priority for trustees of public resources, and a number of wetland restoration sites have been created there. We tested the function of restored sites in the Duwamish estuary for juvenile Chinook salmon by comparing fish densities from enclosure nets or beach seines at three paired restored/un-restored sites and by applying environmental and diet data to a bioenergetics model. We also examined temporal and diet overlap of wild juvenile Chinook salmon with other salmon species and with hatchery-reared Chinook salmon using non-metric multidimensional scaling (NMDS). At a brackish upstream site with a relatively large opening to the river, we found higher densities of juvenile Chinook salmon at the restored site. NMDS results indicated that juvenile Chinook salmon fed on different taxa at the restored sites than at the reference sites. However, modeled growth was similar at restored and reference sites. Co-occurring juvenile chum and Chinook salmon fed differently, with chum eating smaller prey, and Chinook salmon eating larger prey. Co-occurring hatchery and wild juvenile Chinook salmon had similar diets, indicating that they may compete for prey. However, modeled growth was positive and did not differ between hatchery and wild fish, suggesting that food was not limiting. Bioenergetics models indicated that overall juvenile Chinook salmon growth potential at the brackish water site was consistently higher than at more saline sites. Our results suggest that restoration sites in the Duwamish estuary that have larger access openings and are located in brackish water may have increased function over other configurations.     

Use of glacier river-fed estuary channels by juvenile Coho Salmon: transitional or rearing habitats?

Estuaries are among the most productive ecosystems in the world and provide important rearing environments for a variety of fish species. Though generally considered important transitional habitats for smolting salmon, little is known about the role that estuaries serve for rearing and the environmental conditions important for salmon. We illustrate how juvenile coho salmon Oncorhynchus kisutch use a glacial river-fed estuary based on examination of spatial and seasonal variability in patterns of abundance, fish size, age structure, condition, and local habitat use. Fish abundance was greater in deeper channels with cooler and less variable temperatures, and these habitats were consistently occupied throughout the season. Variability in channel depth and water temperature was negatively associated with fish abundance. Fish size was negatively related to site distance from the upper extent of the tidal influence, while fish condition did not relate to channel location within the estuary ecotone. Our work demonstrates the potential this glacially-fed estuary serves as both transitional and rearing habitat for juvenile coho salmon during smolt emigration to the ocean, and patterns of fish distribution within the estuary correspond to environmental conditions.     

Tidal and diel timing of river entry by adult Atlantic salmon returning to the Aberdeenshire Dee, Scotland

The timing of salmon migration from the estuary of the Aberdeenshire Dee into the river in relation to tidal phase and time of day was studied by combined acoustic and radio-tracking of individual fish and by analysing records of untagged fish from a resistivity fish counter 0.8 km upstream from the tidal limit. Up-estuary movements that led to river entry were predominantly nocturnal and tended to occur during the ebb tide. Penetration into the non-tidal reaches of the river also tended to occur at night, but the timing of salmon movements was no longer significantly associated with tidal phase. The tracking data suggested that the reduction in the strength of the association between salmon migration and tidal phase resulted from variability in rates of progress from the estuary to the river. This variability may have been random, or related to changes in migratory behaviour during entry to fresh water. A simulation of upstream progress by groups of salmon illustrated the decay of the relationship between salmon movements and tidal phase and the advance of the average tidal phase of observed salmon movements with increasing distance of the observation point from where movements were initiated. The magnitude of these effects depended on the average rate of upstream progress and variability in the rate of progress, being greatest when upstream progress was slow and variable. These results highlight a limitation of point observations of migration with regard to identifying environmental stimuli for migration and quantifying their effects.     

