Strasburger’s Plant Sciences Strasburgeria robusta Guill.; Strasburgeriaceae named after the founder of this book, Eduard Strasburger © Pete Lowry, Missouri Botanical Garden Andreas Bresinsky, Christian Ko¨rner, Joachim W. Kadereit, Gunther Neuhaus and Uwe Sonnewald

Strasburger’s Plant Sciences Including Prokaryotes and Fungi

With 1100 Figures and 63 Tables Andreas Bresinsky Gunther Neuhaus Botanical Institute Cell University of Regensburg University of Freiburg Regensburg, Freiburg, Germany

Christian Ko¨rner Uwe Sonnewald Institute of Department of Biology University of Basel Division of Biochemistry Basel, Switzerland Friedrich-Alexander-University Erlangen-Nuremberg Erlangen, Germany Joachim W. Kadereit Institut fu¨r Spezielle Botanik und Botanischer Garten Johannes Gutenberg-University Mainz Mainz, Germany

Translation and Copyediting Alison Davies, Stuart Evans (Chapters 1–4, 9, 10) David and Gudrun Lawlor, Stuart Evans (Chapters 5–8) Christian Ko¨rner, Stuart Evans (Chapter 11) Christian Ko¨rner, 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 978-3-642-15517-8 ISBN 978-3-642-15518-5 (eBook) ISBN 978-3-642-15519-2 (print and electronic bundle) DOI 10.1007/978-3-642-15518-5 Springer Heidelberg New York Dordrecht London

This work is based on the 36th German language edition of Strasburger, Lehrbuch der Botanik, by Andreas Bresinsky, Christian Ko¨rner, Joachim Kadereit, Gunther Neuhaus, Uwe Sonnewald, published by Spektrum Akademischer Verlag, Heidelberg 2008.

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© Springer-Verlag Berlin Heidelberg 2013

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Springer is part of Springer ScienceþBusiness Media (www.springer.com) Preface

Eduard Strasburger { *February 1, 1844, – May 19, 1912, Founder of the Lehrbuch der Botanik fu¨r Hochschulen (Botany Textbook for Universities) (Photo by Dr. Wolfram Lobin/Uni Bonn)

The last English translation of Strasburger’s Lehrbuch der Botanik fu¨r 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 fu¨r 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 , Bonn, and Jena, receiving his doctorate in Jena before completing his postdoctoral degree (‘‘Habilitation’’) in Warsaw in 1867. He was appointed professor of botany at the in 1869, at the age of 25, and moved to Bonn University in 1881. 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 fu¨r Hochschulen, in the past often simply referred to as the Bonner Lehrbuch. The Kleine Botanische Praktikum fu¨r Anfa¨nger (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 must be the most important carrier of hereditary factors (1884).

The Authors April 2013

Table of Contents

Preface ...... v List of Topical Insights ...... ix List of Boxes ...... xi

Volume 1

Introduction ...... 1

Part I Structure ...... 11 Gunther Neuhaus

1 Molecular Basics: The Building Blocks of Cells ...... 13

2 The Structure and Ultrastructure of the Cell ...... 39

3 The Tissues of Vascular Plants ...... 129

4 Morphology and Anatomy of Vascular Plants ...... 161

Part II Physiology ...... 237 Uwe Sonnewald

5 Physiology of Metabolism ...... 239

6 Physiology of Development ...... 411

7 Physiology of Movement ...... 531

8 Allelophysiology ...... 569

Volume 2

Part III Evolution and Systematics ...... 607 Joachim W. Kadereit . Andreas Bresinsky

9 Evolution ...... 609

10 Systematics and Phylogeny ...... 665 viii Table of Contents

Part IV Ecology ...... 1041 Christian Ko¨rner

11 Basics of Plant Ecology ...... 1043

12 Plant–Environment Interactions ...... 1065

13 Ecology of Populations and Vegetation ...... 1167

14 Vegetation of the Earth ...... 1217

Timeline ...... 1263 Sources ...... 1267 Index ...... 1273 List of Topical Insights

Topical Insight 5.1: Galactolipids and Membrane Remodeling ...... 370 Christoph Benning

Topical Insight 5.2: Genetically Encoded Biosensors ...... 407 Wolf B. Frommer

Topical Insight 8.1: Host Targets of Bacterial Effectors ...... 598 Mary Beth Mudgett

Topical Insight 9.1: Homoploid Hybrid Speciation ...... 656 Loren Rieseberg

Topical Insight 10.1: Origin and Early Evolution of Flowers ...... 1014 Peter K. Endress . James A. Doyle

Topical Insight 12.1: What Plant Ecologists Can and Cannot Learn from a Satellite’s Eye ...... 1074 Hamlyn G. Jones

Topical Insight 12.2: A World Without Fire ...... 1082 William Bond

Topical Insight 12.3: The Dynamic Pipeline: Coordination of Xylem Safety and Efficiency ...... 1093 Frederick C. Meinzer

