Strasburger s Plant Sciences

Transcription

1 Strasburger s Plant Sciences

2 Strasburgeria robusta Guill.; Strasburgeriaceae named after the founder of this book, Eduard Strasburger Pete Lowry, Missouri Botanical Garden

3 Andreas Bresinsky, Christian Körner, Joachim W. Kadereit, Gunther Neuhaus and Uwe Sonnewald Strasburger s Plant Sciences Including Prokaryotes and Fungi With 1100 Figures and 63 Tables

4 Andreas Bresinsky Botanical Institute University of Regensburg Regensburg, Germany Christian Körner Institute of Botany University of Basel Basel, Switzerland Joachim W. Kadereit Institut für Spezielle Botanik und Botanischer Garten Johannes Gutenberg-University Mainz Mainz, Germany Gunther Neuhaus Cell Biology University of Freiburg Freiburg, Germany Uwe Sonnewald Department of Biology Division of Biochemistry Friedrich-Alexander-University Erlangen-Nuremberg Erlangen, Germany Translation and Copyediting Alison Davies, Stuart Evans (Chapters 1 4, 9, 10) David and Gudrun Lawlor, Stuart Evans (Chapters 5 8) Christian Körner, Stuart Evans (Chapter 11) Christian Körner, Lea Streule (Chapters 12 14) Alison Davies, Garching, Germany David and Gudrun Lawlor, Harpenden, UK Stuart Evans, West Rainton, UK Lea Streule, Basel, Switzerland ISBN ISBN (ebook) ISBN (print and electronic bundle) DOI / Springer Heidelberg New York Dordrecht London This work is based on the 36 th German language edition of Strasburger, Lehrbuch der Botanik, by Andreas Bresinsky, Christian Körner, Joachim Kadereit, Gunther Neuhaus, Uwe Sonnewald, published by Spektrum Akademischer Verlag, Heidelberg Library of Congress Control Number: Springer-Verlag Berlin Heidelberg 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Springer is part of Springer ScienceþBusiness Media (

5 Preface Eduard Strasburger * February 1, 1844, Warsaw { May 19, 1912, Bonn Founder of the Lehrbuch der Botanik für Hochschulen (Botany Textbook for Universities) (Photo by Dr. Wolfram Lobin/Uni Bonn) The last English translation of Strasburger s Lehrbuch der Botanik für Hochschulen (Textbook of Botany for Universities) was published in 1976 (30th Ed.). Since then, six new German editions have been published and were partially translated into Italian, Spanish, Serbo-Croatian, Turkish, and Russian. Considering that plant sciences have developed and expanded considerably since 1976, and that six more German editions have tried to keep pace with these changes, a new English translation was long overdue. The present edition represents a balanced and comprehensive work on the plant sciences, the book s trademark and particular strength. The inclusion of bacteria, archaea, and the various lineages referred to as fungi may not be justified from a phylogenetic perspective when dealing with plants, but is necessary considering the important evolutionary and ecological interactions between plants and these organisms. Strasburger s Lehrbuch der Botanik für Hochschulen has been available for almost 120 years now. Starting with its first edition in 1894, the book has greatly influenced university teaching in Germany and neighboring countries, and its 36 editions also mirror the dynamic history of the plant sciences.the book was first founded by Eduard Strasburger and is still published under his name. From the beginning, it was a multi-author effort, and Strasburger himself invited his colleagues at the Botanical Institute of Bonn University as contributors to the first edition. Since that time more than 20 authors from a number of universities in three different countries contributed to the content. Although clearly all authors of the first and of later editions shaped the book, Strasburger as its founder deserves special recognition. In his honor, a New Caledonian tree, which is shown on page II, was named Strasburgeria. Eduard Strasburger studied the natural sciences in Paris, Bonn, and Jena, receiving his doctorate in Jena before completing his postdoctoral degree ( Habilitation ) in Warsaw in He was appointed professor of botany at the University of Jena in 1869, at the age of 25, and moved to Bonn University in Under his direction, the Botanical Institute at Poppelsdorf Palace established itself as an international center of botany. In 1894, together with his colleagues F. Noll, H. Schenck, and A.F.W. Schimper, he founded the Lehrbuch der Botanik für Hochschulen, in the past often simply referred to as the Bonner Lehrbuch. The Kleine Botanische Praktikum für Anfänger (Short Botanical Practical for Beginners), which also appeared in multiple editions, and the somewhat more extensive Das Botanische Praktikum (Botanical Practical) have dominated microscopical laboratory work at universities for a long time. Strasburger s research interests were primarily in plant ontogeny and cytology. He discovered that the central processes underlying nuclear division (formation, division, and movement of chromosomes) are the same in all eukaryotic organisms (1875), and he was the first to observe that fertilization in flowering plants requires the fusion of the male sperm nucleus with the female egg nucleus. From this he concluded that the cell nucleus must be the most important carrier of hereditary factors (1884). The Authors April 2013

