Salmonid Fisheries

Freshwater Habitat Management

Paul Kemp

• Publisher: Wiley-Blackwell
• Year: 2011
• Print ISBN: 9781405183963
• eBook ISBN: 9781444347906
• Edition: 1
• Topic: Technology & Engineering
• Subtopic: Fisheries & Aquaculture
• Index: Technology & Engineering

Salmonid Fisheries is a landmark publication, concentrating on river management, habitat restoration and rehabilitation, disseminating lessons learnt in relation to the intensively studied salmonids that are applicable to future interventions, not just for salmonid species but for other non-salmonid species, biota and ecosystems. The contents of this book are the product of the Atlantic Salmon Trust's 40 th Anniversary Conference, held in association with the Game and Wildlife Conservation Trust.

Drawing together carefully-edited contributions from many of the world leaders in river restoration from academia, commercial management and government agencies, this important book highlights the need to view river management from the context of the catchment and to adopt an ecosystem-based approach to restoration. The book is broadly divided into two sections which discuss first, the status of current understanding concerning the relationship between lotic habitat management, the response of salmonid fisheries and the theory of river restoration, and secondly, the application of this to habitat management and river restoration.

Salmonid Fisheries is an extremely valuable work of reference for fisheries managers, ecologists, environmental scientists, fish biologists, conservation biologists and geomorphologists. Libraries in all universities and research establishments where biological and earth sciences, and fisheries management are studied or taught should have copies of this book on their shelves.

• Contributions from a wide range of well known experts
• Published in association with the Atlantic Salmon Trust
• Habitat management is crucial for dwindling wild salmon populations
• Of great importance to aquatic ecologists and fisheries managers

Chapter 1

Variation in Habitat Quality for Drift-Feeding Atlantic Salmon and Brown Trout in Relation to Local Water Velocity and River Discharge

John Armstrong

Summary

There is a requirement to determine the effect of water discharge on the qualities of rivers and streams for resident drift-feeding salmon and trout. Two main categories of predictive biological model have been widely considered to address this issue, both of which link to an underlying template of variation in structure of hydrology and physical topology across flows. The first approach, typified by physical habitat simulation modelling (PHabSim), ascribes values to each of the local habitat types as functions of the densities and frequency of occurrence of animals that occupy them. This approach has the advantage of being relatively easily applied but has been criticised on the basis that local fish density can be a poor indicator of patch quality and does not easily relate overall habitat quality to meaningful population parameters. The second approach ascribes values to the local habitat types in terms of the food intakes, net energy gains or fitness of animals that occupy them. This concept has found favour in being potentially more robust in structure than the PHabSim approach, but parameterisation of the models cannot be achieved by simple field observations. Here, the application of energy and fitness value models to salmon and trout is explored. Morphological differences between salmon and trout are related to patch quality in terms of energetics through linking optimal food intake models to energy budgets. Using these models, relationships are established between velocity niche width and population density and nutrient status of the stream. The trout velocity niche is narrower than that of salmon and skewed to lower velocities, particularly at low food availability. The importance of understanding community dynamics in predicting responses of fish to variations in discharge is demonstrated. Consideration is given to factors that further affect the values of patches and their availability to salmon and trout. These factors include fish size, food, among-fish variation in metabolism, diel variation in activity patterns, competition, genetic relatedness of neighbours and mortality risk through predator abundance and availability of shelter. Information on the likely capacities of populations of salmonids to respond to temporal change in the spatial distribution of patch qualities is then considered. Constraints and opportunities are compared between application of PHabSim, patch fitness value and empirical models for recommending river discharge criteria for resident drift-feeding salmon and trout.

1.1 Introduction

Human demands for water and changes in land use and climate influence water discharge (flow) regimes in rivers and affect the habitat available for Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L. Moderation of this impact through planning and implementation of effective water discharge and abstraction regimes should be based on an understanding of the requirements of the fish for water flow. An approach to addressing this issue in part has been to develop an understanding of the relationships between total discharge and local water velocities and other habitat variables throughout the system of interest, and to determine how fish and fish populations respond to changes in discharge and differ among discharge regimes. A main potential advantage of this approach is that by investigating such processes it might be possible to make predictions about the effects of discharge on fish populations on a more robust and wide basis than is possible from using reference to limited empirical observations.

