BOTANY VOLUME 3 - EVOLUTION AND SYSTEMATICS - 2007

11. SYSTEMATICS AND PHYLOGENY

11.2. Bacteria, Fungi, Plants

Originally, The concepts of "animals" and "plants" referred to the two primary systematic groups (taxa) of living organisms (regnum vegetabile and regnum animale, respectively). Today, we know that we are dealing here with grades of Organization that differ in their nutritional physiology, rather than natural groups united by common ancestry. Furthermore, the "plant kingdom" does not even represent a distinct evolutionary Lineage and, consequently, is not a taxon in any strict sense. Plants can be defined as photoautotrophic organisms. Accordingly, botany is the biology of photoautotrophs. Within The Scope of botany, all photoautotrophic organisms are considered, along with those heterotrophic groups that either evolved from autotrophs or are crucial for understanding autotrophic phylogeny.

In the broadest sense, therefore, both Fungi (lichen Symbiosis!) and prokaryotes (endosymbiont hypothesis!) fall within the domain of botany and, by extension, this textbook. Fungi share certain convergent general features with typical plants (see below).

Ultrastructural studies of cellular architecture have revealed two fundamentally distinct organizational plans among living organisms that are currently not connected by transitional forms: protocytes and eucocytes. Relatively recently, these two cellular blueprints served as the basis for dividing all living things into two primary groups (kingdoms): Procaryota (prokaryotes) and Eucaryota (eukaryotes). Recent molecular biology research points to a very early divergence into three major lineages: Archaea, Bacteria, and Eucarya, with Archaea on the Phylogenetic Tree (Fig. 11.9) appearing closer to Eucarya than to Bacteria. However, based on cellular Structure, Archaea and Bacteria are grouped together as prokaryotes in contrast to Eucarya (eukaryotes). All three primary groups (Bacteria, Archaea, Eucarya) are treated here at the rank of kingdoms. To avoid confusion with the traditional concept of "kingdom" (such as the "plant kingdom" contrasted with the "animal kingdom"), the category of "domain" is increasingly used in phylogenetic Classification (e.g., domain Bacteria, etc.).

In the system presented below, we will examine Archaea and Bacteria, and among Eucarya, all autotrophic PLANTS AND THEIR secondarily heterotrophic descendants (plants in the narrow sense), as well as heterotrophic fungi (in the broad sense). Typically, these are sessile organisms with rigid Cell walls that can absorb nutrients only in dissolved (or gaseous) forms. Consequently, this excludes unicellular and Multicellular animals (Archaeozóa, Protozoa, and Metazoa = Zoobionta). It should be noted that delimiting plants, fungi, and animals among lower eukaryotes (= Protobionta, e.g., slime Molds and euglenids, Fig. 11.9) involves considerable difficulties.

Class="center">Fig. 11.9. Phylogenetic tree of plants and fungi: arrows indicate the origins of endosymbioses and, As a result, The Emergence of Mitochondria and Plastids. Arrows pointing to Lichens (Lichenes) show the establishment of ectosymbiosis with cyanobacteria and Chlorophyta: 1 — origin; 2 — acquisition of mitochondria via endosymbiosis; 3 — cyanobacteria as primary endosymbionts, acquisition of "primary plastids"; 4 — red Algae as secondary symbionts, acquisition of "secondary plastids"; 5 — green algae as secondary symbionts, acquisition of "secondary plastids"; 6 — photoautotrophy via ectosymbiosis

Within the kingdoms (régna, domains) discussed here, broad yet unequivocally monophyletic taxa (derived from a single ancestral group) are treated at the rank of subkingdoms (subrégna, subdomains) and phyla. Their names end in -bionta for subkingdoms, -phyta for autotrophic eukaryote phyla, and -mycota for fungi.

The interrelationships and presumed affinities of most groups described in this book are summarized in brief overviews provided at the end of each respective section. An overall scheme of the classification adopted by the authors can be seen in the Table of Contents and in Fig. 11.9.

Older names for major groups (such as algae, fungi, seed plants) are largely inadequate for designating monophyletic evolutionary lineages in the light of modern phylogenetic research. At best, such terms correspond to Levels of organization. Nevertheless, for a structural plan (grade of organization) or a developmental stage (level of organization) characteristic of large groups, these concepts retain a certain utility for denoting specific assemblages and for easily comprehending morphological diversity. Therefore, these earlier designations for grades of organization are explained in dedicated text boxes in this book (11.1 – 11.3; 11.5; 11.8 – 11.10), even though they no longer form The basis of systematic subdivision.

Organisms are assigned to the same grade of organization (regardless of rank) if they share largely identical external (i.e., morphological) or internal (i.e., anatomical and cytological) organizational traits. Grades of organization frequently correspond to levels of evolutionary advancement and, as such, reflect recurrent adaptations to specific living conditions or general progressive evolutionary development.

Thus, grades of organization encompass groups that are clearly heterogeneous. On the other hand, they frequently separate related groups that, from an evolutionary and systematic perspective, should be placed close to one another.

The METABOLISM/13.html">History of the classification of the "plant kingdom" is marked by shifts in its underlying fundamental principles. The best-known artificial system is that proposed by C. Linnaeus (1735) based on reproductive structures. He contrasted 23 classes of flowering plants with a 24th class, Cryptogamia ("hidden marriage"), which included not only the then-little-understood ferns, mosses, algae, and fungi, but also certain higher plants with inconspicuous flowers (Ficus, Lemna) and even corals and Sponges. Linnaeus distinguished subdivisions (taxa) of flowering plants (Phanerogamia, "visible marriage") primarily by the distribution of sexes within the flowers and by the number, fusion, arrangement, and relative lengths of the stamens. Today, cryptogams can be referred to as spore plants, since their DEVELOPMENT OF NEW individuals typically originates from unicellular diaspores (such as spores), whereas phanerogams are better termed flowering or, more accurately, seed plants.

Linnaeus already attempted to construct a natural system of plants, but only A. L. de Jussieu (1789), A. P. de Candolle (1819), St. Endlicher (1836), and others can be regarded as the creators of the major formal systems. Even after the advent of evolutionary theory, the systems of A. Braun (1864), G. Bentham and J. D. Hooker (1862 – 1883), A. W. Eichler (1883), and especially A. Engler's system—which remains widely used today—continued to rely on levels of organization and evolutionary grades for delimiting taxa.

The first attempt at a phylogenetic system was made by R. von Wettstein (1901 – 1908). Modern, universally accepted systems represent various transitional stages on the path from formal to phylogenetic and synthetic classifications.

Even a cursory examination of the diverse, mutually competing classification systems reveals numerous and often profound differences, which demonstrates the extent to which systematics is still a developing science. However, in recent years, comparisons and cladistic analyses of sequence data from various homologous DNA regions of chloroplast, mitochondrial, and nuclear genomes have led to a major breakthrough in clarifying the evolutionary relationships among all groups of organisms.

Consequently, we can hope to achieve a universally accepted and satisfactory natural classification in the foreseeable future.

Similarly, the system presented here represents an attempt to outline the broad evolutionary affinities among major groups. However, given the pedagogical nature of this book, certain simplifications have been made in our descriptions.

To date, approximately 500,000 living plant species are known. Of these, more than two-thirds belong to seed plants (about 700 gymnosperms and 240,000 angiosperms), roughly 10,000 to pteridophytes, and 24,000 to bryophytes. Among Protobionta, the number of described algae is estimated at roughly 23,000, fungi at about 100,000, and lichens at approximately 20,000. Finally, one must account for another 3,000 species of bacteria and 2,000 of blue-green algae. New species are continually being described (especially among fungi and angiosperms!), so it is quite likely that the cataloging of the plant kingdom—far from being complete—will ultimately reveal a species count well exceeding half a million!

I. Kingdom (Domain): Bacteria

The kingdom Bacteria (bacteria, cyanobacteria, prochlorophytes) comprises prokaryotic organisms (Box 11.1) characterized by a unique Cell wall chemistry (murein sacculus).

The two phyla discussed below—Posibacteriota and Negibacteriota—constitute the bacteria in the narrow sense, also referred to as eubacteria (Eubacteria; as opposed to cyanobacteria, etc.).

