CLASSIFICATION AND STRUCTURE OF MICROORGANISMS.

Chair of Microbiology, Virology, and Immunology

Comparison of the three domainsCharacteristic Eubacteria Archaea Eucarya

Cell type Prokaryote Prokaryote Eukaryote

Cell wall Peptidoglycan Varies Varies

Membrane lipids

Unbranched Branched Unbranched

Sensitive to antibiotics?

Yes No No

Circular chromosome?

Yes Yes No (except in mitochondria and chloroplasts)

Histones? No Yes Yes

Prokaryotes

Classification Systems in the Procaryotae

1. Microscopic morphology

2. Macroscopic morphology – colony appearance

3. Physiological / biochemical characteristics

4. Chemical analysis

5. Serological analysis

6. Genetic and molecular analysis• G + C base composition• DNA analysis using genetic probes• Nucleic acid sequencing and rRNA analysis

Bacterial Taxonomy Based on Bergey’s Manual

• Bergey’s Manual of Determinative Bacteriology – five volume resource covering all known procaryotes– classification based on genetic information –

phylogenetic– two domains: Archaea and Bacteria– five major subgroups with 25 different phyla

Taxonomy

• Domain• Kingdom• Phylum• Class• Order• Family• Genus• species

Major Taxonomic Groups of Bacteria

• Vol 1A: Domain Archaea– primitive, adapted to extreme habitats and

modes of nutrition

• Vol 1B: Domain Bacteria • Vol 2-5:

– Phylum Proteobacteria – Gram-negative cell walls

– Phylum Firmicutes – mainly Gram-positive with low G + C content

– Phylum Actinobacteria – Gram-positive with high G + C content

Microbial Phylogeny

• Phylogeny of domain Bacteria– The 2nd edition of Bergey’s Manual of

Systematic Bacteriology divides domain Bacteria into 23 phyla.

Microbial Phylogeny

• Phylogeny of domain Bacteria (cont.) • Phylum Proteobacteria

– The largest group of gram-negative bacteria– Extremely complex group, with over 400 genera and

1300 named species– All major nutritional types are represented: phototrophy,

heterotrophy, and several types of chemolithotrophy– Sometimes called the “purple bacteria,” although very

few are purple; the term refers to a hypothetical purple photosynthetic bacterium from which the group is believed to have evolved

Microbial Phylogeny

• Phylogeny of domain Bacteria (cont.) • Phylum Proteobacteria (cont.)

– Divided into 5 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria

Microbial Phylogeny

• Phylogeny of domain Bacteria (cont.) • Phylum Proteobacteria (cont.)

– Significant groups and genera include:» The family Enterobacteriaceae, the “gram-negative

enteric bacteria,” which includes genera Escherichia, Proteus, Enterobacter, Klebsiella, Salmonella, Shigella, Serratia, and others

» The family Pseudomonadaceae, which includes genus Pseudomonas and related genera

» Other medically important Proteobacteria include genera Haemophilus, Vibrio, Camphylobacter, Helicobacter, Rickessia, Brucella

Microbial Phylogeny• Phylogeny of domain Bacteria (cont.)

• Phylum Firmicutes– “Low G + C gram-positive” bacteria

– Divided into 3 classes» Class I – Clostridia; includes genera Clostridium and

Desulfotomaculatum, and others

» Class II – Mollicutes; bacteria in this class cannot make peptidoglycan and lack cell walls; includes genera Mycoplasma, Ureaplasma, and others

» Class III – Bacilli; includes genera Bacillus, Lactobacillus, Streptococcus, Lactococcus, Geobacillus, Enterococcus, Listeria, Staphylococcus, and others

Microbial Phylogeny

• Phylogeny of domain Bacteria (cont.) • Phylum Actinobacteria

– “High G + C gram-positive” bacteria– Includes genera Actinomyces, Streptomyces,

Corynebacterium, Micrococcus, Mycobacterium, Propionibacterium

• Phylum Chlamidiae– Small phylum containing the genus Chlamydia

Microbial Phylogeny

• Phylogeny of domain Bacteria (cont.) • Phylum Spirochaetes

– The spirochaetes– Characterized by flexible, helical cells with a modified

outer membrane (the outer sheath) and modified flagella (axial filaments) located within the outer sheath

– Important pathogenic genera include Treponema, Borrelia, and Leptospira

• Phylum Bacteroidetes– Includes genera Bacteroides, Flavobacterium,

Flexibacter, and Cytophyga; Flexibacter and Cytophyga are motile by means of “gliding motility”

Procaryotae Kingdom has 4 Divisions according to the structure of cell wall and Gram staining:

