Changing estuaries and impacts on juvenile salmon: A systematic review

Estuaries are productive ecosystems providing important habitat for a diversity of species, yet they also experience intense levels of anthropogenic development. To inform decision‐making, it is essential to understand the pathways of impacts of particular human activities, especially those that affect species such as salmon, which have high ecological, social‐cultural and economic values. Salmon systems provide an opportunity to build from the substantial body of research on responses to estuary developments and take stock of what is known. We conducted a systematic English‐language literature review on the responses of juvenile salmon to anthropogenic activities in estuaries and nearshore areas asking: what has been studied, where are the major knowledge gaps and how do stressors affect salmon? We found a substantial body of research (n = 167 studies; 1,369 comparative tests) to help understand responses of juvenile salmon to 24 activities and their 14 stressors. Across studies, 82% of the research was conducted in the eastern Pacific (Oregon and Washington, USA and British Columbia, Canada) showing a limited geographical scope. Using a semiquantitative approach to summarize the literature, including a weight‐of‐evidence metric, we found a range of results from low to moderate–high confidence in the consequences of the stressors. For example, we found moderate–high confidence in the negative impacts of pollutants and sea lice and moderate confidence in negative impacts from connectivity loss and changes in flow. Our results suggest that overall, multiple anthropogenic activities cause negative impacts across ecological scales. However, our results also reveal knowledge gaps resulting from minimal research on particular species (e.g. sockeye salmon), regions (e.g. Atlantic) or stressors (e.g. entrainment) that would be expedient areas for future research. With estuaries acting as a nexus of biological and societal importance and hotspots of ongoing development, the insights gained here can contribute to informed decision‐making.     

Factors influencing the survival of outmigrating juvenile salmonids through multiple dam passages: an individual‐based approach

Substantial declines of Pacific salmon populations have occurred over the past several decades related to large‐scale anthropogenic and climatic changes in freshwater and marine environments. In the Columbia River Basin, migrating juvenile salmonids may pass as many as eight large‐scale hydropower projects before reaching the ocean; however, the cumulative effects of multiple dam passages are largely unknown. Using acoustic transmitters and an extensive system of hydrophone arrays in the Lower Columbia River, we calculated the survival of yearling Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) passing one, two, or three dams. We applied a unique index of biological characteristics and environmental exposures, experienced by each fish individually as it migrated downstream, in order to examine which factors most influence salmonid survival. High outflow volumes led to involuntary spill in 2011 and created an environment of supersaturated dissolved gas concentrations. In this environment, migrating smolt survival was strongly influenced by barometric pressure, fish velocity, and water temperature. The effect of these variables on survival was compounded by multiple dam passages compared to fish passing a single dam. Despite spatial isolation between dams in the Lower Columbia River hydrosystem, migrating smolt appear to experience cumulative effects akin to a press disturbance. In general, Chinook salmon and steelhead respond similarly in terms of survival rates and responses to altered environmental conditions. Management actions that limit dissolved gas concentrations in years of high flow will benefit migrating salmonids at this life stage.     

Behavioural approaches to demonstrate the ecological significance of exposure of juvenile Pacific salmon (genus Oncorhynchus) to the antisapstain fungicide TCMTB

Simulated stream conditions were used to expose underyearling Pacific salmon (genus Oncorhynchus) to sublethal doses of TCMTB (2-thiocyanomethylthio) benzothiazole; a fungicide used by the lumber industry to protect against discolouration by sapstain fungi. Observed changes in schooling, swimming, and respiration were studied in more detail utilizing progressively more complex and ecologically relevant experimental designs. Laboratory troughs (600 litre) were used to quantify innate shelter-seeking behaviour and susceptibility to predation during salinity stress. Swimming speed, schooling behaviour and responses to salinity and hypoxia were studied in a 4500-litre Water Column Simulator under vertically stratified conditions (fresh water overlying sea water). Finally a similarly stratified 15,500-litre outdoor tank was designed to compare susceptibility to predation during a volitional salinity challenge. Relative to controls, TCMTB-exposed underyearling salmon exhibited a reduction in cover response, were slower to seek shelter from bright light, were more erratic in their swimming behaviour and more likely to be eaten by marine predators. Videotape analyses confirmed that TCMTB reduced exploratory behaviour and swimming speed under both normoxic and hypoxic conditions in the WCS. The ecological consequences of these overt behavioural changes were experimentally linked to a clear increase in risk from predation by yellowtail rockfish (Sebastes flavidus) inhabiting the marine zone below the halocline of the 15,500-litre tank. These techniques illustrate our most recent efforts to correlate cumulative sublethal physiological stress with ecologically meaningful behavioural dysfunction.     