Topical Insight 12.4: From Where Do Plants Take Their Water? ...... 1096 Todd E. Dawson

Topical Insight 12.5: Leaf Nitrogen: A Key to Photosynthetic Performance ...... 1107 John R. Evans

Topical Insight 12.6: Plant Life in the P-Poor Part of the World ...... 1114 Hans Lambers

Topical Insight 12.7: Diversity of Traits: A Functional Link to Adaptation, Community Assembly, and Ecosystem Structure and Function ...... 1131 Peter B. Reich

Topical Insight 12.8: Using Stable 13C Isotopes to Study Carbon and Water Relations ...... 1137 Rolf Siegwolf

Topical Insight 13.1: Forest Structure and Gap Models ...... 1202 Hank H. Shugart

List of Boxes

Box 2.1: Cell Fractionation ...... 42 Box 2.2: The Nuclear Spindle ...... 71 Box 3.1: Residual Meristems and Meristemoids ...... 131 Box 4.1: Inflorescence Morphology ...... 183 Box 4.2: Types of Stele ...... 195 Box 4.3: The Leaves of Carnivorous Plants ...... 218 Box 4.4: Root Metamorphoses ...... 229 Box 5.1: Electrophysiology Methods ...... 272 Box 5.2: Important Units in Photobiology ...... 342 Box 6.1: Thale Cress: Arabidopsis thaliana (L.) ...... 418 Box 6.2: Conventions in Naming Genes, Proteins, and Phenotypes ...... 422 Box 6.3: Production of Transgenic Plants ...... 423 Box 6.4: Application of Transgenic Plants ...... 429 Box 6.5: Evolution of Plant Receptors ...... 528 Box 8.1: Cauliflower Mosaic Virus ...... 589 Box 8.2: Biology of Crown Gall Tumors ...... 593 Box 9.1: Recording and Analyzing Phenotypic and Genetic Variation ...... 628 Box 9.2: Population Genetics ...... 641 Box 10.1: The Origin of Life ...... 676 Box 10.2: Phylogeny of Plants and Fungi ...... 678 Box 10.3: From Unicellular Organisms to Multicellular Organisms ...... 695 Box 10.4: Occurence and Habit of Fungi (Including the Cellulose Fungi) ...... 748 Box 10.5: Uses of Algae ...... 775 Box 10.6: Occurence and Diversity of Habits in Algae ...... 779 Box 10.7: Occurence and Ecology of Mosses ...... 816 Box 10.8: Occurence and Ecology of Ferns and Fern Allies ...... 874 Box 10.9: Seed Plants (Spermatophytina) ...... 880 Box 10.10: Poales: The Evolution of Habitat Ecology and Pollination Biology ...... 949

Box 10.11: Chenopodiaceae: The Evolution of C4 Photosynthesis ...... 961 Box 10.12: Asterales: Evolution of Secondary Pollen Presentation ...... 1007 Box 10.13: Mass Extinctions ...... 1018 Box 11.1: Classification of Soils ...... 1061

Box 12.1: Effects of CO2 on Plant Growth ...... 1151 Box 13.1: Metapopulations: Consequences of Habitat Fragmentation for Survival of Species ..... 1173 Introduction

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

A. Bresinsky et al., Strasburger’s Plant Sciences, DOI 10.1007/978-3-642-15518-5, # Springer-Verlag Berlin Heidelberg 2013 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 (Â380)

a system. Below the complexity level of the cell there ● Motion. Every actively living organism and every indi- is no independent life. The cells always contain vidual cell shows signs of motion (motility). However, information-bearing structures, an array of various many cells/organisms are able to switch to a latent enzymes, and are separated from their environment phase, forming seeds, spores, or cysts. During these by a selectively permeable membrane. It is not contra- stages of life there are no obvious signs of motility and dictory to say that in most multicellular plants there almost all criteria for life are arrested. are plasmodesma (plasma canals in the cell walls) ● Stimulus perception and response. All organisms and between the tissue cells that are united into cells must be able to receive and respond to signals a supercellular symplast. from their environment. The diversity of mechanisms ● Nutrition. Organisms are rather ‘‘unlikely’’ construc- evolved to do this is incredible. tions in terms of energy and entropy. They are made ● Development. Organisms are incapable of retaining up of energy-rich, highly unstable molecules; their a particular structure indefinitely. No organism looks high structural and functional organization represents the same throughout all its life phases. A newly formed low entropy. The support of this labile condition is cell, arising from cell division, grows to the size of its only possible with the input of energy. Living systems mother cell (growth). Multicellular organisms usually are therefore basically open systems; i.e., they take up start their individual development from just a single energy-rich photons or materials and release energy- cell (fertilized egg cell, a zygote; spore). Then they