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7 Table of Contents Preface.... v List of Topical Insights...ix List of Boxes......xi Volume 1 Introduction... 1 Part I Structure Gunther Neuhaus 1 Molecular Basics: The Building Blocks of Cells The Structure and Ultrastructure of the Cell The Tissues of Vascular Plants Morphology and Anatomy of Vascular Plants Part II Physiology Uwe Sonnewald 5 Physiology of Metabolism Physiology of Development Physiology of Movement Allelophysiology Volume 2 Part III Evolution and Systematics Joachim W. Kadereit. Andreas Bresinsky 9 Evolution Systematics and Phylogeny

8 viii Table of Contents Part IV Ecology Christian Körner 11 Basics of Plant Ecology Plant Environment Interactions Ecology of Populations and Vegetation Vegetation of the Earth Timeline Sources Index

9 List of Topical Insights Topical Insight 5.1: Galactolipids and Membrane Remodeling Christoph Benning Topical Insight 5.2: Genetically Encoded Biosensors Wolf B. Frommer Topical Insight 8.1: Host Targets of Bacterial Effectors Mary Beth Mudgett Topical Insight 9.1: Homoploid Hybrid Speciation Loren Rieseberg Topical Insight 10.1: Origin and Early Evolution of Flowers Peter K. Endress. James A. Doyle Topical Insight 12.1: What Plant Ecologists Can and Cannot Learn from a Satellite s Eye Hamlyn G. Jones Topical Insight 12.2: A World Without Fire William Bond Topical Insight 12.3: The Dynamic Pipeline: Coordination of Xylem Safety and Efficiency Frederick C. Meinzer Topical Insight 12.4: From Where Do Plants Take Their Water? Todd E. Dawson Topical Insight 12.5: Leaf Nitrogen: A Key to Photosynthetic Performance John R. Evans Topical Insight 12.6: Plant Life in the P-Poor Part of the World Hans Lambers Topical Insight 12.7: Diversity of Traits: A Functional Link to Adaptation, Community Assembly, and Ecosystem Structure and Function Peter B. Reich Topical Insight 12.8: Using Stable 13 C Isotopes to Study Carbon and Water Relations Rolf Siegwolf Topical Insight 13.1: Forest Structure and Gap Models Hank H. Shugart

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11 List of Boxes Box 2.1: Cell Fractionation Box 2.2: The Nuclear Spindle Box 3.1: Residual Meristems and Meristemoids Box 4.1: Inflorescence Morphology Box 4.2: Types of Stele Box 4.3: The Leaves of Carnivorous Plants Box 4.4: Root Metamorphoses Box 5.1: Electrophysiology Methods Box 5.2: Important Units in Photobiology Box 6.1: Thale Cress: Arabidopsis thaliana (L.) Box 6.2: Conventions in Naming Genes, Proteins, and Phenotypes Box 6.3: Production of Transgenic Plants Box 6.4: Application of Transgenic Plants Box 6.5: Evolution of Plant Receptors Box 8.1: Cauliflower Mosaic Virus Box 8.2: Biology of Crown Gall Tumors Box 9.1: Recording and Analyzing Phenotypic and Genetic Variation Box 9.2: Population Genetics Box 10.1: The Origin of Life Box 10.2: Phylogeny of Plants and Fungi Box 10.3: From Unicellular Organisms to Multicellular Organisms Box 10.4: Occurence and Habit of Fungi (Including the Cellulose Fungi) Box 10.5: Uses of Algae Box 10.6: Occurence and Diversity of Habits in Algae Box 10.7: Occurence and Ecology of Mosses Box 10.8: Occurence and Ecology of Ferns and Fern Allies Box 10.9: Seed Plants (Spermatophytina) Box 10.10: Poales: The Evolution of Habitat Ecology and Pollination Biology Box 10.11: Chenopodiaceae: The Evolution of C 4 Photosynthesis Box 10.12: Asterales: Evolution of Secondary Pollen Presentation Box 10.13: Mass Extinctions Box 11.1: Classification of Soils Box 12.1: Effects of CO 2 on Plant Growth Box 13.1: Metapopulations: Consequences of Habitat Fragmentation for Survival of Species

