BACTERIA. PROTISTS. FUNGAL AND VIRUSES

Microbiology is the study of microorganisms, a collection oforganisms that are generally only be visible with a microscope.

Members of the microbial world are very diverse and include:bacteria, protists, fungi and viruses.

MICROSCOPES:

• Microscopes permit extremely small objects to be seen, objects measured in the metric system in micrometers (um) and nanometers(nm).

• A micrometer is equivalent to a millionth of a meter, while a nanometer is a billionth of a meter.

• Bacteria, fungi, protozoa, and unicellular algae are normally measured in micrometers, while viruses are commonly measured in nanometers.

• A typical bacterium measures about 2 micrometers in length and 1micrometer in width.

There are various types of microscopes available for use in microbiology:

1. light microscope: the common light microscope used in lab is the compound microscope because it contains two types of lenses (ocular and objective)

2. Electron microscope: source of energy is a beam of electrons:2types:

• a. transmission electron microscope: (TEM) scans internalstructures of the organism

• b. Scannins electron microscope: (SEM) scans externalstructures of an organisms

• • Both TEM and SEM give a 3D view of microorganisms but the draw back is the organisms must be dead.

• The ability to see clearly two items as separate objects under the microscope is called resolution.

• The resolving power of a lens refers to the size of thesmallest object that can be seen with that lens.

• Most microscopes exhibit parfocal which means thatthe microscope remains in focus when one switchesfrom one objective to the next objective.

• The total magnification of a microscope is theobjective power times the ocular power.

• The numerical aperture (NA) refers to the widest coneof light that can enter the lens; the NA is engraved onthe side of the objective lens.

• To increase the resolution with oil-immersion lens (one that is exceedingly narrow, and most light missesit and is poorly seen without the resolution) immersion oil is used (it has the same light-bending ability as the glass slide, so keeps light in a straight line as it passes through the glass slide.

STAINING TECHNIQUES:

• Because microbial cytoplasm is usually transparent, it is necessaryto stain microorganisms before they can be viewed with a lightmicroscope.

• In some cases, staining is unnecessary, for example whenmicroorganisms are very large or when motility is to be studied, anda drop of the microorganisms can be placed directly on the slide andobserved...this is called a wet mount.

• A wet mount can also be prepared by placing a droop of culture on acover slip and then inverting it over a hollowed-out slide....this iscalled a hanging drop.

• In preparation for staining, a small sample of microorganisms is placed on a slide and permitted to air dry.

• The smear is heat fixed by quickly passing it over aflame.

• Heat fixing kills the organisms, makes them adhere to the slide, and permits them to accept the stain.

• Simple stain techniques can be performed with basic dyes such as crystal violet or methylene blue, positively charged dyes that are attracted to the negatively charged materials of the microbial cytoplasm.

• Differential staining distinguish two kinds of organisms ex gram stains.

CLASSIFICATION:

• Morphological characteristics are useful in the identification of microorganisms, especially when aided by differential staining techniques.

• The possession of various enzymes as determined by biochemical tests is used in the identification of the microorganism.

• Serological tests, involving the reactions of microorganisms with specific antibodies, are useful in determining the identity of strains and species as well as relationships between organisms.

BACTERIA:

• Bacteria are divided into four divisions.1. . Archaebacteria live in harsh conditions, 2. Eubacteria-true bacteria,3. Cyanobacteria- blue-green algae, 4. Prochorobacetia-new group little known)

• A group of bacteria derived from a single cell is called a strain.• Closely related strains constitute a species.

• Bacteria are divided into sections based on Gram-stain reaction,cellular morphology, oxygen requirements, and nutritionalproperties.

• The entire kingdom is composed of prokaryotes.

• > Characteristics include:1. Unicellular prokaryotes2. both heterotrophic and autotrophic3. Cell shape includes;• a. bacillus: rod shape• b. coccus: sphere shape• c. spirillium: spiral shape4. Cell grouping includes:• a. Staphlo: clustersb. Strepto: chain• Both aerobic and anaerobic

Spirochetes and Spirilla:

• Spirochetes have a spiral shape, a flexible cell wall andmotility mechanisms based on structures called axialfilaments.