Sea-lice infection models for fishes

As free-living sea-lice larvae are difficult to sample directly, lice abundances on fish have recently been used to study larvae in the water. In the KLV problem, juvenile wild salmon migrate past a salmon farm, and the change of infection with distance along the migration route is used to estimate larvae production from the farm. In the farm problem, time-varying infection of sea-cage fish is used to estimate the time-variation of free-living larvae in waters near the farm. Both inverse problems require good forward models for infection. In the farm problem, hosts are relatively large and lice pathogenesis is seldom mortal, whereas in the KLV problem hosts are small and lice-induced host mortality can affect lice abundance; thus, infection models for the farm problem are special cases of models for the KLV problem. Here I give an infection model for the KLV problem that explicitly includes lice clumping and host mortality, showing that Krkosek et al. (Proc R Soc B 272:689-696, 2005) (KLV) probably underestimated larvae production by the salmon farm, and further, that if lice development rates were known from laboratory data, lice abundance field data could be directly inverted for lice-induced host mortality during migration. If lice-induced host mortality is negligible, or if lice are Poisson distributed, infection models of arbitrary complexity reduce to Erlang models. I give two useful Erlang models with their solutions for non-zero initial conditions.     

The effect of salmon farming on the benthos of a Scottish sea loch

The effects of waste from a salmon farm on the benthos of a fjordic sea loch on the western coast of Scotland have been studied. Within 3 m of the floating cages the sediment was highly reducing, and dissolved oxygen content of the water overlying the sediment ranged from 35 to 75% saturation. At ⩾ 15 m from the cages the sediment was oxygenated, and the dissolved oxygen content of the water overlying the sediment was 50–85% saturation. Sedimentary redox potential and dissolved oxygen content of bottom water showed a seasonal variation. The benthic fauna showed marked changes in species number, species diversity, faunal abundance, and biomass in the region of the fish farm, with four zones of effect identified. Directly beneath, and up to the edge of the cages, there was an azoic zone. A highly enriched zone, dominated byCapitella capitata (Fabricius) andScolelepis fuliginosa (Claparède), occurred from the edge of the cages out to as 8 m. A slightly enriched ″transitional ″ zone occurred at ⩽ 25 m, and a “clean” zone at distances > 25 m. This study showed that salmon farming had similar effects on the benthos as other forms of organic enrichment, but the effects were limited to a small area in the immediate vicinity of the cages     

Movements of Atlantic salmon, Salmo salar L., in an estuary in south-west England

In the years 1985–1987, salmon were tracked in the estuary of the River Fowey, Cornwall using the 'sonar buoy' system developed at the M.A.F.F. Fisheries laboratory and described by Solomon & Potter (1988). Sixty-one salmon were caught and tagged in the estuary, 25 with radio and 36 with combined radio and acoustic transmitters. About half these fish were not recorded entering the freshwater reaches of the R. Fowey, and from tag recoveries it seems likely that about 27% were returning to other rivers. For fish returning to the R. Fowey the time between tagging and entry into fresh water varied between 9 h and 130 days. In the estuary the fish largely moved in the same direction as the tidal currents, although movements over the ground against the current were more common in the bottom 2 km and the top 2 km. During periods of low river-flow in summer all salmon tracked in the estuary dropped back out to sea where they stayed for varying periods: some of these made several sorties past the estuary mouth and on occasions well up the estuary before finally entering fresh water. During periods of higher river discharge, in both the summer and the autumn, some fish remained in the estuary for longer periods, sometimes holding position in deep, sheltered water. Most fish entered fresh water at night during periods of increased freshwater discharge, although at very high flows fish also entered in daylight.     

Immediate response of fish communities and water chemistry to causeway breaching and bridge installation in the Kaouk River estuary,British Columbia,Canada

The Kaouk River estuary is located on the northwest coast of Vancouver Island, British Columbia, Canada, in the Treaty Settlement Lands of the Ka:'yu:'k't'h'/Che:k'tles7et'h First Nations. Stretching across the widest point of this estuary is a causeway providing road access to Fair Harbour. This causeway was observed to decrease habitat connectivity throughout the estuary, specifically limiting juvenile salmon access to high‐quality rearing habitat in the tidal marsh. As such, the causeway was breached in 2019 and a bridge was installed. Juvenile salmon were observed using the new connection and were captured both up and downstream of the causeway immediately following breaching. Postbreach water chemistry (dissolved oxygen, pH, salinity, and temperature) near the causeway was recorded within the range of values observed throughout the estuary. Use of the breach by juvenile salmon and homogenized water chemistry indicate the project succeeded in improving habitat connectivity within the Kaouk River estuary and has enhanced juvenile salmon access to 2.7 km² of wetland rearing habitat.     