12 Introduction Botany: A Biological Science Botany is the science of plants. The term was coined in the first century by Dioscorides, who used it to mean a (medicinal) herbal science. In fact, Greek botáne means grass, as a common forage or economic plant. The general Greek term for plant is phýton. These days it is much more common to use the synonymous term plant science than to use botany. Plants are primarily defined as those organisms whose cells contain plastids as well as having true nuclei with a nuclear membrane and several chromosomes. Plastids may occur as chloroplasts, or organelles that may become plastids under the right conditions. Chloroplasts are photosynthetic organelles that are able to convert light energy into chemical energy and to fix carbon dioxide. Green plants are photoautotrophic. Unlike other heterotrophic (organotrophic) organisms, green plants are able to survive without organic nutrition. Fungi are also traditionally included in botany even though they do not have any plastids. They are heterotrophic and behave saprotrophically (feed off dead organic material), parasitically, or symbiotically (feed off living organisms). Even though fungi are phylogenetically closer to animals, they share some features with plants, e.g., they possess vacuoles in their cell-wall-bound cells, they have a sessile life style and they take up dissolved nutrients. Fungi can also form practically obligate symbiotic relationships with plants (mycorrhiza). It can be rather problematic to differentiate between animal and plant among the single-celled protists. Among the flagellates, even between closely related species in the same genus, there can be forms with and without plastids: phytoflagellates and zooflagellates, respectively. The cells of bacteria and archaea are generally smaller and fundamentally more simply organized than the cells of animals, fungi, and plants (> Fig. 1). Bacteria and archaea do not have a true cell nucleus and do not undergo cell multiplication by nuclear or cellular division in the way that all other organisms do, nor do their phototrophic forms have plastids. The cells in these groups are distinguished as prokaryotic cells from the eukaryotic cells of all other organisms. Bacteria and archaea are thus prokaryotes, whereas all other organisms (plants, fungi, animals; all protists with a true cell nucleus) are eukaryotes. There are no intermediate forms between the prokaryotes and the eukaryotes in modern living organisms. Even so, the oldest eukaryotes were derived from the prokaryotes. The investigation of microscopically small organisms, both prokaryotic as well as eukaryotic, is a scientific discipline of its own microbiology. This includes viruses, viroids, and prions subcellular systems that hover at the boundary between the animate and the inanimate. Despite all the differences between prokaryotic cells and eukaryotic cells, and the even more pronounced differences between the various forms and functions of the cells of higher animals and plants, there are many basic commonalities. All organisms share similar molecules and many fundamental systems essential to life. This also applies for genes (hereditary factors). This basic uniformity across all life forms indicates a shared phylogenetic origin: all living organisms (probably) arose from a single lineage (monophyletic origin). What Is Life? Every living system is defined by a particular series of features. However, only all of these features together allow the differentiation of an animate from an inanimate organization. The classic signs of life include: Chemical composition. The dry mass of all organisms is dominated by proteins, nucleic acids, polysaccharides, and lipids. Additionally, there is a wealth of heterogeneous organic molecules and ions. Organic molecules, especially macromolecules, are only synthesized by living organisms (biosynthesis with the help of special catalysts, the enzymes). Systematically constructed complex structures. Life is intrinsically linked to cellular organizational forms. Even the simplest living organisms are characterized by complex structures. This means the molecular and supramolecular components are functionally linked and dependent on each other. Only by functioning together properly are they able to bring something to life. None of the single components alone would be able to fulfill this. The system is thus more than just the sum of the parts, and life is always a product of A. Bresinsky et al., Strasburger s Plant Sciences, DOI / , # Springer-Verlag Berlin Heidelberg 2013

13 2 Introduction. Fig. 1 Size comparison of prokaryotic cells and eukaryotic cells. (a) Bacterial cells (Escherichia coli). (b) Cells of an Elodea canadensis leaf. Three plant cell characteristics can be seen: cell walls, chloroplasts, and central vacuoles. Both images are highly magnified (380) a system. Below the complexity level of the cell there is no independent life. The cells always contain information-bearing structures, an array of various enzymes, and are separated from their environment by a selectively permeable membrane. It is not contradictory to say that in most multicellular plants there are plasmodesma (plasma canals in the cell walls) between the tissue cells that are united into a supercellular symplast. Nutrition. Organisms are rather unlikely constructions in terms of energy and entropy. They are made up of energy-rich, highly unstable molecules; their high structural and functional organization represents low entropy. The support of this labile condition is only possible with the input of energy. Living systems are therefore basically open systems; i.e., they take up energy-rich photons or materials and release energypoor material (e.g., CO 2,H 2 O). This metabolism is intrinsically linked with energy exchange. The metabolism results in a constant energy imbalance (dynamic balance with irreversible subprocesses: so-called flux equilibrium). Metabolism and energy exchange allow the energy-demanding construction of (macro) molecules (anabolism) by linking it to an energyproducing process such as the capture of solar energy and/or the breaking up of energy-rich compounds (catabolism). The low entropy capacity of the organisms is sustained by the donation (dissipation) of excessive entropy into the surrounding environment. By using a dissipative structure, the organisms avoid fatal chaotic events. Thus, life is not really a condition but is rather a continuous process. Whereas the outer form of organisms changes rather slowly, there is continuous turnover at the molecular level. Motion. Every actively living organism and every individual cell shows signs of motion (motility). However, many cells/organisms are able to switch to a latent phase, forming seeds, spores, or cysts. During these stages of life there are no obvious signs of motility and almost all criteria for life are arrested. Stimulus perception and response. All organisms and cells must be able to receive and respond to signals from their environment. The diversity of mechanisms evolved to do this is incredible. Development. Organisms are incapable of retaining a particular structure indefinitely. No organism looks the same throughout all its life phases. A newly formed cell, arising from cell division, grows to the size of its mother cell (growth). Multicellular organisms usually start their individual development from just a single cell (fertilized egg cell, a zygote; spore). Then they grow by cell division until they reach their final size, changing their shape in the process. Ontogeny, the development to a sexually mature multicellular organism, is associated with morphological processes at the cellular level that result in the differentiation of the initially similar embryonic cells. Reproduction. The succession of generations is made up of successive life or reproductive cycles. Life is perpetuated in this way, in spite of the inability of individuals to permanently retain a particular developmental phase and despite the inescapable fact that all individuals must eventually die. Death is the last stage in an individual s development. Unlike catastrophic death, physiological death is often a result of inner processes undergoing a program of selfdestruction. Conversely, organisms may only arise as progeny of conspecific ancestors. Abiogenesis, or