Gracilicutes (gracilis - thin, cutis - skin) – Gram-negative bacteria,

Firmicutes (firmus - firm) – Gram-positive bacteria,

Tenericutes (tener – soft, tender) – microbes without cell wall,

Mendosicutes (mendosus - mistaket) – microbes with atipical peptidoglican

Bacterial Nomenclature

• Binomial naming system– Two word naming system

• First word is genus name– Always capitalized

• Escherichia• Second word is species name

– Not capitalized• coli

• When writing full name genus usually abbreviated– E. coli

• Full name always italicized– Or underlined

Species is population of microbes, which have the only source of origin, common genotype, and during the present stage of evolution are characterized by similar morphological, biochemical, physiological and other signs

If deviations from the typical species properties are found on examination of the isolated bacteria, then culture is considered a subspecies.

Infrasubspecies subdivisions

serovar (antigenic properties)

morphovar (morphological properties)

chemovar (chemical properties)

biovar (biochemical or physiological properties)

pathovar (pathogenic properties)

phagovar (relation to phages)

The term clone was applied to population of cells derived from a single cell

Population is an elementary evolutional unit (structure) of a definite species

The term strain designates a microbial culture obtained from the different sources or from one source but in different time

Or: A subgroup within a species with one or more haracteristics that distinguish it from other subgroups in the species

Morphological Classification of Bacteria

Bacteria (Gk. bakterion - small staff) are unicellular organisms lacking chlorophyll.

Morphologically, bacteria possess four main forms:

spherical (cocci)

rod-shaped (bacteria, bacilli, and clostridia)

spiral-shaped (vibrios, spirilla and spirochaetes)

thread-shaped (non-pathogenic)

Cocci groupings

Coccus

Diplococcus

Streptococcus

Tetrad

Sarcinae

Staphylococcus

Cocci (Gk. kokkos berry). These forms of bacteria are spherical, ellipsoidal, bean-shaped, and lanceolate. Cocci are subdivided into six groups according to cell arrangement, cell division and biological properties

Micrococci (Micrococcus). The cells are arranged singly or irregularly. They are saprophytes, and live in water and in air ( M. roseus, M. luteus, etc.).

Diplococci (Gk. diplos double) divide in one plane and remain attached in pairs. These include: Meningococcus (causative agent of epidemic cerebrospinal meningitis, and gonococcus, causative agent of gonorrhoea and blennorrhoea) Pneumococcus (causative agents of pneumonia)

Streptococci (Gk. streptos curved, kokkos berry) divide in one plane and are arranged in chains of different length. Some streptococci are pathogenic for humans and are responsible for various diseases.

Tetracocci (Gk. tetra four) divide in two planes at right angles to one another and form groups of fours. They very rarely produce diseases in humans.

Staphylococci (Gk. staphyle cluster of grapes) divide in several planes resulting in irregular bunches of cells, sometimes resembling clusters of grapes. Some species of Staphylococci cause diseases in man and animals

Sarcinae (L. sarcio to tie) divide in three planes at right angles to one another and resemble packets of 8, 16 or more cells. They are frequently found in the air. Virulent species have not been encountered

Rods. Rod-shaped forms are subdivided into:

bacteria,

bacilli,

clostridia

Bacteria include those microorganisms which, as a rule, do not produce spores (colibacillus, and organisms responsible for enteric fever, paratyphoids, dysentery, diphtheria, tuberculosis, etc.).

Bacilli and clostridia include organisms the majority of which produce spores (hay bacillus, bacilli responsible for anthrax, tetanus, anaerobic infections, etc.)

According to their arrangement, cylindrical forms can be subdivided into three groups: monobacteria monobacilli

E. coli Y. pestis

C. tetani

C. botulinum

diplobacteria diplobacilli

K. pneumoniae

streptobacteria streptobacilli

Haemophilus ducreyi

(chancroid)

Bacillus anthracis

(anthrax)

Spiral-shaped bacteria

Vibriones (L. vibrio to vibrate) are cells which resemble a comma in appearance. Typical representatives of this group are Vibrio cholerae, the causative agent of cholera, and aquatic vibriones which are widely distributed in fresh water reservoirs.

Spirilla (L. spira coil) are coiled forms of bacteria exhibiting twists with one or more turns. Only one pathogenic species is known {Spirillum minus} which is responsible for a disease in humans transmitted through the bite of rats and other rodents (rat-bite fever, sodoku)

Spirochaetes (L. spira curve, Gk. chaite cock, mane) differ from bacteria in structure with a corkscrew spiral shape

Borrelia. Their cells have large, obtuse-angled, irregular spirals, the number of which varies from 3 to 10. Pathogenic for man are the causative agents of relapsing fever transmitted by lice (Borrelia hispanica), and by ticks (Borrelia persica, etc.). These stain blue-violet with the Romanowsky-Giemsa stain

Leptospira (Gk. leplos thin, speira coil) are characterized by very thin cell structure. The leptospirae form 12 to 18 coils wound close to each other, shaping small primary spirals. The organisms have two paired axial filaments attached at opposite ends (basal bodies) of the cell and directed toward each other.