Eubacteria (see Fig. 2.93) are prokaryotes whose overwhelming majority of species are heterotrophic (see 9.1); furthermore, they are minute (see Fig. 1.1) and morphologically poorly differentiated. The various cell shapes found in bacteria can be derived from a basic spherical form, as well as from straight or curved cylinders (see Fig. 11.10).

There are spherical cocci, which can aggregate into simple colony-like groups; rod-shaped forms whose spore-bearing variants are called bacilli; and shapes ranging from curved (vibrios) to helically twisted rods (spirilla).

In some bacteria, Cells remain interconnected after division, forming cell clusters, packets (sarcinae, Fig. 11.10, F), filaments (Fig. 11.10, H), or networks. Thus, even among bacteria, one can observe a trend toward The Development of more complex structures. However, true division of labor among such multicellular forms is rarely implemented (cf. Chlorochromatium).

Filaments consisting of multiple cells can be simple or branched; some are embedded in mucous sheaths or bear flagella. The branched, multicellular filaments of actinomycetes represent a striking convergence with the mycelium of eukaryotic fungi (Fig. 11.10, K). Myxobacteria are flexible prokaryotes that glide across substrate surfaces. Similarly to certain eukaryotic slime molds, individual cells of some of these forms aggregate to form fruiting bodies up to 1 mm in size (Fig. 11.10, L – N).

Box 11.1. Types of prokaryotic organization

Prokaryotic Cells (protocytes) lack a true, membrane-bounded nucleus (hence their former name, Anucleobionta, i.e., enucleate organisms), yet they possess one to several nuclear equivalents—the nucleoid(s). DNA lies freely as a genophore within the so-called nucleoplasm. Mitosis and Meiosis are absent. The compartmentalization of The Cell into distinct reaction spaces is less pronounced than in eukaryotes: Chloroplasts and mitochondria are lacking. Some prokaryotes possess locomotor Organelles, but their structure differs significantly from that of analogous eukaryotic organelles. The Introduction/4.html">Prokaryotic Cell wall consists of heteropolymeric substances that

have not yet been identified in any eukaryotic organisms. The cell wall is a giant, sac-like polysaccharide molecule of varied chemical composition, cross-linked into a reticulate structure via primary valence bonds (see 2.3.3).

While eukaryotes are strictly dependent on oxygen for their survival, the relationship with this substance varies greatly among prokaryotes. They exhibit a spectrum ranging from complete oxygen intolerance to an obligate requirement for it. The widespread ability to fix atmospheric nitrogen is found exclusively among prokaryotes.

Prokaryotes include bacteria, cyanobacteria, prochlorophytes, and archaea.

Fig. 11.10. Bacteria. Bacterial morphologies: A — Staphylococcus; B — Lactobacillus; C — Bdellovibrio; D — Spirillum; E — Caulobacter (4,000x); F — Sarcina; G — J — Sphaerotilus; G — motile stage (700x), H — Sphaerotilus form (330x), J — onset of Cell Division (800x); K — Streptomyces; L — N — Chondromyces: L — rods (200x), M, N — fruiting bodies (30x)

Morphological differentiation points to an evolution toward more complex structures. Although they by no means attain the complexity characteristic of eukaryotes, one already encounters eukaryotic-like forms that evolved as adaptations to specific living conditions (colonies, filaments, branched filaments, mycelia, fruiting bodies, spores, flagella). Nevertheless, reductive trends leading down to virus-like dimensions also occur.

Nucleoid and Plasmids. Bacterial DNA is not distributed diffusely throughout the Cytoplasm, but is localized in a specific region of the cell—the nucleoplasm. The nucleoid is a tangle of fine filaments bordering directly on the cytoplasm; a nuclear envelope is lacking. Due to genophore Replication outpacing cell division, bacterial cells frequently contain 2 to 4 nucleoids. In Escherichia coli, the genophore consists of a single closed circular DNA molecule 1.4 mm in length. Bacterial genophore division is apparently preceded by its attachment to The cell membrane (with no mitosis or meiosis involved!). In addition to the main genophore, bacterial cells harbor smaller, autonomously replicating DNA rings known as plasmids.

In view of numerous distinctive features in bacteria—unlike eukaryotes—one should by no means speak of "cell nuclei" and "Chromosomes," as is unfortunately still frequently done. Conversely, bacterial DNA largely corresponds in Structure and function to the DNA of all other organisms (see 1.2). During rapid replication, The rate of de novo DNA Synthesis reaches 33 µm (chain length) per minute. Bacteria are the organisms from which the most fundamental insights of Molecular Genetics have been derived. Genetic maps have already been established for E. coli, Salmonella typhimurium, and other bacteria.

Fig. 11.11. Bacteria. Flagellar arrangement in bacteria: A — Monotrichous (Vibrio metchnikovii, 7,000x); B — portion of a flagellum (Bordetella bronchiseptica, 60,000x); C — basal granule at the flagellar attachment site (Rhizobium radicicola, 20,000x); D — lophotrichous (Spirillum undula, 8,000x); E — peritrichous (Proteus vulgaris, cell contents partially autolyzed, 10,000x)

The cytoplasm is separated from the cell wall by a multilayered cytoplasmic membrane (Plasmalemma), much like in all other organisms. The cytoplasm contains the nucleoid (occasionally multiple ones), various membrane systems, and cellular inclusions. Bacterial Ribosomes, measuring 16 × 18 nm, consist of approximately 60% RNA and 40% protein. They occur in the cell in numbers ranging from about 5,000 to 50,000. These ribosomes sediment in an ultracentrifuge at 70S (where S stands for the Svedberg unit, a coefficient used to determine molecular mass). In contrast, eukaryotes possess 80S ribosomes in their cytoplasm, and 70S ribosomes in their Mitochondria and chloroplasts. The intracellular membranes of bacteria form a reticular network (insofar as this has been investigated).

Mesosomes arise from invaginations of the cytoplasmic membrane; they have been described specifically as mesosomes and tubular bodies. In phototrophic bacteria, photosynthetically active vesicles analogous to the thylakoids of green plant chloroplasts have also been observed (Fig. 11.12); in some species, they are even stacked in a similar manner. Thylakoid membranes harbor light-absorbing pigments (bacteriochlorophylls and carotenoids) as well as components of The electron transport and Photophosphorylation systems during Photosynthesis. However, bacterial thylakoids are never enclosed by a common envelope; thus, we are not dealing here with true plastids. Gas vacuoles are also found in some bacteria (e.g., Chromatiaceae).

Fig. 11.12. Bacteria. Photoautotrophic bacterium Rhodopseudomonas with thylakoids: CM — cytoplasmic membrane; Po — polyphosphate body; W — cell wall

Cell wall components. Substances deposited within the cell are partly reserve Materials. Many bacteria store Glycogen-type Polysaccharides. Lipophilic granules consist of poly-β-hydroxybutyric acid. Mycobacterium and Actinomyces accumulate predominantly Neutral Fats and Waxes. Phosphoric acid is stored in the form of polyphosphate granules ("volutin") (see Fig. 2.93).

The Bacterial cell wall (see Fig. 2.98) is approximately 20 nm thick. It lacks the fibrillar structure characteristic of the cellulosic cell walls of higher plants. Its mechanical strength is generally provided by a sac-like envelope. The latter consists primarily of the murein polymer, built from subunits of N-acetylmuramic acid and N-acetylglucosamine linked in an alternating β-1,4-glycosidic sequence into polyglycan strands. Cross-linking of these strands via short Peptides (tetra- or pentapeptides containing D- or L-Amino Acids) generates a reticulate macromolecule, the "murein sacculus." Peptidoglycan is a component of the cell envelope in all bacteria (including cyanobacteria) in more than 100 variants (peptidoglycan types). In some bacteria, the surface develops a thick layer of slime (zoogloea) or "capsules" of diverse composition (mostly polysaccharides or Polypeptides). The cells of Acetobacter xylinum are bound together into a pellicle by Cellulose; in Sarcina ventriculi, the cells are likewise interconnected by cellulose.

