Chemical Ecology E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 353

Veröffentlichungsjahr: 2016

Beschreibung

The book features comparative perspectives on the field of chemical ecology, present and future, offered by scientists from a wide variety of disciplines. The scientists contributing to this book -biologists, ecologists, biochemists, chemists, biostatisticians - are interested in marine, freshwater and terrestrial ecosystems and work on life forms ranging from micro-organisms to mammals, including humans, living in areas from the tropics to polar regions. Here, they cross their analyses of the present state of chemical ecology and its perspectives for the future. Those presented here include complex, multispecies communities and cover a wide range both of organisms and of the types of molecules that mediate the interactions between them. Up to now, no book has presented a solid scientific treatment of a wide range of examples. This book illustrates a diverse panel of the most advanced aspects of this rapidly expanding field.

Leseprobe

Table of Contents

Cover

Title

Copyright

Foreword

Introduction

1 Biodiversity and Chemical Mediation

1.1. Systematic and integrative taxonomy from chemical ecology

1.2. Scent communication between sexual partners

1.3. Scent communication between species

1.4. Chemical mimicry, to enhance reproduction

1.5. A dialog that sometimes evolves into an interaction network

1.6. Conclusions

1.7. Bibliography

2 Chemical Ecology: An Integrative and Experimental Science

2.1. Semiochemicals

2.2. Chemical ecology in multitrophic networks and co-evolution between species

2.3. Contribution of chemical ecology to the study of tropical plant diversification

2.4. When chemical ecology sheds light on the process of biological invasion – an example demonstrating integration between chemistry and ecology

2.5. Protection is in the air: how plants defend themselves against phytophagous insects through VOC emissions

2.6. Conclusions

2.7. Bibliography

3 Scents in the Social Life of Non-Human and Human Primates

3.1. Primate societies and their complex systems of communication

3.2. The role of odors in human communication

3.3. The senses of smell and taste in the search for food and remedies

3.4. Conclusions – the adaptive functions of the sense of smell in “microsmatic” species

3.5. Bibliography

4 Microbiota and Chemical Ecology

4.1. The protagonist microorganisms of chemical ecology

4.2. Strategies for the study of microbiota

4.3. The molecular dialog of microorganisms

4.4. Chemical communication between microorganisms and their hosts

4.5. Regulations and evolution of the interactions in changing ecosystems and environments

4.6. Conclusions – from chemical ecology to future applications: impacts of the study of the microbiota

4.7. Bibliography

5 From Chemical Ecology to Ecogeochemistry

5.1. Balance between primary and secondary metabolism

5.2. Role of secondary metabolites in biotic interactions and community structure

5.3. Secondary metabolites and ecosystem functioning: plant soil relation – brown food chain

5.4. Integration of biotic and abiotic dynamics: benthic marine microhabitats

5.5. Conclusions

5.6. Bibliography

6 Omics in Chemical Ecology

6.1. Introduction: the different “omic” technologies

6.2. From “omics” to signals: identifying new active molecules

6.3. From “omics” to the ecology of communities: identifying chemical interactions of organisms in their environment

6.4. From “omics” to molecular bases: revealing the genetic and molecular bases of chemical interactions

6.5. From “omics” to physiology: characterizing the modes of production and the modes of reception of active molecules

6.6. From “omics” to the role of environment: understanding the impact of biotic and abiotic factors on interactions

6.7. From “omics” to evolution: understanding and predicting the adaptive value of chemical interactions

6.8. Conclusions and perspectives

6.9. Bibliography

7 Metabolomic Contributions to Chemical Ecology

7.1. Definition of metabolomics

7.2. Different strategies of the metabolomic approaches

7.3. The different steps for conducting a metabolomic study

7.4. Applications of metabolomics

7.5. Conclusions

7.6. Bibliography

8 Chemical, Biological and Computational Tools in Chemical Ecology

8.1. Chemical tools

8.2. Sequencing tools

8.3. Databases: biodiversity in silico

8.4. Conclusions

8.5. Bibliography

9 Academic and Economic Values of Understanding Chemical Communication

9.1. Nature as a model

9.2. Nature as a model for development of new molecules of interest

9.3. Chemical ecology and sustainable development

9.4. Conclusions

9.5. Bibliography

Conclusion: Looking Forward: the Chemical Ecology of Tomorrow

Glossary

List of Authors

Index

End User License Agreement

List of Tables

8 Chemical, Biological and Computational Tools in Chemical Ecology

Table 8.1.

