Users Guide to Ecohydraulic Modelling and Experimentation: Experience of the Ecohydraulic Research Team (PISCES) of the HYDRALAB Network

Users Guide to Ecohydraulic Modelling and Experimentation has been compiled by the interdisciplinary team of expert ecologists, geomorphologists, sedimentologists, hydraulicists and engineers involved in HYDRALAB IV, the European Integrated Infrastructure Initiative on hydraulic experimentation which forms part of the European Community’s Seventh Framework Programme. It is designed to give an overview of our current knowledge of organism-environment interactions in marine and freshwater aquatic systems and to provide guidance to those wishing to use hydraulic experimental facilities to explore ecohydraulic processes. By highlighting the current state of our knowledge, this design manual will act as a guide to the use of living organisms in physical models and experiments and help scientists and engineers understand limitations on the use of surrogates. It incorporates chapters on the general decisions that need to be taken when designing an ecohydraulic experiment as well as specific chapters on the main aquatic and marine organisms likely to be of interest. Each of the chapters reviews current knowledge in a defined area of ecohydraulic experimental research. It excludes consideration of fish and mammals and does not deal with plankton, as it focuses on the sediment-water interface and the influences of biota in this complex area. Its primary purpose is to disseminate the extensive knowledge and experience of the team of ecohydraulic experimentalists involved in HYDRALAB IV as part of the PISCES research project as well as some of the important advances being made in this fast developing field of research.

Table of Contents:
Foreword List of symbols and abbreviations Periodic table of the elements Contributors Acknowledgements 1 Introduction 1.1 Introduction 1.2 Rationale for the book 1.3 Reasons for using physical modelling in ecohydraulics 1.4 Audience for the book 1.5 Choice of facility 1.6 Choice of materials 1.7 Choice of measurement equipment 1.8 Layout of the book 1.8.1 Methods, materials and measurement 1.8.2 Organism-specific considerations 1.9 Conclusion: Decision-making framework SECTION 1 Methods, materials and measurement 2 Maintaining the health and behavioural integrity of plants and animals in experimental facilities 2.1 Introduction: The importance of husbandry 2.1.1 Introduction and general considerations 2.1.2 Tolerance levels 2.1.3 Sources of information 2.2 Important considerations when designing experiments with organisms 2.2.1 Housing organisms prior to experiments 2.2.2 Size of the experimental area 2.2.3 Water quality 2.2.4 Sediment sources and properties 2.2.5 Water temperature 2.2.6 Light levels 2.2.7 Sourcing and selecting the organisms 2.2.8 Selecting flow velocity and discharge 2.2.9 Nourishing organisms 2.2.10 Selecting population density 2.2.11 Ensuring natural behaviour 2.3 Conclusions 3 Using surrogates, including scaling issues, in laboratory flumes and basins 3.1 Introduction 3.2 Using physical surrogates 3.2.1 The benefits of using physical surrogates 3.2.1.1 Surrogates simplify the physical structure of organisms 3.2.1.2 Using surrogates avoids concerns about organism husbandry and acclimatisation 3.2.1.3 Surrogates can allow for the use of a greater number/density of organisms 3.2.1.4 Surrogates allow complete control over “organism” position and preclude behavioural complications 3.2.1.5 Surrogates allow detailed measurements near the “organism” 3.2.1.6 Surrogates allow replication of experiments 3.2.2 The limitations of using physical surrogates 3.2.2.1 Surrogates simplify the physical structure of organisms 3.2.2.2 Surrogates do not replicate all organism responses 3.2.2.3 The importance of considering unexpected organism interactions 3.2.3 Mimicking plants 3.2.3.1 Flexible full-scale surrogates 3.2.3.2 Scaled physical surrogates of plants 3.2.4 How previous experiments have mimicked animals 3.2.5 The questions that should be asked before using physical surrogates 3.3 Using alternative organisms as surrogates 3.3.1 The benefits of using other, living organisms as surrogates 3.3.2 The limitations on using biological surrogates 3.3.3 Commonly-used biological surrogates 3.3.4 Considerations before using a biological surrogate 3.4 Conclusions 3.5 Appendix 4 Flow measurement around organisms and surrogates 4.1 Introduction 4.1.1 Time and space scales of turbulent flows: Implications for measurement 4.1.2 Measurement uncertainties in turbulent flows 4.1.3 Problems of measuring flows within and around live biota 4.1.4 Technique overview 4.2 