Quantifying fluid and bed dynamics for characterizing benthic physical habitat in large rivers

Sturgeon use benthic habitats in and adjacent to main channels where environmental conditions can include bedload sediment transport and high near‐bed flow velocities. Bed velocity measurements obtained with acoustic Doppler instruments provide a means to assess the concentration and velocity of sediment moving near the streambed, and are thus indicative of the bedload sediment transport rate, the near‐bed flow velocity, and the stability of the substrate. Acoustic assessments of benthic conditions in the Missouri River were conducted at scales ranging from the stream reach to individual bedforms. Reach‐scale results show that spatially‐averaged bed velocities in excess of 0.5 m s⁻¹ frequently occur in the navigation channel. At the local scale, bed velocities are highest near bedform crests, and lowest in the troughs. Low‐velocity zones can persist in areas with extremely high mean bed velocities. Use of these low‐velocity zones may allow sturgeon to make use of portions of the channel where the average conditions near the bed are severe. To obtain bed velocity measurements of the highest possible quality, it is necessary to extract bottom‐track and GPS velocity information from the raw ADCP data files on a ping‐by‐ping basis. However, bed velocity measured from a point can also be estimated using a simplified method that is more easily implemented in the context of routine monitoring. The method requires only the transect distance and direction data displayed in standard ADCP data‐logging software. Bed velocity estimates obtained using this method are usually within 5–10% of estimates obtained from ping‐by‐ping processing.     

Glacial rivers: physical habitat and ecology

1. This review examines the physical habitat and ecology of glacial rivers which have been relatively unstudied compared with rivers originating from other sources. 2. Typical glacial rivers have summer temperatures below 10°C, a single seasonal peak in discharge, which in the Northern Hemisphere typically occurs in July, a diel fluctuation in flow which usually peaks in late afternoon, and turbidity levels in summer that exceed 30 NTU. These variables contrast with those in snowmelt/rainfall streams, particularly in summer, and make conditions more extreme for the biota. 3. Where maximum temperatures are 2°C benthic invertebrate communities are dominated by Diamcsa (Chironomidae). Downstream, temperatures increase, channels become more stable and valley floors become older. Orthocladiinae (Chironomidae), Simuliidae, Baetidae, Nemouridae and Chloroperlidae become characteristic members of the invertebrate community. 4. Fauna may be displaced, or at least colonization delayed, by channel instability; the variable age structure of the valley floor will influence the faunal gradient, which may also be reset by the effects of tributaries, lakes and valley confinement. 5. We propose a qualitative model that outlines zoobenthic community gradients determined by two principal variables, water temperature and channel stability, as a function of distance downstream, or time since deglaciation.     

Linking local ecological knowledge and habitat modelling to predict absolute species abundance on large scales

Assessing the spatial structure of abundance of a species is a basic requirement to carry out adequate conservation strategies. However, existing attempts to predict species abundance, particularly in absolute units and on large scales, are scarce and have led to weak results. In this work we present a scheme to obtain, in an affordable way, a predictive model of absolute animal abundance on large scales based on the modelling of data obtained from local ecological knowledge (LEK) and its calibration. To exemplify this scheme, we build and validate a predictive absolute abundance model of the endangered terrestrial tortoise Testudo graeca in Southeast Iberian Peninsula. For that purpose, we collected distribution and relative abundance data of T. graeca using a low cost methodology, such as LEK, by means of interviewing shepherds. The information from LEK was employed to build a predictive habitat-based model of relative abundance. The relative abundance model was transformed into an absolute abundance model by means of calibration with a classical absolute abundance sampling method such as distance sampling. The obtained absolute abundance model predicted the observed absolute abundances values well in independent locations when compared with other works (R ² = 36%) and thus can offer a cost-effective predictive ability. Our results show that reliable habitat-based predictive maps of absolute species abundance on regional scales can be obtained starting from low cost sampling methods of relative abundance, such as LEK, and its calibration.     