Bacterial locomotion is powered by extremely delicate flagella (see 2.3.2; Fig. 2.96), which appear at specific developmental stages in many bacteria and ensure active directed cell movement. Under Electron Microscopy, these bacterial flagella reveal a helical surface structure (Fig. 11.11, B); they are composed of several ultra-fine longitudinal fibrils twisted together. They lack the "2 + 9" structure characteristic of true eukaryotic flagella (see Fig. 2.16). Motility is driven by a contractile protein (flagellin) similar to Muscle cell Myosin. Flagellar diameter is typically 10 to 20 nm, and length reaches up to 20 µm. They are distributed on the cell in various ways: singly at the cell pole (monotrichous, Fig. 11.11, A) or in tufts (lophotrichous, as in Spirillum, Fig. 11.11, D); they may also be distributed uniformly over the entire cell surface (peritrichous, Fig. 11.11, E). Attachment to the cell can be polar (Fig. 11.11, C), bipolar, lateral, or slightly subterminal (subpolar). Each flagellum originates (insofar as is known) from a basal body (Fig. 11.11, C) embedded in the cell envelope (see Fig. 2.97). The number of flagella can depend on environmental conditions: for instance, under nutrient deprivation, Proteus vulgaris bears 2 subpolar flagella instead of the numerous flagella distributed across the entire surface under normal conditions. Tufts typically comprise 2 to 50 flagella (polytrichous).

Locomotion. Swimming speeds driven by flagella can reach up to 200 µm/s in Bacillus megatherium, for example—roughly 50 times the cell's own length. A Spirillum can rotate around its axis 13 times in a single second. During this process, the flagella execute 40 revolutions, matching the rotational speed of an electric motor. Movement is usually generated by a thrust action similar to a ship's propeller, though it can also be replaced by a pulling motion akin to an airplane propeller. It occurs predominantly in liquid media, and more rarely across moist surfaces (as seen in peritrichously flagellated Proteus vulgaris moving on Agar). Depending on the external stimulus, movement manifests as chemotaxis (see 8.2.1.1), aerotaxis, phototaxis (see 8.2.1.2), and magnetotaxis (see 8.2.1.3). Stimulus-directed movements allow motile forms to aggregate in regions with optimal concentrations of beneficial substances. From structural and evolutionary Perspectives, the motility of flagellated prokaryotic cells can be viewed as an instance of convergence with analogous Eukaryotic cells. Gliding motility is capable in non-flagellated, cyanobacteria-like yet heterotrophic bacteria. This gliding movement is very slow (approximately 250 µm/min) and is associated with the secretion of mucous sheaths. The naked-protoplast-type motility of myxobacteria was mentioned above.

In addition to flagella, some bacteria possess numerous finer filaments ("fimbriae" or "pili"), whose function remains largely unclear. In Escherichia coli, so-called F-fimbriae, or sex pili, mediate parasexual conjugation (Fig. 11.13, A, B).

Physiology. Bacterial Nutrition can vary depending on the energy source, electron donor, and carbon source. Energy acquisition takes place

either via The breakdown of substances within the substrate (chemotrophy, see 6.9) or through the Utilization of Light energy (phototrophy, see

6.4). Organic (organotrophy) or inorganic substances, such as NH₃, H₂S, or Fe+⁴ (autotrophy), serve as electron Donors. Depending on their electron donor and energy source, autotrophic bacteria are classified as chemolithotrophs or phototrophs. Strictly anaerobic species can neither grow nor reproduce in the presence of oxygen. Facultative anaerobes can survive without oxygen; microaerophilic forms tolerate only very low oxygen concentrations. Oxygen is absolutely essential for obligate aerobic bacteria. The ability to fix atmospheric nitrogen (see 9.2.1) is widespread and found exclusively in prokaryotes.

Reproduction generally occurs through binary cell division into two; in elongated forms, this always takes place perpendicularly to the longitudinal axis. First, a transverse septum forms from the edge of the cell toward the center (centripetally), separating the cells from one another (hence the old name "fission bacteria" or Schizophyta). In almost all bacteria studied to date, the peptidoglycan capsule (where present) participates in septum formation from the very beginning. Following division, cells may remain joined in loose chains (e.g., Streptococcus).

To survive unfavorable conditions, certain forms produce resting cells, or spores. In some rod-shaped bacteria, spores develop intracellularly as endospores; they differ from vegetative cells by a lower stainability and strong light refraction. The primary significance of endospores lies in their heat resistance, allowing them to remain undamaged, for instance, during prolonged boiling. Conversely, vegetative cells of spore-forming forms are killed even by pasteurization (heating to 80 °C for 10 min). Spore formation inside a bacterial cell begins with various chemical transformations within the mother cell, during which 75% of its Proteins are broken down. This is followed by the division of the mother cell into two unequal daughter cells. Spore formation is completed by the development of a thick wall around the smaller cell, which becomes the spore and can account for up to 50% of its volume and dry mass. Thermoresistant spores accumulate a characteristic dipicolinic acid, which enhances both thermoresistance and light refraction.

Sporulation is determined by external conditions and occurs, for example, when nutrients are scarce. The readiness of spores to germinate increases upon storage and heating. Spores have been successfully germinated from dated soil samples containing bacterial spores (such as soil on herbarium specimens) after 200–320 years of dry storage. However, when soil samples were stored in a dry state, 90% of the spores lost their viability within 50 years.

A partial transfer of genetic material ("parasexuality") can occur in bacteria: DNA fragments may be transferred from a donor cell to a recipient cell directly via conjugation, by means of Bacteriophages, or in an extracted form via transformation (Fig. 11.13, B; regarding the function of sex pili, or fimbriae: Fig. 11.13, A).

Fig. 11.13. Escherichia coli. DNA transfer from a donor cell to a recipient cell (A, B). Bacteriophages (C–E): A — electron micrograph. The donor cell and recipient cell (the latter on the left) are connected to each other via a sex pilus (conjugative fimbria) (3,500x); B — diagram of DNA transfer. Top — sex pilus, bottom — recipient. Donor DNA (shown in black) splits into two strands, one of which penetrates the recipient cell. Replication (light line) of the single-stranded DNA (dark line) takes place in the sex pilus and the recipient. Certain Gene loci are marked with circles and letters (Cat, Lac, T, Az′, L); C, D — reproduction of bacteriophages within the host cell accompanied by its destruction (lysogenic cycle). When switching back to the lytic cycle, Transduction may occur, i.e., The transfer of bacterial DNA to released phages; E — individual T₂ phages (40,000x)

In contrast to the generally larger bacteria (see 1.2.5), Viruses are significantly smaller, pass through bacterial filters, and are not independent organisms. They develop from the genetic material of cells. Viruses act essentially as emancipated genes that have taken over the function of controlling the host cell's metabolism for their own synthesis. It is possible, at least for some viruses, that they even originated through extreme reduction from pathogenic bacteria. While bacteria contain DNA and RNA in a ratio of approximately 1 : 3.5%, viruses always contain only a single type of nucleic acid — either DNA or RNA. Viruses can replicate only inside living cells; they exhibit neither growth nor division and are insensitive to penicillin and sulfonamides. Electron micrographs reveal a complete absence of all structures characteristic of bacteria (despite sometimes highly complex morphological organization). Well-known Examples of viral diseases include tobacco mosaic (cf. Fig. 3, vol. 1), FOOT-and-Mouth disease, rabies, yellow fever, hepatitis, Influenza, smallpox, and herpes. Retroviruses are RNA viruses in which single-stranded RNA is transcribed onto a DNA double helix (i.e., the reverse of normal DNA-to-RNA Transcription). This group includes, in particular, the causative agents of immunodeficiency (AIDS, HIV) and tumor-inducing oncoviruses.