• They are very slender and difficult to see under the light microscope.

• They are cultivated with great difficulty (some not at all) andare classified based on morphology and pathogenicity.

• Certain spirochetes inhabit water environments while othersare parasites of arthropods and warm blooded animals

• Ex of a spirochete is • Borrelia burgdorferi {agent of lyme

disease), • Treponema pallidum (agent of syphilis) and

Leptospira interrosans (agent of leptospirosis)• Spirillia have spiral shape, a rigid cell wall, and motility

mechanisms based on polar flagella.• The genera Spirillum, Aquaspirillum and Azospirulum are

widely dispersed, all being aerobic• Ex include Spirillum minor ( rat bite fever),

Camplobacter jejuni (intestinal infection accompanied by diarrhea)

Gram-Negative Rods and Cocci

1. Bdellovibrios are aerobic gram-negative, curved rods that prey on other bacteria. They attach to the surface of a bacterium, rotates, and bores a hole through the host cell wall. Ex Bdellovibrio bacteriovorus

2. Pseudomonads: aerobic, gram-negative rods, motility is with polarflagella. Ex Pseudomonas aersinosa which causes urinary tract infections and infections of burned tissue

3. Azotobacter and Rhizobium: important for their ability to fix nitrogen in the environment.

4. Enterobacteria: facultatively anaerobic, inhabit the human intestinesEx Salmonella ( agent for salmonellosis) Klebsiella (agent pneumonia),E. coli

5. Vibrios: curved, gram-negative, facultatively anaerobic rods. Ex Vibrio cholerae (cholera)

6. Pasteurellas: small size and enable to move. Ex Haemophilus influenza (meningitis)

7. Sulfur bacteria: important in sulfur cycle for their ability to use sulfur and convert it to other compounds that can be used by plants to synthesize sulfur-containing amino acids.

8. Veillonella: gram negative cocci, anaerobic diplococci, part of the normal flora of the mouth and gastrointestinal tract.

9. Gliding bacteria: move by gliding in a layer of slime, which theyproduce

10.Mvxobacteria: gliding bacteria, aerobic rods, nonphotosynthetic

11. Sheathed bacteria: filamentous bacteria with cell walls enclosed in a sheath of polysaccharides and lipoproteins.

12.Photoautotrophic bacteria: obtain their energy from sunlight Ex Cyanobacteria

13..Chemoautotrophic bacteria: gram negative bacteria deriving their energy from chemical reactions involving inorganic material. Ex Nitrobactera

GRAM-POSITIVE BACTERIA:

1. Streptococci: spherical bacteria, aerobic, certain species partlydestroy the red blood cells ( alpha-hemolytic) others completelydestroy the blood cells (beta-hemolytic), Ex Streptococcuspneumoniae (bacterial pneumonia), Streptococcus pyosenes (strepthroat)

2. Staphylococci: normally associated with the skin and mucousmembranes, certain species cause boils and abscesses. ExStaphylococcus aureus (food poisoning)

3. Lactobacilli: rod-shaped single cells or chains, produce lactic acid,associated with the flora of the mouth

4. Bacillus and Clostridium species: gram positive rod shaped bacteria, produce highly resistant endospores, found in the soil, air ex Bacillus anthracis (anthrax), Clostridium (tetanus)

5. Corynebacteria: gram positive rods ex Corynebacterium diptheria (human diptheria)

6. Actinomyces and Arthrobacter: Actinomyces are positive rods, assumes many shapes and usually form branching filaments, cause lumpy jaw. Arthrobacter: found in soil and many degradeherbicides and pesticides.