A comparison of habitat diversity and interannual habitat dynamics in actively and passively restored mountain rivers of Germany

We compared habitat diversity and morphodynamics of ‘actively’ restored reaches (including removal of bank fixation, widening and large wood placement) with ‘passively’ restored reaches (abandonment of channel maintenance) and adjacent non-restored control reaches in medium-sized Central European mountain rivers. Habitat diversity and river morphology were mapped in two consecutive years and changes in habitat composition (channel features, substrates) and morphological changes (active depth and width) were quantified. In both years, habitat diversity was generally higher in the restored reaches compared to their non-restored counterparts, and significantly differed between restoration approaches, with average values in actively restored reaches being about 60% larger than in passively restored reaches. Channel feature composition differed significantly, both between restored and unrestored reaches, and between restoration approaches, whereas substrate composition was similar in all investigated reaches, indicating that restoration had a higher effect on mesohabitat than on microhabitat conditions. Interannual habitat dynamics in respect to channel feature composition were larger in the actively restored compared to the passively restored reaches, while substrate composition remained fairly constant in all reaches. Regarding morphodynamics, changes in depth and width of actively restored reaches differed significantly from changes in passively restored ones in three of the four elements compared. Our findings imply increased habitat richness, diversity and habitat dynamics in the restored reaches, especially in actively restored ones. Analysis of discharge data suggests that flood events exceeding critical shear stress of the bed material, and the time span since restoration determine the potential for morphological changes.     

Synthesis of habitat restoration impacts on young-of-the-year salmonids in boreal rivers

Reviews in Fish Biology and Fisheries - River restoration offers the potential to enhance biological integrity, often measured as fish population changes. We used a meta-analytical approach to...     

Determinants of habitat use in large roach

In this study gillnet catches of large roach Rutilus rutilus and their potential predators, large perch Perca fluviatilis , pikeperch Sander lucioperca and pike Esox lucius , in combination with data on food resources and abiotic variables were used to reveal the variables influencing the habitat use of large roach in Lake Großer Vätersee. The occurrence of large roach was negatively coupled with the occurrence of potential predators. Although almost all roach studied were larger than those actually fed on by the predators, high roach catches never coincided with high predator catches. Since the overall habitat-specific distribution of roach and its predators was nevertheless highly similar, this indicated that large roach obviously avoided the immediate vicinity of the predators without being forced to a full habitat shift. The behavioural response to predators of roach in Lake Großer Vätersee was clearly length dependent, since the patterns of diel habitat use differed between large and small roach. For lake-wide estimates of trophic interactions, size groups of prey should be separated, since size-dependent trait changes may impact habitat-specific resources in a contrasting way.     

Dissolved reactive phosphorus in large rivers of East Asia

Dissolved reactive phosphorus (DRP) concentrations in large pristine rivers of East Asia (370 samples) are reported and the relationship to lithology (phosphorites, igneous apatite-bearing deposits), relief, climate (precipitation, temperature), and population density are investigated. The DRP concentration and yield of 93% of our samples were distinctly low (<0.06–0.89 μM DRP and <0.0008–800 mol DRP/km²/year). The samples with relatively high DRP (∼7% of our samples) were most likely from point sources of human sewage rather than P-rich lithology. The principal component analyses using DRP, dissolved major elements, pH, Sr, and ⁸⁷Sr/⁸⁶Sr found DRP best grouped with dissolved Si and K. However, the correlation between DRP and dissolved Si is still not strong enough to justify using Si as a proxy of DRP export by chemical weathering. The large rivers draining the eastern Tibetan Plateau—the headwaters of the Mekong, Yangtze, and Yellow—together supplied 3.0 × 10⁷ mol DRP/year, 7%, 3%, and 17% of those at mouths, respectively, and were not dominant source regions of DRP. The mouth values of the East Siberian rivers were especially low and this was due to multiple factors, e.g., low precipitation and sparse population. Stepwise regression of various parameters like precipitation, temperature, runoff, population density and relief indicated that the concentrations were not affected by any single factor, but precipitation and secondarily population density explained up to 44% of the variability in the DRP yield of the East Asian rivers.     

