Chapter
23.2.2 General Procedures
23.2.2.1 Influence of Urbanization on Food Webs
23.2.2.2 Gradients in δ13C and δ15N in Basal Resources
23.2.2.3 Use of δD in Stream Food Web Studies
23.2.2.4 Use of Mixing Models to Quantify Food Web Transfers
23.3.1 Basic Method: Comparison of Stream Food Webs Using Stable Isotopes of C and N
23.3.2 Advanced Method 1: Tracing Use of a Novel Terrestrial Particulate Organic Matter Source in a Stream Food Web
23.3.3 Advanced Method 2: Tracing Spatial Variation in Diet Sources for Food Webs
23.3.4 Advanced Method 3: Tracing Shifts in Basal Resources of Stream Food Webs Using δD
23.5 MATERIALS AND SUPPLIES
24 - Dissolved Organic Matter
24.2.1 Site Selection and Study Design
24.2.2 Sample Collection and Analysis
24.3.1 Basic Method 1: A Stream and Its Multiple Sources of Dissolved Organic Matter
24.3.2 Advanced Method 1: Heterotrophic Activity of Dissolved Organic Matter
24.3.2.1 Dark Incubation to Assess Bioavailability
24.3.3 Advanced Method 2: Enzymatic Characterization of the Dissolved Organic Matter Demand
24.3.3.1 Enzyme Collection
24.3.3.2 Enzyme Activity Measurement
24.3.4 Advanced Method 3: Fluorescent Analysis of Dissolved Organic Matter Composition
24.3.5 Advanced Method 4: Limitations to Degradation
24.3.5.2 Photolysis/Photobleaching
24.3.6 Advanced Method 5: Sorption of Dissolved Organic Matter in Soils
24.5 MATERIALS AND SUPPLIES
25 - Transport and Storage of Fine Particulate Organic Matter
25.2.2 Fine Benthic Organic Matter
25.2.4.1 Fine Benthic Organic Matter
25.3.1 Basic Method 1: Seston Concentration
25.3.1.1 Protocol for Seston Sampling in Streams and Small Rivers
25.3.1.2 Protocol for Seston Sampling in Large Rivers
25.3.1.3 Standard Processing Protocols
25.3.1.4 Particle Size Separation Protocols
25.3.1.5 Optional Experiment A: Seston Export
25.3.1.6 Optional Experiment B: Seston Sampling During Storms
25.3.2 Basic Method 2: Fine Benthic Organic Matter
25.3.2.1 Protocols for Field Collection of Fine Benthic Organic Matter
25.3.2.2 Fine Benthic Organic Matter Processing Protocols
25.3.3 Advanced Method 1: Linkages of Sestonic Fine Particulate Organic Matter to the Biota
25.3.3.1 Field Release and Larval Collection
25.3.3.2 Laboratory Analysis
25.4.2 Fine Benthic Organic Matter
25.4.3 Linkages of Sestonic Fine Particulate Organic Matter to the Biota
25.5 MATERIALS AND SUPPLIES
26 - Coarse Particulate Organic Matter: Storage, Transport, and Retention
26.3.1 Basic Method 1: Coarse Particulate Organic Matter Storage and Measurement
26.3.1.1 Field Measurements
26.3.1.2 Laboratory Processing
26.3.2 Basic Method 2: Coarse Particulate Organic Matter Transport and Retention
26.3.2.1 Laboratory Preparation
26.3.2.2 Field Physical Measurements
26.3.2.3 Field Coarse Particulate Organic Matter Releases
26.3.2.5 Option to Basic Method 2: Single-Particle Releases
26.3.3 Advanced Method 1: Enhancement of Stream Retentive Capacity
26.3.3.1 Laboratory Preparation
26.3.3.2 Field Measurements-Deployment of Retention Devices
26.3.3.3 Field Measurements-Related Ecosystem Measurements
26.3.4 Advanced Method 2: Measurement of Organic Carbon Spiraling
26.3.4.2 Field Measurements-Transported Organic Carbon
26.3.4.3 Field Measurements-Benthic Organic Carbon
26.3.4.4 Field Measurements-Organic Carbon Turnover
26.3.4.5 Field Measurements-Physical Characteristics of the Stream
26.3.4.6 Laboratory Processing
26.5 MATERIALS AND SUPPLIES
27 - Leaf-Litter Breakdown
27.3.1 General Protocol for Leaf-Litter Breakdown Experiments
27.3.2 Basic Method 1: Leaf Breakdown for One or More Leaf Species
27.3.3 Basic Method 2: Effects of Spatially Varying Stream Features on Leaf Breakdown Rates