14 Introduction 3 spontaneous generation, of a living system from inanimate material is, at least on today s Earth, inconceivable and has never been proven: omne vivum e vivo ( every life originates from another life ). This rather obvious standpoint is relatively new. Until the groundbreaking work of L. Pasteur and H. Hoffmann around 1860, it was assumed that microorganisms, even fungi and nematodes (worms) in fermenting and rotting liquids, had arisen spontaneously. Replication. Reproduction is normally connected with replication. This ensures the perpetuation of a species in spite of the loss of individuals as a result of changing environments. The replication rates are often astounding in smaller organisms. Under optimal conditions, bacterial cells can divide every 20 min. This means that with unrestricted replication of a single cell, its progeny would form a cell mass the volume of Earth in less than 2 days. Larger organisms tend to replicate more slowly, but the individuals are better protected by a variety of different mechanisms. Inheritance. Ontogeny happens in much the same way from generation to generation. The genetic information is amplified and transmitted in the process. It contains the program for the course of species-specific ontogeny. The genetic information of all cellular organisms prokaryotes and eukaryotes is saved (stored) in the bases and nucleotide sequences of deoxyribonucleic acid (DNA). These are linear or circular double-stranded macromolecules. Viruses can store their genetic information in a single-stranded DNA molecule and in ribonucleic acid (RNA; single stranded or double stranded). Evolution. Copying (replication) and transmission of the genetic information happens with great precision. However, over many successive generations, changes can occur that may be inherited (mutations). These changes can be induced by environmental factors. These can be partly a result of inherited switching on (activation) and off (deactivation) of genes (epigenetics). In the long term, quite big differences can develop in a population that can differently affect the reproductive ability of individuals. This natural selection results in changes in the characteristics of the members of a species and in the end can result in the establishment of new species: evolution and phylogeny. A superior criterion for life in all organisms is their reproductive ability. All remaining characteristics are either critical to or a result of this central attribute. The genetic information of all organisms contains the developmental plan for complex molecular machinery, whose prime function is its own reproduction. Life is (at least on today s Earth) only conceivable and verifiable as a continuum. This knowledge is supported by the irreversibility of individual death and the extinction of species. There is nothing comparable in inanimate nature. Origin and Evolution of Life The living organisms that exist today are the result of a long evolutionary process. On the basis of radioactivity and the composition of rock formations, the age of Earth has been calculated as being about 4.6 billion years. The study of the remains of organisms (fossils; paleontology) in various old sediments has shown that other sorts of plants and animals lived on Earth during earlier geological epochs. The phylogenetic continuity can be seen in the floras and faunas of past epochs of the living organisms: the older they are the more different they are. Larger, multicellular organisms first appeared toward the end of the Precambrian (about 570 million years ago). Until then single-celled organisms had dominated, and these were mostly prokaryotes. There is evidence that extensive colonies of cyanobacteria were already present in the Archean (more than 3 billion years ago): the relevant sediments in Australia and South Africa contain layered stromatoliths over 30 cm in size. These are characteristic biogenic sediments, which are still formed today in warm waters, and were built by dense layers of phototrophic cyanobacteria. How could life have arisen? Answers to this fundamental question are sought by trying to recreate or simulate the primeval conditions that would have existed on Earth at that time. A condition for the formation of a simple self-replicating system was the presence of organic (macro) molecules. In contrast to today, the conditions on the still hot planet (Hadean eon) would have enabled organic molecules to form abiogenically. The first atmosphere contained water vapor as well as carbon dioxide, nitrogen, and smaller fractions of reducing gasses, but practically no free oxygen; therefore, there was no ozone layer that could have filtered the energy-rich UV radiation from the sun. These conditions would have enabled various organic compounds to form. Abiogenic acetic acids and energy-rich thioesters are even formed in watery mixtures of carbon monoxide, sulfuric acid, and metal sulfides, like those thrown out by deep-sea thermal vents. Certain places on primitive Earth would have become enriched in such compounds as long as life did not exist to digest them and no oxidation destroyed them.

