Table of Contents

Cover

Title

Foreword

1 For a Systemic and Transdisciplinary Approach to the Environment

1.1. Introduction
1.2. A complex and vulnerable ocean system
1.3. Suitable observation tools
1.4. Conclusion
1.5. Acknowledgments
1.6. Bibliography

2 Vulnerability to Global Change: Observation Strategies for the Marine Environment

2.1. Introduction
2.2. Marine environment observation strategies
2.3. Some large observation domains
2.4. Satellite contribution to observation strategies
2.5. In situ observation
2.6. Observation strategies
2.7. What next?
2.8. Bibliography

3 Fishing Technology for Fisheries Research

3.1. Introduction
3.2. The methods employed to measure selectivity
3.3. The tools and observation methods of fishing gear
3.4. Computer simulation tools
3.5. Perspectives
3.6. Bibliography

4 Acoustics to Detect and Measure Underwater Organisms

4.1. Introduction
4.2. How animals use acoustics
4.3. How researchers use acoustics
4.4. Practical uses of acoustics
4.5. Acknowledgments
4.6. Bibliography

5 “Bio-logging” as a Tool to Study and Monitor Marine Ecosystems, or How to Spy on Sea Creatures

5.1. Introduction
5.2. The variety of sensors and measurements
5.3. Attachment methods: limits and ethics
5.4. Current challenges
5.5. Some examples of discoveries resulting from bio-logging
5.6. Conclusion
5.7. Bibliography

6 Modeling Strategies for Ecosystems

6.1. Definition of mathematical modeling
6.2. Mathematical formalization
6.3. Metabolic foundations of population dynamics
6.4. Modeling complexity
6.5. Conclusion
6.6. Acknowledgments
6.7. Bibliography

7 The Ecosystem Approach to Fisheries: Reconciling Conservation and Exploitation

7.1. The ecosystem approach to fisheries: a shared view on the management of marine resources
7.2. The way marine ecosystems work
7.3. EAF and research on marine ecosystems
7.4. Ecological indicators Marine Strategy Framework Directive (MSFD)
7.5. Implementing the EAF: the Benguela and Humboldt examples
7.6. Dynamic approaches to the ecosystem management of fisheries
7.7. Bibliography

8 Modeling in Contemporary Sciences: Efficiency and Limits Examples from Oceanography

8.1. Introduction
8.2. A language to describe reality
8.3. Relationships between models and reality
8.4. What about marine ecological systems and their management?
8.5. Interdisciplinarity, transdisciplinarity and modeling
8.5. Bibliography

List of Authors

Index

End User License Agreement

List of Tables

3 Fishing Technology for Fisheries Research

Table 3.1. Different kinds of instruments used according to their applications

4 Acoustics to Detect and Measure Underwater Organisms

Table 4.1. Range of EK60 echosounders used for fisheries research on RV Thalassa (range for which the volume backscattering strength (Sv) caused by noise is -70 dB for a celerity of c = 1494 m/s)
Table 4.2. Summary of the measurements and processes active acoustics can provide information about and their usage for ecosystem-based management. The spatiotemporal scales are those of ecosystem-based management. Adapted from [TRE 11]
Table 4.3. List of acoustic equipment together with their characteristics and application fields

6 Modeling Strategies for Ecosystems

Table 6.1. List of parameters and functions used for Soetaert and Herman’s NPZD model [SOE 09] (*Einstein: quantity of energy linked to the flux of photons within the range of wavelengths used)
Table 6.2. Parameters and variables of a DEB model for the species Crassostrea gigas [POU 06]. J = Joule, chl = chlorophyll a (measurement of the biomass of plankton)
Table 6.3. Summary of some models that take into account the complexity of ecosystems and have been used as examples throughout the chapter. The categories used are modified with respect to those used by Travers et al. [TRA 07]

7 The Ecosystem Approach to Fisheries: Reconciling Conservation and Exploitation

Table 7.1. Abundance and relative mass difference of the stable isotopes of hydrogen, carbon, nitrogen, oxygen and sulfur
Table 7.2. Isotope compositions of universal standards. R represents the ratio of heavy isotope/light isotope
Table 7.3. Functional responses used in models of marine ecosystems [SHI 10]
Table 7.4. A presentation of the criteria and indicators of the MSFD descriptor “food web”

