Effects of woody debris on the habitat of juvenile masu salmon (Oncorhynchus masou) in northern Japanese streams

1. The effects of woody debris on stream habitat of juvenile masu salmon ( Oncorhynchus masou ) were examined at two spatial scales, stream reach and channel unit, for first to thirdorder tributaries of the Teshio River in northern Hokkaido, Japan. The fortyeight study reaches were classified into three distinct types: coarsesubstrate steppool (CSP), coarsesubstrate poolriffle (CPR) and finesubstrate poolriffle (FPR) reaches. Each reach type included reaches with different riparian settings, broadly classified as forest (relatively undisturbed forest and secondary forest after fires) or grassland (bamboo bushland and pasture).
2. The reachscale analyses showed that neither total pool volume nor pooltopool spacing was correlated with woody debris abundance in any of the three reach types. Masu salmon density was positively correlated with both woodydebris cover area and total cover area, but not with total pool volume in the reaches.
3. Channelunitscale analyses revealed that woody debris reduced nonpool velocity, increased pool depth and retained fine sediment in pools in FPR reaches, where the size of woody debris was very large relative to the substrate material size. However, woody debris did not influence any of the hydraulic variables (depth, velocity, substrate) in either nonpools or pools of CSP and CPR reaches. Habitat use by masu salmon in nonpools or pools was affected by woodydebris cover area or total cover area rather than by hydraulic variables in any of the reach types.
4. The effects of woody debris on habitat at the reach and channelunit scales in the study area were less than those indicated by previous work in the Pacific Northwest, North America, owing to the relatively small size of the riparian trees. However, the overall results suggested that woody debris in the study area contributed to masu salmon habitat by providing cover at the smaller, microhabitat scale.     

Habitat structure along channel-unit sequences for juvenile salmon: a subunit-based analysis of in-stream landscapes

1. Habitat structure and habitat use by juvenile masu salmon, Oncorhynchus masou Brevoort, in small streams in northern Hokkaido, Japan, were examined by considering 'subunits' (patches within channel units) as structural elements of stream reaches.
2. Whole wetted channel surfaces of three study reaches were divided into 0.5 × 0.5 m quadrats, which were grouped into eight subunit types according to water depth and velocity, and substratum conditions by a cluster analysis. The subunit distribution showed a regular mosaic pattern corresponding to the channel-unit sequence in each of the three reaches.
3. Juvenile masu salmon exhibited a strong preference for a subunit type characterized by greater depth and moderate current velocity (deep–moderate subunit; mean depth = 0.29 m; mean velocity = 0.19 m s⁻¹). This subunit type usually occurred downstream of stretches with fast current. The preference of masu salmon for the deep–moderate subunit could be because of its usual spatial position in relation to other subunit types as well as to the characteristics of the subunit itself.
4. The results suggest that the value of a habitat is determined not only by the characteristics of the habitat itself, but also by those of adjacent habitats. Therefore, habitat use by stream fish should be studied in the context of the whole 'in-stream landscapes'.     

Effects of longitudinal variations in stream habitat structure on fish abundance: an analysis based on subunit-scale habitat classification

SUMMARY 1. Stream reaches contain assortments of various habitat types that can be defined at different spatial scales, such as channel unit (e.g. pools, riffles) and subunit (patches within channel units). We described longitudinal (upstream–downstream) patterns of stream habitat structure by considering subunits as structural elements, and examined their effects on the abundance of masu salmon ( Oncorhynchus masou ) and rosyface dace ( Leuciscus ezoe ) in a third-order tributary of the Teshio River in northern Hokkaido, Japan.
2. Nine subunit types were determined on the basis of water depth, current velocity and substrate, using 0.5 × 0.5 m grids. Although both masu salmon and rosyface dace used pools as a major habitat, the former preferred a subunit type occurring at pool heads (PH subunit) while the latter preferred a slow-current edge type (SE-2 subunit).
3. Along the course of the stream, slow-edge subunits (SE-1, 2 and 3) increased in frequency downstream while fast-edge subunits (FE-1 and 2) decreased, suggesting a downstream development of slow-current edges. Regression analyses indicated that longitudinal variation in masu salmon abundance was explained by the area of PH, rather than pools. Masu salmon density increased with the area of PH. Rosyface dace abundance was explained by a combination of water depth and the area of SE-2, both effects being positive.
4. Longitudinal variations in the abundance of both species were related to the abundance of their preferred habitat at the subunit scale, rather than channel-unit scale. The results emphasise the importance of fine-scale patchiness when examining stream fish habitats.     

