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CHAPTER 2

Prokaryotic microorganisms

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Overview of microorganisms The Earth is 4.6 billion years old and microbial life is thought to

have first appeared between 3.8 and 3.9 billion years ago; in fact, 80% of Earth's history was exclusively microbial life. Microbial life is still the dominant life form on Earth. It has been estimated that the total number of microbial cells on Earth on the order of 2.5 × 1030 cells, making it the major fraction of biomass on the planet.

There are various hypotheses as to the origin of prokaryotic and eukaryotic cells. Because all cells are similar in nature, it is generally thought that all cells came from a common ancestor cell termed the last universal common ancestor (LUCA). These LUCAs eventually evolved into three different cell types, each representing a domain. The three domains are the Archaea, the Bacteria, and the Eukarya.

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Overview of microorganisms In any event, it is accepted today that there are three distinct

domains of organisms in nature: Bacteria, Archaea, and Eukarya.

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2.1 Bacteria and Archaea

Bacteria are prokaryotic cells. Like the Eukarya, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages. The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain peptidoglycan.

Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to most antibiotics that affect Eukarya.

Bacteria contain rRNA that is unique to the Bacteria as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Eukarya.

Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-negative bacteria.

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Membrane Lipids of Archaea, Bacteria, and Eukarya

The Bacteria and the Eukarya

have membranes composed of

unbranched fatty acid chains

attached to glycerol by ester

linkages.

The Archaea have membranes

composed of branched

hydrocarbon chains attached to

glycerol by ether linkages.

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Bacteria and Archaea

Archaea are prokaryotic cells. Unlike the Bacteria and the Eukarya, the Archaea have membranes composed of branched hydrocarbon chains (many also containing rings within the hydrocarbon chains) attached to glycerol by ether linkages. The cell walls of Archaea contain no peptidoglycan. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are sensitive to some antibiotics that affect the Eukarya.

Archaea contain rRNA that is unique to the Archaea as indicated by the presence molecular regions distinctly different from the rRNA of Bacteria and Eukarya.

Archaea often live in extreme environments and include methanogens, extreme halophiles, and hyperthermophiles. One reason for this is that the ether-containing linkages in the Archaea membranes is more stabile than the ester-containing linkages in the Bacteria and Eukarya and are better able to withstand higher temperatures and stronger acid concentrations.

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2.1.1 Sizes, Shapes, and Arrangements of Bacteria

Bacterial cell shape is determined primarily by a protein called MreB. MreB forms a spiral band – a simple cytoskeleton – around the interior of the cell just under the cytoplasmic membrane. It is thought to define shape by recruiting additional protens that then direct the specific pattern of bacterial cell growth. For example, bacillus-shaped bacteria that have an inactivated MreB gene become coccoid shaped, and coccus-shaped bacteria naturally lack the MreB gene.

Gram Stain of Escherichia coliGram Stain of Staphylococcus aureus

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Sizes, Shapes, and Arrangements of Bacteria

Most bacteria come in one of three basic shapes: coccus, rod or bacillus, and spiral.

Exceptions to the above shapes: Trichome-forming, sheathed, stalked, filamentous, square, star-shaped, spindle-shaped, lobed, and pleomorphic.

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Sizes, Shapes, and Arrangements of Bacteria

Coccus: The cocci are spherical or oval bacteria having one of several distinct arrangements based on their planes of division. Diplococcus, tetrad, sarcina, staphylococcus.

An average coccus is about 0.5-1.0 micrometer (µm) in diameter.

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Sizes, Shapes, and Arrangements of Bacteria

Bacillus: Bacilli are rod-shaped bacteria. Bacilli all divide in one plane producing a bacillus, streptobacillus, or coccobacillus arrangement.

An average bacillus is 0.5-1.0 µm wide by 1.0-4.0 µm long.

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Sizes, Shapes, and Arrangements of Bacteria

Spirals: Spirals come in one of three forms, a vibrio, a spirillum, or a spirochete.

Spirals range in size from 1 µm to over 100 µm in length.

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Vibrio Curved or comma-shaped rod A vibrio appears as a curved bacillus (arrows).

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Spirillum

Thick, rigid spiral.

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Spirochaeta

thin, flexible spiral. The spirochete Borrelia (arrows) in a blood smear.

