Effects of water depth and hydrodynamics on the growth and distribution of juvenile cyprinids in the littoral zone of a large pre-alpine lake

In enclosure experiments in the littoral zone of Lake Constance, Germany, juvenile cyprinids showed significantly reduced somatic growth in the shallow eulittoral zone (0·5 m depth) compared to the sublittoral zone (1·6 m depth). Growth was especially reduced in larger and more deep-bodied fish groups, providing evidence that this is due to increased hydrodynamic stress, induced by ship and wind waves, in the shallow habitats compared to the deep habitat. Other factors such as water temperature and food availability seemed to be of minor importance for the observed growth differences. Gillnet catches at the experimental site and an adjacent site showed that most juvenile cyprinids, including the species from the enclosure study, bream Abramis brama and dace Leuciscus leuciscus , nonetheless prefer shallow habitats compared to deeper sublittoral habitats. Juvenile cyprinids in Lake Constance may prefer these shallow habitats as refuges against larger piscivorous predators, mainly perch Perca fluviatilis , despite the cost in terms of reduced somatic growth indicating that juvenile cyprinids first of all optimize survival rate instead of somatic growth rate.     

Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river

We reared juvenile Chinook salmon for two consecutive flood seasons within various habitats of the Cosumnes River and its floodplain to compare fish growth in river and floodplain habitats. Fish were placed in enclosures during times when wild salmon would naturally be rearing in floodplain habitats. We found significant differences in growth rates between salmon reared in floodplain and river enclosures. Salmon reared in seasonally inundated habitats with annual terrestrial vegetation experienced higher growth rates than those reared in a perennial pond on the floodplain. Growth of fish in the non-tidal river upstream of the floodplain varied with flow in the river. When flows were high, there was little growth and high mortality, but when the flows were low and clear, the fish grew rapidly. Fish displayed very poor growth in tidally influenced river habitat below the floodplain, a habitat type to which juveniles are commonly displaced during high flow events due to a lack of channel complexity in the main-stem river. Overall, ephemeral floodplain habitats supported higher growth rates for juvenile Chinook salmon than more permanent habitats in either the floodplain or river. Variable responses in both growth and mortality, however, indicate the importance of providing habitat complexity for juvenile salmon in floodplain reaches of streams, so fish can find optimal places for rearing under different flow conditions.     

The distribution of salmonids in upland streams in relation to depth and gradient

The distribution of various age classes of salmon and trout was assessed in upland streams by electrofishing. Water depths and site gradients were measured and correlated to fish densities. The fry of both species were significantly more abundant in shallow water; up to 75·3% of salmon fry and 72·2% of trout fry were captured in sites of mean depth < 20 cm. Older trout were found mainly in the deeper areas, with a maximum of 7·4% captured in sites < 20 cm mean depth. Yearling fish were found in all the depth-ranges sampled, but with a tendency for higher numbers in mid-range depths. There were similar correlations in the abundance of each age class with the actual areas of shallow, mid-range and deep water habitat available within sites. Correlations of fish density with gradient indicated that trout were limited in their distribution to areas of lower flow, whereas salmon were not. Since depth and gradient were significantly negatively correlated, there was an apparent preference of trout for slightly deeper habitats than the equivalent year classes of salmon. The observed habitat segregation is discussed in terms of competition and selection.     

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.     

Main stem and off‐channel habitat use by juvenile Chinook salmon in a sub‐Arctic riverscape

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Beavers (Castor canadensis) influence habitat for juvenile salmon in a large Alaskan river floodplain

Our aim was to determine how beavers affect habitats and food resources for juvenile salmon in the Kwethluk River in western Alaska.

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Zooplankton ecology and trophic resources for rearing native fish on an agricultural floodplain in the Yolo Bypass California,USA

Out-migrating juvenile Chinook Salmon Oncorhynchus tshawytscha in California’s Central Valley lack frequent access to historical off-channel habitats such as floodplains. However, many regions have agricultural floodplains that may provide habitat value to young salmon. To determine the suitability of agricultural floodplain, this study tested whether winter-inundated rice fields in a historic flood basin in California’s Central Valley could provide adequate food resources for rearing juvenile Chinook Salmon. We examined the suitability of flooded rice fields for three post-harvest habitat types: stubble, fallow, and disced. Soil emergent and pelagic zooplankton communities were compared to determine colonization sources. Winter-inundated rice fields had high densities of zooplankton, which increased over the course of the study. Daphnia pulex, a large-bodied cladoceran and an excellent forage species of juvenile Chinook Salmon, was abundant in our study. Cladocerans colonized via source water while ostracods likely colonized from a soil egg bank. Overall, there was no discernable effect of habitat type on zooplankton community structure or density, except for D. pulex. Our results suggest that flooded agricultural rearing habitat can support juvenile Chinook Salmon based on high densities of zooplankton and other suitable habitat conditions have the potential to support a robust aquatic food web.     