List of Illustrations

1 For a Systemic and Transdisciplinary Approach to the Environment

Figure 1.1. Semantic proliferation of environmental research
Figure 1.2. Conceptual framework for a systemic and transversal approach (from ANR-ESS SSC)
Figure 1.3. Schematic overview of the structure of the Seas and Oceans set
Figure 1.4. Conceptual framework proposed for the management, protection and restoration of the North Sea [OSP 06]
Figure 1.5. Example of PREMIVER cartographic output showing the concentration of chlorophyll-a in surface waters (2/10/2015)
Figure 1.6. Salmon instrumented with an acoustic beacon allowing us to find out its location in the body of water in 3D
Figure 1.7. Interaction between a hydrodynamic model (arrows) and a reconstruction of the salmon’s journey (white line) in the estuary of the Adour [MAH 10]

2 Vulnerability to Global Change: Observation Strategies for the Marine Environment

Figure 2.1. Simplified pattern of thermohaline circulation [GIE 10]
Figure 2.2. a) Reflection seismology records the echoes of the waves reflected by different subsoil strata; b) seismic refraction records the echoes of the waves refracted on the interfaces of different subsoil strata
Figure 2.3. Examples of bathymetric maps (on the left) and of marine habitats (on the right)
Figure 2.4. Earthquakes in metropolitan France
Figure 2.5. The European Multidisciplinary Seafloor Observatory network
Figure 2.6. A map of the distribution of surface floats (Argos system)
Figure 2.7. Networks of measurements taken by merchant ships fitted with thermo salinographs
Figure 2.8. Simplified diagram of a drifting buoy followed by the Argos satellite
Figure 2.9. An example of the structure of an ARGO deep-sea profiler
Figure 2.10. ARGO floats in operation at the end of 2010 (those submerged by France are shown in yellow)
Figure 2.11. Distribution of profile measurements taken by instrumented marine mammals in the circum-Antarctic area
Figure 2.12. The French SEAEXPLORER “glider”
Figure 2.13. European Center of Submarine Technology “glider” fleet
Figure 2.14. Working principle of a “glider” (source: IFM-GEOMAR). The “glider” dives into deep waters (up to 1000 meters) and then resurfaces, all the while measuring physicochemical parameters. Upon reaching the surface, it sends the data obtained during the submersion to a satellite and recovers information from the control center, piloted by a “gliderman”, for its next dive
Figure 2.15. Front view of the manned Nautile submarine
Figure 2.16. View of the ROV Victor 6000
Figure 2.17. View of the AUV Idefx
Figure 2.18. The Hybrid ROV, able to reach depths of 3000 meters
Figure 2.19. The “Sea Explorer”, a French glider

3 Fishing Technology for Fisheries Research

Figure 3.1. An example of modern bottom trawl with its different parts
Figure 3.2. “Everything is linked”
Figure 3.3. The T90 is a kind of mesh rotated 90° in relation to the normal orientation N of the diamond mesh (on the left). The mesh T90 (on the right) will remain open even when it is stretched in water by the drag of the trawl. The diamond mesh with a normal orientation will tend to close when under traction
Figure 3.4. Mesh gap and gauge measurement: a) the “mesh gap” measured by the gauge; b) triangular manual gauge; c) ICES mechanical gauge (P. Larnaud)
Figure 3.5. The OMEGA gauge
Figure 3.6. Typical example of the selectivity curve of a trawl
Figure 3.7. Example of cod-end with a small-mesh “trawl blinder”
Figure 3.8. Example of trawl cod end with small-mesh cover pocket
Figure 3.9. Example of a small-mesh collection pocket above a square-mesh otter door
Figure 3.10. An example of a Siamese trawl
Figure 3.11. An example of twin trawls
Figure 3.12. An example of a sampling beam trawl
Figure 3.13. A “mesopelagos” scientific trawl
Figure 3.14. The principle of gillnetting
Figure 3.15. Fish in a gillnet laid on the seafloor
Figure 3.16. Typical selectivity curve of a gillnet
Figure 3.17. Principle of trammel nets
Figure 3.18. Typical selectivity curve of a trammel net
Figure 3.19. Example of surface longline
Figure 3.20. Example of bottom longline
Figure 3.21. 180-degree view of the basin of Boulogne sur Mer and mock-ups of trawl otter doors (source: Ifremer/B. Gaurier). On the right, view of the basin of Lorient
Figure 3.22. Excitation and 3D trajectography system set up to study the dynamics of a trawl otter door in the basin of Lorient
Figure 3.23. View of a basin and of its main components
Figure 3.24. Testing a mock-up trawl and an actual size fist pot in a basin
Figure 3.25. EROC (Engin Remorqué pour l’Observation des Chaluts or Towed Vehicle for the Observation of Trawls) on deck of the Thalassa
Figure 3.26. EROC images, classic trawl otter door, Jumper otter door with low floor impact, footrope and headrope of a trawl, IFREMER images
Figure 3.27. Towed vehicle used by the “Aberdeen Marine Laboratory” [MAI 77]
Figure 3.28. Installation of a video system on a selective trawl device; a square-mesh panel
Figure 3.29. On the right: tensionsensors on the bracket of an experimental trawl, positioning system, system used to measure distance between the otter doors and their depth, otter door angle sensor (vertical cylinder). On the right: acoustic beacons working as master-slave to measure the horizontal opening of a pelagic trawl in relation to its rigging
Figure 3.30. Operating phases of a software simulation program: preparation of data, processing through computer algorithms, analysis of the results in the virtual environment
Figure 3.31. Six-panel bottom trawl simulated by the Ifremer commercial software DynamiT, used by several authors for fishing research purposes [DAN 09, TRU 15]. The colors of the cables represent their internal tension
Figure 3.32. The shape of a Danish seine changing during a turning maneuver