Salmon and trout require different flows at different stages of their life cycles (Armstrong et al. 2003) and plans for seasonal provision of water would need to take this factor into account. The focus here is on the requirement for trout and salmon to obtain food, largely from drifting invertebrates, during their development and growth within rivers and streams. The overall aims are to outline the relevant factors, through reference to literature and derivation where appropriate, and to seek a structure for moving forward the development of models to predict optimum discharge regimes.

The first part of this chapter provides a context for interpreting local responses of salmon and trout to water velocities by considering scale of impacting factors and variation in population dynamics across time and space. Then two approaches to quantifying habitat quality are considered. First, assessment of patch (area of stream) quality on the basis of local population densities is evaluated (PHabSim). Second, the approach of assessing patch quality on the basis of the fitness value to fish occupying it is discussed. This latter approach is expanded by development of an energetics model to estimate patch quality for growth as a function of the station holding mode of occupants, specifically as a comparison of typical trout and salmon behaviour types. This model is then used to consider the potential for predicting change in patch quality across discharges, with emphasis on the importance of linkages to the wider community of animals, particularly invertebrate prey.

The chapter then considers some of the biological parameters of trout, salmon and their environments that can be expected to influence local patch quality independent of water velocity. Consideration is also given to evaluation of mortality risk in combination with growth as a component of fitness and to the abilities of salmon and trout to move in response to changes in patch qualities. Finally, some consideration is given to routes for development of practical models for predicting the consequences of change in flow rates on populations of salmon and trout.

1.1.1 Habitat requirements of salmon and trout

The numbers, growth and size distributions of Atlantic salmon, S. salar L., and brown trout, S. trutta L., are strongly influenced by their habitats. Their basic needs for growth, survival and reproduction in fresh water include food, shelter, oxygen, clean water and suitables pawning conditions (reviewed in detail by Armstrong etal. 2003). Food, primarily in the form of invertebrates but also including fish, provides energy to fuel metabolism and growth. Shelter may be afforded by factors such as low light, physical obstructions and camouflage that make the fish less accessible to predators and physical trauma, for example from suspended solids and high water flows. Oxygen is required to enable a physiological scope for maintenance, feeding, processing food and evading predators. Water must be sufficiently clean that there is no significant impedance to the physiological processes that enable growth, minimise tissue maintenance costs and facilitate other key functions, such as imprinting on and detecting odours (Sutterlin & Gray 1973). Composition of the substratum determines local water velocities and shelter. There is a vast complexity of interacting biotic and abiotic factors that influence accessibility to these basic requirements (Armstrong et al. 2003), one of which is local water velocity.

1.1.2 Integrating across scales of influence

The habitat at any particular location in a stream is influenced by processes that occur across a broad range of spatial and temporal scales (Frissell et al. 1986). For example, at a given point in time at the local scale of perhaps 10 cm, a fish may be affected by the velocity of the flow from which it must extract food in competition with others. Yet the amount of such food and the rate of the flow may be influenced by the whole-catchment land use and underlying continental geology, which may be under the influence of geomorphic processes that have occurred across millions of years and human influence over thousands of years (Armstrong et al. 1998b).

Fine-scale processes are also crucially important in understanding the effects of water flow on fish. For example, early investigations of flow limitations on trout and salmon focused on the velocities needed to displace fish completely and were conducted on fine substratum in almost laminar flow in which there were no refuges (Ottaway & Clarke 1981). Such an approach is clearly not readily transferable to rough river beds in which velocity varies dramatically over small space scales providing refuge areas.

