Présentation de l’éditeur Ecological sciences deal with the way organisms interact with one another and their environment. Using sensors to measure various physical and biological characteristics has been a common activity since long ago. However the advent of more accurate technologies and increas- ing computing capacities demand a better combination of information collected by sensors on multiple spatial, temporal and biological scales. This book provides an overview of current sensors for ecology and makes a strong case for deploying integrated sensor platforms. By covering technological challenges as well as the variety of practical ecological applications, this text is meant to be an invaluable resource for students, researchers and engineers in ecological sciences. This book benefited from the Centre National de la Recherche Scientifique (CNRS) funds, and includes 16 contributions by leading experts in french laboratories. Key features • An overview of sensors in the field of animal behaviour and physiology, biodiversity and ecosystem. • Several case studies of integrated sensor platforms in terrestrial and aquatic environments for observational and experimental research. • Presentation of new applications and challenges in relation with remote sensing, acoustic sensors, animal-borne sensors, and chemical sensors. Sensors for ecology Towards integrated knowledge of ecosystems Jean-François Le Galliard, Jean-Marc Guarini, Françoise Gaill Sensors for ecology Towards integrated knowledge of ecosystems Centre National de la recherche scientifique (CNRS) Institut Écologie et Environnement (INEE) www.cnrs.fr Acr1932688304928-24242.pdf 1 20/03/12 16:12 Photographie de couverture / Cover Picture © CNRS Photothèque – AMICE Erwan UMR6539 – Laboratoire des sciences de l’environnement marin – LEMAR – PLOUZANE “A diver inspects a queen conch Strombus gigas during a scientic expedition in Mexico. The queen conch is equipped with acoustic sensors, here nearby a receptor, in order to collect information on its behaviour and physiology in nature.” © CNRS, Paris, 2012 ISBN : 978-2-9541683-0-2 sensors-001-344.indd 6 20/03/12 13:10 Contents Foreword ................................................................................................ 11 I Ecophysiology and animal behaviour Chapter 1 : Bio-logging: recording the ecophysiology and behaviour of animals moving freely in their environment Yan Ropert-Coudert, Akiko Kato, David Grémillet, Francis Crenner ... 17 Chapter 2 : Animal-borne sensors to study the demography and behaviour of small species Olivier Guillaume, Aurélie Coulon, Jean-François Le Galliard, and Jean Clobert ................................................................................... 43 Chapter 3 : Passive hydro-acoustics for cetacean census and localisation Flore Samaran, Nadège Gandilhon, Rocio Prieto Gonzalez, Federica Pace, Amy Kennedy, and Olivier Adam ............................................... 63 Chapter 4 : Bioacoustics approaches to locate and identify animals in terrestrial environments Chloé Huetz, Thierry Aubin ................................................................. 83 8 Contents II Biodiversity Chapter 1 : Global estimation of animal diversity using automatic acoustic sensors Jérôme Sueur, Amandine Gasc, Philippe Grandcolas, Sandrine Pavoine 99 Chapter 2 : Assessing the spatial and temporal distributions of zooplankton and marine particles using the Underwater Vision Profiler Lars Stemmann, Marc Picheral, Lionel Guidi, Fabien Lombard, Franck Prejger, Hervé Claustre, Gabriel Gorsky .................................... 119 Chapter 3 : Assessment of three genetic methods for a faster and reliable monitoring of harmful algal blooms Jahir Orozco-Holguin, Kerstin Töbe, Linda K. Medlin ......................... 139 Chapter 4 : Automatic particle analysis as sensors for life history studies in experimental microcosms François Mallard, Vincent Le Bourlot, Thomas Tully ........................... 163 III Ecosystem properties Chapter 1 : In situ chemical sensors for benthic marine ecosystem studies Nadine Le Bris, Leonardo Contreira-Pereira, Mustafa Yücel ................ 185 Chapter 2 : Advances in marine benthic ecology using in situ chemical sensors Nadine Le Bris, Leonardo Contreira-Pereira, Mustafa Yücel ................ 209 Chapter 3 : Use of global satellite observations to collect information in marine ecology Séverine Alvain, Vincent Vantrepotte, Julia Uitz, Lucile Duforêt- Gaurier ................................................................................................ 227 Contents 9 Chapter 4 : Tracking canopy phenology and structure using ground-based remote sensed NDVI measurements Jean-Yves Pontailler, Kamel Soudani .................................................... 