4 Acoustics to Detect and Measure Underwater Organisms

Figure 4.1. The relation between the size of a target and the volume insonified by an echosounder placed on the hull of a ship (on the left) and an image of the echoes received by the same echosounder (on the right): a) single targets (individual fish) < insonified volume; b) multiple targets (fish school or plankton layer) > insonified volume. θ represents the opening angle of the echo-sounder. The thickness of the insonified volume depends on pulse duration and celerity C of the signal emitted by the echosounder
Figure 4.2. Target strength as a function of the emission frequency for different marine organisms. This curve is called frequency response curve (redrawn from [STA 10] and modified)
Figure 4.3. A multibeam ME70 acoustic antenna (part of the Simrad echosounder)
Figure 4.4. Beam pattern of a Simrad ES -1207C transducer at 120 kHz in polar coordinates, the 7° angle at -3 dB is shown by the crosses on the main lobe (at the center, 0°), the side lobes (small side beams) have been optimized to less than -25 dB by the manufacturer
Figure 4.5. Echogram of a tungsten sphere and its weight used to stabilize the sphere for a multibeam ME70 echosounder configuration with (left) and without (right) minimization of side lobes. In the latter case, the double echoes of the targets and the seafloor significantly complicate data analysis
Figure 4.6. Spectrogram of a whistle produced by an Indo-Pacific bottlenose dolphin (Tursiops aduncus)
Figure 4.7. Spatiotemporal scope of a single observation unit for different observation methods. The lower left-hand corner of each polygon shows the resolution and the upper right-hand corner the range. The dark green area indicates the overlap between the volumes sampled by passive and active acoustics to drawn from [TRE 11] and modified
Figure 4.8. A herring school diving on approach of the survey vessel. a) 3D view, b) 2D lateral view
Figure 4.9. Echosounders installed on the hull of RV Thalassa
Figure 4.10. Volume sampled by a vertical fisheries echosounder
Figure 4.11. Seafloor maps obtained with a Simrad ME70 multibeam echosounder; a) a bathymetric image; b) reflectivity image
Figure 4.12. Environmental Acoustic Reader (EAR) in a coral reef
Figure 4.13. Digital Acoustic Recording Tag (DTAG) on an Atlantic bottlenose dolphin (Tursiops truncatus)
Figure 4.14. Transect design of the acoustic survey carried out in the Bay of Biscay. The diameter of the circles is proportional to the biomass of acoustically detected anchovies
Figure 4.15. Installation plan of a fixed station in the south of the Bay of Biscay designed to observe an artificial reef
Figure 4.16. Flow diagram of acoustic data acquisition and processing for biomass index estimation. The solid-lined boxes correspond to examples of specific software programs
Figure 4.17. 3D representation of fish schools above the seafloor

5 “Bio-logging” as a Tool to Study and Monitor Marine Ecosystems, or How to Spy on Sea Creatures

Figure 5.1. An example of a picture taken by a micro-camera attached directly to a Cape gannet (Morus Capensis). The picture was taken as the animal fitted with it was diving (it is possible to see the bird’s back and wings in the foreground), and shows a fellow gannet about to capture a prey in the presence of a dolphin (Delphinus capensis)
Figure 5.2. A Peruvian booby (Sula variegata) fitted with a miniaturized GPS recorder (which weighs 12 grams)