15 4 Introduction Even the simplest cells, such as those of the (recently arisen) saprobiotic mycoplasmas (see below), are very complex. Their origin from a chaotic mixture of molecular building blocks via a single chance event is highly improbable. However, a likely scenario is that this happened in a process of hypothetical intermediate steps (multistep theory): if the necessary individual steps in this prebiotic evolution were small enough, then the likelihood of them having really happened over a vast timescale is sufficiently large. Some molecules which could have arisen abiogenetically show signs of enzymatic activity; i.e., they function as biocatalysts. Certain RNA molecules (ribozymes) can catalyze changes in themselves and, together with heavy metal ions, can even initiate their own propagation, albeit rather haphazardly (RNA world). The decisive step toward independent life was made when protein catalysts made the effective and precise replication of nucleic acids possible and the key to the synthesis of these enzyme proteins was carried by the nucleic acids. This double-step advance, which was probably a cumulative result of many small steps, formed a link between proteins and nucleic acids that is absolutely fundamental for life in its current form. Thus, there was a genetic code that could translate nucleotide sequences from nucleic acids into protein sequences, and the separation of gene (hereditary factor) from phene (a character based on the hereditary information) was completed. The first systems capable of self-replication, the hypothetical progenotes and the subsequently evolved prokaryotes, were able to live organotrophically as long as the abiotic formation of organic molecules continued. However, increasing exploitation of resources to the point where they became exhausted meant that phototrophic forms became more prominent. Among these were some forms that were able to split water to release oxygen during photosynthesis. This slowly created an oxidative atmosphere, allowing a much more effective energy acquisition from organic molecules by cell respiration. At the same time, an ozone layer was formed in the stratosphere that absorbed the heavily mutagenic UV radiation from the sun and enabled the colonization of the ocean surfaces and the land. Fossil evidence from the long Precambrian evolution is, not surprisingly, rather rare and incomplete. However, sequence comparisons from proteins and nucleic acids of related living organisms can be used to reconstruct phylogeny. The more differentiated the sequences, the earlier the last common ancestor of the organisms must have lived. Evolutionary changes have occurred at different rates in different parts of the (partial) sequences. Therefore, only sequences (or partial sequences) that change very slowly over time and are fairly similar even between living, quite distantly related organisms, are used in the reconstruction of early phylogeny. The comparison of these highly conserved sequences shows that the split between archaea and bacteria happened more than 3 billion years ago. Modern eukaryotic cells have plastids and mitochondria, photosynthetic and cell-respiration organelles, their own genetic code, and synthesize some of their proteins themselves. These organelles can only self-replicate and thus have a semiautonomous position in eukaryotic cells. They also have numerous prokaryotic properties, such as the mode of division, and details of their composition. Plastids seem to be descendants of once-free-living bacteria, which became integrated into the cells of primitive eukaryotes as intracellular symbionts more than one billion years ago and gradually developed into cell organelles (Endosymbiont theory). Remains of multicellular macroorganisms are first found in sediments that are less than a billion years old. These organisms are, without exception, eukaryotes. Even their evolution, which can be increasingly better reconstructed with molecular systematic techniques, has been a result of the interaction between chance mutations and directional selection (Darwinism). This is based on the assumption that evolution is a result of the sum of numerous small steps (gradualism). Even so, these have been interspersed by major evolutionary transitions. These do not differ from the small steps in terms of how they arise, but differ rather in the gross effect of many gradual evolutionary changes. They have been rarer events than the other gradual evolutionary transitions but have been more momentous. It seems that, repeatedly, reproductive units that achieved independence at a certain point in time have merged to form large, more complex units. Thus, completely novel systems have emerged that can form the basis of alternative, distinct lineages. Limits of Life The question for the limits of life has two components. First, one can ask for the distributional limits of life, and second for both lower and upper size limits of individuals. The first aspect an ecological component is that, despite a phenomenal range of adaptive strategies, general conditions for life have quite narrow limits. They are determined by maxima and minima of water content, temperature, and light. The optimum for most organisms is median temperatures (10 40 C) and high water content. For this reason, it is possible to store food at cool temperatures (fridge, freezer) or by drying