Habitat use of Atlantic salmon Salmo salar parr in a dynamic winter environment: the influence of anchor‐ice dams

The effect of anchor‐ice dams on the physical habitat and behavioural responses of Atlantic salmon Salmo salar parr in a small, steep stream was investigated. Anchor‐ice dams formed periodically, leading to a dynamic winter environment as the study reach alternated between riffle and walk dominated habitat. Parr demonstrated large individual variation in habitat use, utilizing most of the wetted stream width, and were generally unaffected by diel changes in the mesohabitat composition. Furthermore, parr displayed high site fidelity in areas with low embedded substrata, and demonstrated few large movements between the three mesohabitat classes present: shallow riffle, walk and pool. Findings from this study question the importance of hydraulic variables such as water depth, flow velocity and dynamic ice formation as single habitat features for juvenile stream salmonids during winter and emphasize the importance of access to substratum cover.     

Habitat selection by juvenile Atlantic salmon: the interaction between physical habitat and abundance

The effect of physical river habitat variables on the distribution of juvenile Atlantic salmon Salmo salar L. in the Rivière de la Trinité, Québec, Canada, was examined using generalized additive modelling. A survey of Atlantic salmon fry and parr densities and habitat variables (flow velocity, water column depth and substratum size) was conducted in the summer months from 1984 to 1992. Clear patterns of habitat use existed: specific ranges of habitat variables were selected, with parr preferring greater velocities, depths and substratum sizes than fry. There was a large variation, however, in juvenile densities for given velocities, depths or substratum sizes, with this variation being greatest in optimal habitats. On examination of an individual year, interaction between the variables was found to explain some of the variation. On a year‐to‐year basis the juvenile Atlantic salmon population was found to exhibit an 'Ideal Free Distribution', which resulted in greatest variation in optimal habitats with year‐to‐year changes in population abundance.     

Assessing the transferability of hydraulic habitat models for juvenile Atlantic salmon

Hydraulic habitat models are logistically and technically challenging and expensive to produce. They are therefore frequently transferred between rivers, often with different environmental conditions, without validation. Although studies have recognised problems with model transfer, few have assessed the consequences for model predictions. This study investigated the local (within sub-catchment) transfer of hydraulic habitat models developed for Atlantic salmon (Salmo salar) fry. Two adjacent reaches were chosen for the study, each containing pool, riffle, glide and run habitats. Detailed topographic surveys were used to develop hydraulic models for the study reaches. Substrate and cover were characterised using transects. Seasonal fish habitat use was characterised by electrofishing. Uniform saturation stocking was employed to ensure standard starting densities across all habitats. Generalised additive models were fitted to fry abundance data. Depth, velocity, dominant substrate and cover were used as predictor variables. The distribution of depth, velocity, dominant substrate and cover differed between the two reaches, but was consistent within reaches across seasons. Substrate exhibited the greatest inter-reach difference. Velocity and depth were the most important individual predictors of fry abundance, with the highest densities observed at moderate velocities (∼0.4 m s⁻¹) and low depths (∼0.1 m) across all seasons. When models were transferred locally between reaches, those that were adjusted for inter-reach differences in mean fry abundance (i.e. those predicting changes in relative abundance) performed better than those transferred without adjustment. Complex models that included substrate and cover typically explained some of the variation in abundance in the transferred reach but performed less well than models containing hydraulic parameters alone. This potentially reflected inter-reach differences in the distribution of substrate and cover. This study suggests that (1) uniform stocking is useful for examining habitat-abundance relationships free from the influence of patchy egg deposition; (2) habitat models should be developed at sites offering maximum environmental complexity at a local level; (3) scientists and managers should avoid transferring models between locations with different environmental characteristics, especially in the absence of model validation; (4) complex models should be avoided, and those containing hydraulic variables alone should be considered, if predictions of habitat quality are to be made at new sites.     