27.3.4 Advanced Method 1: Effects of Anthropogenic Activities on Leaf Breakdown Rates
27.3.5 Advanced Method 2: Assessing Relationships Among Leaf Breakdown Rates and Shredders
27.3.6 Advanced Method 3: Assessing Microbial Activity During the Litter-Breakdown Process
27.5 MATERIALS AND SUPPLIES
28 - Riparian Processes and Interactions
28.2.1 Quantifying Riparian Vegetation Communities
28.2.2 Attenuation of Solar Radiation-Shading
28.2.3 Input and Decomposition of Coarse Organic Matter
28.2.4 Transfer of Dissolved Organic Matter and Nutrients
28.2.5 Remote Sensing of the Riparian Zone
28.3.2 Basic Method 1: Quantifying Riparian Vegetation Communities
28.3.2.1 Point-Centered Quarter Method
28.3.3 Basic Method 2: Attenuation of Solar Radiation-Shading
28.3.3.1 Pyranometer or Quantum Sensor
28.3.3.2 Spherical Densiometer Measurements
28.3.3.3 Hemispherical Photo Measurements
28.3.4 Basic Method 3: Input and Decomposition of Coarse Particulate Organic Matter
28.3.4.1 Leaf Litter Traps
28.3.4.2 Measurement of Coarse Particulate Organic Matter Decomposition Rates
28.3.4.3 Assessment of Detritivore Standing Crops
28.3.5 Advanced Method 1: Transfer of Dissolved Organic Matter and Nutrients from the Riparius to the Stream
28.3.5.1 General Measures of Dissolved Organic Matter and Nutrient Transfer
28.3.5.2 Nitrogen Mineralization Potential
28.3.5.3 Stable Isotope Analysis
28.3.6 Advanced Method 2: Remote Sensing of the Riparian Zone
28.3.6.1 Satellite Imagery
28.3.6.2 Airborne-Based Imagery
28.3.6.3 Light Detection and Ranging
28.3.6.4 Classification of Vegetation and Riparian Patches
28.5 MATERIALS AND SUPPLIES
29.1.1 Dynamics of Wood in Streams
29.1.1.2 Breakdown and Decomposition
29.1.2 Models of Wood Dynamics
29.1.3 Humans and the Dynamics of Wood
29.2.2 Marking Techniques for Repeated Surveys
29.3.1 Basic Method 1: Estimation of Standing Stocks of Wood
29.3.2 Basic Method 2: Line-Intersect Estimation of Large Wood
29.3.3 Basic Method 3: Long-Term Wood Retention and Transport
29.3.4 Advanced Method 1: Modeling Wood Accumulation
29.3.5 Advanced Method 2: Modeling Effects of Timber Harvest on Wood Accumulation
29.3.6 Advanced Method 3: Modeling Wood Abundance in a River Network
29.5 MATERIALS AND SUPPLIES
30 - Conservative and Reactive Solute Dynamics
30.1.1 Conservative Solute Dynamics
30.1.2 Reactive Solute Dynamics
30.2.3 Release Techniques
30.3.1 Basic Method: Dynamics of Conservative Solutes
30.3.1.1 Laboratory Preparation
30.3.1.2 Field Preparation-Prerelease
30.3.1.3 Field Procedure-Pulse Release
30.3.1.4 Field Procedure-Constant-Rate Release
30.3.1.5 After the Release
30.3.1.6 Estimating Discharge
30.3.1.7 Estimating Other Hydraulic Parameters
30.3.1.8 Transient Storage
30.3.2 Advanced Method: Reactive (Nonconservative) Solute Dynamics
30.5 MATERIALS AND SUPPLIES
31 - Nutrient Limitation and Uptake
31.1.1 Elevated Nutrient Loading to Streams
31.1.2 Capacity for Nutrient Retention in the Landscape
31.1.3 Overview of Chapter
31.2.1 Index of Limitation: Nutrient Diffusing Substrata
31.2.2 Short-Term Nutrient Addition
31.2.3 Short-Term 15N Tracer Release
31.3.1 Basic Method: Nutrient Diffusing Substrata
31.3.1.1 Laboratory Procedures
General Laboratory Protocol
Agar Preparation (see Table 31.2)
Attaching Cups to L-Bars and Storage
31.3.1.2 Field Procedures
Placement of Nutrient Diffusing Substrata in Stream (Fig. 31.3)
31.3.1.3 Metabolism Incubation of Discs
31.3.1.4 Chlorophyll a and Ash-Free Dry Mass Analysis on Discs
31.3.1.5 Modifications and Enhancements
31.3.2 Advanced Method 1: Short-Term Nutrient Release
31.3.2.1 General Preparations