16 Introduction 5 (legumes, cereals, flour, bread, hay) or by pasteurization (milk). In nature, the dry and cold regions are particularly poorly colonized. Many organisms can survive temperatures down to the freezing point of water by having latent or dormant phases, but still die between 0 C and 10 C. Psychrophilic organisms (e.g., some snow algae) have optimal growth temperatures between 1 and 2 C. Temperatures over 100 C, which are rarely found on Earth s surface (hot springs, volcanoes), can support thermophilic organisms. Some archaea have temperature optima around 100 C, possibly an adaptive relict from primeval Earth. As phototrophic organisms are mainly responsible for the production of organic material (biomass), life is more-or-less restricted to the well-illuminated regions of Earth s surface and oceans. Earth is coated with a comparatively thin biosphere that accounts for less than 0.01% of its volume. The largest life forms (both fossil and living) are found among the vertebrates (dinosaurs, baleen whales) but also larger and in greater numbers among the conifers and deciduous trees as well as among clonal organisms such as poplar (Populus), reed grass (Phragmites), bracken (Pteridium), and fungi. The giants among the trees (Sequoia, Cryptomeria, some Eucalyptus) are also the heaviest life forms. A more significant question for theoretical biology is how small can a life form be? What is the lower limit of complexity for self-replicating biosystems? The smallest cells are prokaryotic. They are found in mycoplasmas. The diameter of these cell-wall-less prokaryotic cells is about 0.3 mm and their DNA can only code for about 500 different proteins. This is about the absolute minimum possible for DNA replication, the realization of the genetic information stored therein, the support of a heterotrophic metabolism and energy exchange, and a simple cell structure (theoretically about 350 genes). In comparison, the cells of a typical bacterium have a diameter of 2 mm and contain over 3,000 different proteins; the diameter of most eukaryotic cells lies between 10 and 100 mm, and the cells can form over 30,000 different proteins. The complete sequenced genome of the model plant Arabidopsis thaliana has about 25,000 genes, 11,000 more than the fruit fly Drosophila. Viruses are much more simply organized and most of them are even smaller. A virion (a viral particle) is not a cell. Whereas, e.g., the simplest cell has both DNA (information storage) and RNA (information retrieval), a virion has neither DNA nor RNA. The nucleic acid is often only associated with molecules of a single protein type such as in the tobacco mosaic virus (> Fig. 2), or it may be surrounded by a protein sheath (capsid) made up of a single protein or only a few different proteins. This sort of capsid often has a crystalline symmetry. Viruses or (bacterio)phages (viruses that attack prokaryotic cells) only partially fulfill the conditions necessary for life. They have no metabolism or energy exchange, no ability to replicate or synthesize proteins, and no ability to reproduce independently. They can only reproduce by using the metabolism and energy exchange of a living cell they are obligate parasites ( borrowed life ). The dispersal forms virions that exist outside living cells represent lifeless organic systems. The simplest organizational level is achieved by the viroids. These are infectious nucleic acids (RNA) with no associated proteins. The short, ring-shaped RNA molecules do not code for any proteins. Some of the most dangerous plant parasites known are viroids. In spite of their particularly simple organization, neither viruses nor viroids can be considered to be the most primitive forms of life, as their reproduction depends on the existence of living cells. Rather, they are genetic elements that became independent of their support cells (vagabond genes). In fact, there are segments of genetic information in most (if not all?) eukaryotic cells and prokaryotic cells that are inherited independently of the gene-carrying structures (chromosomes, genophores), or at least that are able to temporarily disassociate themselves from the structures. This heterogeneous group includes the plasmids of many bacteria and some eukaryotes, as well as the so-called insertion sequences and transposons (jumping genes). Biology as a Natural Science Living nature is impressive because it supports a huge diversity of life forms. Recording, describing, and systematically organizing all living and extinct organism types (species) is the enormous, as yet unfinished, task of biology, in particular, systematics. But biology is not just restricted to the description of what is there, even more, it strives to explain this diversity. Besides observation and comparison, there is the experiment. An experiment is the observation of a process under artificial predetermined or controlled varied conditions. Data from experiments and observations provide the raw material for constructing hypotheses and theories, contributing toward the explanation of causal relationships. (H. Poincaré: A heap of facts is as much a science as a heap of stones make a house. ). By forming a repeatedly questioned theoretical construct (see below), the discovery of correlating laws and their final formulation into natural laws can incorporate lots of observations into short, clear units that can then be

17 6 Introduction. Fig. 2 Tobacco mosaic virus particles can be seen as rod-shaped particles under an electron microscope (EM). Every virion contains a helical RNA molecule. In the uninjured state, it is made up of a series of 2,130 identical protein molecules each with 158 amino acids. The central axial canal formed in the RNA helix is clearly visible in this negative-contrast slide. Scale bars (a) 0.1 mm, (b) 0.02 mm (EM images from a F. Amelunxen and b C. Weichan) considered. It would be impossible to intellectually penetrate the real world with all its basically nonrecordable structures and experiences without this type of abstraction. Thus, the natural sciences have become enormously significant in recent times, especially modern biology (keywords biotechnology, gene technology ). The sum of recognized natural laws and their interpretation forms the scientific world view, a simplified reflection of nature presented in perceptions, symbols, and ideas. This world view is the highest expression of our understating of nature. It enables mental operations (thought experiments) that would be too dangerous or expensive to conduct in the real world. The scientific world view is thus fundamentally dynamic, as novel information is acquired by research, and new interpretations can be expanded and altered. It is perforce preliminary and fragmentary and cannot (should not) ever be seen as being complete. Even so, it is the best that humankind can offer. The fragmentary character (nature) of the scientific world view is affected not just by the selection (even if subconscious) and use of limits of scientific endeavor, but also by the limits of methodology and primarily by the limitations imposed by the type of research. These are indirect in fundamental research as the aims and results are initially unknown. Indirect aims are researched in that testable hypotheses are postulated (Greek hypóthesis, to suppose). A hypothesis, a scientific concept, can never be proven because the data will never be enough. However, a general theorem can be rejected on the basis of one contradictory event (asymmetry of verification and falsification; see K.R. Popper). The assumption all roses are red cannot be proven even with 1,000 red roses, but can be rejected on the observation of a single yellow or white rose. Correlations are based on laws of relationships derived from observed events (e.g., cigarette smoking/lung