poor material (e.g., CO2,H2O). This metabolism is grow by cell division until they reach their final size, intrinsically linked with energy exchange. The metab- changing their shape in the process. Ontogeny, the olism results in a constant energy imbalance (dynamic development to a sexually mature multicellular organ- balance with irreversible subprocesses: so-called flux ism, is associated with morphological processes at the equilibrium). Metabolism and energy exchange allow cellular level that result in the differentiation of the the energy-demanding construction of (macro) initially similar embryonic cells. molecules (anabolism) by linking it to an energy- ● Reproduction. The succession of generations is made producing process such as the capture of solar energy up of successive life or reproductive cycles. Life is and/or the breaking up of energy-rich compounds perpetuated in this way, in spite of the inability of (catabolism). The low entropy capacity of the organ- individuals to permanently retain a particular devel- isms is sustained by the donation (dissipation)of opmental phase and despite the inescapable fact that excessive entropy into the surrounding environment. all individuals must eventually die. Death is the last By using a dissipative structure, the organisms avoid stage in an individual’s development. Unlike ‘‘cata- fatal chaotic events. Thus, life is not really a condition strophic death,’’ physiological death is often a result but is rather a continuous process. Whereas the outer of inner processes undergoing a program of self- form of organisms changes rather slowly, there is con- destruction. Conversely, organisms may only arise as tinuous turnover at the molecular level. progeny of conspecific ancestors. Abiogenesis, or Introduction 3

spontaneous generation, of a living system from inan- developmental plan for complex molecular machinery, imate material is, at least on today’s Earth, inconceiv- whose prime function is its own reproduction. Life is (at able and has never been proven: omne vivum e vivo least on today’s Earth) only conceivable and verifiable as (‘‘every life originates from another life’’). This rather a continuum. This knowledge is supported by the irre- obvious standpoint is relatively new. Until the ground- versibility of individual death and the extinction of breaking work of L. Pasteur and H. Hoffmann around species. There is nothing comparable in inanimate nature. 1860, it was assumed that microorganisms, even fungi and nematodes (worms) in fermenting and rotting liquids, had arisen spontaneously. Origin and Evolution of Life ● Replication. Reproduction is normally connected with replication. This ensures the perpetuation of The living organisms that exist today are the result of a species in spite of the loss of individuals as a result a long evolutionary process. On the basis of radioactivity of changing environments. The replication rates are and the composition of rock formations, the age of Earth often astounding in smaller organisms. Under optimal has been calculated as being about 4.6 billion years. The conditions, bacterial cells can divide every 20 min. study of the remains of organisms (fossils; paleontology) This means that with unrestricted replication of in various old sediments has shown that other sorts of a single cell, its progeny would form a cell mass the plants and animals lived on Earth during earlier geological volume of Earth in less than 2 days. Larger organisms epochs. The phylogenetic continuity can be seen in the tend to replicate more slowly, but the individuals are floras and faunas of past epochs of the living organisms: better protected by a variety of different mechanisms. the older they are the more different they are. Larger, ● Inheritance. Ontogeny happens in much the same multicellular organisms first appeared toward the end of way from generation to generation. The genetic infor- the Precambrian (about 570 million years ago). Until then mation is amplified and transmitted in the process. It single-celled organisms had dominated, and these were contains the program for the course of species-specific mostly prokaryotes. There is evidence that extensive ontogeny. The genetic information of all cellular colonies of cyanobacteria were already present in the organisms – prokaryotes and eukaryotes – is saved Archean (more than 3 billion years ago): the relevant (stored) in the bases and nucleotide sequences of sediments in Australia and South Africa contain layered deoxyribonucleic acid (DNA). These are linear or cir- stromatoliths over 30 cm in size. These are characteristic cular double-stranded macromolecules. Viruses can biogenic sediments, which are still formed today in warm store their genetic information in a single-stranded waters, and were built by dense layers of phototrophic DNA molecule and in ribonucleic acid (RNA; single cyanobacteria. stranded or double stranded). How could life have arisen? Answers to this funda- ● Evolution. Copying (replication) and transmission of mental question are sought by trying to recreate or simu- the genetic information happens with great precision. late the primeval conditions that would have existed on However, over many successive generations, changes Earth at that time. A condition for the formation of a can occur that may be inherited (mutations). These simple self-replicating system was the presence of organic changes can be induced by environmental factors. (macro) molecules. In contrast to today, the conditions on These can be partly a result of inherited switching on the still hot planet (Hadean eon) would have enabled (activation) and off (deactivation) of genes (epige- organic molecules to form abiogenically. The first atmo- netics). In the long term, quite big differences can sphere contained water vapor as well as carbon dioxide, develop in a population that can differently affect nitrogen, and smaller fractions of reducing gasses, but the reproductive ability of individuals. This natural practically no free oxygen; therefore, there was no ozone selection results in changes in the characteristics of layer that could have filtered the energy-rich UV radiation the members of a species and in the end can result from the sun. These conditions would have enabled vari- in the establishment of new species: evolution ous organic compounds to form. Abiogenic acetic acids and phylogeny. and energy-rich thioesters are even formed in watery mix- tures of carbon monoxide, sulfuric acid, and metal A superior criterion for life in all organisms is their sulfides, like those thrown out by deep-sea thermal vents. reproductive ability. All remaining characteristics are Certain places on primitive Earth would have become either critical to or a result of this central attribute. enriched in such compounds as long as life did not exist The genetic information of all organisms contains the to digest them and no oxidation destroyed them. 4 Introduction