Site Selection and Solute Decisions
Calculating the Amount of Salt to Be Added to the Carboy (see Table 31.3)
Laboratory Preparations for the Field
31.3.2.2 Field Procedures
Before Turning on the Dripper
Adding Injectate to Stream and Sampling at Plateau
31.3.2.3 Laboratory Procedures
Analysis of Water Samples
Calculating Nutrient Uptake Length (Sw)
31.3.2.4 Modifications and Enhancements
31.3.3 Advanced Method 2: Short-Term 15N Stable Isotope Tracer Addition
31.3.3.1 General Preparations
Isotope Purchase and Site Selection
Presampling and Preliminary Information for Calculations
31.3.3.2 Field Procedures
Before Turning on the Dripper
Adding Injectate to Stream and Sampling at Plateau
31.3.3.3 Laboratory Procedures
Sample Processing for Selected Rapid-Turnover Compartment (e.g., Filamentous Green Algae)
31.3.3.4 Potential Modifications to Protocols
31.3.3.5 Calculation of 15N Uptake Length
31.3.3.6 Modifications and Enhancements
31.4.1 Basic Method: Nutrient Diffusing Substrata
31.4.2 Advanced Method 1: Short-Term Nitrogen Release
31.4.3 Advanced Method 2: Short-Term 15N Tracer Release
31.5 MATERIALS AND SUPPLIES
32 - Nitrogen Transformations
32.1.2 Small-Scale Assays for Fluxes
32.2.1 Basic Method 1: Denitrification-Determining Unamended Denitrification and Denitrification Enzyme Activity Rates
32.2.2 Basic Method 2: Nitrification-Determining Gross and Net Nitrification Rates
32.2.3 Basic Method 3: Nitrogen Fixation
32.2.4 Advanced Methods: Isotopes for Flux Rate Measurement
32.3.1 Basic Method 1: Denitrification
32.3.1.1 General Preparation
32.3.1.2 Denitrification Rate Procedures (Laboratory)
Incubation, Sampling, and Analyses
Calculation of Denitrification Rate
32.3.2 Basic Method 2: Nitrification
32.3.2.1 Gross Nitrification Procedure
Day 3 Laboratory Procedures
Calculation of Nitrification Rate
32.3.2.2 Net Nitrification Procedure
Day 3 Laboratory Analyses
Calculation of Nitrification Rate
32.3.3 Basic Method 3: Nitrogen Fixation
32.3.3.1 General Preparation
Gas Chromatograph Configuration
Site Selection, Preparation, and Incubation Decisions
32.3.3.2 Field Procedures
32.3.3.3 Laboratory Procedures
Analysis of Headspace Samples via Gas Chromatography
Calculating N2 Fixation Rates (Based on Capone, 1993)
32.3.4 Advanced Method 1: Using 15N to Measure DNRA
32.3.4.1 General Preparation
Analytical Considerations (Prepare ﹥1Month Prior to Experiment)
32.3.4.2 Field Procedures
32.3.4.3 Laboratory Procedures
Adding 15N to Incubations
32.3.5 Advanced Method 2: Using MIMS to Measure Net N2 Flux
32.3.5.2 Running MIMS Samples
32.3.5.3 Calculations (Adapted From Kana et al., 1998)
32.5 MATERIALS AND SUPPLIES
32.5.4 Dissimilatory Nitrate Reduction to Ammonia
33 - Phosphorus Limitation, Uptake, and Turnover in Benthic Stream Algae
33.1.1 Assessment of P Limitation
33.1.4 Overview of Chapter
33.2.1 Basic Method 1: Phosphatase Activity
33.2.2 Basic Method 2: Chemical Composition (C:P Ratio in Algal Tissue)
33.2.3 Basic Method 3: Net Nutrient Uptake-Stable Phosphorus
33.2.4 Advanced Method 1: Gross Nutrient Uptake (Phosphorus Radiotracer)
33.2.5 Advanced Method 2: Phosphorus Turnover
33.3.1 Basic Method 1: Phosphatase Activity
33.3.1.1 Preparation Protocol
33.3.1.2 Field Collection Protocol
33.3.1.3 Laboratory Protocol
33.3.2 Basic Method 2: Chemical Composition
33.3.2.1 Preparation Protocol
33.3.2.2 Field Collection Protocol
33.3.2.3 Laboratory Protocol
33.3.3 Basic Method 3: Net Nutrient Uptake (Stable Phosphorus)
33.3.3.1 Preparation Protocol
33.3.3.2 Field Collection Protocol
33.3.3.3 Laboratory Protocol
33.3.3.4 Soluble Reactive Phosphorus Analysis (Adapted From APHA et al., 1995)