6 Modeling Strategies for Ecosystems

Figure 6.1. The result of a simulation of a prey/predator system based on a Lotka-Volterra equation: a) evolution of the two variables over time; b) phase plan ad velocities
Figure 6.2. The evolution of a variable x in relation to a Verhulst’s equation for two different initial values
Figure 6.3a–b. a) Diagram representing the bio-interactions between the state variables of Soetaert and Herman’s NPZD model [SOE 09], b) the result of a simulation showing the variable dynamics over time
Figure 6.3 c The representation of the same results in a phase plan
Figure 6.4. a) Functional diagram of the processes and state variables of a Dynamic Energy Budget (DEB) model, b) an example of simulation of individual growth and reproduction for different temperature and food values (phytoplankton)

7 The Ecosystem Approach to Fisheries: Reconciling Conservation and Exploitation

Figure 7.1. Major institutional steps of the advancement in the construction of ecosystem approach to fisheries
Figure 7.2. Diagram of the main ecological and socio-economical inner workings of the “fishery system”
Figure 7.3. Bottom-up control or control through primary production in a simplified four-level food chain in a marine ecosystem
Figure 7.4. Top-down control or trophic cascade in the food chain for four trophic levels in a marine ecosystem
Figure 7.5. a) Wasp-waist control in a simplified four-level food chain in a marine ecosystem. b) The abundance of prey fish (small pelagic fish), which depends on the environment, controls at once the abundance of predators and primary producers
Figure 7.6. A diagram of the concept of bottom-up transfer of spatial structuring
Figure 7.7. An example of sea-surface temperature fields (in ºC) simulated thanks to the Regional Ocean Modeling System model in the south-western Pacific (on the left) and in two specific regions illustrated by the black frames in the left-hand graph. We can see the presence of a large number of eddies and fronts that structure very significantly the oceanic landscape
Figure 7.8. A conceptual model which describes the relative importance of self-organization and environmental constraints in relation to the spatial organization of gregarious fish depending on the scale considered. The diagram is plotted around two axes, one based on self-organization (on the left) and the other on environmental forcing
Figure 7.9. Vertical and horizontal integration of end-to-end models
Figure 7.10. An example of alternative food chains: a) drawn from [PAR 02], b) drawn from [VAN 06], and c) drawn from [MUR 077]
Figure 7.11. The perimeter of the four French marine sub-regions of the MSFD (drawn from DRIEE Ile de France and modified)
Figure 7.12. A presentation of the eleven MSFD descriptors and their indicators of state (s), pressure (p), and impact (i) (from [BOR 10])
Figure 7.13. A diagram of the environmental scenarios in the Humboldt Current ecosystem (from [BER 11])
Figure 7.14. A 3D structure of the habitat of anchovies, defined by the area of cold coastal waters and the depth of the oxycline. This 3D habitat is estimated on the basis of scientific research at sea employing multi-frequency acoustics. The image shown was taken during scientific research conducted in winter 2005 (austral) and the volume of the anchovy habitat is estimated at 9138 km³ (from [BER 10])
Figure 7.15. Probability of encountering breeding birds of three different species according to the sites considered. The size of the circles represents the breeding probability of each species (in %, Guanay cormorants in black, gannets in red, pelicans in blue). Islands are shown in green and peninsulas in red. For ease of reference, the coastline is shifted longitudinally and is shown in yellow
Figure 7.16. Warm and cold ecological scenarios triggered by oceanic Kelvin wave forcing on the Humboldt Current coastal system. ST: surface temperature, CCW DC: average distance of cold coastal waters from the coast, Dist. coast: average distance of anchovies from the coast, Spatial conc.: spatial concentration index for the biomass of anchovies, School depth: average depth of the schools of anchovies (from [BER 08b])

8 Modeling in Contemporary Sciences: Efficiency and Limits Examples from Oceanography

Figure 8.1. Diagram of the spatialized dynamics of fishing resources showing the boundary conditions from which solutions of the model may be studied
Figure 8.2. Smith’s model compared to historical data on whaling (Clark, op. Cit.). The fishing effort E is assumed to be equal to the number of ships. This model provides for certain parameter values a fixed point, which is a stable focus. Data coming from logbooks of ships do not contradict this result
Figure 8.3. Intermittencies in population dynamics: the example of sardines in the Pacific Ocean estimated from sedimentary marine deposits off of the coast of California (see Ferrière and Cazelles [FER 99]). Years are before present (2000)

First published 2016 in Great Britain and the United States by ISTE Ltd and John Wiley & Sons, Inc.

Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the Copyright, Designs and Patents Act 1988, this publication may only be reproduced, stored or transmitted, in any form or by any means, with the prior permission in writing of the publishers, or in the case of reprographic reproduction in accordance with the terms and licenses issued by the CLA. Enquiries concerning reproduction outside these terms should be sent to the publishers at the undermentioned address:

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The rights of André Monaco and Patrick Prouzet to be identified as the author of this work have been asserted by them in accordance with the Copyright, Designs and Patents Act 1988.

