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Tables of Contents for Ices Zooplankton Methodology Manual
Chapter/Section Title
Page #
Page Count
List of Contributors
xvii
Preface
xix
Introduction
1
32
Introduction
1
1
General definitions
1
2
Size classification
3
2
Main systematic groups
5
1
Species diversity
6
2
Ecological position
8
2
Distribution pattern
10
1
Growth and metabolism
10
2
Reproduction and development
12
1
Standing stock and production
12
1
Conclusion
13
17
References
30
3
Sampling and experimental design
33
22
Introduction
33
1
Conceptual issues
34
6
Increased emphasis on species dynamics
34
1
Integration of disciplines: zooplankton, between physics and fish
35
1
Integration of scales: from climatic to turbulent
36
1
Integration of approaches: from theory to field
37
1
Integration of pattern and process
38
1
Integration of technologies and methods
39
1
Design of oceanographic cruises and surveys
40
15
Survey design considerations
40
1
Survey design types
41
1
Systematic design
41
1
Random design
42
1
Stratified random design
42
1
Preferential design
42
1
Other design types
42
1
Sampling in flow fields
43
1
Examples of field programs
44
5
References
49
6
Collecting zooplankton
55
28
Introduction
55
2
A survey of sampling devices
57
10
Pumps and traps
57
1
Nets and serial samplers
58
1
Simple net samplers
58
1
Multiple sample instruments
58
4
Multiple net samplers
62
5
Factors influencing mesozooplankton samples
67
5
Extrusion of zooplankton from nets
67
3
Clogging of net mesh
70
1
Avoidance
70
2
Effect of ambient light
72
1
Mesh and frame color
72
1
Handling towed samplers
72
2
Care of towing cables
74
1
Handling samples and sample preservation
74
2
Collection of live zooplankton for experimental studies
76
1
Copepods
76
1
Other zooplankton instruments used in conjunction with nets
77
1
Optical plankton counter
77
1
References
78
5
Biomass and abundance
83
110
Introduction
83
2
Shipboard sample treatment
85
2
Biovolume and biomass determinations (W. Hagen)
87
60
Volumetric methods
88
1
Settling volume
88
1
Displacement volume
89
1
Gravimetric methods
90
1
Wet mass, fresh mass and live mass
90
1
Dry mass
91
3
Ash-free dry mass
94
1
Biochemical methods
94
3
Sample preparation
97
1
Elemental analysis
97
4
Organic carbon (and hydrogen)
101
2
Organic nitrogen
103
2
Organic phosphorus
105
2
Organic compounds
107
1
Proteins
107
6
Lipids (W. Hagen)
113
6
Carbohydrates
119
3
Energy content
122
9
Adenosine triphosphate ATP
131
8
Conversion factors and equations
139
8
Abundance and species identification
147
7
Analysis of community structure (H. Fock)
154
20
Estimation of species numbers
155
3
Diversity and similarity indices
158
6
Classification and ordination: the detection of groups
164
1
Multivariate classification techniques
164
2
Recurrent group analysis
166
2
Matching species and samples: indicator species analysis
168
1
Analysis of spatial and temporal formations
169
4
Examination of processes within communities by network analysis
173
1
Acknowledgment
174
1
References
174
19
Sampling, preservation, enumeration and biomass of marine protozooplankton
193
30
Introduction
193
3
Collection methods
196
5
Nano-and microzooplankton
196
1
Planktonic sarcodines
197
4
Preservation and enumeration
201
5
Nanozooplankton
201
1
Preservation
201
1
Nanozooplankton enumeration
202
1
Microzooplankton
203
1
Microzooplankton preservation
203
1
Microzooplankton enumeration
204
1
Planktonic sarcodines
205
1
Larger planktonic sarcodine preservation
205
1
Larger planktonic sarcodine enumeration
206
1
Determination of biomass: conversion factors
206
4
Nanozooplankton
206
1
Microzooplankton
207
1
Planktonic sarcodines
208