243 IV Integrated studies Chapter 1 : Integrated observation system for pelagic ecosystems and biogeochemical cycles in the oceans Lars Stemmann, Hervé Claustre, Fabrizio D’Ortenzio ......................... 261 Chapter 2 : Tropical rain forest environmental sensors at the Nouragues experimental station, French Guiana Jérôme Chave, Philippe Gaucher, Maël Dewynter .................................. 279 Chapter 3 : Use of sensors in marine mesocosm experiments to study the effect of environmental changes on planktonic food webs Behzad Mostajir, Jean Nouguier, Emilie Le Floc’h, Sébastien Mas, Romain Pete, David Parin, Francesca Vidussi ...................................... 305 Synthesis and conclusion Jean-François Le Galliard, Jean-Marc Guarini and Françoise Gaill ...... 331 NB: When cited in the text, a chapter of this book is identified accord- ing to the part it belongs to. For example, (III, 3) refers to the chapter 3 by Alvain et al. in the third (III) part of this book about Ecosystem properties. Foreword Altogether explorer, scientist, philosopher and one of the first world citi- zen, the German naturalist Alexander von Humboldt (1769-1859) is often considered as a founder of ecological sciences, though the word “ecology” was only coined several decades later by another German scientist, Ernst Haeckel (1834-1919). Equipped with the best sensors (thermometers, barometers, and so on) and familiar with advanced metrology techniques of its time, von Humboldt pioneered the field of plant biogeography, a discipline at the meeting point between botany, geography, climatology and geology. Von Humboldt major conceptual and methodological con- tributions consisted in collecting physical and geological data along with plant distribution maps to determine the physical and historical condi- tions favouring specific plant assemblages all over the world. With this approach, he ventured into previously unsuspected complex interactions between plants and their physical surroundings. Two centuries later, researchers are still striving to understand the ecological and evolutionary mechanisms that determine the distribution of plant and animal species. Indeed, an accurate quantification of how organisms interact with each other and with their environment is at the heart of several grand chal- lenges in modern ecological sciences from the description of bio-geochem- ical balances to the prediction of ecosystem dynamics. However, contrary to von Humboldt and his followers, we can now explore thoroughly the natural world, thanks to major technological improvements in our ability to measure physical, chemical and biological quantities. Sensors are now part of the standard toolbox of most ecological studies, and play an impor- tant role in both exploratory studies of nature, experimental approaches, and the development of predictive ecological models. With the advent of more advanced technologies and the strong opportunities offered by nowadays available computing capacities, we are in a better position to integrate ecological information from sensors across multiple spatial, tem- poral and biological scales. This book, sponsored by the Centre National de la Recherche Scientifique (CNRS) in France, presents an up-to-date overview of the use sensors for ecology by some leading CNRS laborato- 12 Foreword ries. The book covers some of the main technological challenges in our field from bio-loggers attached on animals to remote sensing imaging capacities installed on satellites, and provides many examples of practi- cal applications chosen from ongoing CNRS programs. It is also tightly connected with the current frontiers in ecology and evolution throughout the world. We hope that the book will become an invaluable resource to students, researchers and engineers in ecological sciences. Few books have reviewed methods and issues in the field of sensors for ecology. The reason is easy to understand: a great deal of techniques and sensor types do exist and are covered in specific reviews or journals. Keeping pace with the increasing number of sensors and technologies currently available is therefore a difficult task. Yet, this book provides in a synthetic way a balanced description of the new applications and challenges in ecological research that the use of remote, acoustic, animal- borne, chemical and genosensors represents. Here, we adopted a broad view on sensors – usually defined as a device that measures a physical quantity and converts it into a signal – to describe a quantity of tools including image and video analyses, biodiversity and life history sensors, and other less traditional methods. Furthermore, this book contains technical descriptions of some sensors even though it is not a handbook about sensor technologies.