Even the simplest cells, such as those of the (recently similar even between living, quite distantly related organ- arisen) saprobiotic mycoplasmas (see below), are very isms, are used in the reconstruction of early phylogeny. complex. Their origin from a chaotic mixture of molecular The comparison of these highly conserved sequences building blocks via a single chance event is highly improb- shows that the split between archaea and bacteria hap- able. However, a likely scenario is that this happened in pened more than 3 billion years ago. Modern eukaryotic a process of hypothetical intermediate steps (multistep cells have plastids and mitochondria, photosynthetic and theory): if the necessary individual steps in this prebiotic cell-respiration organelles, their own genetic code, and evolution were small enough, then the likelihood of them synthesize some of their proteins themselves. These organ- having really happened over a vast timescale is sufficiently elles can only self-replicate and thus have a semiautono- large. Some molecules which could have arisen mous position in eukaryotic cells. They also have abiogenetically show signs of enzymatic activity; i.e., they numerous prokaryotic properties, such as the mode of function as biocatalysts. Certain RNA molecules division, and details of their composition. Plastids seem (ribozymes) can catalyze changes in themselves and, to be descendants of once-free-living bacteria, which together with heavy metal ions, can even initiate their became integrated into the cells of primitive eukaryotes own propagation, albeit rather haphazardly (RNA as intracellular symbionts more than one billion years world). The decisive step toward independent life was ago and gradually developed into cell organelles made when protein catalysts made the effective and pre- (Endosymbiont theory). cise replication of nucleic acids possible and the key to the Remains of multicellular macroorganisms are first synthesis of these enzyme proteins was carried by the found in sediments that are less than a billion years old. nucleic acids. This double-step advance, which was prob- These organisms are, without exception, eukaryotes. ably a cumulative result of many small steps, formed a link Even their evolution, which can be increasingly better between proteins and nucleic acids that is absolutely fun- reconstructed with molecular systematic techniques, has damental for life in its current form. Thus, there was been a result of the interaction between chance mutations a genetic code that could translate nucleotide sequences and directional selection (Darwinism). This is based on from nucleic acids into protein sequences, and the sepa- the assumption that evolution is a result of the sum of ration of gene (hereditary factor) from phene (a character numerous small steps (gradualism). Even so, these have based on the hereditary information) was completed. been interspersed by major evolutionary transitions. The first systems capable of self-replication, the hypo- These do not differ from the small steps in terms of how thetical progenotes and the subsequently evolved pro- they arise, but differ rather in the gross effect of many karyotes, were able to live organotrophically as long as gradual evolutionary changes. They have been rarer events the abiotic formation of organic molecules continued. than the other gradual evolutionary transitions but have However, increasing exploitation of resources to the been more momentous. It seems that, repeatedly, repro- point where they became exhausted meant that ductive units that achieved independence at a certain phototrophic forms became more prominent. Among point in time have merged to form large, more complex these were some forms that were able to split water to units. Thus, completely novel systems have emerged that release oxygen during photosynthesis. This slowly created can form the basis of alternative, distinct lineages. an oxidative atmosphere, allowing a much more effective energy acquisition from organic molecules by cell respira- tion. At the same time, an ozone layer was formed in the Limits of Life stratosphere that absorbed the heavily mutagenic UV radiation from the sun and enabled the colonization of The question for the limits of life has two components. the ocean surfaces and the land. Fossil evidence from the First, one can ask for the distributional limits of life, and long Precambrian evolution is, not surprisingly, rather second for both lower and upper size limits of individuals. rare and incomplete. However, sequence comparisons The first aspect – an ecological component – is that, from proteins and nucleic acids of related living organisms despite a phenomenal range of adaptive strategies, general can be used to reconstruct phylogeny. The more differen- conditions for life have quite narrow limits. They are tiated the sequences, the earlier the last common ancestor determined by maxima and minima of water content, of the organisms must have lived. Evolutionary changes temperature, and light. The optimum for most organisms have occurred at different rates in different parts of the is median temperatures (10–40C) and high water (partial) sequences. Therefore, only sequences (or partial content. For this reason, it is possible to store food at sequences) that change very slowly over time and are fairly cool temperatures (fridge, freezer) or by drying Introduction 5