33.3.4 Advanced Method 1: Gross Nutrient Uptake (Phosphorus Radiotracer)
33.3.4.1 Preparation Protocol
33.3.4.2 Field Collection Protocol
33.3.4.3 Laboratory Protocol
33.3.5 Advanced Method 2: Phosphorus Turnover
33.3.5.1 Preparation Protocol
33.3.5.2 Field Placement and Collection (Option 1)
33.3.5.3 Chamber/Aquarium Placement and Collection (Option 2)
33.3.5.4 Laboratory Protocol (Applicable for Both Options 1 and 2)
33.4.1 Limitation: Phosphatase Activity
33.4.2 Limitation: Chemical Composition
33.4.3 Net Uptake: Stable Phosphorus
33.4.4 Total Uptake: Radiolabeled Phosphorus
33.5 MATERIALS AND SUPPLIES
34.2.1 Basic Method: Stream Metabolism
34.2.1.1 Site Selection and Data Collection
34.2.2 The Fundamental Metabolism Equation
34.2.3 Air-Water Gas Exchange
34.2.4 Advanced Analyses: Inverse Modeling of Ecosystem Metabolism
34.3.1 Basic Method: Stream Metabolism
34.3.1.1 In the Field: Site Parameters and Diel O2 Data
34.3.1.2 In the Field: Gas Exchange From Tracer Additions
34.3.1.3 In the Laboratory: Gas Exchange From Tracer Additions
34.3.1.4 On the Computer: Gas Exchange From O2 Data
34.3.1.5 On the Computer: Estimating Metabolism
34.3.1.6 Advanced Method: Metabolism Modeling
34.5 MATERIALS AND SUPPLIES
35 - Secondary Production and Quantitative Food Webs
35.1.1 Biomass Turnover and the P/B Concept
35.1.2 Utility of Secondary Production in Ecosystem Studies
35.2.1 Population Density
35.2.2 Population Size Structure
35.2.3 Individual and Population Biomass
35.3.2 Noncohort Techniques: Size-Frequency Method
35.3.3 Noncohort Techniques: Instantaneous Growth Rate Method
35.3.4 ``Shortcut'' Approaches
35.3.5 Statistical Approaches
35.3.6 Quantification of Food Webs
35.5 MATERIALS AND SUPPLIES
36 - Elemental Content of Stream Biota
36.2.2 Elemental Composition of Food Web Compartments
36.2.3 Measuring Nutrient Release Rates of Stream Biota
36.2.4 Estimating Threshold Elemental Ratios for Stream Invertebrates
36.3.1 Basic Method 1: Estimating C, N, and P Content of Food Web Compartments
36.3.1.1 Protocol for Field Collection
36.3.1.2 Protocol for Laboratory Preparation
36.3.1.3 Sample Analysis11Wear personal protective equipment (PPE), including lab coat, eyewear, and gloves, whenever conducting lab ...
36.3.1.4 Data Analysis and Assessment of Consumer-Resource Imbalances
36.3.2 Basic Method 2: Measuring Organismal Nutrient Release Rates
36.3.2.2 Laboratory Protocol: Excretion
36.3.2.3 Laboratory Protocol: Egestion
36.3.3 Advanced Method 1: Measuring C, N, and P Content in a Single Sample With the ``One-Vial Technique''
36.3.3.2 Recrystallize the Potassium Persulfate (24h Before Analysis)
36.3.3.5 Nitrogen and Phosphorus Analysis
36.3.4 Advanced Method 2: Evaluating the Relative Importance of Animal Excretion at the Ecosystem Scale
36.3.4.1 Metrics of Relative Ecosystem-Level Importance of Animal Excretion
36.3.5 Advanced Method 3: Accounting for the Effects of Fasting and Stress on Organismal Excretion Rates
36.3.6 Advanced Method 4: Estimating Threshold Elemental Ratios
36.3.6.1 Periphyton Incubation
36.3.6.2 Growth Experiment
36.3.6.3 Experimental Procedure
36.5 MATERIALS AND SUPPLIES
37 - Ecological Assessment With Benthic Algae
37.2.1 Ecological Assessment
37.2.3.2 Field Sampling and Laboratory Assays
37.2.4 Data Analysis Plan
37.3.1 Basic Exercise 1: Rapid Periphyton Survey
37.3.1.1 Field Assessment
37.3.2 Basic Exercise 2: Genus-Level Periphyton Assays and Index of Biotic Condition
37.3.2.1 Collecting Periphyton Samples
37.3.2.2 Subsampling for Different Assays
37.3.2.3 Identifying Diatom Genera and Counting Cells
37.3.2.4 Calculating Diatom Metrics