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Scanning Electron Micrograph of Leptospira interrogans

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Exceptions to the above shapes

Trichome -forming, sheathed, stalked, filamentous, square, star-shaped, spindle-shaped, lobed, and pleomorphic.  

Alysiella filiformis Filamentous Bacterium

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2.1.2 Cell Structure of Bacteria

The mycoplasmas are the only bacteria that naturally lack a cell wall. Mycoplasmas maintain a nearly even pressure between the outside environment and the cytoplasm by actively pumping out sodium ions. Their cytoplasmic membranes also contain sterols that most likely provide added strength.

All other bacteria have a cell wall. The Bacteria, with the exception of the Chlamydias, have a semirigid cell wall containing peptidoglycan. Peptidoglycan prevents osmotic lysis.

The Archaea, that are often found growing in extreme environments, also have a semirigid cell wall but it is composed of chemicals distinct from peptidoglycan such as protein or pseudomurein.

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The Gram-Positive Cell Wall

Prokaryotic Cell (Bacillus megaterium).

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Electron Micrograph of a Gram-Positive Cell Wall

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Structure of a Gram-Positive Cell Wall

The Gram-positive cell wall appears as dense layer typically composed of numerous rows of peptidoglycan, and molecules of lipoteichoic acid, wall teichoic acid and surface proteins.

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The Gram-Negative Cell Wall

Freeze-Facture of a Gram-Negative Bacterium Showing the Various Layers of the Cell Wall and Cytoplasmic Membrane (View from the Top).

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The Gram-Negative Cell Wall

Freeze-Facture of a Gram-Negative Bacterium Showing the Various Layers of the Cell Wall and Cytoplasmic Membrane (Views from the Inside).

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Electron Micrograph of a Gram-Negative Cell Wall

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Structure of a Gram-Negative Cell Wall

The Gram-negative cell wall is composed of a thin, inner layer of peptidoglycan and an outer membrane consisting of molecules of phospholipids, lipopolysaccharides (LPS), lipoproteins and sutface proteins. The lipopolysaccharide consists of lipid A and O polysaccharide.

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Gram-Positive Cell Wall & Gram-Negative Cell Wall

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Structure of an Acid-Fast Cell Wall

In addition to peptidoglycan, the acid-fast cell wall of Mycobacterium contains a large amount of glycolipids such as mycolic acid, arabinogalactan-lipid comlex, and lipoarabinomannan.

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A Peptidoglycan Monomer

The peptidoglycan monomer in E. coli, most gram-negative bacteria, and many gram-positive bacteria. These monomers join together to form chains and the chains are then joined by cross-links between the tetrapeptides to provide strength.

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Peptidoglycan of Staphylococcus aureus

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Peptidoglycan of Escherichia coli

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Structure of Peptidoglycan

Peptidoglycan is composed of chains of peptidoglycan monomers (NAG-NAM-tetrapeptide). These monomers join together to form chains and the chains are then joined by cross-links between the tetrapeptides to provide strength.

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Specific staining

Most bacteria can be placed into one of three groups

based on their color after specific staining procedures

are performed: Gram-positive, Gram-negative, Acid-

fast.

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Gram-positive

Retain the initial dye crystal violet during the Gram stain

procedure and appear PURPLE when observed through the

microscope.

Common gram-positive bacteria of medical importance

include Streptococcus pyogenes, Streptococcus pneumoniae,

Staphylococcus aureus, Enterococcus faecalis, and

Clostridium species.

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Gram Stain of Staphylococcus aureus

Note gram-positive (purple) cocci in clusters.

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Gram-negative

Decolorize during the Gram stain procedure, pick up the

counterstain safranin, and appear pink when observed through

the microscope.

Common Gram-negative bacteria of medical importance include

Salmonella species, Shigella species, Neisseria gonorrhoeae,

Neisseria meningitidis, Hemophilus influenzae, Escherichia coli,

Klebsiella pneumoniae, Proteus species, and Pseudomonas

aeruginosa.

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Gram Stain of Escherichia coli

Note gram-negative (pink) bacilli.

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A Gram Stain of a Mixture of Ggram-Positive and Gram-Negative Bacteria

Note gram-negative (pink) bacilli and gram-positive (purple) cocci.

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Acid-fast

Acid-fast bacteria stain poorly with the Gram stain procedue,

appearing weakly gram-positive or gram-variable. They are

usually characterized using the acid-fast staining procedure.

