Evaluation of instream habitat enhancement options using fish habitat simulations: case-studies in the river Pas (Spain)

In the northern coast of Spain there are rivers with Atlantic salmon populations. In the upper reaches of one of these streams, river Pas, the effectiveness of habitat enhancement measures was evaluated, under different instream flow conditions. By means of the Instream Flow Incremental Methodology and using a two dimensional hydraulic model (River2D, Steffler P (2000) Software River2D. Two Dimensional Depth Averaged Finite Element Hydrodynamic Model. University of Alberta, Canada), the potential value of stream habitat for different salmon development stages requirements was measured by Weighted Useable Area (WUA). This habitat evaluation was carried out for the unmodified stream reach, which represent the control or natural conditions. Habitat improvement measures (alternate deflectors and low dams) were simulated in the original riverbed topography. Over this modified base, habitat was estimated running River2D again. By comparing the salmon habitat evaluations in the control conditions with those obtained under those improvement conditions we have been able to assess the effectiveness of each one, and the instream flow environment at which maximum improvement is reached. The maximum habitat improvement was obtained around 10 m³/s for the adult salmon, and for the fry and parr it was around 6 m³/s. However, the habitat simulation results show that with both improvement measures, under a natural flow regime the mean annual habitat increases around 1% of the WUA in relation to the control conditions, which is not a significant improvement. A similar small WUA increase was obtained when changing the bed topography, considering geomorphological adjustments due to the new erosion and sedimentation areas caused by the presence of these structures. Therefore, these types of habitat improvement measures are not recommended in these stream reaches.     

Cypriniform fish in running waters reduce hyporheic oxygen depletion in a eutrophic river

1. The hyporheic zone is an important habitat for benthic invertebrates and early-developmental stages of gravel spawning fish. However, the eutrophication of running waters and, in turn, the excessive periphyton biomass leads to its biological clogging. The result of these processes is oxygen depletion and a reduction in the habitat quality of the hyporheic zone.
2. This study assessed whether top-down effects of two important European river fish species, the large herbivorous cypriniform common nase (Chondrostoma nasus, L.) and the large omnivorous cypriniform European chub (Squalius cephalus, L.), can reduce eutrophication effects in the hyporheic zone. A 4-week mesocosm-based field experiment in a eutrophic river was conducted using cage enclosures stocked or not with either nase or chub.
3. The top-down control of periphyton was expected to reduce biological clogging and thereby increase oxygen availability in the hyporheic zone. Accordingly, we hypothesised that in enclosures stocked with either fish the concentrations of dissolved oxygen in the hyporheic zone would be higher and the periphyton biomass would be lower than in enclosures without fish stocking.
4. Hyporheic oxygen concentrations were significantly higher in enclosures stocked with either nase or chub than in enclosures without fish stocking. However, periphyton ash-free dry mass was significantly reduced only in enclosures stocked with nase, not in those stocked with chub. Thus, the positive effects of nase and chub on hyporheic oxygen availability were caused by different mechanisms.
5. Our results demonstrate that nase and chub can reduce eutrophication effects in the hyporheic zone of running waters. Hence, protecting and enhancing stocks of herbivorous and omnivorous fish will contribute to restoring the hyporheic zone in efforts to preserve biodiversity in eutrophic rivers.

     

Mortality induced by electrofishing and handling in five young‐of‐the‐year cyprinids: effect of the fish size,species and anode size

Immediate mortality induced by electrofishing and handling of young‐of the‐year (YOY) fish of five cyprinid species (bitterling Rhodeus amarus, chub Leuciscus cephalus, bleak Alburnus alburnus, barbel Barbus barbus, roach Rutilus rutilus) was quantified during routine YOY fish monitoring (point abundance sampling with backpack electrofisher, in situ identification and measurement). Sampled, identified and measured fish were held in screened containers immersed in the river for 5 h after electrofishing. Bleak exhibited significantly higher mortality (17%) than all other species (1–3%). Mortality decreased significantly with fish length; fish <35 mm exhibited the highest mortality. Anode size (10, 20, and 30 cm diameter) had no direct effect on mortality. Point abundance electrofishing with in situ identification and measurement is a safe method for sampling riverine YOY cyprinids.     