1.1.3 Bottlenecks as functions of time and space

The effect of habitat on fish populations can depend critically on the relationship between local densities and sizes of fish and the numbers of fish of those sizes that the habitat potentially could support. This relationship can vary across time, in terms of fish development stage (Armstrong & Nislow 2006), and across space as a function of distance from spawning areas independent of other habitat features (Armstrong 2005). At critical periods, such as after emergence of fry in some populations (Elliott 1989) and after attaining a certain size in others (Rincón & Lobón-Cerviá 2002), fish may saturate available habitat required for their specific size. The population may then continue to saturate the habitat in a self-thinning process, such that individuals can grow only if numbers of fish decrease due to increased individual resource requirements with size (Grant & Kramer 1990). Alternatively, the population may fall below the carrying capacity, but individual growth rates may nevertheless relate inversely to density in some cases (Grant & Imre 2006). The cohort strength may be maximised at intermediate density and size due to size-dependent survival at some stage, for example over the winter period (Crisp 1995, Armstrong 2005).

1.1.4 Local variation in population densities and dynamics

A basic practical significance of these processes is that unless spawning is abundant and homogeneous, there is likely to be substantial spatial variation in numbers, weights, dynamics and even year class number of salmon and trout regardless of local habitat quality (Armstrong 2005). A test of this prediction by field experiment in replicated streams at two levels (clumped and dispersed) confirmed empirically the importance of even local-scale patchiness of egg distribution on population dynamics (Einum et al. 2008). This spatial variation has three important consequences for investigation of habitat for salmonids. First, it is likely that models relating suites of habitat variables to local population density, weight and biomass will result in substantial residual unexplained variation and transfer poorly between different systems (with their different spatial arrangements of habitat types for the different life stages). This expectation is realised in empirical analyses (Fausch et al. 1988). Second, it is essential that in field trials to test for any local effect of a particular habitat variable, there is a substantial number of independent replicates to overcome the expected high degree of background variation in local densities, sizes, growth rates and age class strengths. Third, models to predict the consequences of varying habitat features, such as discharge, should be designed to operate across a broad range of population levels in relation to carrying capacity.

1.2 Defining local habitat quality

1.2.1 Defining patch quality in terms of local fish density

Streams can be considered as assemblages of patches of habitat. The scale at which patches can be assigned can vary and has a large influence on measurement and understanding of physical and biological processes (Folt et al. 1998). A patch may include only the space between two adjacent boulders, for example, and constitute less than the scale of a fish territory, or it may include an area of similar habitat such as a pool and may accommodate several fish territories. For measuring density of fish it may be appropriate in small patches to record likelihood of a fish being present whereas in larger patches the density of fish in occupancy may be an appropriate measure. The density experienced by a fish depends on its distance from nearest neighbours.

An influential approach for predicting consequences of variation in discharge has been through the application of Physical Habitat Simulation (PHabSim) (Bovee 1986) and similar models (e.g. Capra et al. 1995). PHabSim comprises physical and biological components. The physical model includes data from spatially referenced measurements of instream parameters, generally including local flow velocity and water depth, and can predict how these vary across discharges. Overlain on the network of physical habitat structure are estimates of the quality of the local habitat for fishes, from so-called preference curves. The preference curves may be derived from direct measurement in the study site at one or more discharges, imported from studies of other sites, or evolved from peoples’ opinions (‘expert opinion’), which is usually of unknown bias.

The model includes three major assumptions. First, density of fish in a habitat type is a true reflection of the value of that habitat (preference). Second, preference for each particular habitat type is constant across discharges. Third, that fish freely move to best available habitats when discharge changes. A fourth assumption that is implicit in application of the models is that the output (weighted usable area) has some meaning in terms of the fish population, for example the biomass, growth and densities that can be supported by the overall habitat.

Regarding the first assumption, Atlantic salmon and brown trout compete aggressively for high quality feeding patches within streams and tend to form dominance hierarchies in which the top-ranking fish can exclude others from preferred habitat (Sloman & Armstrong 2002). At low densities there may be a direct relationship between patch quality and density (Girard et al. 2004). However, as numbers of fish increase, densities become highest in more marginal areas, due, for example, to dominant fish holding the best stations and displacing other individuals (Greenberg 1994, Bult et al. 1999, Holm 2001, Blanchet et al. 2006, Stradmeyer et al. 2008, see also Baker & Coon 1997).