(legumes, cereals, flour, bread, hay) or by pasteurization of a single protein or only a few different proteins. This (milk). In nature, the dry and cold regions are particularly sort of capsid often has a crystalline symmetry. poorly colonized. Many organisms can survive tempera- Viruses or (bacterio)phages (viruses that attack pro- tures down to the freezing point of water by having latent karyotic cells) only partially fulfill the conditions neces- or dormant phases, but still die between 0C and À10C. sary for life. They have no metabolism or energy exchange, Psychrophilic organisms (e.g., some snow algae) have no ability to replicate or synthesize proteins, and no ability optimal growth temperatures between 1 and 2C. Tem- to reproduce independently. They can only reproduce by peratures over 100C, which are rarely found on Earth’s using the metabolism and energy exchange of a living cell surface (hot springs, volcanoes), can support thermo- – they are obligate parasites (‘‘borrowed life’’). The dis- philic organisms. Some archaea have temperature optima persal forms – virions – that exist outside living cells around 100C, possibly an adaptive relict from primeval represent lifeless organic systems. Earth. As phototrophic organisms are mainly responsible The simplest organizational level is achieved by the for the production of organic material (biomass), life is viroids. These are infectious nucleic acids (RNA) with no more-or-less restricted to the well-illuminated regions of associated proteins. The short, ring-shaped RNA mole- Earth’s surface and oceans. Earth is coated with cules do not code for any proteins. Some of the most a comparatively thin biosphere that accounts for less dangerous plant parasites known are viroids. than 0.01% of its volume. In spite of their particularly simple organization, neither The largest life forms (both fossil and living) are found viruses nor viroids can be considered to be the most prim- among the vertebrates (dinosaurs, baleen whales) but also itive forms of life, as their reproduction depends on the larger and in greater numbers among the conifers and existence of living cells. Rather, they are genetic elements deciduous trees as well as among clonal organisms such that became independent of their support cells (vagabond as poplar (Populus), reed grass (Phragmites), bracken genes). In fact, there are segments of genetic information in (Pteridium), and fungi. The giants among the trees most (if not all?) eukaryotic cells and prokaryotic cells that (Sequoia, Cryptomeria, some Eucalyptus) are also the are inherited independently of the gene-carrying structures heaviest life forms. (chromosomes, genophores), or at least that are able to A more significant question for theoretical biology is temporarily disassociate themselves from the structures. ‘‘how small can a life form be?’’ ‘‘What is the lower limit of This heterogeneous group includes the plasmids of many complexity for self-replicating biosystems?’’ The smallest bacteria and some eukaryotes, as well as the so-called inser- cells are prokaryotic. They are found in mycoplasmas. The tion sequences and transposons (jumping genes). 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 Biology as a Natural Science possible for DNA replication, the realization of the genetic information stored therein, the support of a heterotrophic Living nature is impressive because it supports a huge metabolism and energy exchange, and a simple cell struc- diversity of life forms. Recording, describing, and system- ture (theoretically about 350 genes). In comparison, the atically organizing all living and extinct organism types cells of a typical bacterium have a diameter of 2 mm and (species) is the enormous, as yet unfinished, task of biol- contain over 3,000 different proteins; the diameter of most ogy, in particular, systematics. But biology is not just eukaryotic cells lies between 10 and 100 mm, and the cells restricted to the description of what is there, even more, can form over 30,000 different proteins. The complete it strives to explain this diversity. Besides observation and sequenced genome of the model plant Arabidopsis thaliana comparison, there is the experiment. An experiment is the has about 25,000 genes, 11,000 more than the fruit fly observation of a process under artificial predetermined or Drosophila. controlled varied conditions. Data from experiments and Viruses are much more simply organized and most of observations provide the raw material for constructing them are even smaller. A virion (a viral particle) is not hypotheses and theories, contributing toward the expla- a cell. Whereas, e.g., the simplest cell has both DNA nation of causal relationships. (H. Poincare´: ‘‘A heap of (information storage) and RNA (information retrieval), facts is as much a science as a heap of stones make a virion has neither DNA nor RNA. The nucleic acid is a house.’’). By forming a repeatedly questioned theoretical often only associated with molecules of a single protein construct (see below), the discovery of correlating laws and type such as in the tobacco mosaic virus (> Fig. 2), or it their final formulation into natural laws can incorporate may be surrounded by a protein sheath (capsid) made up lots of observations into short, clear units that can then be 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 pene- offer. The fragmentary character (nature) of the scientific trate the real world with all its basically nonrecordable world view is affected not just by the selection (even if structures and experiences without this type of abstrac- subconscious) and use of limits of scientific endeavor, but tion. Thus, the natural sciences have become enormously also by the limits of methodology and primarily by the significant in recent times, especially modern biology limitations imposed by the type of research. These are (keywords ‘‘biotechnology,’’ ‘‘gene technology’’). indirect in fundamental research as the aims and results The sum of recognized natural laws and their inter- are initially unknown. Indirect aims are researched in that pretation forms the scientific world view, a simplified testable hypotheses are postulated (Greek hypo´thesis,to reflection of nature presented in perceptions, symbols, suppose). A hypothesis, a scientific concept, can never and ideas. This world view is the highest expression of be proven because the data will never be enough. However, our understating of nature. It enables mental operations a general theorem can be rejected on the basis of one (thought experiments) that would be too dangerous or contradictory event (asymmetry of verification and falsi- expensive to conduct in the real world. The scientific fication; see K.R. Popper). The assumption ‘‘all roses are world view is thus fundamentally dynamic, as novel infor- red’’ cannot be proven even with 1,000 red roses, but mation is acquired by research, and new interpretations can be rejected on the observation of a single yellow or can be expanded and altered. It is perforce preliminary white rose. and fragmentary and cannot (should not) ever be seen as Correlations are based on laws of relationships being complete. Even so, it is the best that humankind can derived from observed events (e.g., cigarette smoking/lung Introduction 7 cancer; but also the frequency of storks and human birth form ideas about real life or nature remained a mystery for rates in some regions). Correlations can mean there is a long time. (A. Einstein: ‘‘The incomprehensibility of the a causal relationship, but this does not have to be the world lies in its comprehensibility.’’). 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 Special Position of Biology correlated but not causally, only coincidentally. Although the lack of a correlation implies the lack of a causal rela- The uniqueness of life in nature gives biology a special tionship, a correlation is not evidence for one; therefore, it position among the sciences. Time and again it has been cannot be used for the verification of an assumption. questioned whether living systems and systems of abiotic The asymmetry of verification and falsification means nature adhere to different laws, and special life forces that forward steps in knowledge are achieved indirectly, (vitalism) have often been postulated. However, to date not directly, as inappropriate or inapplicable hypotheses there is no known case where physical and chemical laws are rejected (method of trial and error). The aim, the have been disobeyed by living organisms. On the other appropriate knowledge and explanatory reasons, can hand, organisms are incredibly complex systems, which only be achieved through disappointment and via detours means that biological systems obey laws that would oth- (Greek methodos means not only thorough research but erwise not be observed. One speaks of emerging attri- also detour). butes. An important consequence of living systems is that With every failed falsification attempt, the probability biological materials cannot be logically or mathematically of finding the right hypothesis increases. When the hypoth- penetrated in the same way as objects in physics and esis can be applied to other areas independently of the chemistry. Biology is an exact science based on the recog- original research, it becomes more plausible. Comprehen- nition of natural laws, but observation, description, and sive hypotheses that, despite many attempts, remain comparison play a much greater role than in physics. nonfalsifiable become theories. Theories are elements in However, a complete derivation of all biological phenom- the scientific world view. A theory, e.g., the central biolog- ena from chemical and physical laws, in the sense of ical theory of descendancy or evolution, allows many events a consistent reductionism, would be illusory. to be explained and enables the formulation of numerous The definition of life as a self-replicating system is testable postulates. From a theoretical scientific viewpoint, further supported by a fact that emphasizes the unique- a theory presents a disciplinary matrix or paradigm that ness of the organism – biological teleonomy. Life forms provides the intellectual framework for further experi- behave purposefully, they react expediently, and appear to mental work in an area of interest. Surprisingly, even be constructed sensibly. Besides the question ‘‘why?’’ though specific observations and appropriate experiments (causality), biology (and only biology among the sci- are made on the basis of hypotheses and theories, most ences) also justifiably asks ‘‘what for?’’ (finality). This research is not inductive (based on experience and under- touches on the cyclical development of life; compare the standing) but deductive. It is not primarily targeted at terms ‘‘developmental cycle,’’ ‘‘reproductive cycle,’’ and discovering the unknown or novel, but serves to check ‘‘generation cycle.’’ From any given starting point, these and refine an existing paradigm. Of course, existing cycles proceed along genetically predetermined develop- ‘‘tested’’ theories can be falsified. Then a new more com- mental lines until they return to a comparable starting prehensive theory has to be developed. These scientific point (e.g., egg cells, spores). This results in semicyclical revolutions (see L. Fleck; T.S. Kuhn) are only successful if events and chains of cause and effect. For example, they can also explain why the previous theory appeared to a particular developmental stage B can arise not only as explain so much. Often it becomes apparent that the older a result of the previous stage A but also via the subsequent theory does in fact still hold true within certain limits. The stages C, D, etc., also as a cause for the renewed occurrence history of scientific biology has many examples of such of stage A (even if it is chronologically out of sequence). scientific revolutions, such as in the developments of cell The final viewpoint bears as much weight as the causal biology and genetics. approach in biology. In inanimate nature, cyclical systems The teachings of the potential and limits of human (e.g., oscillations) do not have mechanisms whereby losses knowledge (as outlined above) form part of epistemology, are compensated for by energy gains, and they finally stop which is an important tenet in theoretical science as well as altogether. Life forms, on the other hand, can replicate by in philosophy (see, e.g., I. Kant). Even so, the potential to reproduction. Even in the research of evolution and the use knowledge from independent logic or mathematics to origins of life, biology finds itself in an unusual position. 8 Introduction