ACID FAST BACILLI:

1. Mycobacteria: are rod-shaped, the presence ofmycoloic acid makes the bacteria very difficult to stain, but when heat or other agents are used to force carbolfuschsin (stain) into the cytoplasm, the bacteria resisted colorization with a dilute acid-alcohol solution.

• Therefore,they are called acid-fast. Ex Mycobacteria tuberculosis(tuberculosis) M. leprae (leprosy)

2. Norcardioforms: include nine genera of aerobic, acid fast rods form short filaments, found throughout nature in many types of soil and aquatic environments. Ex N. asteroids (infection of human lungs)

ARCHAEBACTERIA:

• Differ from all other bacteria (Eubacteria)• Ex include:• 1) methanogens (anaerobic found in swamps,

sewage2) halobacteria (high-salt environment)

• 3) extreme thermophiles (live at extremely high temperatures)

SUBMICROSCOPIC BACTERIA:1. Rickettsiae:• Obligate intracellular parasite, rod or coccoid shaped,

cannot be seen with light microscope, gram stain not used foridentification (however walls are characteristically gram negative),cultivation in lab difficult

• This pathogen is responsible for RockyMountain spotted fever, epidemic typhus, Q fever and ehrlichiosis

2. Chlamydia: • an extremely tiny bacteria, acts as an obligate

intracellular parasite, gram stain not used for identification (typically gram negative) growth cycle takes place within host cell.

• Responsible for: psittacosis (disease of lung tissue), trachoma(disease of eye) and chlamydia (infection of reproductive tract)

3. Mycovlasmas:• extremely small bacteria, lacks cell walls, vary in

shape (pleomorphic), causes mild pneumonia in humans, andproblems with the respiratory tract and urinary tract

VIRUSES:

• Depending on one's viewpoint, viruses may be reguarded as complex aggregates of nonliving chemicals, or very simple living microbes.

• Viruses are not placed in a kingdom.• They are not composed of cells and are incapable of

growth without a host cell• They are noncellular genetic elements that use a living

cell for their replication and have an extracellular state.

• Viruses are ultramicroscopic particles containing nucleic acid surrounded by protein, and in some cases other macromolecular components such as a membrane-like envelope.

• The virus particle is also known as a virion.

• The viron is metabolically inert and does not grow or carry on respiratory or biosynthetic functions.

• There are no technical names for viruses.

Viral Structure and Replication:

• Viruses vary in size and shape (smallest viruses are about 0.02um, largest .3 um) (poll virus among smallest, smallpox among largest)

• Certain viruses contain RNA, while other viruses have DNA.

• The Nucleic acid portion of the viruses is known as the genome.

• The genome of the virus is surrounded by a protein coat known as a capsid, which is formed from a number of individual protein molecules called capsomeres.

• The combination of genome and capsid is called the viral nucleocapsid

• Some kinds of viruses contain envelopes ( encloses the nuceocapsid)

• The envelope contains viral-specified proteins that make it unique (ex herpes, chickenpox, infectious mononucleosis)

The nucleocapsid of the virus is constructed according to certain symmetrical patterns: Examples

1. rabies is helical (lone rods,with thir capsids as hollow cylinders surrounding nucleic acids)

2. polio and head colds have icosahedral symmetry meaning the capsid is composed of 20 faces, each shaped as an equilateral triangle),

3. polyhedral viruses (adenovirus such as herpes) are many sided)

• Projections from the envelope are known as spikes, which sometimes help the virus attach to the host cell exAIDs

• Bacteriophases are viruses that multiply within bacteria

• During viral replication, a virus induces a living host cell to synthesize the essential components for the synthesis of new viral particles.

Steps of viral replication include:

1. Attachment: virus adsorbs to a susceptible host cell

2. Penetration: of virus or viral genome in the cell.

3. Replication: protein capsid is stripped away from the genome, and the genome is freed in the cell cytoplasm.

4. Assemble: Once the viral genomes and capsomeres have been synthesized, they are assembled to form new virions. After the assembly is complete, the virions are ready to be released into the environment.