Example of new techniques of headspace by enrichment

Table 8.2.

NGS technologies and their main applications

Table 8.3.

Metabolomic database links

Guide

Cover

Table of Contents

Begin Reading

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Series EditorFrançoise Gaill

Chemical Ecology

Edited by

Anne-Geneviève Bagnères

Martine Hossaert-Mckey

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:

ISTE Ltd27-37 St George’s RoadLondon SW19 4EUUK

www.iste.co.uk

John Wiley & Sons, Inc.111 River StreetHoboken, NJ 07030USA

www.wiley.com

© ISTE Ltd 2016

The rights of Anne-Geneviève Bagnères and Martine Hossaert-Mckey 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: 2016945010

British Library Cataloguing-in-Publication Data

A CIP record for this book is available from the British Library ISBN 978-1-84821-924-3

Foreword

The consequences of the global changes affecting our planet are not limited to climate change or to changes in composition of the atmosphere. In perturbing all ecosystems, and thereby the species that constitute them, these changes affect all the dynamics of life. These effects in turn have impacts, notably on interactions between species or between individuals of a single species, interactions that are indispensable for the maintenance of communities and ecosystems, in which chemical mediation plays a predominant role.

Chemical ecology can be defined as the art of decrypting this invisible, impalpable chemical mediation that permits living organisms to communicate among themselves within their environment. A great diversity of molecules, ranging from very simple compounds to highly complex mixtures, is involved in organisms’ perception of the environment, in communication between individuals, and in the defense mechanisms that have evolved in those interactions that are antagonistic. This scientific domain has successfully reconciled ecology and chemistry, a tour de force that has required a resolutely interdisciplinary approach.

Chemical ecology also provides us with a framework to better interpret, extend and use our knowledge about the diversity of natural substances. Researchers are beginning to understand the roles of these compounds in processes of communication in a diverse range of habitats, both aquatic and terrestrial, and between organisms in all the kingdoms of life: animals, plants, fungi, bacteria and archaea. Beyond such fundamental advances in knowledge, chemical ecology is a source of inspiration for new biosourced applications and helps us conceive of the future ecotechnologies that will be necessary for the resolution of a number of environmental problems.

The research in chemical ecology discussed in this book has been conducted by an internationally recognized, dynamic and original community of French scientists. Chemical ecology has been clearly recognized in recent years as a field that promises to contribute pioneering research, situated at the crossroads of multiple competences shared not only by ecologists and chemists, but also by physiologists, biochemists, ethologists, and ethnologists, among others.

This book will allow the reader to explore the myriad facets of the language of molecules that unites biodiversity and chemodiversity, and thereby discover a new dimension of the living world.

Stéphanie THIÉBAULTFrançoise GAILLInstitute of Ecology and Environment CNRSJune 2016

Introduction

The association of the two terms “ecology” and “chemistry” has recently become evident for researchers, biologists and chemists alike, working at the interface of biology and chemistry. Chemical ecology is now an entire area of research. It is a recent discipline, born during the 1970s/80s, and its development was associated with major progress in analytical chemistry during the same period. This discipline has greatly deepened our understanding of semiochemicals emitted by microorganisms, plants and animals.

To survive and adapt, all living things, from the simplest to the most complex, must intercept the information emitted in their perimeter of perception. The majority of living species communicate among themselves by molecules and chemical signals that we may term “chemical mediators”. In effect, any ecosystem is a dynamic assembly promoted by interactions that are, therefore, essentially founded on trophic exchanges such as molecular exchanges, involving complex substances that often transmit simple messages.

