BOTANY, VOLUME 3 - EVOLUTION AND SYSTEMATICS - 2007

11. SYSTEMATICS AND PHYLOGENY

11.2. Bacteria, Fungi, Plants

II. Kingdom (Domain): Archaea

Superficially, Archaea resemble Bacteria despite fundamental differences between them (which is why they were previously called archaebacteria). However, Archaea (comprising about 80 species) exhibit a great diversity in Cell wall and membrane structures, and muramic acid—a typical component of the eubacterial cell wall—is always absent. Depending on the genus, they form protein and polysaccharide coats, protein sheaths (envelopes), as well as cell walls, sometimes containing pseudomurein, whose component is not muramic acid, but L-talosaminuronic acid. Only L-Amino Acids have been detected. Due to this distinct cellular architecture, Archaea are resistant to penicillin, D-cycloserine, and Other Antibiotics that disrupt murein Biosynthesis. Other specific compounds include branched, phytanyl-containing Lipids with ether linkages, complex RNA polymerases, and a high proportion of modified NUCLEOTIDES in ribosomal Nucleic Acids. The results of rRNA nucleotide sequence analysis indicate that Archaea are highly distinct from eubacteria.

Similar, and even matching, Morphology and physiological features in Archaea and eubacteria have evidently arisen through independent evolutionary development. Both groups include cocci, rods, sarcinae, spirilla, and filamentous forms.¹ Archaea also feature plate-shaped Cells, with frequent transitions from one form to another. Some representatives are capable of active motility, most often due to the presence of a single flagellum (e.g., Methanobacterium mobile). Like bacteria, Archaea include aerobic and anaerobic, heterotrophic, sulfur-dependent, and phototrophic forms. Furthermore, some representatives are extremely thermophilic, acidophilic, or halophilic. In accordance with tradition and established nomenclature rules, archaeal taxa often have misleading name endings such as -bacterium or -bacteriales.

¹ Prochlorophytes were discovered relatively recently (in the 1970s), and this discovery was a genuine sensation at the time. However, molecular biology data indicate their close affinity to certain cyanobacteria, so in many modern systems they are not considered a distinct taxon at all, but are integrated into the cyanobacterial system: unicellular forms are placed in Chroococcales, and filamentous forms in Oscillatoriales (see above). — Translator's Note.

Based on differences in 16S rRNA composition, modern studies of individual representatives suggest a strong divergence during the evolution of Archaea, bacteria, and eukaryotes (excluding their METABOLISM/14.html">Chloroplasts and Mitochondria) (see Fig. 11.9). Nevertheless, A number of biochemical traits show that Archaea are more closely related to eukaryotes than to bacteria, which further emphasizes their isolated position among prokaryotes.

The evolutionary divergence of Archaea apparently occurred about 4 billion years ago, since the oldest known fossil records of cyanobacteria are about 3 billion years old, and Archaea, based on 16S rRNA data, must have originated before the split into eu- and cyanobacteria. During this early temporal window of life's differentiation (more than 3 billion years ago), methane-producing bacteria could have existed in Earth's largely reducing atmosphere (H₂ from the atmosphere; CO₂ from primitive Fermentation processes in ancient seas).

Archaea encompass ancient Ecological and Physiological adaptive types that (probably through progressive evolutionary development) have survived to the present day in corresponding biotopes (for example, methanogenic bacteria in sapropel and the rumen of ruminants). The relict Nature of the representatives of this group that have survived to the present day Supports taxonomic division into early and deeply diverged evolutionary lineages.

First Phylum: Crenarchaeota

Most frequently thermophilic (thermoacidophilic) and sulfur-dependent representatives of this phylum are apparently closest to the ancestors of Archaea. From the standpoint of molecular phylogenetics, they are characterized by a distinctive ribosomal Introduction/21.html">RNA Structure, Setting them apart from the second phylum (Euryarchaeota).

The upper Temperature limit for these organisms, adapted to primeval living conditions, is determined by Water availability as well as the stability of cellular components. Cells of Pyrodictium occultum (Sulfolobales), 0.3 — 2.5 µm in diameter, range from disk-shaped to cup-shaped; they are enclosed in a network of hollow fibrils, with an optimal growth temperature of 100°C and an upper temperature limit for growth of 110°C. Water at such high temperatures remains liquid only under pressure, for example, near the ocean floor or deep within solfatara fields. Pyrodictium was discovered in volcanically heated deep-sea waters. It is a strictly anaerobic Organism that reduces sulfur to hydrogen sulfide. Sulfolobus acidocaldarius is an aerobic and extremely acid-thermophilic species; it is facultatively autotrophic, partly utilizing organic substrates for Respiration and partly oxidizing sulfur to sulfuric acid using oxygen and water. The temperature minimum for its growth is 60°C (for Pyrodictium occultum, 82°C). Acidothermus infernus can produce hydrogen sulfide or sulfuric acid depending on oxygen availability. Thermoplasma acidophilum (Thermoplasmales) is an organism isolated from smoking coal refuse piles and hot springs. These cell wall-deficient archaea die in neutral environments; their optimal pH for growth is 1 — 2, and temperature is 59°C. Their cells, which reproduce by budding, are highly variable: from strongly elongated to irregularly coccoid. Forms with a tuft of flagella have also been discovered. Disk-shaped cells of Thermoproteus and Thermofilum (Thermoproteales) can even grow into filaments exceeding 100 µm in length.

Second Phylum: Euryarchaeota

Representatives of this phylum inhabit a wide spectrum of extreme biotopes. From the standpoint of molecular phylogenetics (rRNA), they differ from the species of the preceding phylum.

1. Methanogenic archaea — anaerobes that produce methane; upon exposure to air, they die faster than anaerobic bacteria. Spore formation has not been observed. This is a morphologically diverse, yet physiologically very homogeneous group capable of an autotrophic lifestyle utilizing CO₂ and H₂ as the sole carbon and Energy Sources. Simple carboxylic acids and alcohol can also serve as alternative carbon sources. Furthermore, they are distinguished by the presence of two specific Cofactors found nowhere else, of which one (CoM, 2-mercaptoethanesulfonic acid) acts as a methyl carrier during methanogenesis, and the other (F₄₂₀) acts as a hydrogen carrier. Forms of Methanobacterium (Methanobacteriales) range from coccoid to narrow rod-shaped; moreover, all species are Gram-positive and possess a pseudomurein sheath. Subsequent genera are Gram-negative. The genus Methanospirillum (Methanomicrobiales) unites organisms in the form of long, twisted rods; their protein sheath does not participate in septum formation (cf. septum formation in eubacteria). Methanosarcina possesses unusually large cells grouped in packets with a heteropolysaccharide sheath. Methanococcus (not to be confused with Methylococcus) — the type genus of Methanococcales — forms cocci; instead of a rigid cell wall, it has a surface layer composed of protein components. Thus, the majority of "methanobacterial" genera have solved The problem of cell envelope construction in different ways. In addition, these forms bear virtually no resemblance in overall chemical composition, nor do they show similarity to eubacteria.

2. Halophilic archaea (Halobacteriales) survive even in dried salt and occur in hypersaline bodies of water. Halobacterium halobium can grow even at a 12% NaCl concentration. At pH 5.5, halobacteria can no longer live; their temperature optimum lies within 40 — 45°C. Under certain conditions, they can carry out phosphorylation (see 6.4.9) and, due to their carotenoid content, impart a red color to saline water.