HANDBOOK OF SCALING METHODS IN AQUATIC ECOLOGY MEASUREMENT, ANALYSIS, SIMULATION - PART 1 pptx

Scaling Methods in Aquatic Ecology HANDBOOK OF Measurement, Analysis, Simulation © 2004 by CRC Press LLC CRC PRESS Boca Raton London New York Washington, D.C. EDITED BY Laurent seuront Peter G. Strutton Scaling Methods in Aquatic Ecology HANDBOOK OF Measurement, Analysis, Simulation © 2004 by CRC Press LLC Cover: Mount Fuji from the OfÞng, also known as The Great Wave off Kanagawa, from the series of block prints 36 Views of Mount Fuji (1823–1829) by Katsushika Hokusai (1760–1849). Senior Editor: John Sulzycki Production Editor: Christine Andreasen Project Coordinator: Erika Dery Marketing Manager: Nadja English This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. 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QH541.5.W3H36 2003 577.6¢072—dc21 2003051467 © 2004 by CRC Press LLC Visit the CRC Press Web site at www.crcpress.com Preface Aquatic scientists have always been intrigued with concepts of scale. This interest perhaps stems from the nature of ßuid dynamics in oceans and lakes — energy cascades from spatial scales of kilometers down to viscous scales at centimeters or less. Turbulent processes affect not only an organism’s perception of, and response to, the physical environment, but also the interaction between species, both within and across trophic levels. Our ability to understand processes that act across scales has traditionally been technically limited by the availability of appropriate instruments, suitable analysis, modeling and simulation techniques, and sufÞcient computing power. In some respects we have also lacked a theoretical framework for conducting these observations, analyses, and simulations. Since the 1970s these problems have partially been overcome and our understanding of the relationship between scale and aquatic processes has advanced accordingly. In fact, it was in the early 1970s that the Þrst applications of spectral analysis to biological oceanographic data emerged. This initial work described the scale-dependent nature of biological– physical interactions and stimulated investigations of such interactions across a vast array of time and space scales. However, even if the increase in computer power during the last three decades has opened new perspectives in space–time complexity in aquatic ecology, it is still unfortunately not sufÞcient. For example, a realistic framework for turbulence simulations will still require several decades of technical improvements, simply to be able to handle high Reynolds number ßows, while a theoretical framework for intermittent processes — increasingly recognized as playing a crucial role in aquatic ecosystems — still does not exist. Only in recent years has aquatic ecology begun to incorporate new, exciting, and often interrelated observational, analysis, modeling, and simulation techniques. These include the following: •Development of techniques to observe small-scale biological processes such as bacterial chemo- taxis, zooplankton behavior, and organisms’ responses to turbulence • Increasing availability and use of satellite data to view the other end of the spatial spectrum æ basin scale dynamics • Incorporation of nonlinear analysis techniques and application of concepts from chaos theory to problems of spatial and temporal processes • Advancement of models and simulations to mimic and hence understand complex biological processes This volume compiles a comprehensive selection of papers, illustrating some of the recent advances that have been made toward understanding physical, biological, and chemical processes across multiple time and space scales. The chapters cover a range of ecosystems, both oceanic and freshwater, from pelagic to benthic/rocky intertidal to seagrass beds. The scale of processes considered ranges from the microscopic to almost global, spanning topics such as physiological cues in individual phytoplankton