While the highest priority is typically the search for natu- Radially symmetrical forms (in the strictest sense) only ral laws – reflected in the regular repetition of structures or occur in sessile or aquatic species. The specialization of processes – in fact here it is the singular, chance event that tissues and organs is highly advanced. Even meristems are is decisive. This is related to the reproduction and selec- specifically determined for the formation of particular tion of organisms. Natural mutations are chance events cells (stem cells of blood and immune systems, the skin, and not predictable. Such mutations can remain neutral the intestinal epithelium, etc.). The lifetime of even large for a very long time until such time as the conditions animals is limited. Regenerative potential is often quite suddenly change, making the mutations have negative or low in highly developed animals. Some highly differenti- positive effects on the organism. If the mutation has ated cells remain active throughout the animals’ lifetime a favorable effect on the bearer, then according to evolu- and are normally not regenerated in the adult phase (large tion by natural selection in successive generations, the neurons, striated muscle fibers, cells of the optical lens). mutation will become fixed. Life forms are, in this respect, A typical plant is usually ‘‘rooted’’ in one place for the very effective enhancers: all their observable inheritable whole of its lifetime. The pollen, seeds, or spores of the traits are derived from improbable and thus rare chance plant have, theoretically, limitless distribution possibili- events (singularities) whose effects are retrospectively ties. The body area is maximized by unfolding and enhanced by reproductive processes. 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 Animals and Plants all shoot tips, annual rings in the wood, etc.). Metabolic waste products have to be removed by each cell individu- Since the historically based (rather than factually based) ally; instead of centralization there is localized cellular tendency to specialize has been superseded, modern biol- excretion. The body is mostly radially symmetrical. ogy is dominated by interdisciplinary cooperation. There is an enormous regenerative potential; each shoot Knowledge drawn from genetics, biophysics, and bio- apex can, in principle, grow a complete new plant. This chemistry as well as physiology contributes to a broad aspect is used extensively in horticulture and agriculture foundation for general biology. Even evolutionary and for the vegetative propagation of plants by grafts, cuttings, developmental biology, as well as molecular and cell biol- scions, bulbs, bulbils, etc. Furthermore, novel shoot apices ogy, have grown beyond the boundaries of the classical may arise in injury-related callus growths (tissues gener- disciplines of botany and zoology. However, this connec- ated by chaotic cell proliferation). Thus, cell cultures (even tivity should not be allowed to disguise the fact that the from single vegetative cells) can be used to successfully typical animal and typical plant (both terms used in the generate whole plants, something that is not possible from colloquial sense) have numerous differences. animal cells or tissues. It is not unusual to find plants that The typical animal is able to migrate. Its body is live to 100 or even 1,000 years of age. Clones are immortal. compactly constructed, with all organs except those Thus, e.g., all apples of the same variety are perpetuated, required to interpret environmental signals being posi- by grafts, from the same genetic clone as from the apple (of tioned inside. In order to see them, the animal’s body that sort) that was first discovered, regardless of where it is has to be opened (‘‘anatomy’’ is derived from the Greek now cultivated. word meaning ‘‘to separate and cut up’’). The large surface Plants and animals also differ significantly in the struc- areas necessary for breathing, nutrient resorption, and ture and function of their cells. A general comparison excretion are folded inside the body cavity. The outer shows that plants cells are not only distinct as a result of surface area is reduced, and so the animal is a ‘‘closed’’ possessing plastids. They are not only phototrophic but organism. The compact body structure enables the devel- are also osmotrophic (only able to take up substances that opment of central organs for circulation and excretion. are dissolved), whereas animal cells are phagotrophic (able Even the nervous system, which enables rapid coordina- to take up nutrients in particulate form). Flagellates tion, shows a tendency to become centralized over include mixotrophic species that are able to take up nutri- evolutionary time. Most organs are formed in a limited ents in both ways (> Fig. 3). The plant cell has, in its fully number and are at least rudimentarily present in the grown state, a central vacuole that makes up over 90% of embryo, growing proportionately with the growing the cell volume, and a . The cell wall absorbs the organism. Body symmetry is predominantly bilateral and hydrostatic pressure of the vacuole (turgor) that would dorsiventral, as expected when the two perpendicularly otherwise cause the cell to burst. Turgor is a consequence oriented vectors of gravity and motility are present. of osmosis; the molar total concentration of the cell sap in Introduction 9