Bacteriophages are highly organized, relatively large viruses (length 150–110 µm). They consist of a DNA-containing "HEAD," a sheath, and a protein "tail" (Fig. 11.13, E). The tip of the tail attaches to The surface of the bacterial cell, and only then is the DNA contained in the head injected into the bacterial body through the hollow tail. Within a few minutes, the first signs of newly formed phage parts become visible, and after approximately the same amount of time, several hundred new phages are released from the bacterial cell as a result of its destruction (lysis). They arise not through division, but through de novo assembly from bacterial plasma. This phenomenon is based on the incorporation of phage DNA into the host's metabolism, where it influences the host's genetic apparatus, leading to the Synthesis of specific phage components instead of normal bacterial components. Inside the host cell, phages can alter their biochemical properties through Mutations; they can also be crossed and recombined. It was once thought that phages might represent an early evolutionary stage of life. However, they lack their own Metabolism and Energy systems (e.g., Respiration is absent), and they are therefore currently regarded as sequestered pieces of bacterial DNA that have acquired the ability to self-replicate and even persist outside the cell in a completely inactive (latent) state until they re-enter the host's metabolism. Significant confirmation of this hypothesis came, in particular, from the discovery that not all bacteriophages are lethal to bacteria; instead, the DNA of so-called "temperate" phages can replicate along with the bacterial DNA for long periods without harming the host (Fig. 11.13, C, D). The "genetic material" of phages and bacteria shares significant partial similarity.

Systematic subdivision of eubacteria. Given the prevailing scarcity of morphological features for classifying bacteria according to putative phylogenetic relationships, biochemical and physiological criteria are of paramount importance alongside available morphological data. The comparison of nucleic acid sequences plays a crucial role (see 1.2).

Bacteria are divided into Gram-negative and Gram-positive — groups that can be considered at the rank of phylum. Their identification relies on the so-called Gram stain (proposed by H. C. J. Gram, 1853–1938). Gram-positive bacteria are those that retain the aniline dye within the cell, whereas in Gram-negative bacteria, the dye can be washed out. The Gram stain is not applicable to cell wall-deficient bacteria, which can arise either spontaneously or experimentally (cf. Mycoplasmas).

First phylum: Gram-positive bacteria (Posibacteriota)

The multilayered murein layer of Gram-positive eubacteria does not lose its stain during Gram staining. Their cell envelope (see Fig. 2.98, A)

is characterized by the following features. The multilayered murein network constitutes up to 30–70% of the cell wall's dry mass. A notable feature of their Amino Acid Composition is that diaminopimelic acid is frequently replaced by Lysine. Polysaccharides are either absent or covalently bound. Protein content is lower. Teichoic Acids — polymers of ribitol phosphate or glycerophosphate linked via phosphodiester bonds to muramic acid — are frequently encountered. Gram-positive bacteria encompass a wide diversity of all morphological and physiological types known among bacteria. The most complex morphological organization is achieved by actinomycetes, whose vegetative body forms a branching mycelium. However, fruiting body formation, as seen in myxobacteria, and the capacity for photosynthesis are absent. Endospore formation occurs only in certain rod-shaped Gram-positive bacteria. An Overview of The Diversity of forms belonging to this phylum is provided by their subdivision into the following artificial groups.

1. Cocci. Gram-positive cocci (similar to Fig. 11.10, A, C) may occur either as single cells or grouped in pairs, tetrads, or packet-like clusters (in Sarcina ventriculi, up to 64 cells held together by cellulose). These are obligate or facultative anaerobes, occasionally aerobes. Example: lactic acid bacteria (such as Streptococcus lactis) from the family Streptococcaceae. This group also includes Deinococcus (see 1.1.23).

2. Non-spore-forming rods. This group comprises rod-shaped (see Fig. 11.10, B) anaerobic or facultatively anaerobic lactic acid bacteria belonging to the family Lactobacillaceae (Lactobacillus).

3. Spore-forming rods are capable of producing endospores. They belong to a single family — Clostridiaceae (Bacillus, Clostridium). These are either non-motile or motile (via lateral or peritrichous flagella), soil-dwelling aerobic, or facultatively anaerobic bacteria. Many of them also form cell chains or filaments.

4. Coryneform bacteria (including Actinomycetales). Coryneform bacteria are Gram-positive organisms with highly variable Morphology; that is, the rods may become club-shaped, short, coccoid, or slightly branched. Endospore formation is completely absent. This group includes propionic acid bacteria (Propionibacteriaceae), which occur as anaerobes in the rumen and intestine of ruminants. In Mycobacteriaceae, which already belong to the Actinomycetales, the tendency toward branching is more pronounced compared to the previously discussed forms. While true branching in Mycobacterium occurs only in young cultures, it is the rule in the so-called "ray fungi," or actinomycetes (Actinomycetaceae, Streptomycetaceae, Nocardiaceae). Numerous species of soil actinomycetes develop colonies in artificial culture that frequently reach up to several centimeters in diameter. These are formed by a "mycelium" that often consists of a single cell lacking cross-walls, highly delicate, and typically abundantly branched (filament diameter 0.5–1 µm; see Fig. 11.10, K). Neither Chitin nor cellulose is found in the cell wall. Sometimes the filaments become multicellular and can easily break down into rods that closely resemble certain rod-shaped bacteria. Furthermore, they produce various types of chain-forming exospores (especially in aerial cultures).

Streptomyces Scabies causes scab in potatoes and other ROOT vegetables, visibly manifesting as scabby lesions on the affected plant parts. An actinomycete symbiont (Frankia alni) inhabits the root nodules of alder and species of several other genera, where it assimilates free atmospheric nitrogen (see 9.2.1f). Nocardia species, like Representatives of the genus Mycobacterium, can oxidize ethane (cf. Flavobacterium). Thermomonospora and Thermoactinomyces species grow at high temperatures. Metabolic products of certain actinomycetes find application in medicine as Antibiotics for combating Infections caused by pathogenic bacteria (actinomycin, streptomycin, etc.). Under natural conditions, these substances are presumably important for competing against rival microorganisms. Clavibacter (see 9.3.2) and Rhodococcus (see 7.6.2.1) can also be assigned to the group of coryneform bacteria.

5. Mycoplasmas (e.g., Mycoplasma), formerly also designated as PPLO (pleuropneumonia-like organisms), lack a cell wall and consequently a fixed shape; therefore, they cannot be classified as Gram-positive bacteria based on the Gram stain. However, 16S rRNA sequence data indicate that they evolved from Gram-positive bacteria. This group apparently also includes the genus Metallogenium, species of which participate in The oxidation of manganese in aquatic environments (manganese bacteria, see 6.9.1).

Second phylum: Gram-negative bacteria (Negibacteriota)

In Gram-negative bacteria, the murein network is thin, single-layered, and accounts for less than 10% of the cell wall's dry mass; components taken up during Gram staining are easily washed out. The outer membrane consists of deposited, though non-covalently linked, Lipoproteins, lipopolysaccharides, and other Lipids, which make up to 80% of the cell wall's dry mass. Ca²⁺ ions enhance the Stability of the lipoprotein layer. Teichoic acids (see Fig. 2.90, B) are not detected.

This phylum includes cocci, rods, vibrios, spirilla, spirochetes, and gliding forms. Regarding their mode of energy acquisition, they are either phototrophs or chemotrophs. Unlike Gram-positive bacteria, some members of this phylum are capable of photosynthesis, which occurs without oxygen evolution (unlike cyanobacteria and eukaryotes). Phylogenetic relationships between phototrophic and non-phototrophic Gram-negative bacteria are generally much closer than their relationship with cyanobacteria, which utilize Water as an electron donor during photosynthesis. Among chemotrophic groups, a distinction is made between chemolithotrophic and chemoorganotrophic forms.

The Classification of the phylum is currently under development and only partially reflects true phylogenetic relationships. Along with largely natural orders, there are various families grouped into artificial categories (1–12) based on similarities in morphology and metabolism. We will begin with cocci and/or rods and examine them through the groups of anaerobes (1), facultative anaerobes (2), and aerobes (3). These will be followed by elongated and simultaneously spirally twisted forms, namely rigid spirilla (4) and flexible spirochetes (5), as well as appendaged bacteria (6). Based on morphological features, special groups are designated for chlamydobacteria (7) and gliding species from Cytophagales (8) and Myxobacterales (9), the latter forming fruiting-body-like structures. Based on metabolism, a distinction can be made between chemolithoautotrophic (11) and photoautotrophic (12) bacteria, while obligately parasitic bacteria (10) are distinguished by their lifestyle.