Influence of salinity on the size at maturity for fish species reproducing in contrasting West African estuaries

The influence of salinity on life-history traits was tested using two adjoining West African estuaries: the Gambia with a 'normal' salinity gradient (salinity always <40 and decreasing from the mouth upstream) and the Sine Saloum (Senegal) with an inverse gradient (from 35 at the estuary mouth up to >130 in the upper reaches). The breeding seasons and subsequent fork length ( L _F) at first maturity ( L _F50) were estimated for different fish species reproducing both in the Sine Saloum and in the Gambia River estuaries using a database built from experimental fish samplings between 1990 and 2003 with a purse seine (30 locations in the Sine Saloum and 44 in the Gambia). The database contained 30 553 individuals belonging to 60 different species among which only 20 species reproduced in both estuaries. The breeding seasons peaked just before, or at the beginning of the rainy season (June to July), and there were almost no sexually mature fishes at the beginning of the dry season (November to December). Patterns of differences between L _F50 of the two estuaries did not follow a general trend (positive or negative), but varied in the same way for females and males of a given species. The L _F50 was only systematically reduced with increasing salinity in species living in high-salinity waters (>70). For species living below 70, differences in sizes at first maturity between the two estuaries did not show any clear relationship with salinity. The smallest mature individual found in an environment was a good indicator of the size at first maturity reached in a particular ecosystem because the trend of the species differences between the two ecosystems generally followed that of the differences in size at maturity.     

Exposure of juvenile chinook and chum salmon to chemical contaminants in the Hylebos Waterway of Commencement Bay, Tacoma, Washington

The Hylebos Waterway is an industrialized waterway ofCommencement Bay, Tacoma, Washington, that is severelycontaminated with aromatic and chlorinatedhydrocarbons in the sediment. Juvenile chinook (Oncorhynchus keta) and chum salmon (O.tshawytscha) inhabit this waterway for a few days orweeks during their outmigration from freshwaterstreams to saltwater. The purpose of thisinvestigation was to determine to what degree juvenilechum and chinook salmon captured from the HylebosWaterway might bioaccumulate organic contaminants. These levels of exposure will be compared to previousstudies where such exposures have been linked tobiological dysfunction in juvenile salmon. Theresults showed that juvenile chum and chinook salmonfrom the Hylebos Waterway take up a wide range ofchemical contaminants, compared to fish fromhatcheries or reference estuaries. These contaminantsinclude high and low molecular weight polycyclicaromatic hydrocarbons (PAHs), polychlorinatedbiphenyls (PCBs, including the toxic congeners 105 and118), hexachlorobutadiene (HCBD), hexachlorobenzene(HCB), DDTs, heptachlor, and several pesticides. Immunohistochemical examination of the gill and gut injuvenile chum salmon from the Hylebos Waterway showedthe induction of the P450 metabolizing enzyme. Moreover, concentrations of contaminants in juvenilechinook and chum salmon from the Hylebos Waterway arecomparable to levels previously shown to be associatedwith biological injury in juvenile chinook salmon,such as impaired growth, suppression of immunefunction as demonstrated by reduced B cell function,and increased mortality following pathogen exposure.     

Maternal and environmental influences on egg size and juvenile life‐history traits in Pacific salmon

Life‐history traits such as fecundity and offspring size are shaped by investment trade‐offs faced by mothers and mediated by environmental conditions. We use a 21‐year time series for three populations of wild sockeye salmon (Oncorhynchus nerka) to test predictions for such trade‐offs and responses to conditions faced by females during migration, and offspring during incubation. In years when their 1100 km upstream migration was challenged by high water discharges, females that reached spawning streams had invested less in gonads by producing smaller but not fewer eggs. These smaller eggs produced lighter juveniles, and this effect was further amplified in years when the incubation water was warm. This latter result suggests that there should be selection for larger eggs to compensate in populations that consistently experience warm incubation temperatures. A comparison among 16 populations, with matching migration and rearing environments but different incubation environments (i.e., separate spawning streams), confirmed this prediction; smaller females produced larger eggs for their size in warmer creeks. Taken together, these results reveal how maternal phenotype and environmental conditions can shape patterns of reproductive investment and consequently juvenile fitness‐related traits within and among populations.     