The Interaction between Water Currents and Salmon Swimming Behaviour in Sea Cages

Positioning of sea cages at sites with high water current velocities expose the fish to a largely unknown environmental challenge. In this study we observed the swimming behaviour of Atlantic salmon (Salmo salar L.) at a commercial farm with tidal currents altering between low, moderate and high velocities. At high current velocities the salmon switched from the traditional circular polarized group structure, seen at low and moderate current velocities, to a group structure where all fish kept stations at fixed positions swimming against the current. This type of group behaviour has not been described in sea cages previously. The structural changes could be explained by a preferred swimming speed of salmon spatially restricted in a cage in combination with a behavioural plasticity of the fish.     

Environmental impact of a salmonid farm on a well flushed marine site: II. Biosedimentology

An environmental monitoring study was carried out between 1993, 1995 on the site of a marine trout farm located in the Bay of Cherbourg (English Channel), France. The study dealt with the sea bottom and solid waste from the farm, and concerns the deposition rate, sediment analysis and chemistry (fine fraction < 63 μm, organic matter, carbon, nitrogen and trace metals such as Cu and Zn), bottom oxygen demand, benthic macrofauna, and underwater video surveying. The observed impact was very moderate and localised, and showed no real abnormality. This was mainly due to the strong hydrodynamics characterising the site. A separate phase of the same study dealt with dissolved waste and the water mass (Part One: Current and water quality).     

First results with a new estuarine fish tracking system

A 'sonar buoy' tracking system has been developed at the MAFF Fisheries Laboratory based upon acoustic transmitting tags and relay units which retransmit the pulsed acoustic signal as a radio signal. The output from several such 'sonar buoys' is monitored by a single automatic recording station on the shore. The system has been used on salmon in the estuary of the River Fowey in Cornwall, providing useful data on the behaviour of returning adults before they enter the river. The tags also transmit a radio frequency signal to allow tracking in the river itself. Of fourteen fish tagged in 1985, six were recorded entering the river between 12 h and 41 days after being released. Another fish was recaptured in a coastal net 160 km to the east. These few preliminary results indicated two distinct patterns of behaviour: one fish remained in deep water in the lower estuary for several days, often lying near moored ships or jetties; at other times fish made extensive excursions up the estuary with the tide, usually returning with the ebb.     

Behaviour of adult Atlantic salmon, Salmo salar L., in the estuary of the River Ribble in relation to variations in dissolved oxygen and tidal flow

Twenty adult returning salmon were tracked in the estuary of the R. Ribble using acoustic oxygensensing transmitters during summer when a pronounced dissolved oxygen (DO) sag develops. Excluding two mortalities, 75% of these fish left the estuary to sea. Fish in the estuary moved to and fro with the tides over a 10 km amplitude experiencing cyclical changes in DO. Fish movement was inhibited below 40% of air saturation value (ASV) DO, and there was evidence of avoidance of DO below 55% ASV. The high rate of loss of fish to sea suggests that many of the fish in the estuary are non-Ribble fish en route to other rivers. Adverse conditions in the Ribble therefore are likely to affect stocks in adjacent rivers.     

The environmental impact of Mediterranean cage fish farms at semi-exposed locations: does it need a re-assessment?