Regarding the second assumption, a direct experiment in which positions and local habitat quality of Atlantic salmon parr were measured across a range of discharges provided evidence of the large error that can occur in application of PHabSim to predict changes in overall habitat quality in terms of ‘weighted usable area’ (Holm et al. 2001). It was clear in this experiment that preference curves were not independent of discharge even though density remained constant and a closely controlled environment allowed precise measures of habitat and fish positions.

The third assumption that fish can move in response to change in distribution of habitat patches can be expected to depend on how those patches are juxtaposed in space across discharges, which is not included as part of the PHabSim model. Capacity of salmon to respond to change in habitat is discussed in Section 1.5. The issue of how the output of PHabSim, the weighte duseable area, relates to population processes is unclear and has been a concern for many researchers (Rosenfeld 2003).

The simple function used in PHabSim to predict habitat suitability considers fish to be constant objects and takes no account of variations in their behaviour, physiology and ecology under different physical and biological environments. This is exemplified with reference to observations of Stradmeyer et al. (2008), who monitored behaviour and feeding of salmon and trout in response to abstraction under controlled mesocosm conditions. Decrease in discharge resulted in a change from widespread distribution throughout pool and riffle to almost exclusive use of marginal pool areas and a switch to cryptic inactive behaviour in subordinate fish, which employed a ‘sneaky’ feeding mode under these conditions (Höjesjö et al. 2005). By contrast, dominant fish increased their aggressive activity markedly (Figure 1.1). All fish used pools during low water and observations of how this habitat was used at normal ...

Table of contents

• Cover
• Dedication
• Title Page
• Copyright
• Contributors
• Preface and Acknowledgements
• Chapter 1: Variation in Habitat Quality for Drift-Feeding Atlantic Salmon and Brown Trout in Relation to Local Water Velocity and River Discharge
• Chapter 2: ‘Catchment Consciousness’ – Will Mantra, Metr ic or Mania Best Protect, Restore and Manage Habitats?
• Chapter 3: In-Channel Placement of Structure to Enhance Habitat Complexity and Connectivity for Stream-Dwelling Salmonids
• Chapter 4: Integrating Science and Practice for the Sustainable Management of In-Channel Salmonid Habitat
• Chapter 5: Monitoring Salmon Stream Restoration: Guidelines Based on Experience in the American Pacific Northwest
• Chapter 6: Restoring Ecological Connectivity in Rivers to Improve Conditions for Anadromous Brown Trout (Salmo trutta)
• Chapter 7: Riparian Management: Alternative Paradigms and Implications for Wild Salmon
• Chapter 8: Does Fencing of British Lowland Streams Encourage Greater Salmonid Fish Stocks?
• Chapter 9: Effects of Competing Brown Trout on Habitat Use by Atlantic Salmon Parr: Controlled Investigations in a Laboratory Stream
• Chapter 10: Pool Restoration for Atlantic Salmon (Salmo salar) in Gravel Bed Rivers in New Brunswick, Canada
• Chapter 11: Nutrient Restoration Using Atlantic Salmon Carcasses as a Component of Habitat Management in Scottish Highland Streams
• Chapter 12: Habitat Requirements for Juvenile Salmonids in Chalk Streams: How will Management Best Address Conflicting Interests?
• Chapter 13: Aerial Photography as a Tool for Salmonid Habitat Assessment
• Chapter 14: Lymington River Fish Passage Easements: A Case Study from the New Forest (UK)
• Chapter 15: A Catalyst for Trout Habitat Improvement: A Review of the Wild Trout Trust Advisory Visit Programme
• Chapter 16: Influences of Environmental Variables and Stocking on Atlantic Salmon Upstream Migrations in the River Thames, UK
• Chapter 17: Managing the Effects of Climate Change: Fishery Management’s Greatest Challenge
• Index
• Colour Plates