Ontogenetic changes in schooling behaviour during larval and early juvenile stages of Pacific bluefin tuna Thunnus orientalis

Schooling was first observed at 25–27 days after hatching (26· 2–33· 8 mm, total length) in the Pacific bluefin tuna Thunnus orientalis. At this time, the mode of swimming changed from intermittent sprinting to continuous cruising, and this allowed the fish to adjust to an inertial hydrodynamic environment.     

An analysis of the distribution of juvenile Atlantic salmon (Salmo salar) in nature as a function of relatedness using microsatellites

The major objective of this study was to test the hypothesis that juvenile Atlantic salmon kin occupy adjacent territories in their natural habitat in order to profit from the benefits associated with kin-biased behaviours, as has been observed under controlled laboratory conditions. Microsatellites were used to establish the relatedness of salmon fry (in their first summer of life) and parr (in their second and third summer of life) captured in adjacent territories. We did not observe a relationship between the proximity and the relatedness of either parr of the same cohort or fry in their natural habitat. Although many pairs of fry were identified as being related when sampled immediately after emergence, most family groups did not occupy adjacent territories. The high dispersal potential in rivers, the low occupation rate of the habitat and the incidence of half-sibs in nature most probably reduce the opportunity and advantage of kin-biased behaviour, in contrast to laboratory studies conducted in artificial, high-density conditions.     

Effects of spatial scale and foraging efficiency on the predictions made by spatially-explicit models of fish growth rate potential

Synopsis Spatially-explicit modeling of fish growth rate potential is a relatively new approach that uses physical and biological properties of aquatic habitats to map spatial patterns of fish growth rate potential. Recent applications of spatially-explicit models have used an arbitrary spatial scale and have assumed a fixed foraging efficiency. We evaluated the effects of spatial scale, predator foraging efficiency (combined probabilities of prey recognition, attack, capture, and ingestion), and predator spatial distribution on estimates of mean growth rate potential of chinook salmon,Oncorhynchus tshawytscha. We used actual data on prey densities and water temperatures taken from Lake Ontario during the summer, as well as, simulated data assuming binomial distribution of prey. Results show that a predator can compensate for low foraging efficiency by inhabiting the most profitable environments (regions of high growth rate potential). Differences exist in predictions of growth rate potential across spatial scales of observation and a single scale may not be adequate for interpreting model results across seasons. Continued refinements of this modeling approach must focus on the assumptions of stationary distributions of predator and prey populations and predator foraging tactics.     

Where the fish swim above the birds: configurations and challenges of wetland restoration in the Po Delta,Italy

Wetland and estuary restoration presents a number of complex challenges that are primarily social, cultural, economic, and governance‐related rather than ecological. Here we consider the case of wetland restoration in the Po Delta, Italy. Wetland restoration of the Po Delta is a goal of a broad range of actors in the region and this project is a response to local calls for action. We investigate why local stakeholders are unsatisfied with apparently successful restoration projects, and appraise the factors that favor both the fulfillment of environmental targets and establishment of cooperative relations. We suggest that historical legacies of land use in the Po Delta have influenced current governance practices in a complex and fragmented governance context. Also, patterns of wetland restoration and wetland management practices differ between wetland types, and their outcomes may be influenced by the number of stakeholders involved, funding, and ability to generate direct revenues from management. However, there seem to be no blueprint solutions to successful wetland management and wetland restoration, and results are uneven at the landscape scale and often depending on contingencies. Maintaining traditional practices that retain cultural importance may be seen as part of restoration by local people. As a landscape that is highly anthropogenic and in continuous motion, we argue that the Delta exemplifies some of the challenges that restoration will face in a world increasingly characterized by novel ecosystems. We suggest actions that could contribute to enhancing wetland restoration outcomes in the Po Delta.     

