A geomorphological framework for river characterization and habitat assessment

1. Methods to assess the physical habitat available to aquatic organisms provide important tools for many aspects of river management, including river health monitoring, determination of river restoration/rehabilitation strategies, setting and evaluating environmental flows and as surrogates for biodiversity assessment. 2. Procedures used to assess physical habitat need to be ecologically and geomorphologically meaningful, as well as practicable. A conceptual methodological procedure is presented that evaluates and links instream habitat and geomorphology. 3. The heterogeneity of habitat potential is determined within geomorphic units (such as pools, runs, riffles) by assessing flow hydraulics and substrate character. These two variables are integrated as hydraulic units — patches of uniform flow and substrate. 4. This methodology forms a logical extension of the River Styles framework that characterizes river form and behaviour at four inter‐related scales: catchments, landscape units, River Styles (reaches) and geomorphic units. As geomorphic units constitute the basis to assess aquatic habitat availability, and they form the building blocks of river and floodplain systems, intact reaches of a particular River Style should have similar assemblages of instream and floodplain habitat. 5. An application of the hydraulic unit procedure is demonstrated in gorge, partly‐confined and alluvial River Styles from the Manning catchment in northern New South Wales, Australia. Copyright © 2001 John Wiley & Sons, Ltd.     

Linking watershed and microhabitat characteristics: effects on production of Atlantic salmonids (Salmo salar and Salmo trutta)

The spatial scale of environmental factors influencing population dynamics ranges from microhabitat to continental or even global scales. Integration of multiple spatial scales is important in order to understand links between environmental variation and population processes. In the present study, we investigate how multiscale drivers influence the production of stream‐rearing Atlantic salmonids (Atlantic salmon, Salmo salar L. and brown trout, Salmo trutta L.) measured in terms of abundance. Variation in juvenile production was studied using data from single‐pass electrofishing surveys (measured as biomass per m²) from nine rivers. These data were combined with habitat data ranging from an important in‐stream microhabitat variable (shelter availability) to properties of the catchment. Variation in productivity within and among rivers was affected by both properties of in‐stream habitat and catchment properties. Shelter availability and the proportion of the catchment consisting of cultivated land and lakes influenced biomass positively, while catchment area had the opposite effect. For a different set of rivers (N = 20), river gradient and catchment area were shown to positively affect the amount of shelter. Finally, the variables identified in the two preceding analysis were included in the analysis of population productivity using catch statistics from 160 rivers. The proportion of cultivated land and lakes, estimated shelter availability were found to have positive effects. In addition, temperature had a positive effect, while river width had a negative effect. This study shows that combining multiple‐scale environmental factors can explain a substantial proportion of variation in population productivity among and within the populations of Atlantic salmonids.     

Re‐introduction of structurally complex wood jams promotes channel and habitat recovery from overwidening: Implications for river conservation

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Integrating ecology with hydromorphology: a priority for river science and management

• 1. The assessment of links between ecology and physical habitat has become a major issue in river research and management. Key drivers include concerns about the conservation implications of human modifications (e.g. abstraction, climate change) and the explicit need to understand the ecological importance of hydromorphology as prescribed by the EU's Water Framework Directive. Efforts are focusing on the need to develop ‘eco‐hydromorphology’ at the interface between ecology, hydrology and fluvial geomorphology. Here, the scope of this emerging field is defined, some research and development issues are suggested, and a path for development is sketched out.
• 2. In the short term, major research priorities are to use existing literature or data better to identify patterns among organisms, ecological functions and river hydromorphological character. Another early priority is to identify model systems or organisms to act as research foci. In the medium term, the investigation of pattern–processes linkages, spatial structuring, scaling relationships and system dynamics will advance mechanistic understanding. The effects of climate change, abstraction and river regulation, eco‐hydromorphic resistance/resilience, and responses to environmental disturbances are likely to be management priorities. Large‐scale catchment projects, in both rural and urban locations, should be promoted to concentrate collaborative efforts, to attract financial support and to raise the profile of eco‐hydromorphology.
• 3. Eco‐hydromorphological expertise is currently fragmented across the main contributory disciplines (ecology, hydrology, geomorphology, flood risk management, civil engineering), potentially restricting research and development. This is paradoxical given the shared vision across these fields for effective river management based on good science with social impact. A range of approaches is advocated to build sufficient, integrated capacity that will deliver science of real management value over the coming decades.