1. Anaerobic cocci and bacilli are grouped into the families Veillonellaceae and Bacteroidaceae. The latter family is closely related to organisms of yet uncertain taxonomic position belonging to the genus Desulfovibrio. These are polar mono-, tri-, or polytrichous bacteria that morphologically resemble vibrios (comma-shaped Curved Rods) or spirilla (see below, 4). They belong to a small group of sulfate-reducing bacteria capable of “sulfate respiration” (see 6.7) and live as chemolithoheterotrophs. Species of Desulfovibrio inhabit sapropel (“rotting sludge”).

2. Facultatively anaerobic bacilli include, in particular, members of the family Enterobacteriaceae (Enterobacter, Erwinia, Klebsiella, and the bacterium Escherichia coli, which commonly inhabits the intestine of warm-blooded organisms and is widely used in experimental research). Species of the genera Photobacterium and Beneckea from the family Vibrionaceae have adapted to life in seawater and are known as luminous bacteria (“Bioluminescence”). Fish and cephalopods use these species within their light Organs as symbionts for orientation and deterrence. This group also includes the genera Haemophilus, Yersinia (Box 9.2), and Zymomonas. Flavobacterium, which is also affiliated with this group, is distinguished by its ability to oxidize ethane.

3. Aerobic cocci and bacilli are represented by a great diversity among Gram-negative bacteria. These include, notably, the families Azotobacteraceae (Azotobacter) and Rhizobiaceae, species of which are frequently capable of fixing free atmospheric nitrogen. The former live freely and can fix up to 20 mg of nitrogen per 1 g of consumed sugar. Representatives of Rhizobiaceae (Rhizobium, Azo-, Brady-, Meso-, Sinorhizobium) infect the roots of legumes, which respond by forming root nodules (see 9.2.1). Phyllobacterium rubiacearum, a species belonging to the same family, is a symbiont in the leaves of various Rubiaceae (Psychotria, Pavetta) and Ardisia from the family Myrsinaceae.

The genus Agrobacterium is incapable of fixing molecular nitrogen. Agrobacterium tumefaciens induces galls on flowering plants (Box 9.2, Fig. A). It has been used to generate Transgenic Plants (see chronological table). This group also includes the family Pseudomonadaceae (with the genera Pseudomonas and Xanthomonas), acetic acid bacteria (e.g., Acetobacter aceti), as well as the genera Bordetella, Citrobacter, and Methylomonas.

4. Spirilla (Spirillales with the genus Spirillum) are spirally coiled, rigid rods with a variable number of turns—ranging from a few to many. According to their flagellar arrangement, they are bipolar polytrichs. Most commonly they are aerobes, less frequently facultative anaerobes.

5. Spirochetes (Spirochaetales) are extremely long (up to 500 μm!) and thin (diameter 0.1 – 0.6 μm) anaerobic or aerobic bacteria, spirally coiled like spirilla. In contrast to the latter, they are flexible: their thin cell walls enable them to move actively in the absence of flagella through the contraction of an axial filament located inside the cells.

6. Appendaged bacteria comprise forms of diverse evolutionary affinities that produce unequal-sized daughter cells upon division and form appendage-like rods and outgrowths. The rods consist of mucus, while filamentous outgrowths are formed as a result of cell elongation. Gallionella ferruginea is known as an iron bacterium that forms rusty-brown masses in iron-containing waters in spring. Pedomicrobium manganicum oxidizes manganese (manganese bacteria, see 6.9.1).

7. Chlamydobacteria possess tubular sheaths (vaginas) that hold cells together in chains. A well-known example is the so-called “sewage fungus” Sphaerotilus natans (see Fig. 11.10, G – J). This bacterium (!) grows in heavily polluted waters, such as the settling basins of sugar refineries. By forming filaments, flocs, and even growths resembling dense fur, it can clog pipes and drainage ditches. Leptothrix also belongs to this group.

8. The order Cytophagales. Representatives of this order exhibit gliding motility. Both genera assigned here—Cytophaga and Sporocytophaga—together with the myxobacteria discussed below, are aerobic soil bacteria that decompose cellulose. Unlike myxobacteria, the order Cytophagales does not form any fruiting bodies. Filamentous gliding forms such as Thiothrix (see 6.9.1) and Beggiatoaceae can be affiliated here. For Chloroflexus, see below (group 12).

9. The order Myxobacteria (Myxobacterales) constitutes the main part of the Gliding Bacteria Group. However, evolutionarily they have advanced further than the preceding group because they possess a complex organization in which unicellular forms can produce fruiting bodies. Red or differently colored cell aggregates of myxobacteria, living on soil or in animal dung, represent colonies (“pseudoplasmodium”) composed of small, cell-wall-less, actively flexing rods lacking flagella, which can successfully perform gliding movements through active cell contractions. In some species, the rods aggregate at specific sites during joint creeping to form characteristic, genus-specific morphological and colored, sometimes mucus-bound common clusters—the so-called fruiting bodies, or cystophores. From their interior, motile cells can form once again (e.g., in common species of Myxococcus and Chondromyces, Fig. 11.10, 1 – 19). In culture, some myxobacteria can feed on living microorganisms (e.g., bacteria). Thus, their life cycle shows a remarkable convergence with eukaryotic Acrasiobionta.

10. Obligately parasitic bacteria are grouped into the order Rickettsiales (rickettsiae). Being obligate parasites, rickettsiae cannot be cultivated outside of living cells. They are very small; they differ from viruses in their DNA/RNA ratio (1:3.5); furthermore, their cell wall is sensitive to Lysozyme and contains muramic acid.

Closely related to rickettsiae are likely the agents of psittacosis (parrot fever), which were long considered viruses. These are bacteria adapted to a parasitic lifestyle that possess DNA and RNA, as well as specific substances (e.g., muramic acid).

11. Chemolithotrophic bacteria—in contrast to heterotrophic bacteria (see, for example, group I)—exhibit an obligatory coupling of chemolithotrophy with autotrophic CO₂ fixation (see 6.9). Aerobic Nitrobacteraceae oxidize ammonia to nitrite (Nitrosomonas) or nitrite to nitrate (Nitrobacter). Morphologically they can be cocci, bacilli, or spirilla; if flagellated, their flagella are subpolarly attached or the cells are peritrichous. Bacteria that oxidize reduced sulfur compounds (partially Thiobacillus) or Fe²⁺ to Fe³⁺ (partially Thiobacillus and Siderocapsaceae) can be affiliated with this family. Finally, mention should be made of hydrogen bacteria, or knallgas bacteria (e.g., Alcaligenes eutrophus), which are only facultatively autotrophic. On the one hand, they can grow better on organic nutrient media, but on the other hand, they can also oxidize molecular hydrogen using hydrogenases. In this way, these bacteria obtain energy, carry out reductive synthetic processes, and synthesize specific CARBOHYDRATES by fixing CO₂.

12. Photoautotrophic Rhodospirillales are largely anaerobes. They are distinguished by the presence of various Photosynthetic Pigments (bacteriochlorophylls a – e) and carotenes, which impart a characteristic purple-violet, reddish, brownish, olive, or green coloration. Oxygen inhibits the synthesis and function of bacteriochlorophylls, thereby distinguishing them also from chlorophyll a of cyanobacteria (see Fig. 6.45) and eukaryotes. Organic compounds serve as electron donors in particular (Rhodospirillaceae). These photoautotrophic bacteria, adapted to using light as an energy source and phylogenetically extremely unrelated, occur as cocci, bacilli, or spirilla. When flagella are present, they are located polarly or bipolarly.

The family Rhodospirillaceae consists of sulfur-free purple bacteria. Like the subsequent family, it is characterized by the presence predominantly of bacteriochlorophyll a or b on a cytoplasmic membrane system. Elemental sulfur is generally not oxidized by them. The best-known representatives belong to the genera Rhodospirillum, Rhodobacter, and Rhodomicrobium.