Spatial and temporal patterns in the contribution of fish from their nursery habitats

Because anthropogenic influences threaten the degradation of many ecosystems, determining where organisms live during early life-history stages and the extent to which different areas contribute individuals to adult populations is critical for the management and conservation of a species. Working in Puget Sound, Washington State in the United States, and using a common flatfish (English sole, Parophrys vetulus), we sought to establish (using otolith chemistry) which areas contribute age-0 fish to age-1 population(s), the extent to which this pattern was consistent between two years, and whether this spatial pattern of contribution coincides with surveys of age-0 fish and/or the available area of nearshore habitat. Our study indicated completely different spatial patterns of fish nursery use between the two years of sampling. We highlight that the contribution of individuals from nursery areas is not related to density of recently settled English sole or the available area of nearshore habitat (depth <10 m) in Puget Sound, nor can we draw conclusions based on environmental data (precipitation, water salinity, light transmission, pH, dissolved oxygen, and water temperature). The results of this study highlight (1) the need for assessing the temporal patterns of nursery habitat use, and (2) that, in order to conservatively manage a species and its population(s), it may be necessary to protect several areas that are used intermittently by that species.     

Impact of introduced brown trout on native fish communities in the Pilica River catchment (Poland)

We compared post- and pre-introduction data for the upper Pilica River and its tributaries to investigate the impact of introduced non-native brown trout on native fish communities. Extirpations of species were recorded. More changes concerned differences in abundance and distribution in the investigated rivers rather than extirpations. Human stressors (pollution, regulation) obviously helped the invasion of trout. Repeated introduction to one tributary of the Pilica enabled brown trout to survive for 10 years, despite the presence of pike and the recent appearance of domestic pollution.     

Evidence for an autumn downstream migration and the subsequent estuarine residence of 0+ year juvenile Atlantic salmon Salmo salar L., in England

The use of passive integrated transponder technology facilitated the first observations of the autumn migration of 0+ year Atlantic salmon Salmo salar parr into tidal rearing habitats in the U.K. The quality of these habitats in relation to smolt production and the ecological significance of this alternative life-history strategy are presently not understood.     

Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved

Pancreatic β-cell dysfunction is an early hallmark of type 1 diabetes mellitus. Among the potentially critical factors that cause β-cell dysfunction are cytokine attack, glucotoxicity, induction of endoplasmic reticulum (ER) or mitochondria stress. However, the exact molecular mechanism underlying β-cell's inability to maintain glucose homeostasis under severe stresses is unknown. This study used proinflammatory cytokines, thapsigargin, and rotenone in the presence of high concentration glucose to mimicking the conditions experienced by dysfunctional β-cells in human pancreatic islets, and profiled the alterations to the islet proteome with TMT-based proteomics. The results were further verified with label-free quantitative proteomics. The differentially expressed proteins under stress conditions reveal that immune related pathways are mostly perturbed by cytokines, while the respiratory electron transport chains and protein processing in ER pathways by rotenone. Thapsigargin together with high glucose induces dramatic increases of proteins in lipid synthesis and peroxisomal protein import pathways, with energy metabolism and vesicle secretion related pathways downregulated. High concentration glucose, on the other hand, alleviated complex I inhibition induced by rotenone. Our results contribute to a more comprehensive understanding of the molecular events involved in β-cell dysfunction.     

Contrasting Functional Performance of Juvenile Salmon Habitat in Recovering Wetlands of the Salmon River Estuary, Oregon, U.S.A.