Functional heterogeneity of dry-season fish refugia across a Mediterranean catchment: the role of habitat and predation

SUMMARY 1. Fish in Mediterranean streams survive through the summer in residual surface waters, encompassing a broad range of abiotic and biotic conditions. Yet, the extent to which fish assemblages may be shaped by functional heterogeneity in dry-season refugia is largely unknown. This study addresses this issue, by examining fish assemblage and population attributes, and predation patterns in residual summer habitats (12 pools and six runs) across a Mediterranean catchment in south-west Portugal.
2. Species richness was fairly constant among runs but increased with pool size, with the addition of exotics and rare natives to large pools resulting in nested subsets. The four most common species (chub, nase, loach and eel) were considered generalists in terms of their use of dry-season refugia. Conversely, rare species presented more specialised habitats, with barbel and exotics favouring pools and stickleback favouring runs.
3. Age and size of the two most common species varied among dry-season habitats. Age 0 chub were restricted to runs, where spawning stages (age 2 and older fish) were also more represented. Age 0 nase also concentrated in runs, but the individuals collected in pools exhibited greater growth. Conversely, age 2 and older nase were proportionally more abundant in pools, but with greater growth and better condition in runs.
4. The otter was the main fish predator, consuming fish of all species and size classes, irrespective of habitat. Otter activity concentrated in pools, where predation risk for cyprinids seemed to be much higher than in runs.
5. Dry-season refugia apparently vary in functional importance for different fish species and life stages, acting as complementary units in the landscape. Therefore, the presence of both pool and run refugia trough the summer dry season may play a critical role in promoting the persistence of native species in Mediterranean streams.     

Assessing the effect of Separation Levee Project on Chinese sturgeon (<Emphasis Type="Italic">Acipensor sinensis</Emphasis>) spawning habitat suitability in Yangtze River,China

Chinese sturgeon (Acipenser sinensis) is a protected anadromous fish species. The migration pattern of the fish has been blocked by the construction of Gezhouba Dam, reducing the natural spawning site length to less than 7 km along the Yangtze River. However, the fish has since established an alternative spawning ground in the narrow reach downstream of Gezhouba Dam. To enhance navigation, a Separation Levee Project (SLP) was implemented in the new-found spawning habitat of the fish. To therefore evaluate the effect of the SLP on Chinese sturgeon spawning habitat suitability, the conditions in the spawning habitat were simulated using River2D (a two-dimensional hydrodynamic model). Two main approaches (habitat kinetic energy and circulation metrics) were used in the simulation. The study showed that SLP only slightly changed the physical conditions in the spawning habitat. Using hydrodynamic simulation, the weighted usable area (WUA) before and after the SLP construction was also computed and habitat preference curve developed for water depth and velocity. On the average, SLP reduced WUA—a finding that was consistent with field-measured data. Based on WUA, the habitat conditions were more sensitive to SLP proximity than metrics based on velocity gradients. SLP posed detrimental impacts on the suitability of spawning habitats of Chinese sturgeon. The findings in this study provide further basis for the protection and restoration of Chinese sturgeon spawning habitats in especially the lower reach of Yangtze River.     

Evaluation of physical fish habitat quality enhancement designs in urban streams using a 2D hydrodynamic model

Creating a habitat for a variety of forms of life, such as riparian plants and various fish, is a necessity for stressed river ecosystems. In this study, the hydraulic characteristics of a fish habitat in an urban channel were analyzed using River2D, which is a two-dimensional (2D) depth-averaged finite element hydrodynamic model, to improve the habitat of two target fish in the Daejeon Stream, Korea. These species are Pseudopungtungia nigra, which is an endangered species in the Daejeon Stream, and Zacco platypus, which is a dominant species. In addition, changes in the weighted usable area (WUA) were compared and reviewed as boulders were placed in the stream. The best method for improving the P. nigra's habitat is proposed. A simulation analysis was performed on urban rivers for fish habitats. As a result, a straight and monotonous urban river flow was found to be an appropriate habitat environment for Z. platypus. The WUA for Z. platypus was about 20 times greater than that for P. nigra. Three different fish habitat enhancement methods were evaluated by calculating the WUA for the target fish in the study channel. By calculating the WUA to create fish habitats, the V-type riffle method was found to increase the usable area of the habitat environment for P. nigra by 360%, and the step stone method and single boulder method did so by 60% and 8%, respectively. For the single boulder method, boulders were placed in the channel bed at 3.5-m intervals, which significantly increased habitat availability. Moreover, centralizing the flow pattern in the channel among several types of boulder placements greatly expanded the habitat for P. nigra. Thus, an appropriate placement interval and boulder location that considers the characteristics of the riverbed and target fish species should be researched and implemented.     