cells and mating signals in zooplankton to basin-scale primary productivity. The range of organisms studied is equally diverse, from phyto- and zooplankton to large Þsh dynamics. A broad range of up-to-date observational, data analysis, and simulation techniques is presented. These include (1) new bio-optical, video, acoustic, remote sensing, and synchrotron-based imaging systems, (2) different scaling methods (i.e., fractals, wavelets, rank-order relationship) to assess a broad range of spatial and temporal patterns and processes, and (3) innovative simulation techniques that allow insights into processes ranging from individual behavior to population dynamics, the structure of turbulent intermittency and its effects on swimming organisms, and the effect of large-scale physical forcings on particle distributions at small scales. Measurement, analysis, and simulation at the organismal level might be crucial to © 2004 by CRC Press LLC investigate the poorly understood cumulative effect of Þne-scale processes on broad-scale biosphere processes. This approach may eventually link dynamic processes at several spatiotemporal scales both to understand complex ecological systems and to address old research questions from new perspectives. It is our hope that this compilation will expose exciting new research to those already working in the Þeld, as well as facilitate a type of cross-pollination by introducing other sections of the scientiÞc community to recent developments. We thus believe that the combination of three potentially disparate Þelds — measurement, analysis, and simulation — in one volume will serve to build bridges between experimentalists and theoreticians. Only by the close collaboration of these Þelds will we continue to gain a solid understanding of complex aquatic ecosystems. Laurent Seuront and Peter G. Strutton © 2004 by CRC Press LLC Acknowledgments This book arose out of a special session entitled “Dealing with Scales in Aquatic Ecology: Structure and Function in Aquatic Ecosystems” at the 2001 ASLO Aquatic Science Meeting. We gratefully acknowledge the Organizing Committee chairs, Josef Ackerman and Saran Twombly, for their enthu- siastic support of what was a successful and popular session, and what we hope will be a successful and popular compilation. SpeciÞcally, we thank the contributors to that session for their quality presentations. We acknowledge, in alphabetical order, C. Avois, J.A. Barth, A.S. Cohen, E.A. Cowen, T.J. Cowles, T.L. Cucci, H. Cyr, M.M. Dekshenieks (McManus), P.L. Donaghay, K.E. Fisher, C. Greenlaw, R.E. Hecky, D.V. Holliday, Z. Johnson, P. Legendre, M. Louis, D. McGehee, C.M. O’Reilly, V. P asour, J.E. Rines, F.G. Schmitt, C.S. Sieracki, M.E. Sieracki, J. Sullivan, E.C.U. Thier, A.K. Yamazaki, and H. Yamazaki. Finally, we owe our thanks to the reviewers of the chapters for improving the quality of the published work. © 2004 by CRC Press LLC Editors Laurent Seuront, Ph.D., is a CNRS Research Scientist at the Wimereux Marine Station, University of Lille 1 æ CNRS UMR 8013 ELICO, France. His education includes a B.S. in population biology and ecology from the University of Lille 1 (1992); an M.S. in marine ecology, data analysis, and modelling from the University of Paris 6 (1995); and a Ph.D. in biological oceanography from the University of Lille 1 (1999). Prior to his present position, he was a research fellow of the Japanese Society for the Promotion of Science at the Tokyo University of Fisheries, working with Hidekatsu Yamazaki. Dr. Seuront’s research concerns biological–physical coupling in aquatic/marine systems/environ- ments, particularly with regard to the effect of microscale (submeter) patterns and processes on large- scale processes. Aspects of his work combine Þeld, laboratory, and numerical experiments to study the centimeter-scale distribution of biological (nutrient, bacteria, phytoplankton, microphytobenthos, and microzoobenthos) and physical parameters (temperature, salinity, light, turbulence), as well as the motile behavior of individual organisms in response to different biophysical forcings. His work to date has been the subject of more than 30 publications in international journals and contributed books, more than 30 presentations at international conferences, and invited seminars at more than 20 locations throughout the world. Peter G. Strutton, Ph.D., is Assistant Professor of Oceanography at the Marine Sciences Research Center, State University of New York, Stony Brook. Prior to his current appointment he was Postdoctoral Scientist with Francisco Chavez at the Monterey Bay Aquarium Research Institute. He received his B.Sc. (Honors) and Ph.D. in marine science from Flinders University of South Australia, working with Jim Mitchell, who was in turn a student of Akira Okubo at Stony Brook. Professor Okubo’s legacy is apparent in many of the chapters contained in this volume. Dr. Strutton’s work focuses on the interaction among physics, biology, and chemistry in the ocean at a broad range of time and space scales. Current areas of interest include the spatial and temporal variability of carbon cycling in the equatorial PaciÞc, the inßuence of phytoplankton on the heat budget of the upper ocean, and the biological–physical interactions associated with open ocean iron fertilization. Since 1996 he has authored or co-authored approximately 20 publications and has presented his work at more than 30 meetings and invited seminars. © 2004 by CRC Press LLC Contributors Neil S. Banas School of Oceanography University of Washington Seattle, Washington, U.S.A. Richard T. Barber Nicholas School of the Environment and Earth Sciences Duke University Beaufort, North Carolina, U.S.A. Carlos Bas Institute of Marine Science (CSIC) Paseo Juan de Borbón Barcelona, Spain Alberto Basset Department of Biology University of Lecce Lecce, Italy Mark C. Benfield Department of Oceanography and Coastal Sciences Coastal Fisheries Institute Louisiana State University Baton Rouge, Louisiana, U.S.A. Uta Berger Center for Tropical Marine Ecology Bremen, Germany Olivier Bernard COMORE–INRIA Sophia-Antipolis, France David R. Blakeway Department of Biological Sciences California State University Los Angeles, California, U.S.A. Matthew C. Brewer Department of Zoology University of Florida Gainesville, Florida, U.S.A. Jason Brown School of Biology Georgia Institute of Technology Atlanta, Georgia, U.S.A. Maria Bunta Department of Physics University of Wisconsin–Milwaukee Milwaukee, Wisconsin, U.S.A. Janet W. Campbell Ocean Process Analysis Laboratory University of New Hampshire Durham, New Hampshire, U.S.A. Philippe Caparroy Insect Biology Research Institute CNRS–University of Tours Tours, France Jose Juan Castro Fisheries Research Group University of Las Palmas Las Palmas, Canary Islands, Spain Michael Caun Department of Life Sciences University of California at Santa Barbara Santa Barbara, California, U.S.A. Francisco P. Chavez Monterey Bay Aquarium Research Institute Moss Landing, California, U.S.A. Andrew S. Cohen Department of Geosciences University of Arizona Tucson, Arizona, U.S.A. Timothy J. Cowles College of Oceanic and Atmospheric Sciences Oregon State University Corvallis, Oregon, U.S.A. © 2004 by CRC Press LLC Hélène Cyr Department of Zoology University of Toronto Toronto, Ontario, Canada John Davenport Environmental Research Institute Department of Zoology, Ecology, and Plant Science University College Cork Cork, Ireland Dominique Davoult Biological Station of Roscoff University of Paris 6 and CNRS Roscoff, France Donald L. DeAngelis Biological Resources Division U.S. Geological Survey and Department of Biology University of Miami Coral Gables, Florida, U.S.A. Robert A. Desharnais Department of Biological Sciences California State University Los Angeles, California, U.S.A. Peter J. Dillon Department of Chemistry Trent University Peterborough, Ontario, Canada Michael Doall