18 Introduction 7 cancer; but also the frequency of storks and human birth rates in some regions). Correlations can mean there is a causal relationship, but this does not have to be the case. If two quantities B and C are correlated, then B can cause C or the other way round; B and C could be caused by a third, common, as yet unknown quantity A; they are correlated but not causally, only coincidentally. Although the lack of a correlation implies the lack of a causal relationship, a correlation is not evidence for one; therefore, it cannot be used for the verification of an assumption. The asymmetry of verification and falsification means that forward steps in knowledge are achieved indirectly, not directly, as inappropriate or inapplicable hypotheses are rejected (method of trial and error). The aim, the appropriate knowledge and explanatory reasons, can only be achieved through disappointment and via detours (Greek methodos means not only thorough research but also detour). With every failed falsification attempt, the probability of finding the right hypothesis increases. When the hypothesis can be applied to other areas independently of the original research, it becomes more plausible. Comprehensive hypotheses that, despite many attempts, remain nonfalsifiable become theories. Theories are elements in the scientific world view. A theory, e.g., the central biological theory of descendancy or evolution, allows many events to be explained and enables the formulation of numerous testable postulates. From a theoretical scientific viewpoint, a theory presents a disciplinary matrix or paradigm that provides the intellectual framework for further experimental work in an area of interest. Surprisingly, even though specific observations and appropriate experiments are made on the basis of hypotheses and theories, most research is not inductive (based on experience and understanding) but deductive. It is not primarily targeted at discovering the unknown or novel, but serves to check and refine an existing paradigm. Of course, existing tested theories can be falsified. Then a new more comprehensive theory has to be developed. These scientific revolutions (see L. Fleck; T.S. Kuhn) are only successful if they can also explain why the previous theory appeared to explain so much. Often it becomes apparent that the older theory does in fact still hold true within certain limits. The history of scientific biology has many examples of such scientific revolutions, such as in the developments of cell biology and genetics. The teachings of the potential and limits of human knowledge (as outlined above) form part of epistemology, which is an important tenet in theoretical science as well as in philosophy (see, e.g., I. Kant). Even so, the potential to use knowledge from independent logic or mathematics to form ideas about real life or nature remained a mystery for a long time. (A. Einstein: The incomprehensibility of the world lies in its comprehensibility. ). Special Position of Biology The uniqueness of life in nature gives biology a special position among the sciences. Time and again it has been questioned whether living systems and systems of abiotic nature adhere to different laws, and special life forces (vitalism) have often been postulated. However, to date there is no known case where physical and chemical laws have been disobeyed by living organisms. On the other hand, organisms are incredibly complex systems, which means that biological systems obey laws that would otherwise not be observed. One speaks of emerging attributes. An important consequence of living systems is that biological materials cannot be logically or mathematically penetrated in the same way as objects in physics and chemistry. Biology is an exact science based on the recognition of natural laws, but observation, description, and comparison play a much greater role than in physics. However, a complete derivation of all biological phenomena from chemical and physical laws, in the sense of a consistent reductionism, would be illusory. The definition of life as a self-replicating system is further supported by a fact that emphasizes the uniqueness of the organism biological teleonomy. Life forms behave purposefully, they react expediently, and appear to be constructed sensibly. Besides the question why? (causality), biology (and only biology among the sciences) also justifiably asks what for? (finality). This touches on the cyclical development of life; compare the terms developmental cycle, reproductive cycle, and generation cycle. From any given starting point, these cycles proceed along genetically predetermined developmental lines until they return to a comparable starting point (e.g., egg cells, spores). This results in semicyclical events and chains of cause and effect. For example, a particular developmental stage B can arise not only as a result of the previous stage A but also via the subsequent stages C, D, etc., also as a cause for the renewed occurrence of stage A (even if it is chronologically out of sequence). The final viewpoint bears as much weight as the causal approach in biology. In inanimate nature, cyclical systems (e.g., oscillations) do not have mechanisms whereby losses are compensated for by energy gains, and they finally stop altogether. Life forms, on the other hand, can replicate by reproduction. Even in the research of evolution and the origins of life, biology finds itself in an unusual position.