How relative size and abundance structures the relationship between size and individual growth in an ontogenetically piscivorous fish

While individual growth ultimately reflects the quality and quantity of food resources, intra and interspecific interactions for these resources, as well as individual size, may have dramatic impacts on growth opportunity. Out‐migrating anadromous salmonids make rapid transitions between habitat types resulting in large pulses of individuals into a given location over a short period, which may have significant impact on demand for local resources. We evaluated the spatial and temporal variation in IGF‐1 concentrations (a proxy for growth rate) and the relationship between size and concentration for juvenile Chinook salmon in Puget Sound, WA, USA, as a function of the relative size and abundance of both Chinook salmon and Pacific herring, a species which commonly co‐occurs with salmonids in nearshore marine habitats. The abundance of Chinook salmon and Pacific herring varied substantially among the sub‐basins as function of outmigration timing and spawn timing, respectively, while size varied systematically and consistently for both species. Mean IGF‐1 concentrations were different among sub‐basins, although patterns were not consistent through time. In general, size was positively correlated with IGF‐1 concentration, although the slope of the relationship was considerably higher where Pacific herring were more abundant than Chinook salmon; specifically where smaller individual herring, relative to Chinook salmon, were more abundant. Where Pacific herring were less abundant than Chinook salmon, IGF‐1 concentrations among small and large Chinook salmon were more variable and showed no consistent increase for larger individuals. The noticeable positive effect of relative Pacific herring abundance on the relationship between size and individual growth rates likely represents a shift to predation based on increased IGF‐1 concentrations for individual Chinook salmon that are large enough to incorporate fish into their diet and co‐occur with the highest abundances of Pacific herring.     

Diet,feeding patterns,and prey selection of subyearling Atlantic salmon (Salmo salar) and subyearling chinook salmon (Oncorhynchus tshawytscha) in a tributary of Lake Ontario

Since juvenile Atlantic salmon (Salmo salar) and Chinook salmon (Oncorhynchus tshawytscha) occupy a similar habitat in Lake Ontario tributaries, we sought to determine the degree of diet similarity between these species in order to assess the potential for interspecific competition. Atlantic salmon, an historically important but currently extirpated component of the Lake Ontario fish community, are the focus of a bi‐national restoration effort. Presently this effort includes the release of hatchery produced juvenile Atlantic salmon in Lake Ontario tributaries. These same tributaries support substantial numbers of naturally reproduced juvenile Pacific salmonids including Chinook salmon. Subyearling Atlantic salmon and subyearling Chinook salmon had significantly different diets during each of the three time periods examined. Atlantic salmon fed slightly more from the benthos than from the drift and consumed mainly chirononmids (47.0%) and ephemeropterans (21.1%). The diet of subyearling Chinook salmon was more closely associated with the drift and consisted mainly of chironomids (60.2%) and terrestrial invertebrates (16.0%). Low diet similarity between subyearling Atlantic salmon and subyearling Chinook salmon likely minimizes competitive interactions for food between these species in Lake Ontario tributaries. However, the availability of small prey such as chironomids which comprise over 50% of the diet of each species, soon after emergence, could constitute a short term resource limitation. To our knowledge this is the first study of interspecific diet associations between these two important salmonid species.     

Defining marine habitat of juvenile Chinook salmon, <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>, and coho salmon, <Emphasis Type="Italic">O. kisutch</Emphasis>, in the northern California Current System

We investigated habitat use by juvenile Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) to identify environmental characteristics that may define their optimal marine habitat. We utilized physical and biological data from four cruises in the northern California Current system from Newport, Oregon, to Crescent City, California, in June and August 2000 and 2002. A non-parametric statistical method was used to analyze and select environmental parameters that best defined ocean habitat for each species. Regression trees were generated for all cruises combined to select the most important habitat variables. Chlorophyll a concentration best defined habitat of yearling Chinook salmon, while decapod larvae, salinity, and neuston biovolume defined habitat of yearling coho salmon. Using criteria from the regression tree analysis, GIS maps were produced to show that the habitat of yearling Chinook salmon was widespread over the continental shelf and the habitat of yearling coho salmon was variable and mainly north of Cape Blanco.     