Leptospira interrogans which is pathogenic for animals and man cause leptospirosis

Treponema (Gk. trepein turn, nema thread) exhibits thin, flexible cells with 6-14 twists. The micro-organisms do not appear to have a visible axial filament or an axial crest when viewed under the microscope

A typical representative is the causative agent of syphilis Treponema pallidum

Properties of prokaryotes and eukaryotes

Prokaryotes Eukaryotes

The nucleoid has no membrane separating it from the cytoplasm

Karyoplasm is separated from the cytoplasm by membrane

Chromosome is a one ball of double twisted DNA threads. Mitosis is absent

Chromosome is more than one, There is a mitosis

DNA of cytoplasm are represented in plasmids

DNA of cytoplasm are represented in organelles

There aren’t cytoplasmic organelle which is surrounded by membrane

There are cytoplasmic organelle which is surrounded by membrane

The respiratory system is localized in cytoplasmic membrane

The respiratory system is localized mitochondrion

There are ribosome 70S in cytoplasm

There are ribosome 80S in cytoplasm

Peptidoglycan are included in cell’s wall (Murein)

Peptidoglycan aren’t included in cell’s wall

The structure of procaryotes

Nucleus. The prokaryotic nucleus can be seen with the light microscope in stained material. It is Feulgen-positive, indicating the presence of DNA. Histonelike proteins have recently been discovered in bacteria and presumably play a role similar to that of histones in eukaryotic chromatin

The DNA is seen to be a single, continuous, "giant" circular molecule with a molecular weight of approximately 3 X 109. The unfolded nuclear DNA would be about 1-3 mm long (compared with an average length of 1 to 2 µm for bacterial cells)

Plasmids: R, Col, Hly, Ent, Sal

Plasmids small circular, double-stranded DNA free or integrated into the chromosome duplicated and passed on to offspring not essential to bacterial growth & metabolism may encode antibiotic resistance, tolerance to toxic metals, enzymes & toxins used in genetic engineering- readily manipulated & transferred from cell to cell There may be several different plasmids in one cell and the numbers of each may vary from only one to 100s in a cell

Prokaryotic RibosomeProkaryotic Ribosome

A ribosome (70 S) is a combination of RNA and protein, and is the site for protein synthesis Composed of large (50S) and small (30S) subunits S = Svedverg unit, measures molecular size

The 80S ribosomes of eukaryotes are made up of 40S and 60S subunits.

• Storage granules– Metachromatic

granules – Polysaccharide

granules– Lipid inclusions– Sulfur granules– Carboxyzomes – Magnetosomes

• Gas vesicles

Inclusions, granules

Volutin granules

Corynebacterium diphtheriae

Loeffler's technique Neisser's staining

Composted of A. The cytoplasmic membrane

To act as a physical barrier btw cytoplasm and environments and selectively controls the movement of substaces into and out of the cell“Semipermeable”

B. Cell wallThe rigid layer that protect the fragile cytoplasmic membrane from rupturingTo maintains cell’s shape

C. Capsule or slime layer (glycocalyx)

Cell Envelope

Cell membrane

PeripheralMembraneProtein

IntegralMembraneProtein

PeripheralMembraneProtein

Phospholipid

Bacterial plasma membrane are composed of 40 percent phospholipid and 60 percent protein. The phospholipids are amphoteric molecules with a polar hydrophilic glycerol "head" attached via an ester bond to two nonpolar hydrophobic fatty acid tails, which naturally form a bilayer in aqueous environments. Dispersed within the bilayer are various structural and enzymatic proteins which carry out most membrane functions.

Mesosome

The predominant functions of bacterial membranes are:

1. Osmotic or permeability barrier;

2. Location of transport systems for specific solutes (nutrients and ions);

3. Energy generating functions, involving respiratory and photosynthetic electron transport systems, establishment of proton motive force, and transmembranous, ATP-synthesizing ATPase;

4. Synthesis of membrane lipids (including lipopolysaccharide in Gram-negative cells);

5. Synthesis of murein (cell wall peptidoglycan);

6. Assembly and secretion of extracytoplasmic proteins;

7. Coordination of DNA replication and segregation with septum formation and cell division;

8. Chemotaxis (both motility per se and sensing functions);

9. Location of specialized enzyme system.

• Unique chemical structure– Distinguishes Gram positive from Gram-negative– bacteria and archaea bacterial species