19 8 Introduction While the highest priority is typically the search for natural laws reflected in the regular repetition of structures or processes in fact here it is the singular, chance event that is decisive. This is related to the reproduction and selection of organisms. Natural mutations are chance events and not predictable. Such mutations can remain neutral for a very long time until such time as the conditions suddenly change, making the mutations have negative or positive effects on the organism. If the mutation has a favorable effect on the bearer, then according to evolution by natural selection in successive generations, the mutation will become fixed. Life forms are, in this respect, very effective enhancers: all their observable inheritable traits are derived from improbable and thus rare chance events (singularities) whose effects are retrospectively enhanced by reproductive processes. Animals and Plants Since the historically based (rather than factually based) tendency to specialize has been superseded, modern biology is dominated by interdisciplinary cooperation. Knowledge drawn from genetics, biophysics, and biochemistry as well as physiology contributes to a broad foundation for general biology. Even evolutionary and developmental biology, as well as molecular and cell biology, have grown beyond the boundaries of the classical disciplines of botany and zoology. However, this connectivity should not be allowed to disguise the fact that the typical animal and typical plant (both terms used in the colloquial sense) have numerous differences. The typical animal is able to migrate. Its body is compactly constructed, with all organs except those required to interpret environmental signals being positioned inside. In order to see them, the animal s body has to be opened ( anatomy is derived from the Greek word meaning to separate and cut up ). The large surface areas necessary for breathing, nutrient resorption, and excretion are folded inside the body cavity. The outer surface area is reduced, and so the animal is a closed organism. The compact body structure enables the development of central organs for circulation and excretion. Even the nervous system, which enables rapid coordination, shows a tendency to become centralized over evolutionary time. Most organs are formed in a limited number and are at least rudimentarily present in the embryo, growing proportionately with the growing organism. Body symmetry is predominantly bilateral and dorsiventral, as expected when the two perpendicularly oriented vectors of gravity and motility are present. Radially symmetrical forms (in the strictest sense) only occur in sessile or aquatic species. The specialization of tissues and organs is highly advanced. Even meristems are specifically determined for the formation of particular cells (stem cells of blood and immune systems, the skin, the intestinal epithelium, etc.). The lifetime of even large animals is limited. Regenerative potential is often quite low in highly developed animals. Some highly differentiated cells remain active throughout the animals lifetime and are normally not regenerated in the adult phase (large neurons, striated muscle fibers, cells of the optical lens). A typical plant is usually rooted in one place for the whole of its lifetime. The pollen, seeds, or spores of the plant have, theoretically, limitless distribution possibilities. The body area is maximized by unfolding and branching. The plant is an open organism; perennial plants grow with numerous shoot apices and grow more in every vegetative period (for trees, annual growth from all shoot tips, annual rings in the wood, etc.). Metabolic waste products have to be removed by each cell individually; instead of centralization there is localized cellular excretion. The body is mostly radially symmetrical. There is an enormous regenerative potential; each shoot apex can, in principle, grow a complete new plant. This aspect is used extensively in horticulture and agriculture for the vegetative propagation of plants by grafts, cuttings, scions, bulbs, bulbils, etc. Furthermore, novel shoot apices may arise in injury-related callus growths (tissues generated by chaotic cell proliferation). Thus, cell cultures (even from single vegetative cells) can be used to successfully generate whole plants, something that is not possible from animal cells or tissues. It is not unusual to find plants that live to 100 or even 1,000 years of age. Clones are immortal. Thus, e.g., all apples of the same variety are perpetuated, by grafts, from the same genetic clone as from the apple (of that sort) that was first discovered, regardless of where it is now cultivated. Plants and animals also differ significantly in the structure and function of their cells. A general comparison shows that plants cells are not only distinct as a result of possessing plastids. They are not only phototrophic but are also osmotrophic (only able to take up substances that are dissolved), whereas animal cells are phagotrophic (able to take up nutrients in particulate form). Flagellates include mixotrophic species that are able to take up nutrients in both ways (> Fig. 3). The plant cell has, in its fully grown state, a central vacuole that makes up over 90% of the cell volume, and a cell wall. The cell wall absorbs the hydrostatic pressure of the vacuole (turgor) that would otherwise cause the cell to burst. Turgor is a consequence of osmosis; the molar total concentration of the cell sap in

20 Introduction 9. Fig. 3 Poterioochromonas malhamensis, a mixotrophic flagellate from the order Chrysomonadales (see also Fig ) with two unequal anterior flagella and lobopodium (L) as well as a posterior anchorage appendage (1,160). The cell on the left has a nucleus (N) with a nucleolus, plastid (P), and storage vacuole (V). The cell on the right has a large digestive vacuole with a half-digested algal cell in it (Interference contrast, microflash image from W. Herth) the vacuole is far greater than that of the imbibed water in the cell walls. Animal tissue cells have neither large vacuoles nor tough cell walls that have a stabilizing function for the individual cells. Their turgor is low because they are surrounded by isotonic body and tissue fluids. The mass of intercellular substances of the connective and supporting tissues of animals fixes not cells but supercellular structures. During plant and fungal cell division, the first wall primordium arises between the daughter cells via internal secretion of wall substances. In contrast, typical animal cell division occurs by pinching off daughter cells from the mother cell (cleavage), and, whereas the cells of the plant body are almost without exception anchored to their point of origin, the cells of animals may migrate and be translocated during development. Fungal cells are apart from not having plastids and not exhibiting phototropism more similar to typical plant cells than animal cells. They are vacuolated, osmotrophic cells with stable, nonrupturing cell walls that generally do not cleave but divide by novel cell wall formation (laid down by internal secretions). Classification and Significance of Plant Sciences The investigation of the plant, fungal, and protist world in fact just like for the whole world of organisms can be considered from many different viewpoints. For example, research areas could reflect the hierarchy of structures to be investigated (> Table 1). Basic research aims to gain understanding of the origin, diversity, and connectivity between form and function. This places the research object to the fore. Applied research is more concerned with the use of plants, fungi, and microorganisms in human and animal nutrition; for medicinal, toxic, and drugproducing plants the foundations of pharmacology; plant breeding, genetic manipulation, and biotechnology; for use in agriculture and forestry; for phytopathology, pest and weed control; and for landscaping, nature and animal conservation, and ecology (as defined by the modern media). Basic research provides the essential background knowledge for every type of applied research. In this handbook, the description of the general structural basics is in Part I. This treats the areas from atomic up to macroscopic dimensions: the overview of molecular basics is followed by a discussion of the structure and fine structure of the cell (cytology), followed by discussion of plant tissues (histology) and then the outer structure as seen with the naked eye (morphology). The structures are presented in Part II according to the general function in metabolic and energy exchange, change of form (metamorphosis), and motility. The dynamics of life processes are illustrated by this so-called plant physiology. The discussion of the physiology of metabolism is followed by discussion of developmental physiology and then physiology of movement. An especially current topic is allelophysiology the diversity of physiological relationships that plants have with other organisms. The division of this handbook into parts and chapters should not obscure the fact that modern biology is distinguished by its interdisciplinary approach. Areas that were