Selective Feeding of age-0 Arctic Grayling in Lake-Outlet Streams of the Northwest Territories, Canada

A paucity of information exists on the diet of Arctic grayling, Thymallus arcticus, particularly for young-of-the-year (YOY). We examined the diet of YOY Arctic grayling in relation to food availability, in the Barrenlands region of the Northwest Territories, Canada, where lake-outlet streams serve as nursery habitat for these fish. Given the small size of YOY grayling and the abundance of lake-derived microcrustacea in the drift of these lake-outlet streams, we anticipated that these prey would make up a major component of the YOY's diet. Food selectivity by YOY grayling, however, was strongly sized-biased; although microcrustacea dominated the drift, YOY primarily consumed larger taxa, especially Chironomidae and Simuliidae. Even among these taxa, grayling tended to select the larger individuals. As they grew, YOY grayling took larger numbers of both large and small prey, particularly the larger invertebrates, although prey size range did not change after mid-July. Selection of pupae and avoidance of Ephemeroptera suggest that prey characteristics other than size also contribute to selectivity by YOY grayling. The relatively limited consumption of terrestrial invertebrates and other large prey may reflect the small sizes of fish in this arctic study, as well as differences in prey availability. Despite the abundance of lake-derived prey, instream production of invertebrates should largely determine the productive capacity of Barrenlands streams as fish habitat.     

Effect of water temperature on activity of wintering age‐0 Acipenser transmontanus and A. brevirostrum: An artificial stream study

The effect of water temperature on behaviour and life history of wintering age‐0 = young‐of‐the‐year (YOY) northern sturgeons (populations using winter refuge habitat) is poorly understood. Using artificial stream tanks, we observed the effect of water temperature on 1) day‐time activity of cultured YOY Kootenai River white sturgeon, Acipenser transmontanus, during two winters (2008 and 2009–2010), and 2) observed day‐time activity of cultured YOY Connecticut River shortnose sturgeon, A. brevirostrum, in the winter, 2009–2010. Activity of YOY was measured every 2 to 7 days by visual or video observations on each fish to determine the mean number of 10 cm² square gridlines on the tank bottom crossed by all fish in each replicate tank (two replicate tanks, 10 fish in each tank). Daily water temperature was recorded by a logger in one tank every 20 min, 24 hr per day. In 2008, YOY A. transmontanus activity was positively related to decreasing mean daily temperature (R² = 0.96, p < 0.01) with 0 to 5 gridlines (range) crossed by all fish during observation periods at the coldest temperature (≤3°C). During the winter of 2009–2010, activity of both species was significantly related to decreasing temperature, and again, a mean of 0 to 5 gridlines (range) were crossed by fish at ≤3°C. We accept the hypothesis that YOY of both species are mostly inactive in the day when winter water temperature decreases to ≤3°C. Using the daytime inactivity temperature threshold of 3°C for YOY, and recent temperatures in river reaches where wild wintering YOY likely occur, we predict (a) wild wintering YOY A. transmontanus are moderately active in the day, may be energy challenged due to elevated temperatures from the warm river discharge by Libby Dam, and have poor survival in the regulated Kootenay River, and (b) wintering YOY Connecticut River A. brevirostrum are moderately active most winter months due to elevated natural river temperatures and may be energy challenged. More research is needed on YOY wintering activity and energetics relative to temperature to insure management of river temperature includes conservation of sturgeons.     

