GENERAL MICROBIOLOGY - T.P. Pyrog - 2004

7. PROKARYOTE SYSTEMATICS

7.5. CHARACTERISTICS OF TAXA ACCORDING TO THE NINTH EDITION OF BERGEY'S MANUAL OF SYSTEMATIC BACTERIOLOGY

7.5.1. Division Gracilicutes

This division includes prokaryotes with a complex Cell wall Structure OF THE Gram-negative type. The walls consist of an outer membrane, a thin inner layer of peptidoglycan, and additional components located externally or between these two layers. They are Gram-negative. Cells are spherical, oval, straight or Curved Rods, spirals, or filamentous; some forms may be surrounded by a sheath or capsule. Reproduction occurs by binary fission, although budding is characteristic of certain groups, and multiple fission occurs in some organisms (Рlеirосарsаlеs). Myxobacteria can form fruiting bodies and myxospores. Endospores are not formed. Many representatives are motile (movement via flagella or by gliding). The group includes both phototrophs and non-phototrophs (both lithotrophs and heterotrophs), aerobes, anaerobes, facultative anaerobes, and microaerophiles.

The division is divided into three classes:

Scotobacteria (consisting of 14 parts — Nos. 1...14) (Table 7.1);

Anoxyphotobacteria (consisting of a single part — No. 15);

Oxyphotobacteria (consisting of a single part — No. 16).

Class Scotobacteria

Part 1. Spirochetes. Gram-negative, spiral-shaped cells that are extremely flexible and motile by means of periplasmic flagella rather than flagella protruding from The Cell into the external environment. Chemoorganoheterotrophs. Do not form spores; reproduce by transverse fission. Anaerobes, microaerophiles, facultative anaerobes, or aerobes.

Table 7.1.

Class Scotobacteria

They occur either free-living or in association with animals, Mollusks, Arthropods, or humans. Some species are pathogenic.

Free-living species inhabiting sewage, polluted waters, as well as fresh and marine waters containing hydrogen sulfide, are represented by bacteria of the genus Spirochaeta. They ferment glucose to produce acetic, lactic, oxalic, and formic acids, ethanol, carbon dioxide, and hydrogen.

Associated forms include Representatives of the genus Cristispira, which inhabit the digestive tracts of freshwater and marine mollusks. Among parasites (Treponema, Borreha, Leptospira), there are pathogenic species: Treponema pallidum, the CAUSATIVE AGENT OF Syphilis, and Leptospira interrogans, the causative agent of leptospirosis.

Part 2. Aerobic, microaerophilic, motile, helically curved Gram-negative bacteria. Gram-negative cells are spiral-shaped (with one or more complete turns of the helix) or vibrioid (possessing less than one complete turn of the helix). Motile by means of polar flagella, moving in a straight line with a characteristic corkscrew motion. Aerobes or microaerophiles. Respiratory METABOLISM utilizing oxygen as the electron acceptor. Some are capable of Anaerobic Respiration using nitrate or fumarate as the electron acceptor. Chemoorganotrophs, though some can grow autotrophically using H₂ as an electron donor. Found in soil, fresh and marine Water, plant roots, reproductive Organs, and the digestive tract and Oral Cavity of humans and animals. Some are pathogenic to humans and animals. Certain species are predatory toward other microorganisms.

Representatives of the genus Azospirillum are free-living microaerophilic nitrogen-fixing organisms found on the roots of grasses and legumes, while bacteria of the genus Vampirovibrio inhabit chlorella. Spirilla are mainly Saprophytes, living in stagnant and polluted waters, seawater (Oceanospirillum), on rotting PLANT AND ANIMAL debris, and in rice paddies. Among the parasites are bacteria of the genus Bdellovibrio, notably Bdellovibrio bacteriovorrus, an intracellular bacterial parasite. This is a non-spore-forming, small (0.25-0.4 χ 0.8-1.2 µm), slightly curved rod with a single polar flagellum. The cells are highly motile. They are capable of existing both inside a bacterial cell and saprophytically on a complex nutrient medium supplemented with Yeast extract. B. bacteriovorrus attaches to the host cell, loses its flagellum, penetrates through The cell wall (using envelope-dissolving Enzymes) into the periplasmic space, and multiplies there. The intracellular development cycle lasts 3–5 hours, after which the parasite cells exit the dead cell to either repeat the parasitic phase or enter a resting state by forming cysts. In an environment with an Abundance of host cells, the cysts germinate and repeat the parasitic development phase once again. Bacteria of this genus inhabit soil, marine, and fresh waters, and are utilized to combat pathogens of epidemiological diseases (such as cholera).