Bacteria with an acid-fast cell wall resist decolorization with an

acid-alcohol mixture during the acid-fast staining procedure,

retain the initial dye carbol fuchsin and appear red.

Common acid-fast bacteria of medical importance include

Mycobacterium tuberculosis, Mycobacterium leprae,

Mycobacterium avium-intracellulare complex and Nocardia

species.

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Acid-fast stain of Mycobacterium tuberculosis

Note redish acid-fast bacilli (arrows).

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Teichoic acid

Nature: poly-glycerol-phosphates and poly-ribitol-phosphates with

variable side-groups. Staphylococcus aureus has poly-ribitol-phosphate

substituted with N-acetyl glucosamine. Staphylococcus epidermidis has poly-glycerol-phosphate

substituted with glucose. Location: teichoic acids are covalently linked to the peptidoglycan

molecule and dispersed throughout the wall.

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Teichoic acid

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Lipopolysaccharide

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Lipid A structure

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Cell membrane

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Cytoplasm and nuclear body

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Inclusion body

Gas vacuoles

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Capsule

India Ink Capsule Stain of Klebsiella pneumoniae showing white capsules

(Glycocalyx) surrounding purple cells

Capsule stain of Enterobacter aerogenes

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Flagellum

Vibrio parahaemolyticus E. coli

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Bacterial Flagella Arrangements

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Monotrichous Flagellum of Vibrio cholerae

a single flagellum, usually at one pole

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Spirillum with Lophotrichous Arrangement of Flagella

Note tuft of flagella at arrow.

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Salmonella with a peritrichous arrangement of flagella

Note numerous flagella covering the bacteria

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Structure of a Bacterial Flagellum

The filament of the bacterial flagellum is connected to a hook which, in turn, is attached to a rod. The basal body of the flagellum consists of a rod and a series of rings that anchor the flagellum to the cell wall and the cytoplasmic membrane. In gram-negative bacteria, the L ring anchors the flagellum to the lipopolysaccharide layer of the outer membrane while the P ring anchors the flagellum to the peptidoglycan portion of the cell wall. The MS ring is located in the cytoplasmic membrane and the C ring in the cytoplasm. The Mot proteins surround the MS and C rings of the motor and function to generate torque for rotation of the flagellum. Energy for rotation comes from proton motive force. Protons moving through the Mot proteins drives rotation. The Fli proteins act as the motor switch to trigger either clockwise or counterclockwise rotation of the flagellum and to possibly disengage the rod in order to stop motility.

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Pilus

E.coli 6,105

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Pilus and sex pilus

E.coli 3,645

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Significance of Pili

Flushing Away of Bacteria Lacking Pili Bacteria Resisting Flushing by way of Pili

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Bacteria Altering the Adhesive Tips of Their Pili

By genetically altering the adhesive tips of their pili, certain bacteria are able to: 1) adhere to and colonize different cell types with different receptors, and 2) evade antibodies made against the previous pili.

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Endospore

Endospores are dormant alternate life forms produced by the genus Bacillus, the genus Clostridium, and a number other genera of bacteria, including Desulfotomaculum, Sporosarcina, Sporolactobacillus, Oscillospira, and Thermoactinomyces.

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Endospore stain of Bacillus megaterium

Note red endospores inside colorless streptobacillus.

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Endospore stain of Bacillus megaterium

Note green endospores within pink bacilli. Many spores have already been released from the vegetative cells.

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Endospore stain of Clostridium tetani

Note the endospore within the rod gives the bacterium a "tennis racquet" shape (arrows).

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Electron micrograph of an endospore of Bacillus stearothermophilus

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Endospore Cycle, Step 1

A vegetative bacterium about to enter the endospore cycle.

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Endospore Cycle, Step 2

The nucleoid replicates.

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Endospore Cycle, Step 3

A spore septum forms.

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Endospore Cycle, Step 4

Each nucleoid becomes surrounded by its own cytoplasmic membrane.

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Endospore Cycle, Step 5

The cytoplasmic membrane surrounds the isolated nucleoid, cytoplasm, and membrane from the previous step forming a forespore.

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Endospore Cycle, Step 6

The forespore is completed and the other molecule of DNA is eventually degraded.

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Endospore Cycle, Step 7

A thick protective layer of peptidoglycan called the cortex is synthesized between the inner and outer forespore membranes. Calcium dipicolinate is synthesized and incorporated in the forming endospore.