Livestock grazing affects vernal pool specialists more than habitat generalists in montane vernal pools

Questions

Do livestock grazing and seasonal precipitation structure species composition in montane vernal pools? Which grazing and precipitation variables best predict cover of vernal pool specialists and species with broader habitat requirements? Is vernal pool species diversity correlated with livestock exclosure, and at what spatial scales?

Location

Montane vernal pools, northeast California, USA.

Methods

Vegetation was sampled in 20 vernal pools, including pools where livestock had been excluded for up to 20 years We compared plant species composition, functional group composition and species diversity among sites that varied in grazing history and seasonal precipitation using CCA and LMM.

Results

Although vernal pool specialists were dominant in montane vernal pools, over a third of plant cover was comprised of species that occur over a broad range of wetland or upland environments. The species composition of vernal pool plant communities was influenced by both livestock grazing and precipitation patterns, however the relative effects of these environmental variables differed by functional group. Livestock exclosures favoured perennial vernal pool specialists over annual vernal pool specialists. In contrast, the cover of habitat generalists was more strongly influenced by seasonal precipitation than livestock grazing. At small spatial scales, species richness and diversity decreased as the number of years a pool had been fenced increased, but this relationship was not significant at a larger spatial scale.

Conclusions

Both livestock grazing and seasonal precipitation structure the montane vernal pool plant community. We found that livestock grazing promotes the cover of annual vernal pool specialists, but at the expense of perennial vernal pool specialists. Wetter vernal pools, however, support higher cover of wetland generalist species regardless of whether pools are grazed.     

Spatial expansion and increased population density of masu salmon parr independent of river restoration

Spatial expansion and increased population abundance of masu salmon Oncorhynchus masou have been recently reported following habitat restoration in some rivers, but no studies have examined these types of changes under natural conditions. We found spatial expansion and increased population density of masu salmon parr in rivers of eastern Hokkaido where no habitat restoration had occurred during the period examined. Changes in the distribution and population densities of parr are often regarded as effects of river habitat destruction and restoration, yet such changes should be evaluated while taking into account the effects of other ocean environmental conditions as well.     

The Atlantic salmon in fresh water: spawning,rearing and production

Summary Fluvial salmonids have evolved to use the diversity of habitats in natural streams for different life history stages and at different seasons. Required freshwater habitat of Atlantic salmon can be classified generally as that suitable (i) for spawning, (ii) for feeding during the major growing period, and (iii) for overwintering.Spawning habitat of salmon is usually in rapid water at the tail of pools on the upstream edge of a gravel bar, ideally with depths about 25 cm, in mean water velocities of about 30–45 cm s^-1, with maximum velocities about 2 body lengths s^-1, and with a substrate of irregularly shaped stones of cobble, pebble, and gravel.Underyearling salmon (<7 cm TL) are most common in shallow (<15 cm) pebbly riffles, whereas older and larger parr (>7 cm TL) are usually in riffles deeper than 20 cm with a coarse substrate. Depth preference increases with size. Multiple linear regression models quantifying parr habitat have identified substrate as an important variable, with a positive relationship to an index of coarseness. Negative relationships were found with mean stream width, range of discharge, and overhanging cover. Water chemistry, especially alkalinity, nitrates, and phosphates, are important regulators of production. Although similar variables had importance, coefficients among rivers differed. Interactions occur among variables. Further studies are required to quantify productive capacity of habitat for parr. Results suggest that useful models can be derived and if a river system is mapped, and stratified by habitat, then smolt yield could be predicted and the required egg deposition could be estimated.In winter, young salmon shelter among coarse substrate or move to pools, but continue feeding, with larger parr being more active.Feeding is in general opportunistic. Food consists mainly of insects, taken primarily in the water column, but also from the surface and at the bottom. Young salmon in flowing water are highly territorial but are less so in slow or still waters. In fast water, parr use their large pectoral fins to apply themselves to the substrate, allowing them to occupy this type of habitat with little expenditure of energy. Height above the substrate decreases with water velocity, but increases with temperature and social status. Although riffles are preferred habitat, and are relatively more productive, lentic waters can be occupied where there are few predators or severe competitors and may provide significant smolt yield in some systems. Selective segregation minimizes competition between salmon and brook charr or brown trout, but brook charr and brown trout may have negative effects on underyearling salmon, and on parr in pools, whereas salmon have negative effects on small brook charr and brown trout in riffles and flats. Competition by both interference and exploitation results in interactive segregation when the resource, mainly food, becomes limiting.Limited downstream movement of underyearling salmon may occur during the summer. Older juveniles may make upstream movements, but generally migrate downstream, with most movements in the spring, and a lesser peak of activity in the autumn. Dispersal tends to be mainly downstream, indicating that for full distribution, spawning areas are best located upstream. High densities of yearling parr may have negative effects on growth and survival of underyearlings in some river systems, but apparently not in others, so that future research is required in this regard. Density-dependent growth is evident where food is limiting, and can provide an indicator of densities of cohorts so that if a quantitative relationship has been derived, mean size from a sample can give an estimate of the density at that station, with minimum size occurring at carrying capacity. Such regressions vary between habitats with differing productive capabilities, so that future research could provide useful models for assessing productive capacity of a habitat, and optimum densities. Life history strategies can change with changes in density-dependent growth rates. Present stock-recruitment functions do not take environmental variables into consideration, and have limited applicability. Further research is required to determine optimum spawning requirements for salmon in different types of river systems in different geographical areas.     