Part 3. Non-motile (or rarely motile) Gram-negative curved bacteria. Chemoorganoheterotrophs. Saprophytes. This group encompasses four types of microorganisms:

1) curved or C-shaped bacteria capable of forming rings by overlapping their cell ends. Cells in the shape of coils and spirals may also occur. Gas vacuoles may be present. Aerobes, found in soil and water;

2) vibroid or straight (or curved) rods. They form gas vacuoles. Aerotolerant anaerobes with a strictly fermentative type of metabolism;

3) arc-shaped cells with gas vacuoles arranged in the shape of a cloverleaf. Pretzel-shaped cells can also be found. They inhabit lakes and ponds where sulfide is present and oxygen is absent.

4) slender S-shaped cells that form flattened sigmoid aggregates by closely packing against one another (in numbers of 4 or multiples of 4), making them motile.

They inhabit fresh and brackish waters where sulfide is present and oxygen is absent.

The first group of organisms includes bacteria of the genus Spirosoma, the third includes Brachyarcus, and the fourth includes Pelosigma. A fermentative type of metabolism is characteristic of the genus Meniscus, while a respiratory type is found in Runnella. They form white-beige pigments ({Містку cyclus aquaticus), yellow (Spirosoma linguale), and pink (Flectobacillus major).

Part 4. Gram-Negative Aerobic Rods and Cocci. Chemoorganoheterotrophs, though some can grow autotrophically using H₂ as an electron donor. They do not form prosthecae, stalks, sheaths, or gas vacuoles. Gliding motility is absent. They do not reproduce by budding. They grow in an ambient air atmosphere. Metabolism is respiratory, utilizing oxygen as the terminal electron acceptor. Some species are capable of anaerobic respiration using electron acceptors other than oxygen. They are found in soil, fresh and marine water, plant roots, or in the reproductive organs, intestinal tract, and oral cavity of humans and animals. Some are pathogenic to humans or animals.

The bacteria are grouped into eight families (see Table 7.1). It should be noted that in Bergey's Manual of Determinative Bacteriology (1997), this group of bacteria is divided into 80 genera, 40 of which were not included in Bergey's Manual of Systematic Bacteriology because they were first described after its publication (mainly in 1987–1992).

Pseudomonads (family Pseudomonaceae) are obligate aerobes, though some species are facultatively anaerobic. They do not fix molecular nitrogen, are motile (by polar flagella), and occur as single straight or curved rods. Representatives of the genus Pseudomonas can utilize a wide range of Organic compounds as a carbon source, including heterocyclic and Aromatic Compounds that are not assimilated by other microorganisms (Pseudomonas fluorescens, Pseudomonas putida). Pseudomonas aeruginosa is a pathogenic bacterium capable of causing otitis, Pneumonia, meningoencephalitis, and wound suppuration. Strains pathogenic to plants are grouped within the species Pseudomonas syringae. Bacteria of the genus Xanthomonas are phytopathogenic (pathogenic to plants). Xanthomonas campestris is the producer of xanthan, the world's best-known microbial exopolysaccharide.

Members of the family Azotobacteraceae are rod-shaped cells that change their Morphology depending on age and cultivation conditions. They are capable of forming cysts. Their key feature is The ability to fix molecular nitrogen. Azotobacter chroococcum is the first known aerobic free-living nitrogen fixer (fixing 10 mg or more of nitrogen per gram of consumed carbon). The preparation azotobacterin, manufactured from living cultures of nitrogen fixers, is used to enrich soil with nitrogen and increase crop yields. Azotobacter vinelandii is a producer of the polysaccharide alginate, which is compositionally similar to plant Polysaccharides extracted from seaweeds.