River habitat homogenisation enhances trophic competition and promotes individual specialisation among young of the year fish

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Predicting the spatial distribution of the invasive piscivorous chub (<Emphasis Type="Italic">Opsariichthys uncirostris uncirostris</Emphasis>) in the irrigation ditches of Kyushu,Japan: a tool for the risk management of biological invasions

The piscivorous chub (Opsariichthys uncirostris uncirostris) has widely invaded Kyushu Island in Japan, and its presence in irrigation ditches known as creeks around Ariake Bay has caused particular concern because various native freshwater fishes are also known to exist in the region. In order to examine the habitat characteristics that are related to its occurrence, we developed a species distribution model for piscivorous chub that inhabits creeks in the Kase river catchment by using geographic and habitat variables that were both biotic and abiotic. We then evaluated the model by using a different data set from the adjacent Chikugo river catchment. The resulting multiple logistic regression model, whose performance was supported by a high value of 0.881 for the area under the receiver operating characteristics curve (AUC), indicated that the occurrence of piscivorous chub was strongly affected by the watercourse distance from the source populations in the Kase river. The model’s performance was still high (AUC = 0.792) when tested with the data set from the Chikugo river catchment. We also produced a GIS map that projects the predicted distribution of piscivorous chub across all creeks within the Kase river catchment. The result is likely to reflect the connectivity between static and lentic habitat and is not merely a question of the simple distance from the source populations. We also discuss how the potential distribution map can be applied to the management of piscivorous chub.     

On the use of climate covariates in aquatic species distribution models: are we at risk of throwing out the baby with the bath water?

Species distribution models (SDMs) in river ecosystems can incorporate climate information by using air temperature and precipitation as surrogate measures of instream conditions or by using independent models of water temperature and hydrology to link climate to instream habitat. The latter approach is preferable but constrained by the logistical burden of developing water temperature and hydrology models. We therefore assessed whether regional scale, freshwater SDM predictions are fundamentally different when climate data versus instream temperature and hydrology are used as covariates. Maximum entropy (MaxEnt) SDMs were built for 15 freshwater fishes using one of two covariate sets: 1) air temperature and precipitation (climate variables) in combination with physical habitat variables; or 2) water temperature, hydrology (instream variables) and physical habitat. Three procedures were then used to compare results from climate vs instream models. First, equivalence tests assessed average pairwise differences (site‐specific comparisons throughout each species’ range) among climate and instream models. Second, ‘congruence’ tests determined how often the same stream segments were assigned high habitat suitability by climate and instream models. Third, Schoener's D and Warren's I niche overlap statistics quantified range‐wide similarity in predicted habitat suitability from climate vs instream models. Equivalence tests revealed small, pairwise differences in habitat suitability between climate and instream models (mean pairwise differences in MaxEnt raw scores for all species < 3 × 10^–4). Congruence tests showed a strong tendency for climate and instream models to predict high habitat suitability at the same stream segments (median congruence = 68%). D and I statistics reflected a high margin of overlap among climate and instream models (median D = 0.78, median I = 0.96). Overall, we found little support for the hypothesis that SDM predictions are fundamentally different when climate versus instream covariates are used to model fish species’ distributions at the scale of the Columbia Basin.     

Fish assemblages of interior tidal marsh channels in relation to environmental variables in the upper San Francisco Estuary

Tidal marsh wetlands represent critical habitat for many estuarine fishes and are particularly important to conserving and restoring native and at-risk species. We describe the seasonal and regional variation in the composition and abundance of fishes in interior tidal marsh channels in the upper San Francisco Estuary (SFE), and relate these to variation in environmental conditions. Fish were sampled quarterly using modified fyke nets from October 2003 to June 2005 in 18 interior tidal marsh channels spanning 3 distinct river systems: Petaluma River, Napa River and West Delta. We collected 116 samples and 9452 individuals of 30 fish species. Four non-native species dominated—Mississippi silverside, western mosquitofish, yellowfin goby, and rainwater killifish—with an additional 13 species occurring commonly (represented equally by natives and non-natives, residents and transients). Large seasonal differences in composition and abundance of fishes occurred, with the lowest abundances in winter and spring and highest abundances in summer and fall. Correlation of ordination scores and environmental variables further supported the importance of season, as well as fish species’ status (native vs. non-native), feeding preference (pelagic vs. demersal), and marsh utilization (resident vs. transient), as factors influencing fish assemblage composition. The proximity of the marsh systems to freshwater and marine influences, which largely control salinity and temperature variation, explained 26% of the variation in fish composition, while channel geomorphology explained 22%. We recommend that both edge habitat (which may be beneficial to fish foraging success) and the extent of tidal connectivity (which allows access for fishes), in addition to location along the estuarine gradient, be considered in designing and managing tidal marsh restoration.     