Acoustic techniques: The Doppler shift 4.3 Acoustic techniques: Acoustic Doppler Velocimetry (ADV) 4.3.1 Introduction to ADV 4.3.2 The strengths and weaknesses of ADV 4.3.3 The use of ADVs in ecological studies 4.4 Acoustic techniques: Acoustic Doppler Velocity Profiling (ADVP) 4.4.1 Introduction to ADVP 4.4.2 Strengths and weaknesses of ADVP 4.4.3 Use of ADVP in ecological studies 4.5 Optical techniques: Laser Doppler Anemometry/Velocimetry (LDA) 4.5.1 Introduction to LDA 4.5.2 Strengths and weaknesses of LDA 4.5.3 Use of LDA in ecological studies 4.6 Optical techniques: Particle Image Velocimetry (PIV) 4.6.1 Introduction to PIV 4.6.2 Strengths and weaknesses of PIV 4.6.3 Use of PIV in ecological studies 4.7 Thermal techniques: Hot Film and Hot Wire Anemometry (HFA/HWA) 4.7.1 Introduction to HFA/HWA 4.7.2 Strengths and weaknesses of HFA/HWA 4.7.3 Use of HFA/HWA in ecological studies 4.8 Drag measurements 4.8.1 Introduction to measuring drag 4.8.2 Strengths and weaknesses of drag measurement 4.8.3 Applications in ecological studies 4.9 Conclusions SECTION 2 Organism specific considerations 5 Biofilms 5.1 Introduction 5.2 Biofilms in natural hydro-ecosystems 5.2.1 Composition and structure of biofilms 5.2.2 Biofilms in natural hydro-ecosystems 5.2.3 Factors responsible for biofilm selection and growth 5.2.4 Thermal and photocycle effects 5.2.5 Spatial heterogeneity of biofilms 5.3 Impact of biofilms on the physico-chemical environment 5.3.1 The impact of biofilms on biogeochemical fluxes and ecosystem function 5.3.2 The impact of biofilms on the hydrodynamic environment 5.3.3 The impact of biofilms on the sedimentary environment 5.4 Conclusions 6 Plants, hydraulics and sediment dynamics 6.1 Introduction 6.2 The impacts of plants on the physical environment 6.2.1 Overview 6.2.2 Classification of vegetation forms under the influence of flow 6.2.3 Quantifying the drag force acting on vegetation 6.3 Important plant characteristics for plant-flow interactions 6.3.1 Plant properties 6.3.1.1 Plant shape 6.3.1.2 Stiffness 6.3.1.3 Buoyancy 6.3.2 Vegetation stand properties 6.3.2.1 Areal stem density 6.3.2.2 Configuration 6.3.2.3 Spatial distribution 6.3.2.4 Submergence ratio 6.3.3 Measuring plant properties 6.4 The impacts of plants on unidirectional flows 6.4.1 Impacts on the velocity profile 6.4.2 Impacts on turbulence generation and dissipation 6.4.3 Monami: A special case of turbulence 6.5 The impacts of plants on waves 6.5.1 Impacts on the velocity profile under waves 6.5.2 Impacts on total wave energy 6.6 The impacts of plants on the sedimentary environment 6.6.1 Sedimentation around and within plant stands 6.6.2 Scour and erosion 6.7 Numerical modelling of the interaction between vegetation, mean flow and turbulence 6.8 Conclusions 7 Macrozoobenthos, hydraulics and sediment dynamics 7.1 Introduction 7.2 Drag on and around animals 7.2.1 The significance of drag for animals 7.2.2 Variations in the drag acting on sessile animals 7.2.2.1 Animal morphology 7.2.2.2 Animal texture 7.2.2.3 Animal behaviour 7.2.2.4 Attached organisms (epibionts) 7.2.3 Measuring drag on sessile animals 7.3 Flow generation and bioirrigation of sediments 7.3.1 The environmental significance of flows generated by animals 7.3.2 Factors affecting animal-generated flows 7.3.2.1 Siphonal geometry 7.3.2.2 Ambient flow conditions 7.3.2.3 Seston concentration and quality 7.3.3 Quantifying flows generated by animals 7.4 Sediment mixing by mobile animals (bioturbation) 7.4.1 The significance of bioturbation for aquatic sediments 7.4.2 Controls on bioturbation by mobile benthic animals 7.4.2.1 Size and density of organisms 7.4.2.2 Sediment type 7.4.2.3 Location 7.4.3 Quantifying bioturbation 7.5 Topographic changes due to animals and the hydraulic implications of those changes 7.5.1 Significance of animals in controlling substrate topography 7.5.2 Ways in which animals alter substrate topography 7.5.2.1 Aggregation of sessile animals 7.5.2.2 Animal tracks and surface pellets 7.5.2.3 Pits and mounds 7.5.2.4 Tubes 7.5.3 Quantifying topographic alterations by mobile animals 7.6 The impact of mobile animals on the stability and transport of sediment 7.6.1 The significance of animals for the stability of freshwater and marine sediments 7.6.2 How animals alter sediment stability and sediment transport 7.6.2.1 Suspension of fluff layers 7.6.2.2 Sedimentation and biodeposition 7.6.2.3 Bulk sediment destabilisation 7.6.2.4 Stabilisation of sediments 7.6.2.5 Bioprotection of sediments 7.6.3 Quantifying the effects of animals on sediment stability and transport 7.7 Conclusions 8 Conclusion: Decision-making framework 8.1 Introduction 8.2 Decision-making framework References