Distribution and habitat associations of billfish and swordfish larvae across mesoscale features in the Gulf of Mexico

Ichthyoplankton surveys were conducted in surface waters of the northern Gulf of Mexico (NGoM) over a three-year period (2006-2008) to determine the relative value of this region as early life habitat of sailfish (Istiophorus platypterus), blue marlin (Makaira nigricans), white marlin (Kajikia albida), and swordfish (Xiphias gladius). Sailfish were the dominant billfish collected in summer surveys, and larvae were present at 37.5% of the stations sampled. Blue marlin and white marlin larvae were present at 25.0% and 4.6% of the stations sampled, respectively, while swordfish occurred at 17.2% of the stations. Areas of peak production were detected and maximum density estimates for sailfish (22.09 larvae 1000 m(-2)) were significantly higher than the three other species: blue marlin (9.62 larvae 1000 m(-2)), white marlin (5.44 larvae 1000 m(-2)), and swordfish (4.67 larvae 1000 m(-2)). The distribution and abundance of billfish and swordfish larvae varied spatially and temporally, and several environmental variables (sea surface temperature, salinity, sea surface height, distance to the Loop Current, current velocity, water depth, and Sargassum biomass) were deemed to be influential variables in generalized additive models (GAMs). Mesoscale features in the NGoM affected the distribution and abundance of billfish and swordfish larvae, with densities typically higher in frontal zones or areas proximal to the Loop Current. Habitat suitability of all four species was strongly linked to physicochemical attributes of the water masses they inhabited, and observed abundance was higher in slope waters with lower sea surface temperature and higher salinity. Our results highlight the value of the NGoM as early life habitat of billfishes and swordfish, and represent valuable baseline data for evaluating anthropogenic effects (i.e., Deepwater Horizon oil spill) on the Atlantic billfish and swordfish populations.     

Comparison of zoobenthos and zooperiphyton of large and medium rivers

The results of a study of zoobenthos and zooperiphyton of two rivers of the Ob’ River middle reaches are shown. A comparative analysis of the composition and abundance values of two ecological groups of zoobenthos and zooperiphyton hydrobionts has revealed the difference in their taxonomic compositions and dominant complexes. The similarity in total number and biomass of zoobenthos and zooperiphyton in the large river and the higher values of zooperiphyton quantitative development in a medium river have been identified.     

Water and habitat quality assessment in the Honi and Naro Moru rivers,Kenya, using benthic macroinvertebrate assemblages and qualitative habitat scores

An assessment of water and habitat quality, based on macroinvertebrate assemblage indices and qualitative habitat scores (QHS), was undertaken in the Honi and Naro Moru rivers, Kenya, in 2011. The two rivers are important as water sources for the local communities and as habitat for organisms such as invertebrates in the national parks there. The Naro Moru upstream site (QHS: 83%) is unmodified, with minimal human influence. The Honi downstream site and the Naro Moru midstream and downstream sites experienced moderate to large modifications in habitat and biota (QHS: 40–80%). South African scoring system (SASS) scores ranged from 43 (Naro Moru downstream) to 165 (Honi upstream), and there was a decrease in SASS scores with distance downstream. Based on the multimetric index (MI), the Honi and Naro Moru upstream and midstream sites have good water quality (MI: 0.6–0.8), whereas the Honi midstream and downstream sites, and the Naro Moru downstream site, have moderate water quality (MI: 0.4–0.6). Human activities had a negative effect on water quality and habitats. Preventive and conservation measures should be taken in the usage of the Naro Moru and Honi rivers.     

Metapopulation structure and habitat quality in modelling dispersal in the butterfly Iolana iolas

Quantifying dispersal is fundamental to understanding the effects of fragmentation on populations. Although it has been shown that patch and matrix quality can affect dispersal patterns, standard metapopulation models are usually based on the two basic variables, patch area and connectivity. In 2004 we studied migration patterns among 18 habitat patches in central Spain for the butterfly Iolana iolas, using mark–release–recapture methods. We applied the virtual migration (VM) model and estimated the parameters of emigration, immigration and mortality separately for males and females. During parameter estimation and model simulations, we used original and modified patch areas accounting for habitat quality with three different indices. Two indices were based on adult and larval resources (flowers and fruits) and the other one on butterfly density. Based on unmodified areas, our results showed that both sexes were markedly different in their movements and mortality rates. Females emigrated more frequently from patches, but males that emigrated were estimated to move longer daily dispersal distances and suffer higher mortality than females during migration. Males were more likely to emigrate from small than from large patches, but patch area had no significant effect on female emigration. The effects of area on immigration rate and the within-patch mortality were similar in both sexes. Based on modified areas, the estimated parameter values and the model simulation results were similar to those estimated using the unmodified patch areas. One possible reason for the failure to significantly improve the parameter estimates of the VM model is the fact that resource quantity and butterfly population sizes were strongly correlated with patch area. Our results suggest that the standard VM modelling approach, based on patch area and connectivity, can provide a realistic picture of the movement patterns of I. iolas .     