Bacteria of the genus Rhizobium (rhizobia) are capable of fixing nitrogen in Symbiosis with leguminous plants. The species names of ROOT-nodule bacteria are largely determined by their host plant (Rhizobium leguminosarum, Rhizobium meliloti). Bacteria of the genus Agrobacterium (Agrobacterium tumefaciens) are intracellular parasites that penetrate plant Tissues through wounds and induce tumors on the roots, stems, or leaves of plants.

The family Acetobacteriaceae comprises bacteria capable of oxidizing ethanol to acetic acid in a neutral or acidic environment (pH 4.5).

Bacteria of the genera Neisseria, Moraxella, and Kingella are parasites (causing Gonorrhea, meningitis, and infections of the mucous membranes in humans and warm-blooded animals).

Part 5. Facultatively Anaerobic Gram-Negative Rods. Chemoorganoheterotrophs, though some can grow autotrophically using H₂ as an electron donor. They do not form prosthecae, stalks, sheaths, or gas vacuoles. Gliding motility is absent. They do not reproduce by budding. They are capable of growth in ambient air; their metabolism is respiratory, though they can also grow heterotrophically via Fermentation. They occur as free-living forms as well as in associations with animals, humans, or plants. Some are pathogenic.

The bacteria are grouped into three families (see Table 7.1). In Bergey's Manual of Determinative Bacteriology (1997), the family Enterobacteriaceae comprises 30 genera, half of which were not included in Bergey's Manual of Systematic Bacteriology because these genera were first described after its publication.

The typical genus of the family Enterobacteriaceae is the genus Escherichia (with the type species Escherichia coli, the colon bacterium). To date, this bacterium is the most thoroughly studied of all prokaryotes; it can be called an "open book" as it serves as a primary model object for all molecular biological, genetic, and biochemical research. Escherichia coli is a conditionally pathogenic Organism. In the intestines of vertebrates, it acts as a commensal (commensalism being a form of symbiosis where the microorganism feeds at the expense of the host without causing harm or benefit). However, under certain conditions (such as host immunosuppression), it can cause intestinal diseases. Pathogenic strains of the colon bacterium cause colienteritis in humans. Through gastrointestinal excretions, Escherichia coli enters the environment—water, soil, and food products—and is considered an indicator of fecal environmental contamination.

Pathogenic species are found among members of the genera Salmonella (the causative agent of typhoid fever), Shigella (the causative agent of dysentery), and Klebsiella. Phytopathogenic species occur among bacteria of the genera Erwinia and Enterobacter.

Part 6. Gram-Negative Anaerobic Straight, Curved, and Helical Rods. Chemoorganoheterotrophs. Obligately anaerobic, non-spore-forming, nonmotile or motile rods prone to pleomorphism. They obtain energy through anaerobic respiration or fermentation. In anaerobic respiration, they do not utilize sulfate, other oxidized sulfur compounds, or elemental sulfur as TERMINAL ELECTRON ACCEPTORS.

The bacteria are grouped into a single family, Bacteroidaceae, and 13 genera (Butyriovibrio, Succinivibrio, Bacteroides, Fusobacterium, Leptotrichia, Wolinella, Anaerovibrio, Acetivibrio, etc.). In Bergey's Manual of Determinative Bacteriology (1997), the family Bacteroidaceae consists of 47 genera, over 30 of which were not included in Bergey's Manual of Systematic Bacteriology because they were first described after its publication.

Bacteria of this group inhabit the Oral Cavity and gastrointestinal tract of humans, animals, and insects. Some species are pathogenic (certain Fusobacterium species are associated with purulent and gangrenous infections). Bacteria of different genera differ in their final fermentation products: members of the genus Butyriovibrio produce butyrate from glucose, Succinivibrio produces succinate, and Acetivibrio produces acetate. Fusobacterium accumulate butyric acid as their main fermentation product, Leptotrichia accumulate lactic acid, and Bacteroides produce a mixture of acids (succinic, acetic, formic, etc.).