The chemical language, using semiochemicals much like words, is, in nature, a kind of universal language and appears to be indispensable for maintaining terrestrial and aquatic ecosystems. Chemical communication is by far the most frequently used mode of communication in the living world.

In an attempt to understand this language of nature, ecologists and chemists are confronted with the complexity and the creativity of organisms. Studying an ecosystem – its structure and functioning, the interactions of organisms within it, among themselves and with their physico-chemical environment – requires a multi- and pluridisciplinary approach, an approach indispensable in chemical ecology, which is a natural interface between the two sciences.

An increasingly large amount of data on organisms and the chemicals that mediate interactions between them, in both terrestrial and aquatic environments, continually reinforce our understanding of the biodiversity and chemobiodiversity of living things. The most innovative aspects are linked to the evolution of the species and the mediation of complex interactions in their multitrophic environment, considering each species as an integral part of a community, not as an entity unto itself (Chapter 1). Characterized semiochemicals, either attractants or repellents, selected over thousands of years of evolution and co-evolution for their efficiency, generally have very specific effects on the target organism. Interactions between organisms involve multiple scales; research on chemical ecology therefore relies on a wide range of experimental approaches. Furthermore, given the current loss of biodiversity and ongoing climate change, it is important to understand the functioning of ecosystems and the interaction between their microbial, plant and animal components before considering the effects of human disturbances on these ecosystems (Chapter 2). Work on sociality has allowed the elucidation of a complex evolutionary history of chemical communication in animal behavior, particularly in social species that we think of as microsmatic (i.e. having limited olfactory sense) such as human and non-human primates. In these species, the chemical composition of body odor can reflect individual characteristics. In addition, the use of natural substances by animals for self-medication, which has been shown in arthropods and vertebrates, including non-human primates as well as humans, emerges as an important evolutionary theme. Semiochemicals can, therefore, be considered as a central element of the organization of most animal societies (Chapter 3). Likewise, recent advances in the chemical ecology of the microscopic living world, a theme that was long largely neglected, have in effect modified an overly simplified image of interactions. Microorganisms – prokaryotes (bacteria, cyanobacteria, archaea) or eukaryotes (fungi, protists) – live in communities where intense competition occurs. In response to particular environmental constraints, these microorganisms produce an entire arsenal of molecules. Understanding the mechanisms by which these molecules are produced, and their effects on other organisms, is indispensable to the understanding of the interactions in microbial communities. The study of how microorganisms adapt in sometimes extremely hostile environments often has applications in the field of biotechnology (Chapter 4). The interactions between components of ecosystems can be disturbed by human activities. The active biological and chemical interactions of components in and with the elements of soil, air or water are called ecogeochemical. Ecogeochemistry thus proposes to analyze, by integrative approaches, the complexity of ecological systems and the mechanisms by which the biotic and abiotic components of the ecosystem interact. It complements the classic “biogeochemical” approach of functional ecology by addressing in a single conceptual context the organisms and components of their abiotic environment, particularly the chemical compounds in interaction with these organisms (Chapter 5). For several years, chemical ecology has benefited from the progress achieved in genomics, transcriptomics, proteomics and metabolomics; chemical ecology has thus entered the era of “omics”. “Omics” regularly lead to new tools that are very useful for shedding new light on evolutionary mechanisms. “Omic” approaches in chemical ecology vary greatly and are based on a range of biological models, from the simplest to the most complex (Chapter 6). Metabolomics is the most recent of the “omic” sciences. Metabolomics can be applied without an a priori approach, aiming to analyze the largest possible portion of the metabolome. It can also be applied in a priori approaches targeting a family of metabolites that belong to a particular path of biosynthesis. Metabolomics provides essential information to clarify the key roles played by semiochemicals in the interactions between organisms and their environment, and the mechanisms regulating these interactions. The increasingly powerful analytical, mathematical and statistical tools made available to biologists and chemists thus enable the consideration of increasingly detailed characterization of metabolomes (Chapter 7). The characterization of mediators by increasingly perfected chemical tools, and the new techniques of genome sequencing, have together allowed all these innovative approaches to contribute to better understanding of the living world and its language. Improvements in instrumentation, with gains in sensitivity and resolution, have made it possible to obtain increasingly precise and detailed analyses of primary or secondary metabolites. These approaches generate masses of data, making indispensable automatic comparison with online databases (Chapter 8). The characterization of a chemical mediator of ecological interactions can lead to multiple applications in the fields of applied research such as medicinal chemistry, pharmacology and phytopharmacy. Characterization of the biological target of a semiochemical can lead to the discovery of new biological receptors. In certain cases, nature can adapt to the presence of high levels of pollutants. In ecosystems seriously affected by pollutants, a combined study of the chemistry and ecology of the plants that are able to develop despite pollution can lead to the development of procedures to decontaminate soils, purify water or air (phytoremediation) and restore ecosystem functioning (green engineering) (Chapter 9). At the end of the book (Conclusion), we address the questions that remain unanswered in this constantly changing discipline.