Simple predictions of instream habitat model outputs for fish habitat guilds in large streams

1. In the context of a generalised modification of hydraulic conditions in medium to large streams, modelling the impacts of stream regulation on fish communities in multiple streams is an important challenge for basic and applied freshwater ecology. Conventional instream habitat models such as PHABSIM link a hydraulic model with preference curves for various species to estimate habitat value changes with discharge in stream reaches. Despite world‐wide applications, they have been scarcely used in multiple sites with multiple species. 2. We assigned 21 size classes of European fish species to four habitat guilds (cluster analysis grouping size classes with comparable microhabitat preference curves). Then, we ran a conventional instream habitat model on 28 French stream reaches belonging to the `barbel zone', to estimate habitat values versus discharge curves for the 21 size classes. We summarised the outputs as mean habitat values for guilds, and tested if they were predictable from average characteristics of reaches (discharge, depth, width, particle size). 3. As was obtained elsewhere for populations, habitat values for guilds were strongly related to average, dimensionless characteristics of reaches. The Reynolds number of reaches, equivalent to a discharge per width unit, reflected most of the discharge‐dependent changes in habitat values (within reaches). In particular, habitat values of species preferring bank (respectively midstream) microhabitats decreased (respectively increased) with increasing Reynolds number. The Froude number at median discharge was the major predictor of reach‐dependent but discharge‐independent variations in habitat values. Habitat values of species preferring riffle versus pool or bank microhabitats were higher in reaches with high Froude numbers. These relationships were consistent with existing knowledge on the different species. 4. Such results suggest that the input variables required to estimate habitat values for fish communities can be greatly simplified, as illustrated by a general estimation of the sensitivity of species preferring midstream habitats to discharge changes in any reach. Cost‐efficient alternatives to conventional instream habitat models should facilitate their validation in multiple sites, a point that remains critical in instream habitat modelling of fish communities.     

Development and application of a nutrient-diffusing bioassay for large rivers

1. Laboratory and field experiments were performed to develop and then apply a nutrient-diffusing substratum (NDS) design suitable for use in large, fast-flowing rivers. 2. Initial laboratory experiments quantified diffusion of PO₄ and NO₃ from new and previously used clay pots, which were soaked in deionized distilled water. Mean release rates initially exceeded 2.4 and 725 μmol l^–1 day^–1 P and 0.22 and 18 μmol l^–1 day^–1 N from new and used pots, respectively, but declined rapidly with increasing time spent in deionized distilled water and were below detectable levels after about 18 and 29 days, respectively. 3. A phosphorus (P) dose–response experiment in a P-limited reach of the Athabasca River, Alberta, Canada showed that epilithic biomass and macroinvertebrate density on NDS increased with increasing concentrations of KH₂PO₄ up to about 0.5 m . Beyond this threshold, biomasses and densities were unaffected by initial KH₂PO₄ concentration. Coefficients of variation of epilithic biomass estimates declined with increasing KH₂PO₄ whereas invertebrate density appeared to be unaffected by KH₂PO₄ levels. 4. Release rates of both P and N from NDS filled with 0.5 m KH₂PO₄ or 0.5 m NaNO₃ declined at a log-negative rate from about 5000 μmol N-NO₃ l^–1 day^–1 and 3500 μmol P-PO₄ l^–1 day^–1 on day 2, to 200 μmol l^–1 day^–1 for both N and P on day 32. 5. After development, we used the diffusing substrata to identify spatial patterns in nutrient limitation at seven sites along a 120 km reach in the Athabasca River, that receives two known point-source nutrient inputs. NDS consisting of N, P, N + P and unenriched controls were attached to the river bottom for 22–23 days and then retrieved and sampled for epilithic chlorophyll a. Physicochemical parameters and epilithic biomasses on upper stone surfaces were also quantified when NDS were deployed and retrieved from each site. 6. Sites located immediately downstream of the two point source inputs had higher water column concentrations of PO₄ and epilithic biomasses than the site immediately upstream; epilithic biomass was positively related to PO₄ in the late autumn (r²⁼ 0.58) but not in early autumn. Sites located immediately below nutrient inputs were not nutrient-limited, whereas upstream reference sites were P-limited.     