Copyright © 2007 John Wiley & Sons, Ltd.     

Factors influencing the success of salmonid egg development in river substratum

Interstitial water conditions in the hyporheic zone of the stream bed are determinants of salmonid egg hatching success. We used standardised egg exposures to develop and validate discriminant analysis and generalised linear model models linking the hatching success of brown trout (Salmo trutta) with physicochemical factors of the interstitial zone (e.g., oxygen, specific conductance, nitrate, nitrite, ammonium, pH and redox potential). Interstitial water quality was identified as a limiting factor for egg development (median of relative hatching rates = 0.23). Hatching success was unimodal in hatchery and field references incubated in free‐flowing water, but bimodal (very high or very low hatching success) in natural sediment exposures. The effects of physicochemical factors on the hatching success of Salmo trutta strongly depended on both the time and spatial scale analysed. The variables retained in the models differed between the macroscale (over all rivers), the river‐specific scale (within a river) and the microscale (at different sediment depths). Egg hatching success decreased with increased substratum depth (decrease of 26% in 150 mm compared with 50 mm). Increasingly more variable interstitial water conditions (e.g., oxygen) throughout the egg incubation period suggest progressive degradation rates in the stream substratum during the incubation period at the microscale level. Consequently, consideration of different spatial and temporal scales is necessary for the evaluation of habitat quality in salmonid conservation and catchment management plans.     

Habitat use by a freshwater dolphin in the low‐water season

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Seasonal effects of macrophyte growth on rainbow trout habitat availability and selection in a low‐gradient,groundwater‐dominated river

Rainbow trout habitat use is often described in high‐gradient, runoff‐driven, heterotrophic streams where geomorphic features and overhanging riparian vegetation provide channel complexity and cover. However, many rainbow trout populations thrive in rivers with contrasting aquatic habitat. We describe rainbow trout habitat use in a low‐gradient, groundwater‐dominated tailwater river where river flow management and macrophyte growth and senescence largely govern available trout habitat. In the summers of 2013 and 2014, available aquatic habitat (depth, velocity, macrophyte cover, substrate size) was quantified, while individual trout location was determined by radio telemetry and linked to environmental variables. Detailed habitat surveys indicate that macrophyte cover increases throughout the summer and is a strong determinant of in‐stream habitat characteristics. Paired logistic regression shows that adult rainbow trout prefer greater depths. Water depth increases with macrophyte abundance at both reach and local scales as plants restrict flow, and available trout habitat is linked to this seasonal pattern. When macrophyte abundance is high, adult trout show secondary preference for localised areas of lower macrophyte cover but otherwise show no selectivity for macrophyte cover, velocity or substrate size. Results suggest that submerged aquatic plants increased the quantity and quality of rainbow trout habitat as a source of channel complexity and cover. Macrophytes may play a similar role in other low‐gradient streams and should not be overlooked by fisheries managers considering habitat suitability.     

A comparison of catchment based salmonid habitat survey techniques in three river systems in Northern Ireland

Three survey techniques, a fully quantitative, multivariate study; a shorter or truncated fully quantitative method and a Geographical Information System (GIS) based, semi-quantitative, survey technique, were developed to assess in-river salmonid habitats on a catchment wide basis. These methods were tested and compared on three river systems in Northern Ireland: the Blackwater, the Bush and the Main. The research indicated that the fully quantitative method generated an accurate habitat database but required a high investment in time and resources to complete. The truncated survey approach often produced an inaccurate habitat database. The semi-quantitative technique generated a more accurate habitat dataset with greater productivity and efficiency for the resources invested in the survey.     