During spring and summer 2003, we measured a variety of chemical and biological parameters in five medium-sized, Mediterranean cage farms that exploit semi-offshore conditions, and controlled the supply of fodder. The objective was to assess whether modern cage farms proliferating at semi-offshore sites exert environmental impact levels equivalent to the levels described from more traditional cage farms located in shallow, sheltered sites. In the water column, we examined the concentration of dissolved inorganic nutrients and heterotrophic bacteria in both surface and near-bottom water. At the bottom, we examined the concentrations of benthic chlorophyll a, phaeophytin and organic matter in sediments, the granulometric structure of the sediment, and the taxonomic (at the family level) abundance of benthic macroinvertebrates. For most parameters, we found no substantial differences between farm and control sites. Rather, most variation was explained as a function of depth (surface versus bottom water) or season (spring versus summer conditions). Deviations of farm values from control values, when they occurred, were small and did not indicate any significant impact on either bacterioplankton or benthic chlorophyll. Only one of the five farms studied exerted a detectable impact on the benthic macroinvertebrate community immediately under the cages. These results suggest that medium-sized fish farms located on semi-exposed western Mediterranean coasts have fewer environmental impacts than traditional fish farms located in shallow, sheltered sites. Impact characterization in these new farms may require refinement of the standard approach to deal with rapid dispersal of effluents and sub-lethal levels of environmental disturbance.     

The relationships between hydrodynamics, the concentration of hydrogen sulphide produced by polluted sediments and fish health at several marine cage farms in Scotland and Ireland

Waste products from marine cage salmon farming can cause organic enrichment of the benthos in the immediate area of the farm with potentially deleterious consequences to fish health. The relationships between benthic enrichment and hydro-dynamic parameters - mean current speed, maximum current speed and incidence of low currents - were examined. Benthic impact was assessed on the basis of SCUBA diver observation and measurements of hydrogen sulphide in the water immediately (within 30 cm) overlying the sediment at slack water. Other factors such as maximum site biomass and the age of the site were also considered. At 7 of the 8 salmon farms studied there was a good correlation between mean current speed ( r =−0.877) and incidence of low currents ( r = 0.943) with log mean hydrogen sulphide concentration. The lack of correlation for the remaining site was thought to be due to a combination of high levels of terrigenous organic input to the site and overfeeding.
The relationship between fish growth and mortality with hydrogen sulphide concentration was also examined. Good correlation between both fish growth ( r =−0.819) and cumulative percentage mortality ( r = 0.941), and log mean hydrogen sulphide concentration were found when the data from one exceptional site were excluded.     

Juvenile Salmon Usage of the Skeena River Estuary

Migratory salmon transit estuary habitats on their way out to the ocean but this phase of their life cycle is more poorly understood than other phases. The estuaries of large river systems in particular may support many populations and several species of salmon that originate from throughout the upstream river. The Skeena River of British Columbia, Canada, is a large river system with high salmon population- and species-level diversity. The estuary of the Skeena River is under pressure from industrial development, with two gas liquefaction terminals and a potash loading facility in various stages of environmental review processes, providing motivation for understanding the usage of the estuary by juvenile salmon. We conducted a juvenile salmonid sampling program throughout the Skeena River estuary in 2007 and 2013 to investigate the spatial and temporal distribution of different species and populations of salmon. We captured six species of juvenile anadromous salmonids throughout the estuary in both years, and found that areas proposed for development support some of the highest abundances of some species of salmon. Specifically, the highest abundances of sockeye (both years), Chinook in 2007, and coho salmon in 2013 were captured in areas proposed for development. For example, juvenile sockeye salmon were 2–8 times more abundant in the proposed development areas. Genetic stock assignment demonstrated that the Chinook salmon and most of the sockeye salmon that were captured originated from throughout the Skeena watershed, while some sockeye salmon came from the Nass, Stikine, Southeast Alaska, and coastal systems on the northern and central coasts of British Columbia. These fish support extensive commercial, recreational, and First Nations fisheries throughout the Skeena River and beyond. Our results demonstrate that estuary habitats integrate species and population diversity of salmon, and that if proposed development negatively affects the salmon populations that use the estuary, then numerous fisheries would also be negatively affected.     