Predicting the structure and diversity of young-of-the-year fish assemblages in large rivers

1. Interactions between environmental variables and 0+ fish assemblages in the upper River Garonne (France) were quantified during late August 1995.
2. The abundance and diversity of the fish assemblages in floodplain channels were modelled using Artificial Neural Network (ANN) analysis and nine variables: the abundance of the six dominant species, fish specific richness, overall abundance of 0+ fish and the Shannon index of diversity. Multiple regression analysis was also used to assess ANN performance.
3. Using 596 samples, correlation coefficients ( r adjusted) between observed and estimated values of the nine dependent parameters were all highly significant ( P < 0.01). Expected values from the tested data were significantly related to the observed values. The correlation coefficient between observed and estimated values ( r ) varied from 0.70 to 0.85.
4. The ANN provided a high quality prediction, despite the complex nature of the relationship between microhabitat composition and fish abundance.
5. Garson's algorithm was used to provide the explanatory power needed in ecology when using black-box models. Parameters contained in the models (i.e. weighting) were used to determine the relative contributions of explanatory variables and thus to ascertain the structure of fish communities.     

Local distribution of macrophytes and consequences for sampling methods in large rivers

During the years 2003 and 2004, the distribution of macrophytes was studied at eight sites in two large rivers in the southwest of France (the Dordogne and Garonne). Using a pinpoint method, we obtained 7,083 observations and recorded physical parameters such as depth, distance from bank, water velocity, and substrate type. By using logistic regressions, we showed that a combination of these factors significantly influences the distribution of macrophytes. This enabled us to highlight transversal distribution patterns. Helophyte spermatophytes, free-floating taxa, and most of the nonanchored algae were characteristic of the shallow areas located near the banks. The deepest areas were characterized by a reduced number of species with a majority of submerged spermatophytes which are resistant to high velocity, anchored algae, and bryophytes. These results can be used to implement the Macrophyte Biological Index for Rivers (IBMR) for large rivers. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: S. M. Thomaz     

Survival of migrating salmon smolts in large rivers with and without dams

The mortality of salmon smolts during their migration out of freshwater and into the ocean has been difficult to measure. In the Columbia River, which has an extensive network of hydroelectric dams, the decline in abundance of adult salmon returning from the ocean since the late 1970s has been ascribed in large measure to the presence of the dams, although the completion of the hydropower system occurred at the same time as large-scale shifts in ocean climate, as measured by climate indices such as the Pacific Decadal Oscillation. We measured the survival of salmon smolts during their migration to sea using elements of the large-scale acoustic telemetry system, the Pacific Ocean Shelf Tracking (POST) array. Survival measurements using acoustic tags were comparable to those obtained independently using the Passive Integrated Transponder (PIT) tag system, which is operational at Columbia and Snake River dams. Because the technology underlying the POST array works in both freshwater and the ocean, it is therefore possible to extend the measurement of survival to large rivers lacking dams, such as the Fraser, and to also extend the measurement of survival to the lower Columbia River and estuary, where there are no dams. Of particular note, survival during the downstream migration of at least some endangered Columbia and Snake River Chinook and steelhead stocks appears to be as high or higher than that of the same species migrating out of the Fraser River in Canada, which lacks dams. Equally surprising, smolt survival during migration through the hydrosystem, when scaled by either the time or distance migrated, is higher than in the lower Columbia River and estuary where dams are absent. Our results raise important questions regarding the factors that are preventing the recovery of salmon stocks in the Columbia and the future health of stocks in the Fraser River.     