基于湿周法的西南山区河流生态需水的计算与验证

研究湿周法的适用条件及转折点的确定方法,为计算河流最小生态需水提供参考。收集了我国西南山区岷江和大渡河流域河流上、中和下游共计8个水文站的实测大断面数据,通过建立各断面湿周与流量关系及其拟合曲线,分别采用斜率法、曲率法和经验法分析确定了各断面最小生态需水,并参考相关参数标准对计算结果进行了合理性检验。研究表明,湿周法适用于河床稳定且形态近似抛物线形或矩形的断面,以斜率为1的点(斜率法)确定断面湿周与流量关系曲线的转折点及断面最小生态需水更有利于保护河流生境;对于形态近似为抛物线形或矩形的断面,其计算结果约占多年平均流量的8.9%~13.2%,各断面最小生态需水所对应平均水深、湿周率和平均流速均能满足检验标准。湿周法适用于近似抛物线形或矩形的断面,不建议用于近似三角形或梯形的断面。     

Hydraulic‐habitat modelling for setting environmental river flow needs for salmonids

Abstract There is an increasing demand for tools to assist in the management of environmental flows in rivers. Changes in river discharge act on biota through a hydraulic template, which is mediated by channel morphology. Hence, environmental flow assessments also need to consider channel morphology, especially if morphology has been altered by human activities. Computer models describing the preferences of fish for hydraulic microhabitats have been applied to environmental flow problems since the mid‐1970s. Salmonids have been a particular focus for these methods. Other reviews have provided comprehensive coverage of the basic features and principles of such models. These are briefly discussed focusing on the developments that have occurred in the last 15 years and whose application has so far been infrequent. These include improvements to the representation of hydraulics at reach‐scale and of longer river sections, and improved representation of interacting physical variables that describe habitat. The central theme is the spatial coverage and fundamental granularity of such models. Despite a broad literature, there is a lack of documented examples of the application of hydraulic‐habitat models through all stages in the environmental flow decision‐making process. The review concludes with four short examples that illustrate the use of model output.     

Colonisation tactics of three temperate catadromous species,eel Anguilla anguilla,mullet Liza ramada and flounder Plathychtys flesus,revealed by Bayesian multielemental otolith microchemistry approach

Daverat F, Martin J, Fablet R, Pécheyran C. Colonisation tactics of three temperate catadromous species, eel Anguilla anguilla, mullet Liza ramada and flounder Plathychtys flesus, revealed by Bayesian multielemental otolith microchemistry approach.
Ecology of Freshwater Fish 2011: 20: 42–51. © 2010 John Wiley & Sons A/S Abstract – The colonisation of Gironde (SW France) river catchment by juvenile, eel, Anguilla anguilla, flounder Platychtys flesus and thinlipp mullet Liza ramada was investigated comparatively using Sr:Ca and Ba:Ca composition of otolith. The relation between Sr, Ba and habitat was investigated based on Sr and Ba water composition sampled each month along the estuary‐river gradient. A total of 50 mullets, 30 eels and 47 flounders were collected in the Gironde river catchment. Analysis was performed with a Femtosecond LA‐ICPMS along a trajectory from the core to the edge. Sr and Ba water concentrations discriminated three habitats within the Gironde system, the lower estuary, the upper estuary and the freshwater sites. A signal processing method based on Gaussian hidden Markov models was applied to the multielemental life‐history data. The linear model used to allocate a Gironde habitat to coupled Sr, Ca values was parameterised with seasonal patterns and magnitude of Sr and Ba water values in the different habitats. The results showed that the three species used three different habitats and they had a large diversity of habitat use patterns with resident and nomadic tactics. Resident tactics were less frequent than nomadic tactics that suggested individual fish used two or more habitats. Mullet used a wider range of habitats in the lower part of the estuary than eel and flounder and switched habitats more frequently. Flounders tended to colonise initially freshwater, and then estuarine habitats later in life while mullets used the entire range of available catchment habitats throughout their life.     