Physiological characterization of juvenile Chinook salmon utilizing different habitats during migration through the Columbia River Estuary

Although off-channel habitats in the estuaries of large rivers impart many benefits to fish that rear within them, it is less clear how these habitats benefit migrating anadromous species that utilize these habitats for short periods of time. We evaluated the physiological correlates (nutritional condition, growth, and smoltification) of habitat utilization (main-channel vs. off-channel) by juvenile Chinook salmon Oncorhynchus tshawytscha during emigration. Fish from the off-channel had higher condition factor scores and relative weights than fish from the main-channel throughout the study period. Plasma triglyceride and protein concentrations were significantly different between habitat types and across the sampling period, suggesting that fish utilizing the off-channel habitats were compensating for energy losses associated with emigration as compared to main-channel fish. Growth potential (RNA to DNA ratio) did not vary by habitat or sampling period, presumably due to short residency time. There were no differences in osmoregulatory capacity (gill Na(+), K(+)-ATPase activity) based on habitat type. Our results indicate that short-term off-channel habitat use may mitigate for energy declines incurred during migration, but likely does not impart significant gains in energy stores or growth.     

Conservation planning for freshwater–marine carryover effects on Chinook salmon survival

Experiences of migratory species in one habitat may affect their survival in the next habitat, in what is known as carryover effects. These effects are especially relevant for understanding how freshwater experience affects survival in anadromous fishes. Here, we study the carryover effects of juvenile salmon passage through a hydropower system (Snake and Columbia rivers, northwestern United States). To reduce the direct effect of hydrosystem passage on juveniles, some fishes are transported through the hydrosystem in barges, while the others are allowed to migrate in‐river. Although hydrosystem survival of transported fishes is greater than that of their run‐of‐river counterparts, their relative juvenile‐to‐adult survival (hereafter survival) can be less. We tested for carryover effects using generalized linear mixed effects models of survival with over 1 million tagged Chinook salmon, Oncorhynchus tshawytscha (Walbaum) (Salmonidae), migrating in 1999–2013. Carryover effects were identified with rear‐type (wild vs. hatchery), passage‐type (run‐of‐river vs. transported), and freshwater and marine covariates. Importantly, the Pacific Decadal Oscillation (PDO) index characterizing cool/warm (i.e., productive/nonproductive) ocean phases had a strong influence on the relative survival of rear‐ and passage‐types. Specifically, transportation benefited wild Chinook salmon more in cool PDO years, while hatchery counterparts benefited more in warm PDO years. Transportation was detrimental for wild Chinook salmon migrating early in the season, but beneficial for later season migrants. Hatchery counterparts benefited from transportation throughout the season. Altogether, wild fish could benefit from transportation approximately 2 weeks earlier during cool PDO years, with still a benefit to hatchery counterparts. Furthermore, we found some support for hypotheses related to higher survival with increased river flow, high predation in the estuary and plume areas, and faster migration and development‐related increased survival with temperature. Thus, pre‐ and within‐season information on local‐ and broad‐scale conditions across habitats can be useful for planning and implementing real‐time conservation programs.     

Adult spawners: A critical period for subarctic Chinook salmon in a changing climate