Functional Ecology Laboratory State University of New York at Stony Brook Stony Brook, New York, U.S.A. Douglas D. Donalson Department of Biological Sciences California State University Los Angeles, California, U.S.A. Igor M. Dremin Theory Department Lebedev Physical Institute Moscow, Russia Karen E. Fisher Los Alamos National Laboratory Los Alamos, New Mexico, U.S.A. Rodney G. Fredericks Coastal Studies Field Support Group Louisiana State University Baton Rouge, Louisiana, U.S.A. David A. Fuentes Department of Biological Sciences California State University Los Angeles, California, U.S.A. Vincent Ginot INRA Biometry Unit Domaine St. Paul Avignon, France Mario Giordano Institute of Marine Sciences University of Ancona Ancona, Italy Jarl Giske Department of Fisheries and Marine Biology University of Bergen Bergen, Norway Volker Grimm Department of Ecological Modelling UFZ Centre for Environmental Research Leipzig–Halle Leipzig, Germany Robert E. Hecky Department of Biology University of Waterloo Waterloo, Ontario, Canada Jean-Pierre Hermand Department of Optics and Acoustics University of Brussels (ULB) Brussels, Belgium Carol J. Hirschmugl Department of Physics University of Wisconsin–Milwaukee Milwaukee, Wisconsin, U.S.A. Geir Huse Department of Fisheries and Marine Biology University of Bergen Bergen, Norway © 2004 by CRC Press LLC Oleg V. Ivanov Theory Department Lebedev Physical Institute Moscow, Russia Houshuo Jiang Department of Applied Ocean Physics and Engineering Woods Hole Oceanographic Institution Woods Hole, Massachusetts, U.S.A. Mark P. Johnson School of Biology and Biochemistry The Queen’s University of Belfast Belfast, United Kingdom Daniel Kamykowski Department of Marine, Earth, and Atmospheric Sciences North Carolina State University Raleigh, North Carolina, U.S.A. Sean F. Keenan Department of Oceanography and Coastal Sciences Louisiana State University Baton Rouge, Louisiana, U.S.A. Sophie Leterme Wimereux Marine Station CNRS and University of Lille 1 Wimereux, France Amala Mahadevan Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge, United Kingdom and Ocean Process Analysis Laboratory University of New Hampshire Durham, New Hampshire, U.S.A. Bruce D. Malamud Environmental Monitoring and Modelling Group Department of Geography King’s College London, Strand London, United Kingdom Horst Malchow Department of Mathematics and Computer Science Institute for Environmental Systems Research University of Osnabrück Osnabrück, Germany Alexander B. Medvinsky Institute for Theoretical and Experimental Biophysics Russian Academy of Sciences Pushchino, Moscow Region, Russia Aline Migné Laboratory of Hydrobiology University of Paris 6 and CNRS Paris, France James G. Mitchell School of Biological Sciences Flinders University Adelaide, Australia Wolf M. Mooij Centre for Limnology The Netherlands Institute of Ecology Nieuwersluis, the Netherlands Vladimir A. Nechitailo Theory Department Lebedev Physical Institute Moscow, Russia Roger M. Nisbet Department of Ecology, Evolution, and Marine Biology University of California at Santa Barbara Santa Barbara, California, U.S.A. Catherine M. O’Reilly Environmental Science Program Vassar College Poughkeepsie, New York, U.S.A. Thomas Osborn Department of Earth and Planetary Sciences The Johns Hopkins University Baltimore, Maryland, U.S.A. © 2004 by CRC Press LLC [...]... ζ (1) 0 .1 0. 01 0.0 01 0. 01 0 .1 1 10 1 10 1 10 l 1 ζ (2) 0 .1 0. 01 0.0 01 0.0 01 0. 01 0 .1 l 1 ζ (3) 0 .1 0. 01 0.0 01 0.00 01 0.0 01 0. 01 0 .1 l ( ) q FIGURE 1. 