Integrating climate–hydrology–ecology for alpine river systems

• 1. High climatic sensitivity and lack of significant human impact make alpine river basins important environments for examining hydrological and ecological response to global change.
• 2. This paper is based upon previous and ongoing research within a glacierized, alpine river system (Taillon‐Gabiétous basin, French Pyrenees), which adopts an interdisciplinary approach to investigate the climate–hydrology–ecology cascade. Data are used to advance hypotheses concerning impacts of climate change/variability upon alpine river system hydrology and ecology.
• 3. The snowpacks and glaciers that are the source of Pyrenean streams are climatically sensitive, with glaciers in retreat for most of the historical period. Given anticipated changes in summer air‐mass frequencies, the volume of meltwater may decrease, the nature and rate of glacier drainage may alter, and the timing of peak snow‐ and ice‐melt may shift. However, rainfall‐runoff and groundwater may increase their relative contributions to stream flow.
• 4. The influence of changing water source contributions on physico‐chemical habitat and, in turn, on benthic communities is assessed using an alternative alpine stream classification. This model predicts more rapid downstream change in benthic communities in the future as meltwater contributions decline and, at the basin‐scale, biodiversity may be reduced owing to less spatio‐temporal heterogeneity in water sources contributions and, thus, physico‐chemical habitat. However, predictions are complicated by potential changes in biotic interactions with altered species' distributions.
• 5. Integrated, long‐term research into the climate–hydrology–ecology cascade in other alpine river basins is vital because interdisciplinary science is fundamental to predicting stream hydrology and ecology under scenarios of future climate/variability, to assessing the utility of alpine river systems as indicators of global change, and to developing conservation strategies for these fragile ecosystems.

Copyright © 2006 John Wiley & Sons, Ltd.     

Priority habitats for the conservation of large river fish in the Ganges river basin

• 1. Three classes of habitat used by groups of fish species classified as conservation and management priorities were developed for the Gerua River (also known as the Girwa River, Karnali River) in the Ganges river basin. This river is large (mean annual discharge ca 1500 m³ s^?1, up to 900 m wide), surrounded by protected lands of India and Nepal, and upstream of major diversions and river alterations.
• 2. Fish and habitat sampling was conducted at 45 sites from 2000 to 2003. Data were analysed for 2172 fish of 14 species. Species and life stages found occupying a statistically distinct subset of the river habitats were grouped to identify classes of river habitat for conservation.
• 3. Most species and life‐stage groups specialized on specific habitat conditions revealed by multivariate analyses of variance and a principal component analysis. The most numerous and diverse group (six species, 15 life stages) was associated with deep depositional habitats with sandy substrate. Two species covering three life stages were primarily oriented to erosional habitat marked by fast current velocity with pebble and cobble substrate. A third group of three species of adults and juveniles were intermediate in habitat use.
• 4. River conservation for fish faunas should maintain both erosional and depositional channel habitats with depths, substrates, and current velocity inclusive of the ranges reported. The erosional and depositional nature of the key habitats requires that rivers be maintained with flows capable of channel‐forming functions.

Copyright © 2006 John Wiley & Sons, Ltd.     

A method for applying fluvial geomorphology in support of catchment‐scale river restoration planning

• 1. This paper reports on an extension to the use of Fluvial Audit survey to include a subjective and adaptive multi‐criteria assessment (MCA) process that integrates scientific literature and observational data to develop three reach‐scale indices of: (a) channel modification; (b) channel function (sediment store or source); and (c) naturalness. These indices are nested within an overall conceptual model of channel evolution and used to underpin catchment scale river restoration.
• 2. The approach is described and applied to a small groundwater dominated river in the UK. The results show that over 48% of the total main river was in a degraded state relative to a conceptual model of a natural reference state. Only 23% of the river was in a near‐natural state.
• 3. MCA classifications were translated into a set of management actions necessary to return each reach to a near‐natural condition. These are described.
• 4. The method offers a transparent decision support for stakeholders that can incorporate differing scientific evidence. The use of MCA enables flexibility in terms of the relative importance of scores and weights placed upon factors in the final classification. This makes the approach amenable to stakeholder and public consultation.

Copyright © 2009 John Wiley & Sons, Ltd.     