Bluehead chub nesting activity: a potential mechanism of population persistence in degraded stream habitats

Aquatic biodiversity continues to decline as humans modify the landscape, mainly because of stream habitat alterations and loss caused by urban development. Bluehead chubs may mitigate some effects of instream habitat degradation by providing clean gravel substrate via their spawning nests. We used path analysis, an extension of multiple linear regression, to explore the relationships among instream habitat degradation, adult chub abundance, chub nesting activity, and chub reproductive performance. Age-0 chub abundance was best explained by small adult abundance and nest abundance. Habitat disturbance indirectly and negatively influenced age-0 chub abundance through adult chubs and nest abundance. Percentages of pool and run habitat also had indirect negative effects on age-0 chub abundance. Several metrics of chub nesting activity (nest density [proportion of substrate occupied by nests], average nest size, and number of nests) were explained by both adult chub abundance and nesting site conditions. Variability among stream systems described significant variation in adult chub abundance and nesting characteristics and, if unaccounted for, would have resulted in large unexplained variability. Chub nesting activity served as a link between habitat degradation, adult chub abundance, and their reproductive performance. Our study provides preliminary evidence that bluehead chubs’ nesting activity may be a mechanism of their persistence in degraded stream reaches. We recommend confirmatory studies through in-stream manipulative experiments.     

Fish recruitment in a large,temperate floodplain: the importance of annual flooding,temperature and habitat complexity

1. Large river floodplains are considered key nursery habitats for many species of riverine fish. The lower Volga River floodplains (Russian Federation) are still relatively undisturbed, serving as a suitable model for studying the influence of flooding and temperature on fish recruitment in floodplain rivers. 2. We examined the interannual variability in recruitment success of young‐of‐the‐year (YOY) fish in the lower Volga floodplain in relation to flood pulse characteristics and rising water temperatures in the spring. We sampled four areas with different flooding regimes, in three consecutive years (2006–2008). 3. Extensive areas with a long duration of flooding accommodated high densities of young fish. This suggests that extended inundation improves the recruitment success of river fish. In areas with extensive flooding, the biomass of YOY of most fish species was about three times higher in 2006 and 2007 than in 2008. We hypothesise that low spring temperatures in 2008 may have caused this reduced recruitment and that a flood synchronised with rising temperature enhances recruitment success. 4. Extensive flooding was particularly favourable for species characterised by large body size, delayed maturation, high fecundity and low parental investment, such as pike Esox lucius, roach Rutilus rutilus and ide Leuciscus idus. Gibel carp Carassius gibelio, a species tolerant of high temperature and hypoxia, did particularly well in small waterbodies in the driest parts of the floodplain. 5. Structural characteristics of floodplain waterbodies explained much of YOY fish density. These species–environment associations varied from year to year, but some species such as common bream Abramis brama, roach and gibel carp showed consistent relationships with structural habitat characteristics in all years, despite large interannual fluctuations in flood pulse and spring temperature.     

Complex interactions between native and invasive fish: the simultaneous effects of multiple negative interactions

We suggest that the ultimate outcome of interactions between native species and invasive species (extinction or coexistence) depends on the number of simultaneous negative interactions (competition and predation), which depends on relative body sizes of the species. Multiple simultaneous interactions may constrain the ability of native species to trade fitness components (i.e., reduced growth for reduced risk of predation) causing a spiral to extinction. We found evidence for five types of interactions between the adults and juveniles of introduced western mosquitofish (Gambusia affinis) and the juveniles of native least chub (Iotichthys phlegethontis). We added ten large (23–28 mm) and seven small (9–13 mm) young-of-the-year (YOY) least chub to replicate enclosures with zero, low, and high densities of mosquitofish in a desert spring ecosystem. Treatments with mosquitofish reduced the average survival of least chub by one-third. No small YOY least chub survived in enclosures with high mosquitofish densities. We also performed two laboratory experiments to determine mortality to predation, aggressiveness, and habitat selection of least chub in the presence of mosquitofish. Mean mortality of least chub due to predation by large mosquitofish was 69.7% over a 3-h trial. Least chub were less aggressive, selected protected habitats (Potamogeton spp.), and were more stationary in the presence of mosquitofish where the dominance hierarchy was large mosquitofish>>large least chubsmall mosquitofish>>small least chub. Least chub juveniles appear to be figuratively caught in a vice. Rapid growth to a size refuge could reduce the risk of predation, but the simultaneous effects of competition decreased least chub growth and prolonged the period when juveniles were vulnerable to mosquitofish predation.     