5. Release: of new viral particles (varies ex host cell may becomeexhausted and release virions ,ift he host cell experiences death then it is called a lytic cycle of reproduction

• Lysogenic cycle: certain viruses remain active within their host cells for a long period without replicating. ( virus is called a temperate virus, or proviruse because they do not bring death to host immediately)

• HOST RANGE:• Refers to the spectrum of host cells in which a virus

can multiply(animal virus, bacterial virus plant virus)

• A virus can only infect certain species in each range.

TAXONOMY OF VIRUSE:

• Classification of viruses is based on type of nucleic acid, morphological class, size of capsid, and number of capsomeres.

• Other considerations include: virus's susceptibility to microbial control agents, immunological properties, site of multiplication, andmethod of transmission.

VIRAL MEASUREMENTS:

• Viruses are generally to small to be seen under the light microscope, and thus to determine their number in terms of a detectable effect on a host cell, virus infectious units are expressed per volume of fluid.

ANTIVIRAL AGENTS:

• Antibiotics cannot be used to inactivate viruses because viruses do not perform the biochemical functions that antibiotics interfere with.

• However some drugs can interfere with viral replication.

• Protection against viral disease can be rendered by using a viral vaccine( composed of inactivated( dead) or attenuated (weakened viruses)

ONCOGENY:

• A number of types of cancer are now known to be caused by viruses.

• (oma suffix attached to affected tissue)

• Viruses capable of producing tumors are called oncogenic viruses and include adenoviruses, herpes viruses, pox viruses, and papovaviruses

FUNGI:

• Include several thousand species of eukaryotic, spore bearingorganisms that obtain simple organic compounds by absorption.

• They have no chlorophyll and reproduce by both sexual and asexual means.

• The study of fungi is called mycology, and fungal diseases are called mycoses.

• Together with bacteria, fungi are the major decomposers of organic materials in the soil.

Two major groups of organisms make up the fungi

1. filamentous fungi called mold

2. unicellular fungi called yeasts

STRUCTURE AND PHYSIOLOGY:

• There is considerable variation in the structure, and size of fungi

• Molds consists of long, branching filaments of cells called hyphae (the visible hyphae mat is called a mycelium)

• Yeasts are microscopic unicellular fungi, that reproduce asexually by budding.

• Some species of fungi have the ability to shift from yeast form to the mold form and vice versa... these fungi are called dimorphic.

• Many fungal pathogens exist in the body in the yeast form but revert to the mold form in lab.

• Reproduction in yeasts usually involves spores.• Asexual spores may also be formed within a

sac, in which case they are called sporansiospores.

• Most fungi grow best where there is a rich supply of organic matter, most being saprophytic.

• Most fungi grow best at an acidic pH of about 5 and a temperature of 25 C (room temp), however, pathogenic fungi grow best at a temp of 37C (body temp)

• Fungi store glycogen for their energy needs and are aerobic, exceptfor the fermentation yeasts that grow in both aerobic and anaerobicconditions.

• Asexual reproduction occurs in the fungi when spores form bymitosis, and sexual reproduction allows for compatible nuclei tounite within the mycelium and form sexual spores

CLASSIFICA TION OF FUNGI:

• Fungal spores are important in the identification of the fungus, since the spores are unique in shape, color and size.

1. Division Zygomycota: produce sexual spores known as zygospores as well as asexual sprangiospores. Ex Rhizopus found on fruits vegetables and breads

2. Division Ascomycota; form their sexual spores within a sac called an ascus...and are called sac fungi EX include powdery mildews and fungi that causes dutch elm disease and Saccharomyces(fermentation yeast)

3. Division Basidiomycota: are called basidiomycetes or club fungi because a club shaped structure called a basidium is formed after sexual reproduction.

The spores are called basidiospores . The fruiting bodies are called basidiocarps. Ex of a basidiocarp is a mushroom. One of the organisms of meningitis is the basidiomycete

Cryptococcus neoformans and the mushroom Amanita is poisonous to humans.