Library of Congress Control Number: 2016939646

British Library Cataloguing-in-Publication Data

A CIP record for this book is available from the British Library

ISBN 978-1-84821-778-2

Foreword

We have been asked by ISTE to stimulate work in the area of the environment. Therefore, we are proud to present the “Seas and Oceans” set of books, edited by André Monaco and Patrick Prouzet.

Both the content and the organization of this collection have largely been inspired by the reflection, initiatives and prospective works of a wide variety of national, European and international organizations in the field of the environment.

The “oceanographic” community in France – which is recognized for the academic quality of the work it produces, and is determined that its research should be founded on a solid effort in the area of training and knowledge dissemination – and internationally was quick to respond to our call, and now offers this set of books, compiled under the skilled supervision of the two editing authors.

Within this community, there is a consensus about the need to promote an interdisciplinary “science of systems” – specifically in reference to the Earth’s own “system” – in an all-encompassing approach, with the aim of providing answers about the planet’s state, the way it works and the threats it faces, before going on to construct scenarios and lay down the elementary foundations needed for long-term, sustainable environment management, and for societies to adapt as required. This approach facilitates the shift of attention from this fundamental science of systems (based on the analysis of processes at play, and the way in which they interact at all levels, and between all the constituent parts making up the global system) to a “public” type of science, which is finalizable and participative, open to decision-makers, managers and all those who are interested in the future of our planet.

In this community, terms such as “vulnerability”, “adaptation” and “sustainability” are commonly employed. We speak of various concepts, approaches or technologies, such as the value of ecosystems, heritage, “green” technologies, “blue” chemistry and renewable energies. Another foray into the field of civilian science lies in the adaptation of research to scales which are compatible with the societal, economic and legal issues, from global to regional to local.

All these aspects contribute to an in-depth understanding of the concept of an ecosystemic approach, the aim of which is the sustainable usage of natural resources, without affecting the quality, the structure or the function of the ecosystems involved. This concept is akin to the “socio-ecosystem approach” as defined by the Millennium Assessment (http://millenniumassessment.org).

In this context, where the complexity of natural systems is compounded with the complexity of societies, it has been difficult (if only because of how specialized the experts are in fairly reduced fields) to take into account the whole of the terrestrial system. Hence, in this editorial domain, the works in the “Seas and Oceans” set are limited to fluid envelopes and their interfaces. In this context, “sea” must be understood in the generic sense, as a general definition of bodies of salt water, as an environment. This includes epicontinental seas, semi-enclosed seas, enclosed seas, or coastal lakes, all of which are home to significant biodiversity and are highly susceptible to environmental impacts. “Ocean”, on the other hand, denotes the environmental system which has a crucial impact on the physical and biological operation of the terrestrial system – particularly in terms of climate regulation, but also in terms of the enormous reservoir of resources it constitutes Oceans covering 71% of the planet’s surface, with a volume of 1,370 million km³ of water.

This set of books covers all of these areas, examined from various aspects by specialists in the field: biological, physical or chemical function, biodiversity, vulnerability to climatic impacts, various uses, etc. The systemic approach and the emphasis placed on the available resources will guide readers to aspects of value-creation, governance and public policy. The long-term observation techniques used, new techniques and modeling are also taken into account; they are indispensable tools for the understanding of the dynamics and integral functioning of the systems.

Finally, treatises will be included which are devoted to methodological or technical aspects.

The project thus conceived has been well received by numerous scientists renowned for their expertise. They belong to a wide variety of French national and international organizations, focusing on the environment.

These experts deserve our heartfelt thanks for committing to this effort in terms of putting their knowledge across and making it accessible, thus providing current students with the fundaments of knowledge which will help open the door to the broad range of careers that the area of the environment holds. These books are also addressed to a wider audience, including local or national governors, players in decision-making authorities, or indeed “ordinary” citizens looking to be informed by the most authoritative sources.

Our warmest thanks go to André Monaco and Patrick Prouzet for their devotion and perseverance in service of the success of this enterprise.

Finally, we must thank the CNRS and Ifremer for the interest they have shown in this collection and for their financial aid, and we are very grateful to the numerous universities and other organizations which, through their researchers and engineers, have made the results of their reflections and activities available to this instructional corpus.

André MARIOTTI

Professor Emeritus at University Pierre and Marie Curie
Honorary Member of the Institut Universitaire de France
France

Jean-Charles POMEROL

Professor Emeritus at University Pierre and Marie Curie
France