In representatives of both subsequent families, elemental sulfur or hydrogen sulfide serves as the electron donor. Chromatiaceae accumulate sulfur inside the cells or on their surface. Most often they have a purple color, which is why they are called purple sulfur bacteria. Examples include species of Chromatium and Thiospirillum, whose cells reach considerable sizes (20 – 40 × 3.5 – 4 μm), as well as Thiocapsa. Green sulfur bacteria belonging to the family Chlorobiaceae (genus Chlorobium and several others) can neither accumulate nor deposit sulfur. They contain bacteriochlorophylls (mainly c, or some also have bacteriochlorophyll a in minor amounts) in vesicles located near the cytoplasmic membrane or attached to it. This feature distinguishes them from both preceding families. Special forms are known under the generic name Chlorochromatium. They appear as aggregates of several non-motile green sulfur bacteria and a central colorless bacterium with polar flagella; such an entity moves in space as a single unit. Chloroflexaceae (sulfur-free green bacteria grouped into the genus Chloroflexus) exhibit gliding motility and therefore represent an intermediate stage between groups 8 and 12.

Photoautotrophic bacteria inhabit anaerobic zones in freshwater pools, ponds, and lakes, in slowly flowing watercourses, as well as in marine bays. Purple sulfur bacteria form, for example, pinkish or wine-red films on decaying plant parts at the bottom of water bodies. Sometimes their mass development (“water bloom”) is observed in deeper anaerobic zones of lakes. This occurs under specific Temperature conditions—at sufficiently high concentrations of hydrogen sulfide, carbon dioxide, and organic compounds. Due to their high carotenoid content, purple bacteria can capture penetrating short-wavelength light and use it for photosynthesis. Accordingly, in greater depths of water bodies, purple bacteria predominate, whereas among sulfur bacteria, those with a brown coloration due to higher carotenoid content prevail.

Occurrence and Lifestyle of Bacteria

Bacteria, represented by numerous species (about 3,000) and an immeasurable number of individuals, are found all over the globe: in water, soil, and—carried by dust—everywhere in the atmosphere and on all objects. Their wide distribution is promoted primarily by the following factors: firstly, their small size and the resulting very large surface-to-body-mass ratio, which enables a very high physiological activity and metabolic intensity (e.g., the ability to reproduce very rapidly); secondly, the resistance of their vegetative cells and especially spores to adverse external influences, as well as the diversity of their modes of nutrition. Under optimal conditions, some species (e.g., Vibrio cholerae) can divide several times an hour, so that a single bacterial cell can give rise to several billion new cells within 24 hours.

Bacterial spores are highly resistant to desiccation and extreme temperatures; some withstand exposure to boiling water for several hours (maximum 30 h), as well as to extreme cold. The vegetative cells of many species are also particularly resistant to desiccation. Some can live at high temperatures (90 – 110 °C), for example, in hot springs, and some actively generate significant amounts of heat (“self-heating” to over 60 °C in hay, manure, tobacco, and cotton by species such as Bacillus stearothermophilus or species of the genera Thermomonospora and Thermoactinomyces).

Thermophily. Thermophilic bacteria, such as species of the genera Bacillus, Clostridium, various mycobacteria, and the archaea discussed later, not only tolerate high temperatures but also require them for optimal growth. True thermophily in this sense is found exclusively among prokaryotes.

Moderate thermophiles include bacteria that release thermal energy during metabolism.

Thermophilic bacteria utilize thermostable Proteins and Enzymes characterized by high temperature optima. Protein stability is enhanced, in part, by Metal Ions or binding to cell membranes, as well as by a specific amino acid composition; thus, thermostable proteins contain more Arginine residues than thermolabile ones.

Metabolism. A greater number of metabolic types is found among prokaryotes—and specifically already among eubacteria—than among eukaryotes. The majority of bacteria live heterotrophically—as saprotrophs or parasites. However, obligate parasitism (e.g., in rickettsiae) is rare; most pathogenic species can also reproduce outside of a plant or animal Organism. Therefore, their cultivation on appropriate nutrient solutions (e.g., meat broth with peptone) presents no difficulty. On solid nutrient media (agar, gelatin), bacteria frequently form mucous aggregates of various appearances—“colonies” (see 5.1), which are most often colorless but can also be colored due to pigment secretion. Pigments within cells (in thylakoids, see Fig. 11.12, or in the cytoplasmic membrane) are found only in photosynthetic green bacteria or purple bacteria—analogously to halobacteria among archaea.

Through secreted enzymes, bacteria cause intensive substrate decomposition under either anaerobic or aerobic conditions. Noteworthy Features of the metabolic physiology of various bacteria include, in particular: autotrophy—via either photosynthesis (red and green sulfur bacteria) or Chemosynthesis (see 6.9); heterotrophy in saprotrophs, parasites, or symbioses; aerobic or anaerobic Energy Metabolism; denitrification or desulfurification (see 6.6; 6.7); MOLECULAR Nitrogen Fixation (see 9.2.2). Bacteria carry out numerous Fermentation processes: lactic acid and Butyric acid fermentation, fermentation of cellulose, pectin, and protein, and aerobic acetic acid fermentation (see 6.10.2.2). Bacteria can degrade almost all natural substances, even petroleum, paraffins, and asphalt. Hydrocarbons are degraded the less readily the shorter their chains are; ethane and methane are utilized only by specialized species (see 6.9.1). Only certain synthetic resins and plastics, as well as the particularly resistant sporopollenin (see 2.2.7.6), are largely resistant to bacterial decomposition.

Symbionts. Among symbiotic bacteria, species that fix atmospheric nitrogen are particularly important for many vascular plants (Fabaceae, Alnus, Hippophae, Ardisia, Pavetta, Psychotria; see 9.2.1), including members of the families Rhizobiaceae (Rhizobium, Phyllobacterium) and Actinomycetaceae (Frankia). It is believed that the mitochondria of eukaryotic cells arose via endosymbiosis (with organisms resembling rickettsiae serving as the original endosymbionts).

Pathogens. Numerous species of bacteria cause diseases in animals and humans. The Prevention of such diseases is possible through immunization (vaccination): in active immunization, a weakened pathogen or its toxins is administered to a human (or animal) to stimulate antibody production, whereas passive immunization involves the administration of Antibodies from immunized animals.

Examples of human diseases caused by Gram-positive bacteria include: purulent infections (Staphylococcus), anthrax (Bacillus anthracis), tetanus (Clostridium tetani), diphtheria (Corynebacterium diphtheriae), tuberculosis (Mycobacterium tuberculosis), acne (Propionibacterium acnes), and actinomycosis (Actinomyces bovis). Closely related to Gram-positive bacteria is Mycoplasma pneumoniae, which causes pulmonary infections. Gram-negative bacteria cause Pneumonia and respiratory tract infections (Klebsiella pneumoniae, Bordetella bronchiseptica, Haemophilus influenzae), typhoid fever (Salmonella typhi), paratyphoid fever (Salmonella paratyphi), food poisoning (Salmonella typhimurium), plague (Yersinia pestis), cholera (Vibrio cholerae), Sexually Transmitted Infections (Gonorrhea — Neisseria gonorrhoeae, Syphilis — Treponema pallidum), meningitis (Neisseria meningitidis), and spotted fever (Rickettsia sp.).

Phytopathogenic species invade plants either through Stomata, hydathodes, etc. (especially species of Pseudomonas and Xanthomonas), or by infecting wounds (frost cracks, insect damage, etc., e.g., Erwinia carotovora). Pathogenic bacteria poison the host organism with toxins. The presence or absence of flagella plays no role in pathogenicity; strangely, only rod-shaped, non-spore-forming forms are pathogenic to plants. Pathogenic bacteria typically inhabit intercellular spaces, from which they dissolve the middle lamellae (see 2.2.7.1), causing the isolated cells to die; sometimes this process is further accelerated by toxins. The host tissue thereby transforms into a mushy, rotten mass (soft rots). Relatively few bacteria invade living cells (including Pseudomonas tabaci). Occasionally, bacteria clog vascular bundles, thereby causing wilting and death of the plant, which is most often facilitated by wilting toxins (e.g., Corynebacterium michiganense). Over 200 plant bacterioses are known.

Biotechnology. Bacteria and other microorganisms can be utilized in technical processes and industrial production. These include such fields as Genetic Engineering (transformation), The production of antibiotics (also for cleaving side chains of synthetically obtained precursors), enzymes, and other proteins; waste management (e.g., methane fermentation of sewage sludge); and bioleaching for metal recovery (converting poorly soluble copper and uranium compounds into water-soluble sulfates by Thiobacillus species). Bacteria growing on petroleum-containing substrates can serve as indicators in prospecting for new oil deposits.