For an estuarine restoration project to be successful it must reverse anthropogenic effects and restore lost ecosystem functions. Restoration projects that aim to rehabilitate endangered species populations make project success even more important, because if misjudged damage to already weakened populations may result. Determining project success depends on our ability to assess the functional state or “performance” and the trajectory of ecosystem development. Mature system structure is often the desired “end point” of restoration and is assumed to provide maximum benefit for target species; however, few studies have measured linkages between structure and function and possible benefits available from early recovery stages. The Salmon River estuary, Oregon, U.S.A., offers a unique opportunity to simultaneously evaluate several estuarine restoration projects and the response of the marsh community while making comparisons with a concurring undiked portion of the estuary. Dikes installed in three locations in the estuary during the early 1960s were removed in 1978, 1987, and 1996, creating a “space‐for‐time substitution” chronosequence. Analysis of the marsh community responses enables us to use the development state of the three recovering marshes to determine a trajectory of estuarine recovery over 23 years and to make comparisons with a reference marsh. We assessed the rate and pattern of juvenile salmon habitat development in terms of fish density, available prey resources, and diet composition of wild juvenile Oncorhynchus tshawytscha (chinook salmon). Results from the outmigration of 1998 and 1999 show differences in fish densities, prey resources, and diet composition among the four sites. Peaks in chinook salmon densities were greatest in the reference site in 1998 and in the youngest (1996) site in 1999. The 1996 marsh had higher densities of chironomids (insects; average 864/m²) and lower densities of amphipods (crustaceans; average 8/m³) when compared with the other sites. Fauna differences were reflected in the diets of juvenile chinook with those occupying the 1978 and 1996 marshes based on insects (especially chironomids), whereas those from the 1987 and reference marshes were based on crustaceans (especially amphipods). Tracking the development of recovering emergent marsh ecosystems in the Salmon River estuary reveals significant fish and invertebrate response in the first 2 to 3 years after marsh restoration. This pulse of productivity in newly restored systems is part of the trajectory of development and indicates some level of early functionality and the efficacy of restoring estuarine marshes for juvenile salmon habitat. However, to truly know the benefits consumers experience in recovering systems requires further analysis that we will present in forthcoming publications.     

Influences of sea level changes and volcanic eruptions on Holocene vegetation in Tonga

Here, we investigate Mid- to Late-Holocene vegetation changes in low-lying coastal areas in Tonga and how changing sea levels and recurrent volcanic eruptions have influenced vegetation dynamics on four islands of the Tongan archipelago (South Pacific). To investigate past vegetation and environmental change at Ngofe Marsh (‘Uta Vava’u), we examined palynomorphs (pollen and spores), charcoal (fire), and sediment characteristics (volcanic activity) from a 6.7-m-long sediment core. Radiocarbon dating indicated the sediments were deposited over the last 7700 years. We integrated the Ngofe Marsh data with similar previously published data from Avai’o’vuna Swamp on Pangaimotu Island, Lotofoa Swamp on Foa Island, and Finemui Swamp on Ha’afeva Island. Plant taxa were categorized as littoral, mangrove, rainforest, successional/ disturbance, and wetland groups, and linear models were used to examine relationships between vegetation, relative sea level change, and volcanic eruptions (tephra). We found that relative sea level change has impacted vegetation on three of the four islands investigated. Volcanic eruptions were not identified as a driver of vegetation change. Rainforest decline does not appear to be driven by sea level changes or volcanic eruptions. From all sites analyzed, vegetation at Finemui Swamp was most sensitive to changes in relative sea level. While vegetation on low-lying Pacific islands is sensitive to changing sea levels, island characteristics, such as area and elevation, are also likely to be important factors that mediate specific island responses to drivers of change.     

Community context and the influence of non-indigenous species on juvenile salmon survival in a Columbia River reservoir

Non-indigenous species (NIS) have been called biological pollutants, which implies that reducing their numbers should reduce negative impacts. To test this hypothesis, we used food web models, parameterized with data from field studies, to ask how reducing the number of NIS co-occurring with endangered salmon would affect salmon mortality. Our analyses indicate that predation on Upper Columbia River spring chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss juveniles was affected very little by NIS reduction. The effects of removing NIS were partly or totally offset by indirect food web interactions, and were subtle compared to effects of native predator management. We predict that the most effective way of reducing predation on salmon smolts will involve managing native predators and targeted removals of specific NIS. Minimizing impact of established NIS thus entails not only reducing NIS prevalence, but also considering background management practices and community context.     

Density, aggregation, and body size of northern pikeminnow preying on juvenile salmonids in a large river

Predation by northern pikeminnow Ptychocheilus oregonensis on juvenile salmonids Oncorhynchus spp. occurred probably during brief feeding bouts since diets were either dominated by salmonids (>80% by weight), or contained other prey types and few salmonids (<5%). In samples where salmonids had been consumed, large rather than small predators were more likely to have captured salmonids. Transects with higher catch-per-unit of effort of predators also had higher incidences of salmonids in predator guts. Predators in two of three reservoir areas were distributed more contagiously if they had preyed recently on salmonids. Spatial and temporal patchiness of salmonid prey may be generating differences in local density, aggregation, and body size of their predators in this large river.