The scientists, including biologists, ecologists, biochemists, chemists and biostatisticians, who have contributed to this book are interested in both continental and marine environments, both temperate and tropical ecosystems, and in living things ranging from microorganisms to mammals, all of which are covered in their analyses of chemical ecology and of its perspectives. The work presented herein illustrates the most advanced and varied aspects of this rapidly expanding discipline. Compared with other books available on related themes, which for the most part deal with relatively simple systems, covering pairwise or tritrophic interactions and comprising a small number of model organisms and semiochemicals, our book offers a holistic vision of chemical ecology.

As a final remark, we wish to pay homage to Murray S. Blum, who just recently passed away and who was one of the first to demonstrate the importance of chemical mediation in the living world. Among other things, Murray brought the notion of parsimony into chemical ecology, along with his smile, which he distributed without parsimony.

Introduction written by Anne-Geneviève BAGNÈRES and Martine HOSSAERT-MCKEY.

1Biodiversity and Chemical Mediation

Chemical mediation is a widely used mode of communication that contributes significantly to the organization and functioning of biodiversity. Identifying and classifying species are prerequisites for the study of biodiversity, and as with other morphological or molecular characteristics, the study of traits of organisms related to the production of semiochemicals is regularly used today in integrative taxonomy. One of the important facets of chemical ecology is the study of communication mediated by organic compounds (volatile or not) in the same species (reproduction, meeting sexual partners, etc.) and between species (pollination, predation, parasitism, etc.) with honest or deceptive signals. Identifying the compounds emitted, and understanding their modes of action and their roles in the interactions between individuals and between species, are the objectives of this young pluridisciplinary science, which aims to discover this hidden language of nature [PIC 06, RAG 08]. This interspecies chemical mediation sometimes also allows the creation of complex interactive networks, structuring biodiversity around certain organisms, which often play keystone roles in ecosystems [HOS 10, IVA 11a, IVA 11b]. Ephemeral or stable, from attractive to repulsive, this communication is based on an infinite multitude of combinations of organic compounds, where the game for each species consists of emitting, detecting or even masking a scent.

1.1. Systematic and integrative taxonomy from chemical ecology

A good understanding of biodiversity is a prerequisite for numerous disciplines, such as biology, ecology and even the study of chemical communication between different species. Systematics is the science devoted to the discovery, the interpretation and the classification of biological diversity. This term designates both the methods implemented and the results of their application, and can, therefore, lead to the “classification of living things” in general. Systematics includes taxonomy, which describes living organisms based on their characteristics, most often morphological and/or molecular (sequencing of DNA or RNA is widely used, notably to characterize the infinitely small), and groups these organisms into taxa. Because it is crucial for analyzing and conserving biodiversity so that each taxon has a name, and a specific name never designates multiple taxa, the taxonomic descriptions must be as precise and detailed as possible, integrating complementary types of characteristics. Today, this integrative taxonomy is considered to be the most rigorous approach in systematics because it integrates all the taxonomic, morphological and ecological traits for which scientific information exists to characterize the taxa considered. This method is also the most adaptable, since a small number of the most important traits in the ecology of species concerned may be selected to determine whether two sets of individuals belong to the same species.