Spatial and temporal variation in fish assemblages of drying stream pools: The role of abiotic and biotic factors

Droughts and summer drying create unusual temporary aquatic habitats in the form of isolated pools in many small streams around the world. To examine spatial and temporal variation in fish community structure of drying stream pools, their relation to abiotic environmental variables, and associations among species, fish were sampled during summer 1995 and 1996 from pools of four streams in the Ozark mountains, Arkansas, USA. Redundancy analysis of physical-chemical variables showed significant differences among stream sites, but no significant difference between years or stream site by year interaction. Stream sites separated consistently along axes one (habitat heterogeneity) and two (temperature/canopy cover) in both years. Redundancy analysis of fish species-size class densities showed a significant stream site by year interaction. Groupings of stream sites based on fish assemblages were not well explained by physical-chemical variables measured at the pool scale, but were related to location within the drainage basin, and these groupings differed between years. There were 27 (15.8%) and 10 (5.8%) significant associations found among fish species-size classes in 1995 and 1996, respectively, and all but two significant associations in 1995 were positive. Pool depth, habitat heterogeneity, pool size and dissolved oxygen/canopy cover were important local abiotic factors depending on response variables examined. In both years, large fish total density, large central stoneroller density (80 mm TL), and small sunfish (<80 mm TL) density were positively related to pool depth. Otherwise, there was no consistent relationship between physical-chemical variables and dependent variables (fish density and species richness) within a year or between years for a given dependent variable. These results support the hypothesis that local abiotic factors are important in structuring fish assemblages in harsh environments, but the importance of those factors varies temporally, and regional influences appear to override local abiotic conditions as factors structuring fish assemblages in drying stream pools. Predation by terrestrial vertebrates may also be an important factor structuring these fish assemblages that has been largely overlooked.     

Predator–prey relationships within natural,restored, and created vernal pools

We performed a multiyear monitoring study to compare amphibian habitat quality among four natural, four restored, and six created pools. We used successful reproduction and metamorphosis of two vernal pool indicator species, the wood frog and spotted salamander, to represent desired outcomes. Ordination techniques were used to identify the aspects of habitat quality that were most correlated with desired outcomes. Previously published results indicated that pool depth, volume, and hydroperiod were among the best predictors of success, regardless of pool type. Observations in the first few years of monitoring also suggested that pools with longer hydroperiods had a greater abundance of aquatic predators of eggs and larvae of indicator species. This follow‐up study further explores and compares predator–prey relationships among pool types. We quantified within‐pool predator and prey abundance and diversity and collected another year of data on the reproductive success of indicator species. Our results confirmed that mean predator abundance was eight times higher in pools with longer hydroperiods. We documented a 96% decrease in wood frog survival rates in a semi‐permanent, natural pool following a 41% decrease in overhead canopy cover and an increase in green frog abundance. At the same time, wood frog reproductive success increased in nearby restored pools with lower predator abundance. Pools with the highest mean survival rates for the two indicator species combined were short‐ or long‐cycle pools (i.e. hydroperiod of 12–35 weeks) with low predator abundance (i.e. <1 organism L^?1) and greater proportions of arthropod prey relative to other food items.     