. Fig. 3 Poterioochromonas malhamensis, a mixotrophic flagellate from the order Chrysomonadales (see also Fig. 10.83) with two unequal anterior flagella and lobopodium (L) as well as a posterior anchorage appendage (Â1,160). 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 understanding of the origin, diversity, and connectivity the cell walls. Animal tissue cells have neither large vacu- between form and function. This places the research object oles nor tough cell walls that have a stabilizing function for to the fore. Applied research is more concerned with the individual cells. Their turgor is low because they are the use of plants, fungi, and microorganisms in human surrounded by isotonic body and tissue fluids. The mass of and animal nutrition; for medicinal, toxic, and drug- intercellular substances of the connective and supporting producing plants – the foundations of pharmacology; tissues of animals fixes not cells but supercellular struc- plant breeding, genetic manipulation, and biotechnology; tures. During plant and fungal cell division, the first wall for use in agriculture and forestry; for phytopathology, primordium arises between the daughter cells via internal pest and weed control; and for landscaping, nature and secretion of wall substances. In contrast, typical animal cell animal conservation, and ecology (as defined by the mod- division occurs by pinching off daughter cells from the ern media). Basic research provides the essential back- mother cell (cleavage), and, whereas the cells of the plant ground knowledge for every type of applied research. body are almost without exception anchored to their point In this handbook, the description of the general struc- of origin, the cells of animals may migrate and be tural basics is in Part I. This treats the areas from atomic translocated during development. up to macroscopic dimensions: the overview of molecular Fungal cells are – apart from not having plastids and basics is followed by a discussion of the structure and fine not exhibiting phototropism – more similar to typical structure of the cell (cytology), followed by discussion of plant cells than animal cells. They are vacuolated, plant tissues (histology) and then the outer structure as osmotrophic cells with stable, nonrupturing cell walls seen with the naked eye (morphology). that generally do not cleave but divide by novel cell wall The structures are presented in Part II according to the formation (laid down by internal secretions). 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 physiol- Classification and Significance of ogy. The discussion of the physiology of metabolism is Plant Sciences followed by discussion of developmental physiology and then physiology of movement. An especially current topic The investigation of the plant, fungal, and protist world – is allelophysiology – the diversity of physiological rela- in fact just like for the whole world of organisms – can be tionships that plants have with other organisms. considered from many different viewpoints. For example, The division of this handbook into parts and chapters research areas could reflect the hierarchy of structures to should not obscure the fact that modern biology is distin- be investigated (> Table 1). Basic research aims to gain guished by its interdisciplinary approach. Areas that were 10 Introduction