37.3.3 Advanced Exercise 1: Identification and Counting of All Algae (Optional)
37.3.3.1 Calculating Algal Metrics
37.3.4 Advanced Exercise 2: Species Autecologies and Inferring Environmental Condition (Optional)
37.3.4.1 Calculating an Environmental Optimum for a Species
37.3.4.2 Calculate Inferred Total Phosphorus Concentration for a Stream
37.3.5 Advanced Exercise 3: Biomass Assays (Optional)
37.3.6 Advanced Exercise 4: Analysis and Interpretation of Data
37.3.6.1 Determine Expected Conditions
37.3.6.2 Assess Stream Conditions for Targeted Streams
37.3.6.3 Assess Stream Conditions for the Region
37.3.6.4 Diagnose Likely Causes of Impairment
37.5 MATERIALS AND SUPPLIES
38 - Macroinvertebrates as Biotic Indicators of Environmental Quality
38.1.1 Evaluating Stressors
38.1.2 Advanced Approaches to the Identification of Macroinvertebrates
38.1.2.1 Genetic Approach
38.1.2.2 Species Traits Approach
38.1.3 Volunteer (Citizen-Based) Assessments
38.2.1 Analytical Approaches
38.2.1.1 Multimetric Approach
38.2.1.2 Multivariate Approaches
38.2.2 Habitat Assessment
38.3.1 Basic Method: Assessment of Two Sites
38.3.1.2 Physical Habitat Description
38.3.1.3 Macroinvertebrate Field Collection Option
38.3.1.4 Macroinvertebrate Laboratory-Only Option
38.3.2 Advanced Method: Assessment of Multiple Sites
38.3.2.2 Macroinvertebrate Collections
38.3.2.3 Habitat Assessment
38.3.2.4 Subsampling, Sorting, and Identification
38.3.2.5 Calculate Metrics
38.3.2.6 Comparison of Replicate Samples
38.3.2.7 Generate Ordination Scores
38.4.1 General Questions for Both Basic and Advanced Methods
38.4.2 Questions for Basic Method
38.4.3 Questions for Advanced Method
38.5 MATERIALS AND SUPPLIES
39 - Environmental Quality Assessment Using Stream Fishes
39.1.1 A Brief History of the Index of Biotic Integrity
39.1.2 Patterns in ``Noise'' Versus ``Signal''
39.1.3 Motivation and Regionalization
39.2.2 Regional Calibration
39.2.4 Establishment of Baseline Considerations
39.2.5 Metric Selection and Replacement
39.2.5.3 Correlation With Natural Gradients
39.2.5.4 Responsiveness Test
39.2.5.6 Range Test for Metric Values
39.2.6 Additional Considerations
39.3.1 Basic Method: Application of the Index of Biotic Integrity to a Reference Site and an Impacted Site
39.3.2 Advanced Method: Calibration and Testing a Stream Fish Index of Biotic Integrity
39.4.2 Questions for Basic Method
39.4.3 Questions for Advanced Method
39.5 MATERIALS AND SUPPLIES
40 - Establishing Cause-Effect Relationships in Multistressor Environments
40.1.1 Linking Field Biomonitoring to In Situ Bioassay Experiments
40.1.2 Artificial Stream Approaches
40.2.2 General Procedures
40.3.1 Basic Method: Retrospective Ecological Risk Assessment of an Effluent Discharge
40.3.1.1 Site Characterization
40.3.1.2 Field Assessment of Ecological Effects
40.3.1.3 Laboratory Methods
40.3.2 Advanced Method 1: Determining Nutrient Limitation Using Nutrient Diffusing Substrate Bioassays
40.3.3 Advanced Method 2: In Situ Determination of Sublethal Effects of the Effluent
40.3.4 Advanced Method 3: Separating Nutrient and Contaminant Effects on Benthic Food Webs
40.4.1 Basic Method: Retrospective Ecological Risk Assessment of an Effluent Discharge
40.4.2 Advanced Method 1: Determining Nutrient Limitation Using Nutrient Diffusing Substrate Bioassays
40.4.3 Advanced Method 2: In Situ Determination of Sublethal Effects of the Effluent
40.4.4 Advanced Method 3: Separating Nutrient and Contaminant Effects on Benthic Food Webs
40.5 MATERIALS AND SUPPLIES
Methods in Stream Ecology
：Volume 2: Ecosystem Function
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