Like the morphological or molecular characteristics of an organism, its chemical composition – i.e. its metabolome – can be used as a characteristic (or a set of characteristics) in taxonomy or systematics. Chemotaxonomy (also called chemosystematics) seeks to understand the relationship between the chemical composition of organisms, their taxonomic identity and their systematic classification. The metabolome can be studied as a signature of evolution, and the metabolomic revolution is transforming chemosystematics by making it possible to quickly compare a large number of such chemical signatures (Figure 1.1) [BAG 10a, CAR 12]. The analysis of portions of the metabolome also provides classifications similar to those supplied by molecular systematics based on the analysis of portions of the genome. Thus, it provides support for hypothetical classifications. Chemotaxonomy can also be used to discriminate “sister” species, notably for difficult taxonomic groups in which closely related species are often “cryptic”, owing to the small size of organisms, the absence of morphological variability or, on the contrary, excessive variability.

In the case of sponges of the class Homoscleromorpha, the absence of variation in morphological characteristics classically used in sponge systematics (skeletal spicules) led researchers to search for other informative characteristics. Discovery of variability in up to six different types of characteristics has dismantled the “myth of the cosmopolitan species Oscarella lobularis”, and 15 species of this genus have now been described [IVA 11a, IVA 11b]. Metabolomic approaches combined with traditional and molecular systematics have recently allowed the proposal of a new systematic classification of Homoscleromorpha sponges, and integrative taxonomy is now used to describe many other species of this class of sponges [BOU 14, RUI 14, CAC 15] (see Chapter 7).

Figure 1.1.Metabolomic fingerprints showing interspecific variability of the chemical signal emitted by different sponges of the family Oscarellidae, Class Homoscleromorpha: HPLC-ESI (þ) MS (BPC) with indications of m/z values above the peaks of the major compounds (from [CAR 12])

In the case of Mediterranean orchids, the morphological similarity of the described species sometimes makes their recognition difficult, notably by stakeholders in conservation efforts. Thus, in 2010, 20.6% of the orchid species found in metropolitan France were considered to be supported by “insufficient data” by the IUCN, mainly as a result of problems with taxonomic identification [SCH 14]. Using the integrative taxonomy approach and taking into account, in one analysis, numerous scientifically established taxonomic characteristics (morphology, molecular characteristics, distributional range, flowering period, odor emitted and identity of pollinators), it has progressively become possible, in genus after genus, to clearly identify the taxonomically difficult species. In this context, the variation in the odors emitted by these remarkable flowers is particularly important, because odors of some species attract specific pollinators, whereas those of other species attract a greater diversity of pollinators. These differences have implications for reproductive isolation. Pollinator differences related to variation in floral odor, together with other traits analyzed in the framework of integrative taxonomy, show, for example, how the three described species of the fly orchid group, very close morphologically, can be definitely considered to be distinct species. They differ at the level of their molecular genetics, their habitat preferences, their morphology, the floral scents they emit and their specific pollinators [TRI 13]. Demonstration of these differences shows the importance of implementing conservation programs, because two of these species have restricted distributions (Ophrys aymoninii, endemic to the Grand Causses region in France; O. subinsectifera, endemic to the Franco-Spanish Pyrenees).