. Table 1 natural laws, and causes for the distribution and gregari- Biological fields of research and the complexity of the ousness of plants in space and time. objects studied Plant ecology highlights the significance of plant sci- ences, especially in the modern world. In terms of energy, Structure Fields of research all life on Earth is dependent on phototrophic organisms, Atoms Biophysics in particular, plants: they are the only relevant (in terms of Molecules Biochemistry sheer numbers) producers and are found at the start of Semantic Molecular biology almost all food chains and at the base of all food pyramids. macromolecules This has been true for at least a billion years. Thanks to Genes, chromosomes Genetics their enormous biodiversity, plants support the structure Cells Cell biology and functioning of highly diverse ecosystems under a huge range of conditions, from the Polar Regions to the Tropics. Tissues Histology This diversity and the function of individuals in the Organs Anatomy, physiology biosphere are severely threatened by the no longer negli- Organisms Morphology, developmental gible influence of approximately seven billion people. physiology, systematics, phylogeny, Unsustainable land use and atmospheric changes mean autecology the threat to the biosphere has reached global proportions Populations Reproductive biology, evolutionary (global change). Even humans belong to those organisms biology whose existence as individuals and species entirely Communities Geobotany, community ecology depends on a stable environment. In these circumstances, Ecosystems Biogeochemistry, ecosystem a climate protection scheme based on scientific principles biology is more important than ever. Plant science plays an important role in the develop- ment of biological sciences. Many fundamental biological once separated have grown together and have given rise to principles have been developed on the basis of plant stud- new, especially productive fields of research. This is what ies. These include the discovery of the cell and cell nucleus, happened when, e.g., descriptive cell research (cytology), chromosomes, mitosis, meiosis, osmosis, and laws of biochemistry, and molecular biology came together and genetic inheritance. Even though the solutions to many formed modern cell biology. problems in modern biology have been found using Part III firstly outlines evolution research and deals microorganisms and certain animals with particularly with the natural laws and causes governing speciation and appropriate systems, and many medically relevant ques- its genetic background. Secondly, it is largely taken up tions regarding cancer, immune systems, thought, and with botanical systematics. The study of relationships is consciousness can only be answered using (higher) ani- based on the results of many other disciplines, and sys- mals, botany nevertheless remains a key area of basic tematics describes, names, and classifies more than biological research. This is evidenced by the enormous 500,000 known plant species. The classification is based advances made in modern plant sciences (see the model on the reconstructed phylogeny of the plant kingdom. plant Arabidopsis thaliana). As before, the applied plant Evidence from nucleic acids and proteins (molecular phy- sciences are also immensely important. Plants and fungi logeny) and from plant fossils (paleobotany) plays a domi- play a central role next to bacteria in biotechnology.Itis nant role. The chapter on systematics contains information therefore not surprising that ‘‘green gene technology,’’ the from many different specialized areas that intensively deal application of gene technology in agriculture, has rapidly with individual organismal groups (microbiology, bacteri- become increasingly significant. As everywhere in modern ology, mycology, etc.) as well as applied disciplines that biology, the deciphering of genomes (genomics) is being study the practical uses of plants for humans. continually updated as different protein complements Plant ecology deals with the relationships that plants are discovered (proteonomics) and the metabolites of and plant communities have with their biotic and abiotic different cells in the same organism are analyzed environment. Ecological botany aims to understand facts, (metabolonomics).