Third Division: Blue-green algae, or Cyanobacteria (Cyanobacteriota, Cyanoprokaryota, Cyanophyta)

Representatives of this division resemble algae (hence the name blue-green algae; prokaryotic algae) — they are morphologically simple

organisms capable of photosynthesis. Oxygen is released during photosynthesis (oxygenic photosynthesis). However, unlike eukaryotic algae, their cellular structure largely corresponds to the bacteria discussed earlier; that is, they are prokaryotes, and therefore it is preferable to use the term "cyanobacteria" instead of the outdated name "blue-green algae".

Differences from Eubacteria. Among prokaryotes, cyanobacteria constitute a relatively homogeneous group. Nucleotide sequencing of 16S rRNA reveals a higher level of homogeneity among cyanobacterial genera than between them and other bacteria. Cyanobacteria differ from phototrophic eubacterial genera in their photosynthetic pigments (chlorophyll a instead of bacteriochlorophyll) and the release of oxygen during photosynthesis; however, alongside oxygenic photosynthesis, anoxygenic photosynthesis can also occur under certain conditions. A cyanobacterial cell is, on average, 5 to 10 times larger than a bacterial cell.

Differences from Eukaryotic Algae. Phototrophic cyanobacteria (blue-green algae), which frequently form simple or branched filaments, are prokaryotes and differ from eukaryotic algae (see Box 11.5) in the following features. Their cells lack a defined nucleus, mitochondria, Lysosomes, Endoplasmic reticulum, membrane-bound chloroplasts, and vacuoles with cell sap surrounded by a tonoplast; however, some cyanobacteria, like certain eubacteria, possess gas-filled vesicles called gas vacuoles. Unlike all eukaryotes, however, some cyanobacteria are capable of fixing free atmospheric nitrogen (N₂), much like certain eubacteria. This ability is primarily due to the presence of heterocysts (see 9.2.1), which differ from other cells by the loss of pigmentation, the presence of cellulose, and light-refracting polar bodies (Fig. 11.15, F). Evidently, the nitrogen compounds formed in the heterocysts pass through fine channels in the polar bodies into neighboring cells.

Cell Structure. In the central, colorless part of the cells (the nucleoplasm, or centroplasm), there are granule-, rod-, network-, or filament-like elements containing DNA. Their aggregate, the so-called Chromatin apparatus, represents the functional equivalent of a nucleus. During cell division, this entire complex divides in two (Fig. 11.15, M). The centroplasm is surrounded by a poorly defined peripheral colored chromatoplasm, which, depending on the cell shape, appears as a hollow sphere or cylinder. The chromatoplasm is highly viscous and, unlike the protoplasm of eukaryotic cells, does not exhibit streaming. It contains Cytology/practical/13.html">Ribonucleic acid in diffusely scattered ribosomes, while the assimilation pigments — chlorophylls a and, in individual cases, also c and d — are located in thylakoids. In addition to carotenoids (especially β-carotene, but also zeaxanthin, echinenone, and myxoxanthophyll, though not lutein), accessory pigments include two water-soluble Chromoproteins (phycobiliproteins), whose prosthetic groups (predominantly phycocyanin, along with phycoerythrin) are termed phycobilins. Phycobilins are related to Bile pigments and occur in slightly different forms in the eukaryotic algal divisions Cryptophyta and Rhodophyta. In cyanobacteria, as in red algae, phycobiliproteins are localized in bodies known as phycobilisomes (see Fig. 2.89), which are situated on the thylakoids (Fig. 11.14, A). The latter are positioned at approximately equal distances from one another and are not aggregated into pairs, triplets, or stacks.

Reserve Substances. Cyanobacterial (cyanophycean) starch is stored as particles between the thylakoids that are invisible under light microscopy. It is a glucan close to glycogen and related to the floridean starch of red algae. In addition, microscopically visible cyanophycean granules occur — slightly angular small bodies composed of polymers of the amino acids arginine and asparagine; these evidently serve as nitrogenous reserve materials. Phosphorus in the form of highly polymerized polyphosphates accumulates in volutin bodies, which are constructed of Nucleoproteins. These bodies may also function as energy stores (ATP).

Fig. 11.14. Cyanobacteriota: A — concentric thylakoids (25,000>); B — Cylindrospermum, pore band on a transverse septum (26,000x); L — lipid body; P — phosphate body

The rigid cell wall (= protective layer) consists of murein, with cellulose practically absent (though see above regarding heterocysts). Externally, cyanobacteria frequently feature mucilaginous sheaths (envelopes), which electron microscopy reveals to have a fibrous structure and to contain polysaccharides alongside Amino Acids and Fatty acids. The cell wall consists of four layers and is degraded by lysozyme. In ultrastructure and chemistry, cyanobacterial cell walls occupy an intermediate position between those of Gram-negative and Gram-positive eubacteria.

Morphology. Some cyanobacteria are unicellular (e.g., Dermocarpa). Other forms constitute colonies containing from a few to many cells (Chroococcus, Merismopedia), unbranched filaments without heterocysts (Oscillatoria) or with heterocysts (Nostoc, Anabaena), filaments with heteropolar differentiation (Rivularia), and filaments with false branching (Tolypothrix, Scytonema) or true branching (Hapalosiphon). False branching arises when a mother filament ruptures, and the end of a daughter filament breaks through the mucilaginous sheath and continues to grow laterally, forming a branch (Fig. 11.15, K). In contrast, true branching results from A change in the plane of division. Branching begins with cells that, through division in a different direction, form parallel to the longitudinal axis of the filament and subsequently maintain this division orientation. Some filamentous cyanobacteria possess from a few to many cells in longitudinal and transverse cross-sections and thereby exhibit true branching (Stigonema, certain species with apical growth; Fischerella). Here, cells divide predominantly in more than one direction. In all multicellular species of cyanobacteria, we are essentially dealing with colonies in which individual cells are loosely arranged within a mutually secreted mucilage or within the original cell wall (see 5.1).

Locomotion. The thalli of many species, most frequently filamentous ones, exhibit gliding movements (2 — 11 μm/s). Locomotion is possible only on a solid and, moreover, moist substrate. It is based not merely on the simple secretion of mucilage (cf. movement in desmids, Zygnematophyceae), but apparently also on the action of microfibrils. These structures coil around the filament or cell over the murein layer and impart a rotational movement through friction against the substrate. To gain traction, they utilize their own mucilage secreted through extremely fine pores 10 nm in diameter (Fig. 11.14, B) in the cell wall. Only filamentous Oscillatoriaceae are capable of forward movement accompanied by rotation, whereas representatives of other groups move forward without simultaneous rotation.

Reproduction in cyanobacteria occurs via cell division. Motile stages with flagella are absent. Filamentous blue-green algae grow intercalarily through the division of any cells within the filament. Transverse walls form centripetally in the manner of an iris Diaphragm (Fig. 11.15, N). They consist solely of supportive layer material. Reproduction takes place through nonspecific fragmentation of filaments or via the Separation of hormogonia consisting of a small number of cells (Fig. 11.15, L). Hormogonia — filament fragments composed of young, unspecialized cells — detach from the mother filament, glide away, and grow into new filaments. In some unicellular forms, the contents of an enlarging mother cell divide successively into A large number of spherical endospores, each of which develops into a new individual upon release from the mother cell. In certain species with elongated cells, the basal part remains sterile, while the apical part constantly regenerates to produce spores (Fig. 11.15, D). Cyanobacterial endospores differ from eubacterial endospores in their structure and development. Exospores also occur; they are abjointed from the mother cell. All these spore types lack flagella. To survive unfavorable periods, resting cells, or akinetes, are formed (especially in hormogoniophytes). Individual cells transform into akinetes by accumulating reserve substances while increasing in size and significantly thickening their walls (Fig. 11.15, J). Akinetes germinate into hormogonia. Alternatively, lateral branches of filaments may become entirely enveloped by a tough wall and transform into resting organs, or hormocysts. Thus, various mechanisms exist not only for Vegetative Reproduction but also for The formation of resting structures that may appear in The life cycle under specific (i.e., adverse) conditions.