7 The structure functions DIVFl vs l in log–log plots for q = 1, 2, and 3 (from top to bottom) for the TurboMAP ßuorescence proÞle The slopes of the closed symbols provide estimates of the Þrst, second, and third scaling. .. Hydrobiologia, 3 61, 19 1 19 9 Hanson, A.K and P.L Donaghay, 19 98: Micro- to Þne-scale chemical gradients and layers in stratiÞed coastal waters Oceanography, 11 , 10 17 Holliday, D.V., R.E Pieper, C.F Greenlaw, and J.K Dawson, 19 98: Acoustical sensing of small-scale vertical structures in zooplankton assemblages Oceanography, 11 , 18 –23 Hutchinson, G.E., 19 61: The paradox of the plankton Am Nat., 95, 13 7 14 5 Jackson,... Research Institute Daniel Kamykowski provided useful comments on an early version of this chapter © 2004 by CRC Press LLC 14 Handbook of Scaling Methods in Aquatic Ecology: Measurement, Analysis, Simulation 1. 5 ζ (q ) 1. 0 0.5 0.0 0.0 1. 0 2.0 3.0 4.0 5.0 q FIGURE 1. 8 The empirical scaling exponents z(q) obtained from the TurboMAP ßuorescence proÞle in Lake Biwa (open diamonds) and in Seto Inlet (black... 2 .1 2.2 Introduction 17 Methods 19 2.2 .1 System Description 19 2.2 .1. 1 Camera Housing 19 2.2 .1. 2 Power/Telemetry Housing 19 2.2 .1. 3 Strobed Light Sheet 20 2.2 .1. 4 Environmental Sensors and Frame 21 2.2 .1. 5 Winch and Sea Cable 21 2.2 .1. 6 Command and Control 21 2.2 .1. 7 Image and Data Processing... orientations of individual targets can be determined Nearest neighbor distances can be calculated to estimate the micropatchiness of zooplankton © 2004 by CRC Press LLC 22 Handbook of Scaling Methods in Aquatic Ecology: Measurement, Analysis, Simulation FIGURE 2.2 An example ZOOVIS image containing a marine snow particle displayed within the image processing program White boxes surround all particles... 17 © 2004 by CRC Press LLC 18 Handbook of Scaling Methods in Aquatic Ecology: Measurement, Analysis, Simulation of tens to hundreds of meters and vertical scales of several meters or more, they are generally inadequate to reveal the structure of patches and layers on finer scales Pumps have proved useful for exposing vertical structure on smaller scales than nets (Smith et al., 19 76; Incze et al., 19 96),... To investigate the impact of patchiness, we took Niskin bottle samples at two stations located in the inshore (50°47¢300 N, 1 33¢500 E) and the offshore (50°46¢950 N, 1 16 ¢680 E) waters of the Eastern English Channel during the spring bloom on 16 and 17 April 2002, respectively During the recovery, the Niskin bottles were handled gently to avoid stirring of the water inside the bottles From the 5-l... Handbook of Scaling Methods in Aquatic Ecology: Measurement, Analysis, Simulation FIGURE 2 .1 (Top) The underwater components of ZOOVIS being deployed from the stern of the CCGS Vector in Knight Inlet, British Columbia, Canada A = camera housing; B = telemetry housing; C = strobe housing; D = CTD; E = transmissometer; and F = acoustic transponder/responder The fluorometer is not visible in this image In this... roll off toward high probability related to an oversampling of the most common ßuorescence values is still visible, both the linear behavior and the roll off toward low probability has disappeared, demonstrating the inability of a low-resolution sampling process to capture the microscale structure of ßuorescence distributions © 2004 by CRC Press LLC 12 Handbook of Scaling Methods in Aquatic Ecology: Measurement,. .. Perspectives 4 1. 2 .1 Aquatic Ecosystem Functioning 4 1. 2.2 Impact of the Sampling Process 5 1. 3 Comparison of High-Resolution Data and Conventional Techniques 7 1. 3 .1 Instrument Description 7 1. 3.2 Sensor Deployment 9 1. 3.3 Differential Structure of Standard and High-Resolution Fluorescence Signals 10 1. 4 Conclusion 12 Acknowledgments . States of America 1 2 3 4 5 6 7 8 9 0 Printed on acid-free paper Library of Congress Cataloging -in- Publication Data Handbook of scaling methods in aquatic ecology : measurement, analysis, simulation. Leterme CONTENTS 1. 1 Introduction 3 1. 2 Microscale Structure in Aquatic Ecosystems: Perspectives 4 1. 2 .1 Aquatic Ecosystem Functioning 4 1. 2.2 Impact of the Sampling Process 5 1. 3 Comparison of High-Resolution. Strutton. p. cm. Includes bibliographical references and index. ISBN 0-8 49 3 -1 34 4-9 1. Aquatic ecology Research—Methodology. 2. Aquatic ecology Measurement. 3. Aquatic ecology Simulation methods. I.