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Endospore Cycle, Step 8

Another protective layer called the spore coat and composed of protein is synthesized.

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Endospore Cycle, Step 9

Sometimes a final layer called the exosporium is added. As the vegetative portion of the bacterium is degraded, the completed endospore is released.

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Endospore Cycle, Step 10

With the proper environmental stimuli, the endospore germinates. As the protective layers of the endospore are enzymatically broken down, a vegetative bacterium begins to form and emerge.

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Endospore Cycle, Step 11

The vegetative bacterium now begins to divide by binary fission.

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Endospore Cycle, Step 12

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2.1.3 Colony of Bacteria and Archaea

Bacterial colony is defined as a visible cluster of bacteria

growing on the surface of or within a solid medium,

presumably cultured from a single cell.

Binary Fission

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2.2 Actinomycetes

Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content in their DNA. They can be terrestrial or aquatic. Actinobacteria is one of the dominant phyla of the bacteria. Analysis of glutamine synthetase sequence has been suggested for phylogenetic analysis of Actinobacteria.

Actinobacteria are well known as secondary metabolite producers and hence of high pharmacological and commercial interest.

Some Actinobacteria form branching filaments, which somewhat resemble the mycelia of the unrelated fungi, among which they were originally classified under the older name Actinomycetes.

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Streptomyces

Streptomyces is notable as a source of antibiotics. Substrate mycelium Aerial mycelium Spore mycelium

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Spores of Streptomyces avermitilis

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Actinomycetes morphology

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Actinomycetes morphology

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Colony of Streptomyces coelicolor

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Surface and reverse side of the Streptomyces colony

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Nocardia

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Streptosporangium nondiaststicum

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2.3 Cyanobacteria

Cyanobacteria, also known as blue-green bacteria, blue-green algae, and Cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis.

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Structure of Cyanobacterium (Dermocarpa sp.)

Thylakoids, reserve materials: PHB, cynophycine.

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Heterocyst

Heterocyst-Specialized cells for nitrogen fixation.

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Akinete

Akinetes-Thick-walled resistant stages that remain inactive for sometime. They germinate to form new filaments.

Anabaena free akinete

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Hormogonia

Hormogonium-A short segment of the filament breaks off and forms a new filament.

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Chamaesiphon

Endospore

Endospores are formed in Dermocarpa (Chamaesiphonales) by multiple

fission of a large sperical vegetative cell and subsequently released by

rupture of the parental cell and eventually form new vegetative cells.

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Chroococcus

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Gloeocapsa

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Dermocapa

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Oscillatorua

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Spirulina

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Anabaena

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Hapalosiphon

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2.4 Mycoplasma

Mycoplasma refers to a genus of bacteria that lack a cell wall. Without a cell wall, they are unaffected by many common antibiotics such as penicillin or other beta-lactam antibiotics that target cell wall synthesis. They can be parasitic or saprotrophic. Several species are pathogenic in humans, including M. pneumoniae, which is an important cause of atypical pneumonia and other respiratory disorders, and M. genitalium, which is believed to be involved in pelvic inflammatory diseases. Mycoplasma is the smallest known cell and is about 0.1 µm in diameter.

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Mycoplasma colonies

Mycoplasma colonies apparently commonly possess a "fried-egg" appearance. This colony also observed under the microscope. Magnification approximate 8×.

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Mycoplasma colonies

Tiny colonies (~ 0.5 mm) observed under stereomicroscope and “fried-egg” (see images) morphology.

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Mycoplasma

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Characteristics

Mycoplasmas are unusual among bacteria in that most require sterols for the stability of their cytoplasmic membrane. Sterols are acquired from the environment, usually as cholesterol from the animal host.

Mycoplasmas generally possess a relatively small genome of 0.58-1.38 megabases, which results in drastically reduced biosynthetic capabilities and explains their dependence on a host.

Mycoplasma species are often found in research laboratories as contaminants in cell culture. Mycoplasmal cell culture contamination occurs due to contamination from individuals or contaminated cell culture medium ingredients.