2
Standard protocols
210
2
Collection of nano-and microzooplankton
210
1
Preservation of nanozooplankton
210
1
Staining and enumeration of nanozooplankton
210
1
Preservation of microzooplankton
211
1
Enumeration of microzooplankton
212
1
Acknowledgments
212
1
References
212
11
Acoustical methods
223
36
Introduction
223
1
General discussion of principles, instruments, techniques, and comparative approaches
223
18
Review
223
1
Background
223
1
History
224
1
Basic principles
224
1
Active sonar equation
224
2
Target strength models
226
5
Sources of variability
231
1
Measurement
231
1
Modeling
232
1
Generic instruments
232
1
Echo sounder
232
1
Sonar
233
1
Acoustic Doppler current profiler (ADCP)
233
1
Echo integrator
233
1
Post-processing system
233
1
Methods of data processing and analysis
234
1
Echogram
234
1
Echo integration
234
1
Target strength determination
235
2
Post-processing and data analysis
237
1
Comparisons
238
1
Identification
238
1
Choosing an acoustic instrument
239
1
Single-animal methods
239
1
Multiple-animal methods
240
1
Parameter ranges for scientific echo sounders
240
1
Measurement protocols, model computations, and examples
241
12
Calibration
241
1
Test measurements
241
1
Standard-target method
241
1
Beam pattern measurement
242
1
Elements of echo abundance surveying
243
1
Equipment
243
1
Signal processing
244
1
Equipment use
244
1
Medium
244
1
Scatterer identification
244
1
Survey planning
244
1
Interpretation
244
1
Density measurement
244
1
Interpolation
244
1
Abundance estimation
245
1
System deployment
245
1
Evaluation of sonar performance
245
3
Exemplary model computations
248
2
Echo abundance surveying of Antarctic krill
250
1
Target strength determination by caged-animal measurement: Antarctic krill
251
1
Monitoring zooplankton with a fixed acoustic system
251
1
Acoustic estimates of size distribution using a multi-frequency system
252
1
Acknowledgments
253
1
References
253
6
Optical methods
259
38
Introduction
259
1
General discussion of principles, techniques, and comparative approaches
260
23
Review
260
1
Basic principles
261
1
Light phenomena
261
1
Illumination
262
1
Water as an optical medium
263
1
Light detection
264
1
Magnification and resolution
264
1
Sources of variability
265
1
Instrument effects
265
1
Water medium
265
1
Animal-dependent effects
266
1
Classes of light microscopy
266
1
Imaging
266
1
Bright-field microscopy
267
1
Contrast techniques
267
3
Fluorescence microscopy
270
2
Quantification
272
1
Techniques
272
1
Silhouette photography
272
1
Optical plankton counting
273
2
Video plankton recording
275
6
Comparisons
281
1
Identification
282
1
Imaging versus quantification
283
1
Venue and deployment
283
1
Operating ranges of two systems
283
1
Measurement protocols, model computations, and examples
283
8
Silhouette photography in the laboratory
283
1
Procedures
284
2
Further processing of the film
286
1
Optical plankton counter
286
1
Calibration including comparisons
286
2
Limitations
288
1
Operating scenario
288
1
Applications
288
1
Video plankton recorder
289
1
Calibration including comparisons
289
1
Limitations
290
1
Operating scenario
290
1
Applications
291
1
Acknowledgments
291
1
References
291
6
Feeding
297
104
Introduction
297
1
Feeding mechanisms of zooplankton
297
2
Expression of zooplankton feeding rates and common conversion factors
299
4
Clearance rate (F)
299
2
Ingestion rate (I)
301
1
Daily ration (DR)
302
1
Conversions between units of mass and energy
303
1
Microzooplankton
303
17
Methodological approaches
303
3
Indirect methods to measure assemblage grazing
306
1
Correlation of natural consumer-prey cycles
306
1
Extrapolation of laboratory rates to the field
306
1