Dietary composition of black drum Pogonias cromis in a hypersaline estuary reflects water quality and prey availability

The Baffin Bay estuary is a hypersaline system in the Gulf of Mexico that supports an important recreational and commercial fishery for black drum Pogonias cromis, a benthic predator. Seasonal measurements of water quality variables, benthic macrofauna densities and biomass, and determination of P. cromis food sources using stomach‐content and stable‐isotope analyses were carried out to determine how P. cromis food sources change with water quality and how this may affect P. cromis diet. Gut‐content analysis indicated P. cromis selectively consumed bivalves Mulinia lateralis and Anomalocardia auberiana. Isotope compositions demonstrated that P. cromis relied on these benthic food resources produced in the Baffin Bay estuary year‐round. Biomass and densities of these bivalves were influenced by changes in water quality variables, particularly salinity and dissolved oxygen. Thus, this paper demonstrates the relationship between water quality variables, benthic macrofauna, and their use as food resources by a carnivorous fish species, and emphasizes the need for integrated assessments when studying the effects of water quality on ecosystem function. Holistic approaches such as these can provide important information for management and conservation of fishery resources and can improve predictions of ecosystem response to climate variability.     

The food web in the lower part of the Seine estuary: a synthesis of existing knowledge

The Seine estuary illustrates the alterations to estuaries due to human activities heavy releases of pollutants of various origins and significant morphological changes beginning in the middle of the 19th century. The intertidal mudflat surface has been seriously reduced (< 30km²) since the channels of the Seine River came under management. While the role of the Seine estuary in the dynamics of the eastern English Channel ecosystem is recognized as important, the biological characteristics of the estuary remained relatively unknown until the 1990s. Biological diversity was progressively impoverished from the polyhaline zone to the oligohaline zone. In spite of a heavily contaminated environment, the macrobenthic and planktonic fauna of the Seine estuary remains similar to those of other northeastern Atlantic estuaries. The fauna exhibit clear contrasts between areas with very high abundance and others with very low abundance. The pelagic fauna, especially the copepod Eurytemora affinisand the shrimp Palaemon longirostris, are more abundant in the Seine estuary than in other estuaries. Diversified and abundant, Abra alba-Pectinaria koreni and Macoma balthica benthic communities occur, respectively, in the outer and inner parts of the estuary. In subtidal flats, benthic fauna is especially poor in terms of specific richness, abundance and biomass. Paradoxically, considering the high abundance of prey, fish are particularly scarce. Two food webs have been identified. In the oligohaline zone, where turbidity is maximum, the food web is exclusively planktonic, due to dredging that prevented benthic fauna from settling. In the polyhaline zone, fish populations that feed particularly on benthic fauna benefit from low turbidity and high oxygen concentrations. So, in spite of heavy organic and metallic contamination and human activities, the Seine estuary remains a highly productive ecosystem, which provides a nursery for marine fish and feeding grounds for migratory birds. A global management plan appears to be necessary in order to guarantee that the Seine estuary continues to function as it currently does.     

Ecological Risk Assessment Paradigm for Salmon: Analyzing Immune Function to Evaluate Risk

Wild Pacific salmon populations are in serious decline, and as a result, a number of salmon stocks are listed as threatened or endangered under the Endangered Species Act. Our research identifies and supports the possibility that certain environmental contaminants can alter salmon survival, and as a result may contribute to these species being at risk. We have shown that juvenile chinook salmon (Oncorhynchus tshawytscha) are exposed to polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) as they migrate through a contaminated urban estuary in Puget Sound WA (the Duwamish Waterway estuary). Immune function was analyzed in these fish by examining the ability of their anterior kidney and splenic leukocytes to produce a primary and secondary in vitro plaque-forming cell (PFC) response to the hapten, trinitrophenyl (TNP), and by determining their susceptibility to a marine pathogen, Vibrio anguillarum. We found that fish outmigrating from the urban estuary produced a significantly lower PFC response to TNP and were more susceptible to the pathogen, compared to juvenile salmon collected from a rural estuary during their outmigration. In the laboratory, we exposed juvenile chinook salmon collected from a hatchery to either a PCB technical mixture or a PAH compound to determine if these contaminants have the potential to alter immune function in salmon. Indeed, we found that salmon exposed in the laboratory to either the PCB mixture or the PAH also produced lower PFC responses and were more susceptible to disease compared to animals treated with the solvent vehicle. In summary, contaminants such as PAHs and PCBs are demonstrated to influence salmon health, and thus have the potential to adversely impact salmon populations.