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