Factors affecting the occurrence of smooth‐coated otter in aquatic systems of the Upper Gangetic Plains,India

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Fish assemblages of an African river floodplain: a test of alternative models of community structure

In the Oueme River, a lowland river in Benin, Africa, artificial ponds constructed in the floodplain (whedos) are colonised during the high‐water period by a presumably random sample of fishes from the river channel. As water slowly recedes from the floodplain, fishes are isolated in whedos until they are harvested near the end of the dry season. We surveyed fishes in whedos and adjacent main‐channel and floodplain habitats during two low‐water periods (2008 and 2009) and one falling‐water period (2010–2011) to evaluate the relevance of four alternative metacommunity models to these systems. In 2010–2011, we also measured a suite of physicochemical variables including dissolved oxygen, temperature, specific conductivity and per cent cover of aquatic vegetation. Whedos were covered with dense growth of aquatic vegetation, and dissolved oxygen concentrations were lower in whedos and a natural floodplain depression compared with the main channel. Multivariate analyses revealed that habitat types were distinct with regard to assemblage structure and abiotic conditions. Assemblages in whedos and natural floodplain depressions were differentiated from those of the river channel, with the floodplain habitats being dominated by piscivorous fishes that tolerate aquatic hypoxia. Dispersal, aquatic hypoxia and predation act in concert to shape local community structure. Patch dynamics, species sorting and mass effect models all were consistent with patterns in fish assemblage structure in this system. We conclude that the underlying mechanisms of drift, speciation, selection and dispersal ultimately may be more useful for explaining patterns in ecological communities than alternative metacommunity models.     

Incorporating hydromorphology in strategic approaches to managing flows for salmonids

Abstract Whilst flow is often seen simplistically as a measurable and manageable variable in rivers, the habitat value of flow is delivered by interactions with channel morphology and substrate. The resulting hydromorphology impacts on all salmonid life stages; its proper understanding requires integration between the sciences of hydrology/hydraulics, geomorphology and freshwater ecology, but this integration is scarce. This study describes those features of river channel morphology and dynamics that are most relevant to hydromorphological status, describes progress in field assessment and outlines practical progress in calibrating in‐channel habitat condition as an aid to setting flows. However, the incorporation of the true spatial and temporal variability of hydromorphology awaits further refinement of survey techniques and the long‐awaited interdisciplinary research on causal process links. Meanwhile, amongst the geomorphological tools available to those setting environmental flows are fluvial audits, the definition and mapping of meso‐scale biotopes and the use of realistic river typologies for the local application of general flow rules.     

The significance of meandering channel morphology on the diversity and abundance of macroinvertebrates in a lowland river in Japan

• 1. Many rivers and streams across the world have been channelized for various purposes. Channel cross‐sections of meandering rivers are asymmetrical and have cross‐sectional diversity in their physical environment; cross‐sections of a channelized river are typically trapezoidal and have little cross‐sectional diversity, both in physical and ecological conditions. Several programmes to restore stream meanders have been undertaken to improve river ecosystems degraded by channelization. However, the association between diversification in the physical environment due to meander restoration and the macroinvertebrate community structure is poorly known.
• 2. This study of a lowland river in Japan assessed how the cross‐sectional diversity of the physical environment changed with restoration of a meander in a channelized river, and how the macroinvertebrate communities responded to the changes in physical habitat variation. Comparisons were made between the macroinvertebrate communities of a channelized reach, the restored meandering reach, and a natural meandering reach.
• 3. Natural meandering and restored meandering reaches showed higher cross‐sectional diversity in physical variables and total taxon richness across a reach than did the channelized reach. Almost all taxa observed in the natural and restored meandering reaches were concentrated in the shallowest marginal habitats near the banks. Shear velocity increasing with water depth had a negative association with macroinvertebrate density and richness.
• 4. This study demonstrated that the shallow river bed along the inside of bends formed point bars that provided a highly stable substrate, a suitable habitat for macroinvertebrates in a lowland river. It is concluded that meander restoration could be an effective strategy for in‐stream habitat restoration in lowland meandering rivers.

Copyright © 2007 John Wiley & Sons, Ltd.     

A qualitative ecological risk assessment of the invasive Nile tilapia,Oreochromis niloticus in a sub‐tropical African river system (Limpopo River,South Africa)

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