Part 7. Sulfate-Assimilating or Sulfate-Reducing Bacteria. This group includes chemolithotrophic obligate anaerobes that obtain energy by oxidizing molecular hydrogen under anaerobic conditions, using sulfate as a terminal electron acceptor. There are also chemoorganotrophs that utilize organic acids (lactate, Pyruvate, formate, acetate), alcohols (ethanol, butanol), and CARBOHYDRATES as sources of carbon and energy. They do not form endospores and are predominantly nonmotile.

The bacterial group is represented by the genera Desulfovibrio, Desulfomonas, Desulfobulbus, Desulfobacter, Desulfococcus, and Desulfosarcina.

Desulfosarcina variabilis is capable of autotrophic growth, utilizing CO₂ as its sole carbon source, H₂S for energy, and SO₄^2- as the terminal electron acceptor.

Part 8. Anaerobic Gram-Negative Cocci. Chemoorganoheterotrophs. Anaerobes. Non-spore-forming, nonmotile cells occurring singly, in pairs, in chains, or in clumps. Metabolism is strictly fermentative.

The group is represented by a single family, Veillonellaceae, which consists of three genera: Veillonella, Acidaminococcus, and Megasphaera.

They are parasites of warm-blooded animals and are found in the digestive tracts of humans, ruminants, rodents, and pigs.

Part 9. Rickettsiae and Chlamydiae. Obligate Intracellular Parasites of eukaryotic hosts (vertebrates and arthropods). Cells are rod-shaped, coccoid, or pleomorphic. Many species are pathogenic.

Rickettsiae of the tribe Rickettsieae are pathogenic to humans (causing epidemic typhus and fevers), whereas those of the tribe Ehrlichieae are nonpathogenic. Bacteria of the tribe Wolbachieae are arthropod symbionts and are nonpathogenic, with the exception of the genus Rickettsiella, which comprises pathogens of insect larvae and certain other invertebrates. Rickettsiae of the family Bartonellaceae are found in the erythrocytes of humans and vertebrates. Small rickettsial forms of the family Anaplasmataceae are obligate parasites of the Blood Plasma and erythrocytes of many wild and domestic animals.

Chlamydiae are obligate intracellular parasites of humans and vertebrates that reproduce exclusively within the host Cytoplasm.

Part 10. Gliding Bacteria. Chemoorganotrophic, obligately aerobic bacteria lacking flagella but capable of gliding across solid surfaces. Under nutrient deprivation, cells aggregate to form fruiting bodies composed of mucus and cells, which are often brightly colored and visible to the naked eye. Fruiting bodies range from simple clumps to complex structures featuring sporangia of characteristic SHAPES AND SIZES, arranged singly or in groups on simple or branched stalks. The cells inside the fruiting bodies represent resting stages (myxospores or microcysts).

Fruiting bodies can be formed by representatives of the order Myxobacteriales. Myxobacteria are characterized by a high activity of lytic enzymes that drive the Hydrolysis of Proteins, Nucleic Acids, polysaccharides, etc. Consequently, they actively decompose dead plant residue and lyse both prokaryotic and Eukaryotic cells. They inhabit soil, decaying plant material, and the bark of living trees.

Part 11. Sheathed bacteria. Chemoorganoheterotrophs. Aerobes. Incapable of gliding motility. Characterized by filamentous growth, with cells enclosed in sheaths (tubes or extracellular material). When observed in a wet mount using Phase-contrast Microscopy, the tube appears transparent, resembling a microscopic plastic tube or pipe. Sometimes the sheath is so thin and closely appressed to the cell that it is indistinguishable under phase-contrast microscopy. Upon The addition of 95% ethanol to the preparation, the sheath becomes visible. Sheaths may range in color from yellow to dark brown due to the deposition of iron and manganese oxides within them. Individual cells may be motile via polar or subpolar flagella, or non-motile.