Microsatellite analysis of relatedness structure in young of the year of the endangered Zingel asper (Percidae) and implications for conservation

1. Zingel asper is one of the most endangered freshwater fish of Western Europe. Because of critical habitat loss and fragmentation, stocking or reintroduction protocols are sometimes considered even though few data are available about the behaviour and biology of the species.
2. The present study is the first attempt to explore the population genetic structure of juveniles (young of the year, YOY) of this endangered species using genetic markers (microsatellite loci). In the Beaume River (ardeche, France), Z. asper exhibits very low densities (10–80 fish per hectare), and it was expected that annual recruitment would comprise only few clutches (full- or half-sibs groups).
3. However, sibship reconstruction in one YOY cohort showed that more than 60% of the adult population reproduced. Dispersal rate in early YOY was high: relatedness estimates showed that only few months after hatching, YOY sibs were mixed among study sites. A large number of breeders together with high dispersal rates explain the high genetic variability observed in small populations of Z. asper .
4. Conservation strategies for the species are discussed based on these results, emphasizing the importance of conserving population genetic variability and preserving habitat connectivity for juveniles.     

Differential responses by two closely related native fishes to restoration actions

Globally, river degradation has decimated freshwater fish populations. To help reverse this trend in a southeastern Australia river, we used multiple restoration actions, including reintroduction of instream woody habitat, riparian revegetation, removal of a weir hindering fish movement, fencing out livestock, and controlling riparian weeds. We monitored the responses of native fish at the segment scale (20 km) and reach scale (0.3 km) over 7 years to assess the effectiveness of the different restoration strategies. Two closely related species, Murray cod Maccullochella peeli and trout cod Maccullochella macquariensis, increased at the restored segment compared with the control segment. However, inherent differences between river segments and low sample size hampered assessment of the mechanisms responsible for segment‐scale changes in fish abundance. In contrast, at the reach scale, only M. peeli abundance significantly increased in reaches supplemented with wood. These differential responses by 2 closely related fish species likely reflect species‐specific responses to increased habitat availability and enhanced longitudinal connectivity when the weir improved passage around a fishway. Changes in M. peeli abundance in segments supplemented with and without wood suggest an increase in carrying capacity and not simply a redistribution of individuals within the segment, facilitated the observed expansion. Our findings confirm the need to consider individual fish species' habitat preferences carefully when designing restoration interventions. Further, species‐specific responses to restoration actions provide waterway managers with precise strategies to target fish species for recovery and the potential to predict fish outcomes based on ecological preferences.     

Direct and indirect effects of predatory young‐of‐year fishes in a dryland river food web

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Spatial Variation in Fish Assemblages across small Mediterranean Drainages: Effects of Habitat and Landscape Context

Much debate about assemblage organization in stream fish may stem from analysing the effects of both local and large-scale processes on assemblage attributes over whole geographic regions. This study addresses this issue, by examining the contribution of local habitat attributes and landscape context to fish assemblage variation across small Mediterranean drainages in southern Portugal. Fish abundance and species composition was estimated in 28 sites, across 10 drainages, in both a dry year (1999) and a wet year (2001), and related to two sets of variables reflecting habitat and landscape characteristics. Fish showed responses to both sets of variables with variance partitioning indicating that landscape context had important effects on species richness whereas habitat attributes were the primary determinants of local fish abundance. In general, high species richness was associated with larger drainage area and higher rainfall variability, whereas variation in species abundances mostly reflected the influence of width, depth, conductivity, current velocity, substrate size and emergent vegetation. The relative contributions of both landscape context and habitat attributes to species richness and abundance were generally lower in 1999 than in 2001, with much less diversified species–habitat relationships being found in the former dry year. These results point to the dynamic nature of assemblage organization, emphasizing the importance of innovative, multi-scale approaches in advancing our knowledge of fish assemblage structure in Mediterranean streams.