The pigment budget
307
1
Acid lysozyme assay
307
1
Direct methods to measure per capita grazing rates
308
1
Food tracers: inert particles
308
2
Food tracers: prey cells
310
1
Food tracers: radioisotopes
311
2
Food vacuole contents
313
1
Prey removal
314
1
Direct methods to measure assemblage grazing rates
314
1
Sea water dilution method
314
2
Working procedures for the sea water dilution method
316
3
Size fractionation methods
319
1
Metabolic inhibitor method
320
1
Meso- and macrozooplankton
320
39
Empirical relationships
320
2
Field investigation on gut fluorescence
322
1
Sampling
323
1
Preparation for analysis
323
1
Gut clearance coefficient
323
2
Sorting animals
325
1
Extraction
326
1
Pigment analysis
326
1
Transformation to carbon
327
1
Pigment destruction
327
1
Working procedures for the gut fluoresence method
328
1
Equipment
328
1
Supplies
328
1
Procedure
328
2
Measurement and calculations
330
1
Comments and special precautions
330
1
Gut contents of field sampled consumers
330
1
General procedures
331
1
Special case: copepod mandibles in stomach contents
332
1
Digestion
333
2
Methods based on budgets of material or energy
335
1
Growth
336
1
Egestion
336
1
Excretion
337
1
Respiration
337
1
Assimilation efficiency
337
1
Measurement of assimilation efficiency: direct measurements
338
1
Measurement of assimilation efficiency: indirect calculation
338
1
Measurement of assimilation efficiency: ratio methods
339
1
Non-homogeneous food material
339
1
Food selectivity
339
1
Sloppy feeding
340
1
Losses from fecal material
340
1
Absorbance of IT in the digestive tract
340
1
Production of non-fecal material mixed with feces
340
1
Ash-ratio method
341
1
Chlorophyl-ratio method
341
1
Silica-ratio method
342
1
Radioisotope tracers
342
1
Methodological comparisons
343
1
Working procedures for laboratory experiments with isotopes
343
1
Working procedures for field experiments
344
1
Food removal methods
344
1
Bottle effects during incubations
345
1
Sloppy feeding
346
1
Estimates of community grazing rate
346
4
Working procedures with food removal methods
350
1
Collection of zooplankton
350
1
The food source
351
1
Experiments
351
2
Sub-sampling
353
1
Microscopic examination of sub-samples
354
1
Feeding rate calculations
354
1
Use of film and video to study feeding behavior
355
1
Biochemical indices
356
2
Working procedures for measurement of digestive enzyme activity
358
1
Amylase
358
1
Trypsin
358
1
Difficulties with specific zooplankton groups
359
6
Stomach contents from field samples
359
3
Laboratory experiments
362
3
Omnivory
365
3
A general method to estimate omnivory
365
1
Collection of consumers
366
1
Collection and handling of water
366
1
Sample collection, processing and analysis
366
1
Data analysis
367
1
Gut fluorescence and experimental egg production
367
1
Gut fluorescence and egestion rate
367
1
A method to estimate the importance of copepod prey for predators
367
1
Factors regulating feeding rate
368
9
Abundance of food items
368
1
Functional response. Model I
369
1
Functional response. Model II
370
1
Functional response. Modified model II
370
1
Functional response. Model III
371
1
Design of functional response experiments
371
1
Calculation curve fits in functional response experiments
372
1
Size of food items
373
1
Turbulence
374
1
Consumer body size
374
1
Palatability/toxicity of food organisms
375
1
Physical environmental factors
376
1
Temperature
376
1
Light
376
1
Spatial constraints
377
1
Predation behavioral models
377
1
Concluding remarks
378
1
Acknowledgments
379
1
References
380
21
The measurement of growth and reproductive rates
401
54
Introduction: why measure growth and reproductive rates of zooplankton?