Concurrent, distribution-wide abundance declines of some Pacific salmon species, including Chinook salmon (Oncorhynchus tshawytscha), highlights the need to understand how vulnerability at different life stages to climate stressors affects population dynamics and fisheries sustainability. Yukon River Chinook salmon stocks are among the largest subarctic populations, near the northernmost extent of the species range. Existing research suggests that Yukon River Chinook salmon population dynamics are largely driven by factors occurring between the adult spawner life stage and their offspring's first summer at sea (second year post-hatching). However, specific mechanisms sustaining chronic poor productivity are unknown, and there is a tremendous sense of urgency to understand causes, as declines of these stocks have taken a serious toll on commercial, recreational, and indigenous subsistence fisheries. Therefore, we leveraged multiple existing datasets spanning parent and juvenile stages of life history in freshwater and marine habitats. We analyzed environmental data in association with the production of offspring that survive to the marine juvenile stage (juveniles per spawner). These analyses suggest more than 45% of the variability in the production of juvenile Chinook salmon is associated with river temperatures or water discharge levels during the parent spawning migration. Over the past two decades, parents that experienced warmer water temperatures and lower discharge in the mainstem Yukon River produced fewer juveniles per spawning adult. We propose the adult spawner life stage as a critical period regulating population dynamics. We also propose a conceptual model that can explain associations between population dynamics and climate stressors using independent data focused on marine nutrition and freshwater heat stress. It is sobering to consider that some of the northernmost Pacific salmon habitats may already be unfavorable to these cold-water species. Our findings have immediate implications, given the common assumption that northern ranges of Pacific salmon offer refugia from climate stressors.     

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.     

Ontogeny of Diel Pattern of Stream-Margin Habitat Use by Emerging Brown Trout, Salmo Trutta, in Experimental Channels: Influence of Food and Predator Presence

Age-0 brown trout, Salmo trutta, inhabit shallow and slow-flowing habitats where they can easily maintain stationary swimming positions. However, recent results have shown that they use deeper and faster habitats during daylight than at night, suggesting the occurrence of a nocturnal movement toward stream-margin habitats. Experiments were conducted to describe precisely when this diel pattern of habitat use appears during ontogeny. In two indoor channels, free-embryo brown trout were deposited under the gravel. When emerging, alevins were free to choose between margin (2 cm deep, 0-2 cm s^-1) or deep habitat (12 cm, 2-4 cm s^-1), or to leave the channel (upstream or downstream). During the week of emergence, upstream and downstream catches, fish habitat use (deep habitat or margin), and fish behavior (resting or swimming) were measured by direct observations and trap counts. Three treatments were performed: (1) fish artificially fed on drifting invertebrates, (2) fish exposed to predators (bullhead, Cottus gobio), and (3) control channels (no food, no predator). In control and food channels, a diel pattern of habitat use was observed 1-2 days after the emergence started. Most fish rested in the margin at night, whereas they moved towards the deep habitat during daylight to hold stationary swimming positions. In the presence of bullhead, most trout were cryptic, and visible fish stood in the margin during both daylight and at night. The importance of predation risk and foraging behavior on the ontogeny of the diel pattern of habitat use is discussed. Results support the direct development without larva from free-embryo via alevin in brown trout.     

Shallow water predation risk for a juvenile flatfish (winter flounder; Pseudopleuronectes americanus, Walbaum) in a northwest Atlantic estuary

Many small fish, including several juvenile Atlantic flatfish, are most abundant in shallow areas presumable because these habitats enhance survivorship and/or growth. In this study, we investigated size-dependent depth distributions and the role of shallow habitats as predator refuges for age-0 winter flounder (Pseudopleuronectes americanus) in a northwest Atlantic estuarine nursery. Analysis of trawl surveys performed during the larval settlement period throughout the Navesink River and Sandy Hook Bay, New Jersey, showed that as fish increased in size, depth of occurrence gradually decreased, so that individuals >35 mm standard length (SL) were concentrated in habitats ∼1 m deep. Tethering in structurally simple and adjacent shallow and deep habitats showed that predation risk for flounder (30-50 mm SL) was low in shallow water (<1 m) and increased rapidly with depth. Summer flounder (Paralychthys dentatus), which were more abundant in trammel nets in deep habitats and included winter flounder in their diets, appeared to be important consumers of tethered fish. Our results indicate that following larval settlement, winter flounder emigrate from or suffer high mortality in deeper water to become concentrated in shallow habitats that can serve as predator refuges even when they lack complex physical structures. These results highlight the potential for functional habitat loss when natural and/or anthropogenic factors make shallow habitats unavailable to young fish.     