Static habitat partitioning and dynamic selection by sympatric young Atlantic salmon and brown trout in south-west England streams

Direct underwater observation of micro‐habitat use by 1838 young Atlantic salmon Salmo salar [mean L_T 7·9 ± 3.1(s.d.) cm, range 3·19] and 1227 brown trout Salmo trutta (L_T 10·9 ± 5·0 cm, range 3·56) showed both species were selective in habitat use, with differences between species and fish size. Atlantic salmon and brown trout selected relatively narrow ranges for the two micro‐habitat variables snout water velocity and height above bottom, but with differences between size‐classes. The smaller fishes <7 cm held positions in slower water closer to the bottom. On a larger scale, the Atlantic salmon more often used shallower stream areas, compared with brown trout. The larger parr preferred the deeper stream areas. Atlantic salmon used higher and slightly more variable mean water velocities than brown trout. Substrata used by the two species were similar. Finer substrata, although variable, were selected at the snout position, and differences were pronounced between size‐classes. On a meso‐habitat scale, brown trout were more frequently observed in slow pool‐glide habitats, while young Atlantic salmon favoured the faster high‐gradient meso‐habitats. Small juveniles <7 cm of both species were observed most frequently in riffle‐chute habitats. Atlantic salmon and brown trout segregated with respect to use of habitat, but considerable niche overlap between species indicated competitive interactions. In particular, for small fishes <7 cm of the two species, there was almost complete niche overlap for use of water depth, while they segregated with respect to water velocity. Habitat suitability indices developed for both species for mean water velocity and water depth, tended to have their optimum at lower values compared with previous studies in larger streams, with Atlantic salmon parr in the small streams occupying the same habitat as favoured by brown trout in larger streams. The data indicate both species may be flexible in their habitat selection depending on habitat availability. Species‐specific habitat overlap between streams may be complete. However, between‐species habitat partitioning remains similar.     

Seasonal and spatial microhabitat selection and segregation in young Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L., in a Norwegian river

Seasonal microhabitat selection by sympatric young Atlantic salmon and brown trout was studied by diving. Both species, especially Atlantic salmon, showed seasonal variation with respect to surface and mean water velocities and depth. This variation is partly attributed to varying water flows and water temperatures. In winter the fish sought shelter in the substratum. A spatial variation in habitat use along the river due to different habitat availabilities was observed. Both species occupied habitats within the ranges of the microhabitat variables, rather than selecting narrow optima. It is hypothesized that the genetic basis allows a certain range to the behavioural response. Microhabitat segregation between the two species was pronounced, with brown trout inhabiting the more slow-flowing and partly more shallow stream areas. Atlantic salmon tolerated a wider range of water velocities and depths. Habitat suitability curves were produced from both species. It is suggested that habitat suitability curves that are based on observations of fish occupancy of habitat at median or base flow may not be suitable in habitat simulation models, where available habitat is projected at substantially greater water flows.     

Spatio-temporal patterns of fish assemblages in a large regulated alluvial river

1. The River Durance, the last alpine tributary of the River Rhône, is a large, braided alluvial hydrosystem. Following large-scale regulation, flow downstream of the Serre-Ponçon dam has been maintained at 1/40th of previous annual mean discharge. To assess the effects of historical disturbances, fish assemblages and habitat use were analysed during five summers in a representative reach of the middle Durance.
2. Habitat availability and use were assessed with a multi-scale approach including the variables water depth, current velocity, roughness height of substratum, amount of woody debris and lateral/longitudinal location. Eighteen fish species were sampled by electrofishing in 289 habitat sample units.
3. Partial least square (PLS) regression showed that taxa were mainly distributed according to relationships between their total length and water depth/velocity variables. Fish assemblage composition was also related to roughness height as well as distance from the bank or to the nearest large woody debris. However, PLS regression revealed no significant differences in habitat selection between two periods of varying hydromorphological stability.
4. Fish distribution patterns and density were related to proximity to the bank and cover, indicating that local scale variables need to be considered in conservation and restoration programmes.     