• 4. Division Deuteromycota: lack a known sexual cycle of reproduction and are said to be imperfect.

• When its sexual cycle is discovered, a fungus from this division is usually reclassified.

• EX athlete's foot, ringworms

• Slime mold: have characteristics of both molds and protozoa.

• The amoeba stage is called the plasmodium, which has many nucli.

• The amoeba stage ends when the plasmodium matures or encounters a harsh environment

• Water molds: belong to the group known as oomycetes.

• They resemble other fungi because they have branched filaments and form spores. Certain water molds parasitize fish.

FUNGAL DISEASES:

• Systemic mycoses: fungal infection deep within body and affect many tissues and organs.

1. Subcutaneous mycoses are fungal infections beneath the skin.

2. Cutaneous mycoses affect hair, nails, and skin

3. Superficial mycoses are localized on hair shafts and superficial skin cells.

4. Opportunistic mycoses are caused by normal flora or fungi that are not normally pathogenic...can infect any tissue

UNICELLULAR ALGAE:

• Algae are eukaryotic organisms that have no roots, stems, or leaves, but do have chlorophyll and carry out photosynthesis.

• They can be multicellular or unicellular.• Unicellular algae occur most frequently in water, especially in

plankton.• Reproduction in algae occurs in both asexual and sexual forms,

binary fission also takes place• During sexual reproduction, algae form differentiated sex cells that

fuse to produce a diploid zvsote•

• The zvgote develops into a sexual spore, which germinates under favorable conditions.

DIVISIONS OF UNICELLULAR ALGAE:

• 5 divisions classified in the kingdom protista1. Division Chlorophyta: possess green chlorophyll pigments and

carotenoids. Ex chlamydomonas2. Division Charophyta: EX stoneworts, may be a source of

limestone,cover the bottoms of ponds

3. Division Euslenophyta: Ex euglena, contain chlorophyll andcarotenoid pigments for photosynthesis and reproduce by binaryfission

4. Division Chrysophyta: Ex diatoms, brown and yellow-green algae.Contain chlorophyll and a special carotenoid pigment calledfucoxanthins (golden-brown color)

5. Division Pyrrophvta: Ex dinoflagellates, contain chlorophyll,carotenoid and xanthophylls pigments, cause red tides

PROTOZOA:

• Eukaryotic microorganisms, are heterotrophs and feed on bacteriaand paniculate organic material.

• Asexual reproduction is by fission, budding, sexual reproduction isby conjugation.

• Most are aerobic, but a few anaerobic species can be found inhuman or animal intestines.

• Vary is size and shape,• Many alternate between a free-living vegetative form (trophozoite)

and a resting form (cyst) depending on environmental conditions

• main types of locomotor organelles:flagella, cilia, and pseudopodia.•

CLASSIFICATION OF PROTOZOA:

1. Mastigophora: have 1 or more flagella, reproduction by fission,group members cause intestinal distress. Ex Giardia lamblia,Trypanosoma brucei (sleeping sickness), euglena is also placed here.

2. Sarcodina: move by pseudopodia, but flagella may be present in reproductive stage. Ex Entamoeba histolytica ( amoebic dysentery)

3. Ciliophora: move by means of cilia, Ex paramecium4. Apicomplexa: form spores at one stage in their life

cycle so are also known as Sporozoa. Ex Pneumocvstis carinii (lethal pneumonia in AIDs), malaria and toxoplasmosis are also classified here.

HELMINTHS:

• There are a number of parasitic animals that spend part or all othertheir lives in humans.

• Most of these animals belong to 2 phyla, Platyhelminthes(flatworms), and Aschelminthes (roundworms)...both commonlyreferred to a helminthes.

• Helminths are multicellular eukaryotic heterotrophs generallypossessing digestive, circulatory, nervous, excretory, andreproductive systems (hermaphroditic or dioecious).

• Parasitic helminthes must be highly specialized to live inside theirhosts.