401
2
Factors controlling the dynamics of copepod populations
402
1
Variability in the production of the prey field for fish larvae
402
1
The influence of food availability on growth and egg laying rates, including the linkage between copepod spawning and primary production cycles
402
1
Evaluation of environmental impacts
402
1
Estimation of secondary production
403
1
Models of growth and fecundity
403
4
Physiological or laboratory-derived budgetary models
404
1
Temperature-dependent empirical model
405
1
Global model of in-situ weight-specific growth
406
1
Determination of egg production rate: broadcast spawning copepods
407
11
The basic method
407
2
Procedures: know your species
409
1
Capture and handling
409
1
Duration of incubation
410
1
Incubation containers and density of females
410
3
Temperature
413
1
Light regime
414
1
Food supply
414
1
Statistical considerations
415
1
Estimation of spawning frequency from preserved samples
416
1
Egg viability
416
2
Egg production rates of egg carrying copepods
418
2
Egg ratio method
418
1
Incubation method
419
1
The determination of growth rate
420
5
Estimation of growth rate from preserved samples and demographic information
420
1
Estimation of development time
420
1
Estimation of mean weight
420
1
Limitations and sources of error
421
1
Direct measurement of growth rate
422
1
The basic method
422
1
Procedures
423
2
Biochemical and radiochemical methods
425
14
Ratio of biochemical quantities
425
1
Hormones and growth factors
426
1
Enzyme activities
427
6
Radiochemical methods
433
1
In vitro incorporation
433
2
In vivo uptake
435
1
In vivo injection
436
1
In vivo ingestion
436
3
Measurement of egg production rate of a marine planktonic copepod (Calanus finmarchicus)
439
2
Facilities
439
1
Equipment and supplies
439
1
Procedure
440
1
Capture
440
1
Sorting the catch
440
1
Incubation
441
1
Data analysis
441
1
Direct determination of copepod molting and growth rates in the field
441
3
Facilities and equipment
441
1
Supplies
441
1
Procedure
442
1
`Artificial cohort method'
442
1
`Sorting method'
442
1
Data analysis and interpretation
443
1
Molting rates
443
1
Growth rates
443
1
Notes and comments
443
1
Creation of artificial cohorts: alternative techiques
443
1
Changing the water
444
1
Acknowledments
444
1
References
444
11
Metabolism
455
78
Review
455
1
Oxygen consumption as an index of metabolism
455
3
Conversion of oxygen consumption to carbon and calorific units
458
1
Nitrogen and phosphorus metabolism
458
2
Measuring metabolic rate on live zooplankton
460
19
Technical problems
461
12
Body size and temperature as bases of metabolic comparison
473
3
Metabolic quotients
476
3
Metabolic rate and enzymatic indices
479
10
ETS activity
481
3
Enzymes of intermediary metabolism
484
1
Potential sources of error
485
4
Concluding remarks
489
1
Practice
490
1
T. Ikeda
J. J. Torres
Collection and handling of zooplankton
490
3
Respiration
493
23
Oxygen consumption-Winkler titration
493
6
T. Ikeda
Oxygen consumption-electrodes
499
7
J.J. Torres
Enzymatic method-electron transfer system
506
4
S. Hernandez-Leon
Enzymatic method-lactate dehydrogenase and citrate synthase
510
6
J.J. Torres
S.P. Geiger
Excretion
516
4
T. Ikeda
Single end-point method
516
1
Time-course method
517
1
Ammonia and inorganic phosphate analysis
517
3
References
520
13
Methods for population genetic analysis of zooplankton
533
38
Background
533
1
Technical approaches to determining genetic diversity
534
8
Allozymes
534
1
Restriction fragment length polymorphisms of DNA
535
1
DNA sequence analysis
536
1
Oligonucleotide probe hybidization
537
3
Allele-specific PCR
540
1
Microsatellite DNA
540
1
RAPDs
540
2
New and emerging techniques
542
1
Statistical approaches to assessing genetic diversity and structure
542
7
Statistical measures of genetic diversity
543
2
Statistical measures of genetic structure
545
2
Statistical analysis of gene flow (dispersal)
547
1
Computer methods and software sources
547
2