1.2. Scent communication between sexual partners

Another facet of chemical ecology concerns communication between members of the same species. Recent discoveries have shown that certain plants of the African savanna communicate among themselves the arrival of large herbivores; the first plant that suffers their attacks quickly emits a volatile bouquet perceived by neighbors of the same species, which then quickly synthesize protective tannins. In the time it takes an elephant or a giraffe to graze on several leaves, individuals of the same species in the vicinity have already become repulsive [WAR 02].

However, chemical communication within the same species is most developed in animals, especially at the time of reproduction. Reproduction conditions the capacity of species to settle in an environment and colonize it. In animals, scents have a generally determinant role in the recognition, detection (sometimes at long distance) and choice of a sexual partners. To find soul mates, insects have developed amazing olfactory abilities. This is the case with many night-flying moths that are capable of detecting a sexual partner at very long distances. For example, female silkworms (Bombyx mori) use bombykol to attract males from within a radius of many kilometers. The males of such species are often equipped with long branching antennae that detect the volatile substances emitted by females [BUT 61]. In Drosophila fruit flies, couples find each other on a ripe fruit (Figure 1.2) on which they both come to find food and to use as breeding sites. The mature fruits visited by these flies generally emit phenylacetic acid and phenylacetaldehyde, compounds which act as aphrodisiac stimulants in these small flies. During copulation, the male transmits to the female a pheromone (cis-vaccenyl acetate); as a result, future contenders detecting this compound in an already fertilized female can avoid her and optimize their partner selection. Although the production of these perfumes and the molecular mechanisms by which they are detected present differences between vertebrates and invertebrates, how their nervous systems code and decode signals is sometimes strikingly similar. For example, the Asian elephant uses the same sexual pheromone as numerous butterflies [RAS 96]!

Figure 1.2.A ripe fruit constitutes the ideal place for interaction between male and female drosophila (Drosophila melanogaster) flies (left photo: Jean-Pierre Farine). This food source and breeding site is a substrate particularly adapted for finding a sexual partner (right photo: Sonia Dourlot)

Although the molecules of sexual communication are less well known for vertebrates than for insects, the chemical mediation used by vertebrates includes both small volatile molecules perceived by olfaction and detectable at a distance (such as exo-brevicomin in the mouse) and heavier molecules perceived through contact, such as proteins in the mouse or lipid compounds in several species of Spanish lizards.

A large number of studies have shown that the fragrant bouquets indicate not only the maturity, receptivity and location of the sexual partner but also its quality. Scent variation can even allow olfactory discrimination at the individual scale. It is this property that allows communication of information on the quality of the sexual partner, which is defined, depending on the species, by traits such as its capacity to acquire territory, its social rank, its access to resources, its fertility, its resistance to illness, etc. Numerous examples have been studied not only in cattle and mice (Figure 1.3), but also in social insects (see section 1.5) and primates (see Chapter 3).

Figure 1.3.Left: scent detection in cattle. Here, a male is sniffing the perigenital zone of a female, to detect volatile compounds linked to female receptivity (photo: F. Urbany). Right: in the domestic mouse (Mus musculus), the identity of the sexual partner is perceived via olfaction: a male and a female evaluate each other by sniffing (photo: K. Thonhauser)

1.3. Scent communication between species

However, it is in the case of communication between species that chemical mediation reaches its richest development, giving free rein to complexity, producing what is sometimes described as chemobiodiversity (defined as the chemical diversity of living things) by analogy to biodiversity. The same scent may sometimes be “interpreted” in different manners by the species involved in the interactions. Immobile and often confronted by the necessity to attract pollinators while at the same time repelling “unwanted” visitors such as herbivores, plants are often the overlooked champions of scent manipulation. In some cases, the same bouquet of floral compounds can simultaneously attract pollinators and repel other visitors. In one such example, male plants of the cycad Macrozamia attract their pollinators to cones by the emission of a small quantity of volatile compounds such as β-myrcene [TER 07]. Once the pollinator is attracted, the temperature in the male cones increases, entraining a drastic increase in the emission of β-myrcene and transforming it into a compound that is repulsive to pollinators. These then fly to the cones of female plants,