Application of a bioenergetics model to estimate the influence of habitat degradation by check dams and potential recovery of masu salmon populations

Using a bioenergetics model, we examined how check dams negatively effect masu salmon (Oncorhynchus masou) populations by causing habitat loss in upstream areas and habitat degradation in downstream areas. The potential recovery of masu salmon populations in the upstream area was estimated based on the expected biomass and potential recovery area. We also determined if and how fish carrying capacity is affected by degradation of substrate conditions (armoring and compaction) in the downstream area. Recovery of upstream areas was considered to be effective in enhancing and conserving masu salmon populations. We demonstrated that the dam-induced altered substrate conditions and habitat degradation in the downstream area resulted in a considerable reduction of drifting prey. Simulation analysis revealed that a 40 % increase in the abundance of masu salmon juveniles in the downstream area could be expected if substrate conditions were restored. We concluded that both improvement of migration barriers and restoring the sediment regime would be important in enhancing and conserving wild masu salmon populations.     

Factors influencing use of freshwater pools by otters, Lutra lutra, in a marine environment

Eurasian otters ( Lutra lutra ) inhabiting a marine environment need to wash in freshwater in order to maintain the insulating properties of their fur. Use of freshwater pools by otters on the coast of Skye was studied in order to determine factors influencing pool choice. A number of characteristics were recorded for all pools present. Otter spraints were recorded as an indication of pool use. Only 34% of available pools were utilized by otters. Stepwise logistic regression revealed that choice of pools is influenced by pool depth, the percentage of a pool's substratum composed of flat rock, and the surrounding percentage cover of short grass. Possible reasons for these associations are discussed. The information may be of use when selecting and managing coastal areas for otter conservation.     

Riverine environmental characteristics and seasonal habitat use by adult Sakhalin taimen Hucho perryi

The study identified seasonal habitat use by endangered adult Sakhalin taimen Hucho perryi and the environmental characteristics of their habitat (water depth, amount of riparian forest and sinuosity). Fifteen adult H. perryi with acoustic tags were tracked by towing an acoustic receiver with a canoe in the Bekanbeushi River system in eastern Hokkaido Island, Japan, during each month from late April to late November 2008. Individuals mainly used midstream (shallower than downstream) habitats in all seasons. These locations were generally characterized by relatively dense riparian forests and high sinuosity, indicating the presence of pools. In spring, individuals used habitats with less riparian forest cover compared to mean value of the river channel. From spring to autumn, adult H. perryi selected limnologically complex habitats with meandering channels. From summer to autumn, individuals selected habitats with more riparian forest cover. The inverse relationship between H. perryi detection and riparian forest area in spring was a result of seasonal defoliation in deciduous riparian forests.     

Invertebrate community composition differs between restored and natural vernal pools

The loss of freshwater wetlands worldwide has underscored the importance of restoration to enhance biodiversity and functional objectives. While aquatic invertebrate communities within restored perennial freshwaters are well studied, few studies have occurred in the greatly reduced habitat of seasonal wetlands, such as vernal pools. California vernal pools have experienced high habitat loss and support many threatened or endangered invertebrate species. We compared 90 natural and 90 restored vernal pools of different ages across 10 sites throughout California and Southern Oregon using the Sars' method. Large branchiopod abundance, total invertebrate abundance, class richness, and community composition were assessed between pool types (natural vs. restored) and along environmental gradients (e.g. site, pool depth, surface area, age since restoration). Large branchiopod and total invertebrate abundance were 215 and 274% higher in natural pools than restored pools, but class richness was not different. Community composition was significantly different and driven by greater abundances of vernal pool fairy shrimp, San Diego fairy shrimp, Ostracoda, Cladocera, and Copepoda in natural pools. Few environmental or habitat variables explained patterns in richness or abundance. Our work demonstrates that restored pools, even those decades old, are different than natural pools. Future mitigation and monitoring guidelines for restored vernal pools should include quantitative evaluations for aquatic invertebrates. Restored pools are not adequate compensation for lost natural pools because they do not have the same ecological functions and values.