Differences that distinguish Parasitic Helminths from their free-living relatives:

1. They either lack a digestive system or have a greatly simplified one.

2. Nervous system is reduced due to the lack of need to search for food and respond to the environment

3. Locomotion is either reduced or completely absent due to transfer from host to host

4. Reproductive system is often more complex, it produces more fertilized eggs, by which a suitable host is infected.

PLATYHELMINTHES:

Members are flattened form top to bottom, and have an incomplete digestive system and only one mouth.

Classification of Platvhelminthes:

1. Trematodes: (flukes) named according to the tissue of the definitive host in which the adult live (ex lung fluke, blood fluke)

a. Parasonimus westermanni (lung fluke) lives in the bronchioles,grows to 12mm long and 6mm wide, eggs usually coughed up,swallowed and excreted in feces

b. Clonorchis sinensis: (Chinese liver fluke) eating raw or undercooked fish

c. Schistosoma: burrow through skin of human host and entercirculatory system, usually found in certain abdominal andpelvic veins.

2. Cestoda: (tapeworms) intestinal parasites, composed of a head (scolex) with suckers, body divided into segments(proglottids).

a) Taenia sasinata: (beef tapeworm) lives in humans and can reach lengths up to 6 meters, thefeces of an infected human contains thousands of eggs.

b)Taenia pisiformis: dog tapewormc) Echinococcus granulosus: tiny tapeworm

found in the intestines of dogs, cats ,wolves and foxes., humans sever as the intermediate host and is a dead end for the parasite unless thehuman is eaten by an animal

ASCHELMINTHES: ( ROUNDWORMS)

• Aschelminthes are cylindrical in shape and tapered at each end, have a complete digestive system, consisting of a mouth, an intestine, and an anus,

• Most are dioecious, males being smaller than females and having a hooked tail

• Parasites of humans belong only to the class consisting of nematodes.

NEMATODES:

• Nematode infections of humans can be divided into two categories

a) Those in which the egg is infective

b) Those in which the larva is infective

Parasitic Nematodes include: 1. Ascaris lumbricoides: largest roundworm to infect

humans(intestines), reaches a length of up to 30cm. Is dioecious with male being smaller and having a hooked

tail. Diagnosis is made when adult worms are excreted with feces

2. Enterobius vermicularis: adult pinworm, spends its entire life in human host. Adult pinworms are found in human intestines,females migrate to anus to deposit eggs in perianal skin,

Diagnosis is by using a Graham sticky tape method (tape placed on perianal skin in such a way as to expose sticky side to eggs and then tape is microscopically examined for eggs.

3. Necator americanus: Hookworms, Adults live in small intestines of humans, eggs excreted with feces, larvae hatch and live in soil, they enter host by penetrating host's skin...enter the blood or lymph vessels which transport them to the lungs... where they are coughedup and swallowed, transporting the larvae to the intestines.

Diagnosis is eggs in feces... name is derived from the hooks located around the mouth that are used for attachment and removing food from host tissue. Infect humans in the larvae form.

• Trichinella spiralis: usually acquired by eating encysted larvae in pork or bear meat. In the human digestive tract, the larvae are freed from cyst, mature and reproduce.

• The larvae enter lymph and blood vessels in the intestines and migrate through out the body...theyencyst in muscles and other tissue where they remain until ingestedby another host

ARTHROPODS AS VECTORS:

• Those that carry disease-causing microorganisms are called vectors.

• > Representative classes of arthropods include: >

1. Arachnida: (8 legs) spiders, mites, ticks

2. Crustacea :(4 antennae) crabs, crayfish

3. Chilopoda: (2 legs per segment) centipedes

4. Diplopoda: (4 legs per segment) millipedes

5. Insecta (6 legs) bees, flies

TERMS:

• Definitive host: An organism that harbors the adult, sexually mature form of a helminthic parasite

• Intermediate host: An organisms that harbors the larvae stage of a helminthes