Strategies for preservation of zooplankton samples for genetic analysis
549
3
Preservation and storage in ethanol
550
1
Quick freezing in liquid nitrogen
550
1
Formalin, glutaraldehyde, and other bad things
551
1
Dehydration
551
1
In situ molecular analysis
551
1
General recommendations
552
1
Measurement protocols
553
9
Introduction
553
1
Facilities and equipment
553
1
General laboratory rules
554
1
Procedures
554
1
Sample preservation
554
1
DNA purification
555
2
PCR amplifications
557
2
Gel electrophoresis
559
1
Gel purification of DNA
559
2
Recipes and safety information
561
1
Buffers and frequently used solutions
561
1
Safety information
561
1
Further reading
562
1
Acknowledgments
563
1
References
564
7
Modeling zooplankton dynamics
571
98
Introduction
571
1
Modeling approaches and techniques
572
5
Steps of model building
572
1
Choice of state and forcing variables
572
1
Choice of model units
573
1
Choice of mathematical functions to model the interactions between variables
573
1
Identification of parameters
573
1
The mathematical description of the system
574
1
Systems of equations
574
1
Numerical methods
575
1
Computer programing and languages
576
1
Further reading
576
1
Models of individual bioenergetics and life-history traits
577
18
Individual bioenergetics
577
1
Budget of individual zooplankton
577
1
Ingestion rate
578
7
Assimilation and egestion
585
1
Excretion and respiration -- energetic costs
585
1
Growth and egg production models
586
3
Vital rates
589
1
Developmental stage durations of crustacean zooplankton
590
1
Mortality rates
591
1
Inverse methods to estimate vital rates
592
1
Evolutionary forces on the organism
592
3
Further reading
595
1
Population models
595
17
Populations described by one variable
595
1
Populations described by several variables -- structured population models
595
1
Discrete-time difference equation models and matrix models
596
4
Continuous-time structured population models
600
2
Stage-structured population models based on ODEs
602
4
Delay differential equation models
606
1
Structured population models to estimate demographic parameters
606
1
Stochasticity in structured population models
606
1
Individual-based models of a population
606
1
Building an IBM
607
2
Object-oriented programing (OOP)
609
1
Constraints in behavior
609
1
Models of interactions between zooplanktonic populations
610
1
Interaction model with two variables
610
1
Population interactions using structured population models
611
1
Further reading
611
1
Models of zooplankton communities
612
12
Zooplankton bulk models in ecosystem models
612
1
The representation of herbivorous zooplankton in NPZ-type ecosystem models
612
6
From a single grazer to several grazers
618
2
Size-structured ecosystem models
620
1
Size-structured ecosystem models
620
1
Size spectrum theory
621
2
Size- and stage-structured zooplankton populations in ecosystem models
623
1
Further reading
623
1
Modeling spatial dynamics of zooplankton
624
19
Modeling active behavior and counter-gradient search
624
1
Modeling behavioral mechanisms, aggregation and schooling patches
625
1
Modeling zooplankton behavior at the `micro-scale'
625
2
Evolutionary modeling approaches for optimal spatial distributions
627
6
Models of plankton patchiness generated by population dynamics interactions
633
1
Grid-based models
634
1
Coupling IBMs and spatially explicit models
635
1
Passive particle trajectories from Lagrangian transport in model circulation fields
635
2
Trajectories of actively swimming particles from Lagrangian transport in model circulation fields
637
1
Spatial zooplankton dynamics with advection-diffusion-reaction equations (ADRE)
638
1
Modeling passive dispersion with ADREs
639
1
Modeling active vertical swimming with ADREs
640
2
Modeling the dispersion of a population in circulation models with ADREs
642
1
Spatial distribution of zooplankton in ecosystem models coupled with ADREs
643
1
Further reading
643
1
Acknowledgments
643
1
References
644
25
Index
669