Fig. 11.15. Cyanobacteriota: A — Chroococcus turgidus (400x); B — Aphanocapsa pulchra (500x); C — Merismopedia punctata (600x); D — Dermocarpa clavata, endospore formation; E, F — Nostoc commune: E — colony (1x), F — same, filament with 4 heterocysts (400x); G — Rivularia polyotis, portion of colony (200x); H — Rivularia haematites, portion of colony in cross-section, with lime deposits and growth rings (15x); J — Cylindrospermum stagnale, with elongated resting cell and spherical heterocyst at the filament apex (500x); K — Plectonema wollei with false branching (200x); L — Lyngbya aestuarii, hormogonium formation (500x); M — Stigonema mamillosum, filament apex (250x); N — Oscillatoria princeps, filament apex (300x)

Sexual reproduction is unknown. It remains unclear whether the occasionally observed EXCHANGE OF GENETIC material (specifically, the recombination of Antibiotic Resistance factors from two strains within a single strain) is based on parasexual processes.

Systematics. Classification based on morphological features coincides only partially with molecular phylogenetic data. Cyanoprokaryota (i.e., cyanobacteria) constitute a single class (Cyanophyceae) and, depending on their level of organization, are subdivided into several orders.

1. Order: Chroococcales. This order comprises unicellular forms or simple colonies (spheres, plates, short unbranched filaments). Unbranched short filaments may already combine into a sort of "pseudoparenchyma." Reproduction occurs via cell division; some forms also produce endospores (e.g., Dermocarpa; Fig. 11.15, D) and exospores. If daughter cells do not grow to the normal size of mother cells, reproduction is referred to as taking place via nanocytes. Synechococcus and Synechocystis are unicellular forms. In Chroococcus and Gloeocapsa (see Fig. 5.2), cells remain united after division into colonies of 2, 4, or 8 within common mucilaginous envelopes, which may be layered (see 5.1). In Chroococcus, young daughter cells are hemispherical (Fig. 11.15, A), whereas in Gloeocapsa they are ovoid-rounded and embedded within a very thick mucilaginous envelope. Species of both genera are most frequently found in slimy coatings on damp rocks and walls. In Aphanocapsa (Fig. 11.15, B), Aphanothece, Microcystis, and Merismopedia (Fig. 11.15,

C), the number of cells comprising the colony is larger. Plate-like colonies in Merismopedia species (Fig. 11.15, C) result from cell divisions strictly in a single plane; these species inhabit freshwaters, with some occurring in marine environments.

2. Order: Oscillatoriales. These filamentous forms still lack heterocysts and akinetes, with only the terminal cells differing in appearance from the rest of the filament cells. Cell division always occurs in a single direction, and consequently branching is absent. Filaments of Oscillatoria species, commonly found in water and mud, consist of uniform, frequently disc-shaped cells (Fig. 11.15, M). Growth is intercalary, and reproduction occurs via hormogonia. This order also includes the genera Phormidium, Schizothrix, Spirulina, Trichodesmium, Plectonema, and Lyngbya.

3. Order: Nostocales. Here, cell division occurs similarly to representatives of the previous order, but perpendicular to the longitudinal axis of the filaments (see Fig. 5.1). Reproduction takes place via hormogonia, as in Oscillatoriales. Heterocysts and sometimes akinetes regularly occur as distinct, well-visible cell forms. Species of the genus Nostoc, which form rounded or amorphous lobed colonies in water or on damp soil, are represented by moniliform filaments embedded in a common polysaccharide mucilage (Fig. 11.15, F). Species of the genera Cylindrospermum, Aphanizomenon, and Anabaena, some of which are planktonic, form resting cells (Fig. 11.15, J). In species of Rivularia (Fig. 11.15, G, H), colonies attached to aquatic plants and stones exhibit a clear distinction between the base and the apex of the filament: a heterocyst is located at the lower end, while upwards the filament gradually tapers into a colourless Hair; thus, there is structural differentiation determined by the body plan. Species of Tolypothrix and Scytonema are distinguished by the presence of false branching. The genera Anabaenopsis, Calothrix, and Aulosira also belong to this order (see 9.2.1).

4. Order: Stigonematales. This order includes the most highly differentiated forms. As a result of transverse and longitudinal cell divisions, true branching and the presence of multiseriate filaments are possible and characteristic of them. Reproduction is carried out via hormogonia. Heterocysts or akinetes may occur. In Stigonema (Fig. 11.15, M), the thallus is divided into a base and an apex; the apical cell cuts off segments downwards, which subsequently divide by longitudinal and transverse septa; multiseriate filaments can also form lateral branches. The genera Fischerella, Hapalosiphon, and Mastigocladus also belong to this order.

Occurrence and Lifestyle of Cyanobacteria (Blue-Green Algae)

Cyanobacteria, numbering about 2,000 species, are distributed worldwide. They are often visible to the naked eye as a mucous mass, finely filamentous coatings, water blooms, etc. They inhabit primarily fresh water (even hot springs with temperatures around 75 °C), but are also found on moist and dry soils, tree bark, and rocks—ranging from the Arctic to the Antarctica. Thus, certain species have adapted to life outside of water.

Weathering and Formation of Rocks. Blue-green algae inhabiting calcareous rocks are subject to extreme fluctuations in temperature and humidity. They live here partly On the surface (epilithically) and partly in microscopic cracks (endolithically), often forming dark bands (ink streaks). Some endolithic species can dissolve limestone, while in others (e.g., Rivularia, Schizothrix) calcium carbonate is deposited in their mucilaginous sheaths (Fig. 11.15, H), which in fresh water leads to the formation of chalk and travertine, and in the tidal zone of warm seas, to the deposition of laminated calcareous crusts (stromatolites). Fossil stromatolites have been found in Precambrian deposits, and it is believed that the blue-green algae that formed them already covered large areas and were widely distributed during that geological epoch.

Species occurring in large masses near the surface of fresh and saline waters can cause so-called water blooms. Oscillatoria rubescens causes red water blooms in eutrophic water bodies and is known as the "Burgundy Blood alga". Other species, such as Microcystis aeruginosa and Aphanizomenon flos-aquae, produce toxic peptides that can cause fish kills in freshwaters. The water bloom caused by Spirulina platensis in the saline lakes of South Africa serves as the primary food source for the lesser flamingo. In biological water analysis, an Abundance of cyanobacteria indicates a critical degree of eutrophication (Box 11.7).

Nitrogen Fixation. Many genera (Nostoc, Anabaena, etc.) include species that fix atmospheric nitrogen (see 9.2.1). In waterlogged rice fields, cyanobacteria fix up to 50 kg of nitrogen per hectare annually. Unlike certain eubacteria (Rhizobiaceae), nitrogen-fixing cyanobacteria are completely adapted to a free-living lifestyle. Consequently, THE CONTRIBUTION OF blue-green algae to ecosystem functioning appears to be greater than that of nitrogen-fixing eubacteria. Among cyanobacteria, there is also a higher number of nitrogen-fixing genera and species.

Representatives of several genera enter into symbiotic relationships with other organisms. The algal component of certain lichens (see Mycobionta, Appendix 2) consists of cyanobacteria. Some forms live as endophytes in the tissue cavities of other plants, for example, Anabaena in the leaves of Azolla (see Fig. 11.159, O), and Nostoc in the thallus of certain liverworts (Blasia, Anthoceros, see Fig. 11.127, D), in the roots of Cycas, and in the rhizome of Gunnera (an angiosperm). In these symbiotic associations, cyanobacteria supply their partners with nitrogen.

Fourth Division: Prochlorophytes (Prochlorobacteriota, Prochlorophyta)

Prochlorophytes are unicellular algae living in symbiosis with marine ascidians, lacking phycobilins and possessing chlorophyll b alongside chlorophyll a. Structurally, their cells are typical prokaryotes: a membrane-bound nucleus is absent, and cell walls consist of murein. They reproduce independently in culture. This division also includes free-living filamentous freshwater forms that otherwise correspond to the Diagnosis of Prochlorophyta.