Mangrove Habitat Use by Juvenile Reef Fish: Meta-Analysis Reveals that Tidal Regime Matters More than Biogeographic Region

Identification of critical life-stage habitats is key to successful conservation efforts. Juveniles of some species show great flexibility in habitat use while other species rely heavily on a restricted number of juvenile habitats for protection and food. Considering the rapid degradation of coastal marine habitats worldwide, it is important to evaluate which species are more susceptible to loss of juvenile nursery habitats and how this differs across large biogeographic regions. Here we used a meta-analysis approach to investigate habitat use by juvenile reef fish species in tropical coastal ecosystems across the globe. Densities of juvenile fish species were compared among mangrove, seagrass and coral reef habitats. In the Caribbean, the majority of species showed significantly higher juvenile densities in mangroves as compared to seagrass beds and coral reefs, while for the Indo-Pacific region seagrass beds harbored the highest overall densities. Further analysis indicated that differences in tidal amplitude, irrespective of biogeographic region, appeared to be the major driver for this phenomenon. In addition, juvenile reef fish use of mangroves increased with increasing water salinity. In the Caribbean, species of specific families (e.g. Lutjanidae, Haemulidae) showed a higher reliance on mangroves or seagrass beds as juvenile habitats than other species, whereas in the Indo-Pacific family-specific trends of juvenile habitat utilization were less apparent. The findings of this study highlight the importance of incorporating region-specific tidal inundation regimes into marine spatial conservation planning and ecosystem based management. Furthermore, the significant role of water salinity and tidal access as drivers of mangrove fish habitat use implies that changes in seawater level and rainfall due to climate change may have important effects on how juvenile reef fish use nearshore seascapes in the future.     

Winter behaviour of juvenile Atlantic salmon Salmo salar L. in experimental stream channels: effect of substratum size and full ice cover on spatial distribution and activity pattern

Activity and choice of areas offering different cover (substratum or surface ice) for juvenile Atlantic salmon Salmo salar were studied in experimental stream channels during winter. Channels were completely ice covered between December and March. During this period, the ice thickness increased from 50 to 300 mm after which 50% of the ice was experimentally removed and followed by c. 2·5-fold increase in discharge to simulate the effects of spring flood. Large substrata provided preferred habitats but areas with small substratum sizes were also used when full surface ice provided above-stream cover and the stream discharge was relatively low. The fish remained nocturnal throughout the study but the level of day activity significantly increased as the surface ice became thicker. Maximum movement distance during a 24 h period and homing-at-dawn behaviour remained at a constant level throughout the main winter, but significantly changed during the simulated spring flood (mean ± s . e . maximum extent of movements within 24 h increased from 1·1 ± 0·1 to 3·0 ± 0·5 m; homing behaviour decreased from the highest level of 89·3 to 34·6% during spring flood). Overwinter survival was high (92·9%). Relative mass increase during the study ranged from –8·3 to 28·5%, and 84% of the juvenile Atlantic salmon gained mass. The highest rates of mass increase were associated with frequent movements between areas of different substratum size. The results indicate that during winter: (1) Atlantic salmon parr preferred large substratum cover compared with surface ice cover at the fish densities studied here, (2) juvenile Atlantic salmon were predominantly nocturnal but diurnal activity increased as surface ice became thicker and (3) increase in water discharge during spring altered the behaviour of juvenile Atlantic salmon and may have caused additional habitat shifts.     

Effects of predator and flow manipulation on Chinook salmon (Oncorhynchus tshawytscha) survival in an imperiled estuary

We evaluated the effects of non-native, piscivorous fish removal and artificial flow manipulation on survival and migration speed of juvenile Chinook salmon, Oncorhynchus tshawytscha, emigrating through the eastern Sacramento-San Joaquin Delta of California (Delta) using a Before-After-Control-Impact study design. Acoustically-tagged salmon survival increased significantly after the first predator reduction in the impact reach. However, survival estimates returned to pre-impact levels after the second predator removal. When an upstream control gate opened (increasing flow and decreasing tidal effect) juvenile salmon emigration time decreased and survival increased significantly through the impact reach. Though a short-term, single season experiment, our results demonstrate that predator control and habitat manipulation in the Delta tidal transition zone can be effective management strategies to enhance salmon survival in this highly altered system.     

Juvenile Atlantic salmon in the Varzuga River (White Sea Basin)

In the Varzuga River (Kola Peninsula), juvenile Atlantic salmon occur at a high mean density of 1·1 individuals per m², with a relatively low growth rate, reaching c. 8 g at age 3. They migrate to sea at ages 2–4 before they are fully silvered. Mortality is not high and the fish forage in the estuary where they grow fast and acclimate to the pelagic and high salinity habitat.