Bacteria are either free-floating or attached to submerged plants, stones, and other objects. They occur in wastewater, activated sludge, as well as in marine and freshwater environments. The most common genera are Sphaerotilus, which inhabit wastewater, and Leptothrix, which thrive in environments rich in organic matter and iron.

Part 12. Budding and/or appendaged bacteria. Non-phototrophic organisms are classified as follows:

1) bacteria possessing prosthecae (slender extensions of living cellular material consisting of a cell wall, cytoplasmic membrane, and cytoplasm):

a) reproduction by asymmetric budding. Buds form at the tip of the prostheca or on the cell surface;

b) reproduction by binary transverse fission;

2) bacteria lacking prosthecae:

a) budding bacteria;

b) non-budding bacteria. They form stalks (cytoplasm-free extensions used by the cell to attach to a surface);

a) other bacteria possessing: tapered filaments at the ends encrusted with manganese dioxide; ribbon-like structures not encrusted with metal oxides; stalks (hollow, cone-shaped extensions visible under a Light Microscope).

Prosthecae are formed by bacteria of the genera Caulobacter and Prosthecomicrobium. Bacteria of the genus Hyphomicrobium reproduce by budding. Bacteria of the genus Pedomicrobium accumulate iron and manganese.

Part 13. Gram-negative chemolithotrophic bacteria. Depending on the Chemical Nature of the Inorganic Compounds serving as their energy source, they are divided into the following groups:

1) nitrifiers. They can utilize reduced inorganic nitrogen compounds (AMMONIA AND NITRITE) as an energy source for growth;

2) sulfur-oxidizing bacteria. They can oxidize reduced inorganic sulfur compounds, with many organisms utilizing them as their sole energy source;

3) obligate hydrogen oxidizers, which use molecular hydrogen as an energy source for growth. Organic carbon sources are not utilized;

4) bacteria lacking prosthecae and stalks. They form or accumulate iron and/or manganese oxides on the cell surface or internally;

5) magnetotactic bacteria, which exhibit tactic responses to magnetic fields. The cells contain iron-rich electron-dense inclusions (magnetosomes).

The first group includes bacteria of the family Nitrobacteraceae (genera Nitrosomonas, Nitrospira, Nitrosococcus, Nitrospira, Nitrobacter); the second group includes genera such as Thiobacillus, Thiobacterium, Thiovulum, Thiospira, etc. Bacteria capable of precipitating iron and manganese include representatives of the family Siderocapsaceae (genera Siderocapsa, Siderococcus, etc.).

Nitrifiers inhabit soil, fresh water, and marine environments. Sulfur-oxidizing bacteria live in soil, water, sulfur springs, and sulfur deposits where hydrogen sulfide is produced and sulfur is deposited. Bacteria of the family Siderocapsaceae are found in iron-bearing waters.

Part 14. Endosymbionts. This group of symbiotic bacteria remains insufficiently studied. Based on their host type, they are divided into three groups: endosymbionts of protozoa (Ciliates, flagellates, amoebae), insects, and Fungi and other invertebrates (excluding arthropods). All endosymbionts are adapted to intracellular existence, and most of them are unable to grow in vitro (outside the cell).

Five genera of protozoan endosymbiotic bacteria are known (Halospora, Tectibacter, Lyticum, Caedibacter, Pseudocaedibacter) along with one genus of insect endosymbionts (Blattabacterium).

Class Anoxyphotobacteria

Part 15. Phototrophic bacteria. Bacteria that contain bacteriochlorophyll and carotenoids and are capable of utilizing light as an energy source. They grow in the light under anaerobic conditions and do not release oxygen during Photosynthesis. Some are capable of dark growth via aerobic respiration. They can exist photoautotrophically, photoheterotrophically, and chemoheterotrophically. They cannot use water as a hydrogen donor; instead, they require Donors with a higher oxidation state (hydrogen sulfide, hydrogen, organic compounds). Consequently, their photosynthesis proceeds without oxygen evolution (anoxygenic photosynthesis). They lack phycobiliproteins. This is a morphologically diverse group comprising cocci, rods, curved forms (spirilla, vibrios), both motile and non-motile.