Hydromorphological degradation impact on benthic invertebrates in large rivers in Slovenia

Large rivers are amongst the most degraded ecosystems. We studied a relationship between hydromorphological degradation and benthic invertebrates in large rivers in Slovenia. Five indices of the Slovenian hydromorphological assessment methodology were used to develop a HM stressor gradient. Natural type-specific habitat diversity was considered in the hydromorphological stressor gradient building and thus two hydromorphological types of large rivers were defined. CCA ordination with five HM indices and 315 benthic invertebrate taxa revealed variations in taxa response along the HM stressor gradient. First CCA axis species values were used to develop a taxon-specific river fauna value (Rf_i), whereas tolerance values (biplot scaling) were used to determine a hydromorphological indicative weight (HW_i). Rf_i, HW_i, and log₅ abundance classes were combined using weighted average approach to construct a River fauna index for large rivers (RFI_VR). Several additional benthic invertebrate-based metrics were also tested against the HQM. A Slovenian multimetric index for assessing the hydromorphological impact on benthic invertebrates in large rivers (SMEIH_VR) was constructed from the RFI_VR and a functional metric %akal + lithal + psammal taxa (scored taxa = 100%). The strong relationship between hydromorphological stressor gradient and SMEIH_VR index provides us with an effective assessment system and river management tool.     

Fish habitat preferences in large streams of southern France

1. Relationships between fish and their habitat over whole geographic regions, which are evident from studies of many streams and species, can improve understanding of lotic communities and provide reliable management tools. Nevertheless, most habitat preference studies have been based on single sites, and confined to small streams and to game species.
2. Regional habitat preference models, based on local velocity, depth and roughness, were developed for twenty-four species and their size classes commonly found in large European streams. Fish surveys were conducted in six large streams in southern France over an 8-year period. To limit the influences of habitat variables other than those studied, we estimated fish preferences within each survey and averaged this information across surveys. Preferences were fitted with confidence intervals and their sensitivity to field uncertainty was evaluated.
3. Most species and size classes had significant preferences for local habitat conditions which were consistent across the region. Habitat preferences predominant in the region overall were not always observed at any one site, but habitat conditions preferred on average in the region were never actually avoided locally. These results support the use of regional preference models for fish and the development of similar models for other lotic groups whose sensitivity to local habitat conditions has been reported elsewhere.     

The influence of habitat structure and flow permanence on macroinvertebrate assemblages in temporary rivers in northwestern Zimbabwe

Temporary rivers within the Nyaodza-Gachegache subcatchment in northwestern Zimbabwe were investigated to examine the role of flow permanence and habitat structure on macroinvertebrate community composition. Macroinvertebrate communities of intermittent and ephemeral rivers displayed significant differences in the number of taxa, macroinvertebrate abundance, Shannon and Simpson diversity indices and in size class structure. Intermittent sites were characterised by higher numbers of taxa, diversity and Ephemeroptera and Trichoptera richness compared to ephemeral sites. The fauna of ephemeral sites was dominated by a single taxon (Afrobaetodes) (Ephemeroptera, Baetidae) whilst larger sized taxa (e.g. Elassoneuria (Ephemeroptera, Oligoneuriidae), Dicentroptilum (Ephemeroptera, Baetidae), Aethaloptera (Trichoptera, Hydropsychidae), Pseudagrion (Odonata, Coenagrionidae) and Tholymis (Odonata, Libellulidae) were exclusively restricted to intermittent sites. Clear differences were observed between sand, gravel, cobble and vegetation habitats. Vegetation and cobbles supported distinct communities, with some taxa exclusively restricted either to vegetation (e.g. Pseudagrion, Leptocerina (Trichoptera, Leptoceridae), Cloeon (Ephemeroptera, Baetidae), Afronurus (Ephemeroptera, Heptageniidae) and Povilla (Ephemeroptera, Polymitarcidae) or cobble (e.g. Aethaloptera and Dicentroptilum) habitats. In terms of ensuring optimum diversity within the subcatchment, we consider conservation of critical habitats (cobbles and vegetation) and maintenance of natural flows as the appropriate management actions. Handling editor: D. Dudgeon