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Scientific classification Scientific classificationKingdom: Bacteria

Phylum: Tenericutes or Firmicutes

Class: Mollicutes

Order: Mycoplasmatales

Family: Mycoplasmataceae

Genus: Mycoplasma Nowak 1929

Species

M. gallisepticumM. genitaliumM. haemofelisM. hominisM. hyopneumoniaeM. ovipneumoniaeM. pneumoniaeetc.

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2.5 Rickettsia

Rickettsia is a genus of non-motile, Gram-negative, non-sporeforming, highly pleomorphic bacteria that can present as cocci (0.1 μm in diameter), rods (1–4 μm long) or thread-like (10 μm long).

Being obligate intracellular parasites, the Rickettsia survival depends on entry, growth, and replication within the cytoplasm of eukaryotic host cells (typically endothelial cells).

Rickettsia cannot live in artificial nutrient environments and are grown either in tissue or embryo cultures (typically, chicken embryos are used).

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Rickettsia

Rickettsia species are carried by many ticks, fleas, and lice, and cause diseases in humans such as typhus, rickettsialpox, Boutonneuse fever, African tick bite fever, Rocky Mountain spotted fever, Flinders Island spotted fever and Queensland tick typhus (Australian Tick Typhus). They have also been associated with a range of plant diseases. The name rickettsia is often used for any member of the Rickettsiales. They are one of closest living relatives to bacteria that were the origin of the mitochondria organelle that exists inside most eukaryotic cells.

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Rickettsia conorii

0.5 µm

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Head louse on human hair (Rickettsia carrier)

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Scientific classificationScientific classification

Domain: BacteriaPhylum: ProteobacteriaClass: AlphaproteobacteriaOrder: RickettsialesFamily: RickettsiaceaeGenus: Rickettsia da Rocha-Lima, 1916

SpeciesRickettsia aeschlimanniiRickettsia africaeRickettsia akariRickettsia asiaticaRickettsia australisRickettsia canadensis

Rickettsia conoriiRickettsia cooleyiRickettsia felisRickettsia heilongjiangensisRickettsia helveticaRickettsia honeiRickettsia huliniiRickettsia japonicaRickettsia massiliaeRickettsia montanensisRickettsia parkeri[3]

Rickettsia peacockiiRickettsia prowazekii[3]

Rickettsia rhipicephaliRickettsia rickettsii[3]

Rickettsia sibirica[3]

Rickettsia slovacaRickettsia tamuraeRickettsia typhi[3]

etc.

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2.6 Chlamydia

Chlamydia is a genus of bacteria that are obligate intracellular parasites. Chlamydia infections are the most common bacterial sexually transmitted infections in humans and are the leading cause of infectious blindness worldwide.

The three Chlamydia species include Chlamydia trachomatis (a human pathogen), Chlamydia suis (affects only swine), and Chlamydia muridarum (affects only mice and hamsters).

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Chlamydia

Chlamydia trachomatis inclusion bodies (brown) in a McCoy cell culture.

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Chlamydia

Chlamydial Inclusion under 100× oil objective.

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Life Cycles of Chlamydias

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Life Cycles of Chlamydias, Step 1

An elementary body attaches to the host cell and begins to enter by endocytosis.

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Life Cycles of Chlamydias, Step 2

The elementary body is placed in a vacuole.

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Life Cycles of Chlamydias, Step 3

The elementary body reorganizes to form a larger reticulate body.

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Life Cycles of Chlamydias, Step 4

The reticulate body divides by binary fission.

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Life Cycles of Chlamydias, Step 5

The reticulate bodies convert back to elementary bodies.

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Life Cycles of Chlamydias, Step 6

The elementary bodies are released from the host cell.

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Scientific classification

Scientific classificationDomain: BacteriaClass: ChlamydiaeOrder: Chlamydiales

Family: Chlamydiaceae

Genus: Chlamydia Jones et al. 1945 emend. Everett et al. 1999

Species

Chlamydia muridarum Everett et al. 1999Chlamydia suis Everett et al. 1999Chlamydia trachomatis (Busacca 1935) Rake 1957 emend. Everett et al. 1999

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2.1 Bacteria and Archaea 2.2 Actinomycetes 2.3 Cyanobacteria 2.4 Mycoplasma 2.5 Rickettsia 2.6 Chlamydia

Summery

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Microbiology (5th Edition): Chapter 20 The Archaea Chapter 21 Bacteria:The Deinococci and Nonproteobacteria Gram Negatives Chapter 22 Bacteria:The Proteobacteria Chapter 23 Bacteria:The Low G + C Gram Positives Chapter 24 Bacteria:The High G + C Gram Positives

Further reading