Taxonomy. These bacteria belong to two orders. The first order, Rhodospirillales (purple bacteria), encompasses the families Rhodospirillaceae (non-sulfur purple bacteria) and Chromatiaceae (purple sulfur bacteria); the second order, Chlorobiales (green bacteria), encompasses the families Chlorobiaceae (green sulfur bacteria) and Chloroflexaceae.

Characteristics of representatives. Depending on their ability to use elemental sulfur as an electron donor, they are divided into sulfur and non-sulfur bacteria.

A common feature of the members of the order Rhodospirillales is that their photosynthetic apparatus is located on internal membranes (thylakoids) formed by invaginations of The Plasma Membrane. Members of the order Chlorobiales are characterized by the presence of chlorosomes—pigment-containing Organelles attached to the plasma membrane. Bacteriochlorophyll is specifically housed within these chlorosomes.

Purple and green bacteria inhabit water bodies with a hydrogen sulfide concentration of 20–100 mg/L and higher, which provides anaerobic conditions for their survival. Non-sulfur bacteria thrive in organic-rich aquatic environments. They inhabit both saline and freshwater bodies and are presumably among the oldest bacteria on Earth.

Class Oxyphotobacteria

Part 16. Cyanobacteria. Bacteria that contain chlorophyll a, use light as an energy source, and release oxygen (just like green plants). They are divided into two groups:

1) organisms containing chlorophyll a and phycobiliproteins (allophycocyanin, phycocyanin, and occasionally phycoerythrin), known as cyanobacteria;

2) organisms containing chlorophylls a and b (which are otherwise characteristic only of green Algae and higher plants), but lacking phycobiliproteins, known as prochlorophytes.

Taxonomy. They are divided into two orders—Cyanobacteriales and Prochlorales. Based on morphological features, cyanobacteria are classified into five groups:

1) chroococcalean cyanobacteria—unicellular rods and cocci, occurring singly or in aggregates held together by capsules or slime. They reproduce by binary fission or budding. Genera include Synechococcus, Gloebacter, etc.;

2) pleurocapsalean cyanobacteria—also unicellular forms, but capable of reproduction via multiple fission as well. During this process, numerous small cells called baeocytes develop inside the dividing cell. Genera include Pleurocapsa, Dermocapsa, Myxosarcina, etc.;

3) filamentous cyanobacteria without heterocysts—trichoms consist exclusively of vegetative cells. Genera include Oscillatoria, Spirulina, Plectonema, etc.;

4) filamentous cyanobacteria with heterocysts—genera include Anabaena, Nostoc, etc. In addition to heterocysts, they can form akinetes—resting cells that differentiate from vegetative cells by developing a thick outer wall, increasing in volume, and accumulating cyanophycin, Glycogen, Lipids, and carotenoids. Cells divide in a single plane;

5) filamentous cyanobacteria with heterocysts—differ from group 4 in that their cells divide in more than one plane. Genus Fischerella.

Characteristics of representatives. The photosynthetic apparatus is represented by thylakoids. A hallmark feature of cyanobacteria is the presence of phycobilisomes—disc-shaped structures attached to the outer surface of thylakoids, composed of phycobiliproteins. Phycobilisomes act as light-harvesting antenna pigments. Only a single cyanobacterium, Gloeobacter violaceus, lacks both thylakoids and phycobilisomes.

Cyanobacteria are widespread in various aquatic environments, soil, and rice paddies. Thanks to their ability to fix molecular nitrogen, they can thrive in nutrient-poor habitats such as marine sands and desert rocks. They are remarkably resilient to extreme conditions. Some cyanobacteria are so acid-tolerant and thermophilic that they grow in acidic hot springs (70 °C, pH 4.0).

Prochlorophytes are exosymbionts living on the bodies of marine animals.