• Rigidity of cell wall is due to peptidoglycan (PTG) – Compound found only in bacteria – Archaea –psudomurein or other sugars, proteins,

glycoproteins

• Many antimicrobial interfere with synthesis of PTG

• Penicillin; Lysozyme

Cell wall

• Basic structure of peptidoglycan– Alternating series of two

subunits• N-acetylglucosamin (NAG)• N-acetylmuramic acid (NAM)

– Joined subunits form glycan chain

• Glycan chains held together by string of four amino acids

– Tetrapeptide chain:L-ala-D-glu-DAP-D-ala L-ala-D-glu-Lys-D-ala

• Interpeptide bridge

Structure of peptidoglycan

Structures associated with gram-positive and gram-negative cell walls.

Differences of cell wall structure in Gram-positive and Gram negative cells

L FormsL Forms

Glycocalyx

CapsuleProtects bacteria from phagocytic cells

Slime layerEnable attachment and aggregation of bacterial cells

Capsules Most prokaryotes contain some sort of a polysaccharide layer outside of the cell wall polymer

Only capsule of B. anthracis consist of polypeptide (polyglutamic acid)

CapsuleCapsule

The capsule is covalently

bound to the cell wall.

Associated with virulence in bacteria.

Example:

Streptococcus pneumoniae

Slime LayerSlime Layer

The slime layer is loosely bound to the cell.

Carbohydrate rich material enhances adherence of cells on surfaces

Example:Streptococcus mutans and “plaque formation”

Biofilms Biofilms

The slime layer is associated with cell aggregation and the formation of biofilms

Example:Staphylococcus epidermidis biofilms on catheter tips

•Adhesion•Avoidance of immune response•Protection from dehydration •Protection of bacterial cells from engulfment by protozoa or white blood cells (phagocytes), or from attack by antimicrobial agents of plant or animal origin. •They provide virulent properties of bacteria (S. pneumoniae, B. anthracis)

General capsule function

Flagella

• 3 parts– filament – long, thin,

helical structure composed of proteins

– hook- curved sheath– basal body – stack of

rings firmly anchored in cell wall

• rotates 360o

• 1-2 or many distributed over entire cell

• functions in motility

Flagellar arrangements

1. Monotrichous – single flagellum at one end (cholera vibrio, blue pus bacillus),

2. Lophotrichous – small bunches arising from one end of cell (blue-green milk bacillus,Alcaligenes faecalis)

3. Amphitrichous – flagella at both ends of cell (Spirillum volutans),

4. Peritrichous – flagella dispersed over surface of cell, slowest E. coli, salmonellae of enteric fever and paratyphoids A and B

Bacterial MotilityBacterial Motility

The rotation of the flagella enables bacteria to be motile.

Flagella are important for:

Motility (dispersal)

Antigenic determinant

Number and location species specific

Pili and FimbriaePili and Fimbriae• Short, hair-like structures on the surfaces of procaryotic cells • Proteinaceuse filaments (~20 nm in diameter)• Very common in Gram-negative bacteria

• Functions:– Adherence to surface/ substrates: teeth, tissues– Involved in transfer of genetic information btw cells– Have nothing to do with bacterial movement (Except the twitching move

ment of Pseudomonas)

Fimbriae are smaller than flagella and are important for attachment

Bacterial endospores• Bacterial spores are often called “endospore” (since they are

formed within the vegetative cell)• Produced in response to nutrient limitation or extreme environments• Highly resistant• Highly dehydrated (15% water)• Metabolically inactive• Stable for years• Not reproductive • Functions: to survive under an extreme growth conditions such as

high temperature, drought, etc.

Bacillus, Clostridium, Sporolactobacillus, Thermoactinomyces, Sporosarcina, Desulfotomaculum species sporulate

Spore

Spores

• Key compositions:– Dipicolinic acid (DPA)– Calcium (Ca2+)

• Structure– Core / Cytoplasm– Plasma membrane– Core wall/ spore wall– Cortex – Spore coat– Exosporium

Endospores

The sporulation process begins when nutritional conditions become unfavorable, depletion of the nitrogen or carbon source (or both) being the most significant factor. Sporulation involves the production of many new structures, enzymes, and metabolites along with the disappearance of many vegetative cell components.

Spores are located: 1) Centrally (B. anthracis);

2) Terminally (С. tetani);

3) Subterminally (C. botulinum, C. perfringens)

The spores of certain bacilli are capable of withstanding boiling and high concentrations of disinfectants. They are killed in an autoclave exposed to saturated steam, at a temperature of 115-125 C, and also at a temperature of 150-170 C in a Pasteur hot-air oven.

Important Point: