Unit Two Microorganism PDF

UNIT TWO (2) 2. Microorganisms 2.1. What are Microorganisms?  Microorganisms also called microbes.  Many microbes are simple single-celled organisms, but some can form complex structures, and some are even multicellular.  Are diverse in form and function and they found in every...

UNIT TWO (2) 2. Microorganisms 2.1. What are Microorganisms?  Microorganisms also called microbes.  Many microbes are simple single-celled organisms, but some can form complex structures, and some are even multicellular.  Are diverse in form and function and they found in every environment on Earth that supports life.  The science which study about microbes is called microbiology which study what they are, how they work, and what they do. Microbiology: is the scientific study of microorganisms Biosphere: the regions of the surface and atmosphere of the earth occupied by living organisms. Microscopic organisms: too small to be seen with the naked eye, only visible with a microscope. Most microorganisms are harmless or other are use full. Functions of microorganism  Recycling of nutrients.  Produce about 50% of the oxygen gas we breathe (algae).  Provide other nutrients to many other organisms.  For producing food many of the foods we eat.  Microorganisms and viruses are also in the air we breathe and in the water we drink.  Even, some 100 billion microorganisms inhabit in/on our skin and grow in our mouth, ears, nose, throat, and digestive tract.  The majority of these microbes, called our natural microbiota are actually beneficial in helping us resist diseases, and regulating development and nutrition.  When most of us hear the word “bacterium” or “virus”, we think infection or disease although such pathogens (disease-causing agents) are rare. 2.2. Types of microorganisms  In the life sciences, high priority is placed on the identification and recognition of the different types of microorganisms to treat or use them for various purposes.  Based on evolutionary lines, (Phylogeny tree) there are three main kinds of microorganisms, such as bacteria, archaea, and eukarea.  Phylogeny tree refers to line that show evolutionary relationships between organisms.  It constructed based on (from) small sub unit of rRNA nucleated (gene) sequence.  The three domain System, proposed by Carl Woese, based on: o rRNA nucleotide sequences o Cell's membrane lipid structure and its sensitivity to antibiotics.  Comparing rRNA nucleotide sequences is very useful. Because: o rRNA molecules throughout nature carry out the same function o Their structure changes very little over time.   Therefore similarities and dissimilarities in rRNA nucleotide sequences are a good indicator of different are related or unrelated.  Woese say 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 (protozoa, fungi, plant, and animals). Eubacteria (singular: bacterium)  Means “true bacteria“.  They include all bacteria (except for Archaea bacteria).  Relatively simple, single celled (unicellular) organisms.  Prokaryotic unicellular organisms with no nuclear membrane, mitochondria, Golgi bodies, or endoplasmic reticulum that reproduce by asexual division. General characteristics  They are omnipresent (always present everywhere) i.e. present in soil, air and water.  They are unicellular, prokaryotic microorganism  The cell bears a thick rigid cell wall outside the plasma membrane.  They have great variation in the mode of nutrition i.e. may be autotrophic and heterotrophic  In heterotrophic mode of nutrition they may be, parasite saprophyte or symbiotic in nature  They Lack o true nucleus (nuclear membrane and nucleolus) o mitochondria, Golgi apparatus, plastid and endoplasmic reticulum  Both DNA and RNA present in bacterial cell. Structure of Bacterial Cell Cell Wall:  Cell walls of bacteria are made up of glycoprotein murein.  Its main function providing support, mechanical strength and rigidity to the cell.  It protects cells from bursting in a hypotonic medium. Plasma Membrane:  It is also known as a cytoplasmic membrane (or) cell membrane.  It is composed of phospholipids, proteins, and carbohydrates.  It helps in the transportation of substances including the removal of wastes from the body.  It helps in providing a mechanical barrier to the cell.  Plasma membrane acts as a semi-permeable membrane, allowing only selected material to move inside and outside the cell. Cytoplasm:  Helps in cellular growth, metabolism, and replication.  Cytoplasm is the storehouse of all the chemicals and components used to sustain a bacterium's life. Ribosome:  A tiny granule made up of RNA and proteins.  They are the site of protein synthesis.  They are free-floating structures that help in transferring the genetic code. Plasmid:  Plasmids are a small circle of DNA.  Bacterial cells have many plasmids.  Plasmids are used to exchange DNA between bacterial cells. Flagella:  This is a rigid rotating tail.  It helps the cell move clockwise and anticlockwise forward and also helps the cell spin. The rotation is powered by an H+ gradient across the cell membrane. Pili:  Short protein appendages.  Smaller than flagella.  Fixes bacteria to surfaces.  It also helps in reproduction during conjugation. Capsule:  Capsule is a kind of slime layer, which covers the outside of the cell wall.  They are composed of a thick polysaccharide.  It is used to stick cells together and works as a food reserve.  It protects the cell from dryness and from chemicals. Glycocalyx  is an outer layer external to the Cell Wall  it can take the form of a capsule or slime layer  When the Glycocalyx layer is thick and covalently bonded to the cell, it is called capsule.  When the Glycocalyx layer is thin and loosely attached, it is referred to as a slime layer.  Functions of the Glycocalyx include: o Protection from desiccation (drying out) o Evading immune defenses o Adhesion sites for attachment to host cells, tissues, or surfaces Eukaryotic Microbes  Includes o Species with a wide range of life cycle, morphological specialization and nutritional needs. o More diseases are caused by viruses and bacteria than by microscopic eukaryotes.  Have eukaryotic cell that have o Complex membrane bounded organelles in the Cytoplasmic matrix. o Majority of their genetic material within membrane delimited nuclei o A cytoskeleton composed of microtubules, microfilament and intermediate filaments helps give shape. o Cytoskeleton is also involved in cell movements, intracellular transport and reproduction. o When eukaryotes reproduce, complex processes called mitosis and meiosis. The main difference between eukaryotic and prokaryotic cells Features Prokaryote Eukaryotes Typical organisms Bacteria Protoctista, fungi, plants, animals Typical Size ~ 1-10µm ~10-100 µm Types of nucleus Nuclear body no Real nucleus with nuclear envelope nucleus DNA Ribosomes 70S 80S Cytoplasmic Very few Highly structured by membrane and cytoskeleton structure Mitochondria None 1-100(though RBC’s have none) Chloroplast None In algae and plants Cell division Binary fission Mitosis(normal cell replication (simple division) Meiosis(gamete production) Bacterial Shapes In fact, phenotypically bacteria are classified based on numerous features.  Cell shape  Nature of multi cell aggregates,  Motility  Formation of spores, and  Reaction to the gram stain is some of the most important features that are used to classify bacteria. Therefore, based on their shape bacteria classified into three groups: A. Cocci (singular, coccus) – spherical bacteria B. Bacilli (singular, bacillus) – rod-shaped bacteria C. Spirochaetes – spiral or corkscrew-shaped bacteria D. Comma_ Vibrio cholera Based on their gram stain, bacteria classified into: gram positive and gram negative bacteria. Gram’s staining: a test for distinguishing bacteria (named after Hans Christian Gram, who developed the technique in 1884) Gram negative Gram positive Have thin peptidoglycan Have thick peptidoglycan Cell wall surrounded by outer membrane/ Have no outer membrane lipo-polysaccharide & Porin protein Antibiotics resistant Susceptible to antibiotics Secrete endotoxin Do not secrete endotoxin Difficult to treat Easy to treat except TB Lose crystal violet Do not lose crystal violet Pink in color purpie in color Eg. Eg. All staphylococci,  All streptococci and  Some listeria species Wall teichoic acid and lipoteichoic acid are two cell wall teichoic acids found in Gram-positive bacteria.  Wall teichoic acids are attached to peptidoglycan while lipoteichoic acids are anchored in the Cytoplasmic membrane by a lipid anchor The Gram staining process includes five basic steps 1. Heat fix/attach the bacteria to the slide 2. Applying a primary stain (crystal violet) 3. Adding a mordant (Gram’s iodine) 4. Rapid decolorization with ethanol, acetone or mixture of both 5. Counter staining with safranin Differential staining: is a staining procedure that distinguishes organisms based on their staining properties Peptidoglycan: The rigid layer of the cell walls of Bacteria, a thin sheet composed of N- acetylglucosamine, N-acetylmuramic acid, and a few amino acids. Endotoxin: the lipopolysaccharide portion of the cell envelope of certain gram negative bacteria, which is toxin to human when solubilized. 2.1.2. Nutritional types of bacteria Bacteria use different mechanism of metabolism to obtain energy and nutrient for growth and reproduction. Most of metabolic mechanism may be placed in one of five nutritional classes; based on the primary source of carbon, energy and electrons. 1. Carbon source  Inorganic carbondioxide_____Autotrophs  Organic molecule like glucose__heterotrophs 2. Energy source  Sunlight_photoautotrophs  Inorganic chemicals__chemoautotrophs 3. Electron source  Reduced inorganic compounds _Lithotrophs  Reduced organic compounds__Organotrophs A. Photolithoautotrophs/ often called photoautotrophs  Carbon source_ use inorganic carbondioxide as carbon source  Energy source_ sun light as energy source  Electron source- inorganic –e donor (H2O, Hydrogen sulfide)  Representative__ Purple, green sulfur bacteria, Cynobacteria B. Photoorganoheterotrophs/  Carbon source_ organic molecule like glucose  Energy source_ Sun light  Electron source__Organic matter  Representative__Purple non sulfur bacteria, Green non sulfur bacteria  Some of these bacteria also can grow as photolithoautotrophs with molecular hydrogen as an electron donor. C. Chemolithoautrotrophs  Carbon source is inorganic carbon dioxide  Energy source inorganic chemical.  Electron source inorganic –e donor.  Representative__Sulfur oxidizing bacteria, Hydrogen oxidizing bacteria, Methanogens, Nitrifying bacteria, iron oxidizing bacteria D. Chemolithoheterotrophs  Carbon source __from organic sources  Energy source  Electron source reduced inorganic molecules  Representative___Some sulfur oxidizing bacteria  These groups contribute greatly to the chemical transformation of elements.  For example__ ammonia to nitrate, sulfur to sulfate  Representative: some sulfure oxidizing bacteria. E. Chemoorganohetrotrophs /Chemoheterotrophs/ Chemoorganotrophs  Organic compound as a source of carbon, hydrogen, electron and energy.  Representative___ nearly all pathogenic MOs, fungi, many Protista and Archaea 2.1.3. Reproduction of bacteria 2.1.3.1. Asexual reproduction There are five types of asexual reproduction in bacteria. These are: 1. Binary fission 2. Reproduction through conidia 3. Budding 4. Reproduction through cyst formation 5. Reproduction through endospore formation Type of Reproduction Description Examples The most common method; the bacterial cell Escherichia coli, 1. Binary Fission divides into two identical daughter cells. Bacillus subtilis Bacteria produce asexual spores called conidia, 2. Reproduction through Streptomyces which are released and can develop into new Conidia species individuals. A new organism develops from an outgrowth Hyphomicrobium 3. Budding (bud) of the parent, which eventually detaches. species Bacteria form protective cysts that can survive 4. Reproduction through harsh conditions; under favorable conditions, Azotobacter species Cyst Formation they can germinate into active cells. Certain bacteria form endospores, which are 5. Reproduction through highly resistant structures that can survive Clostridium, Endospore Formation extreme conditions; when conditions improve, Bacillus species they can germinate into vegetative cells. 1. Binary fission  Most bacteria reproduce by this means.  It occurs after a period of growth in which the cell doubles in mass.  At this time, the chromosome (DNA) replicates and the two DNA molecules separate.  Chromosome segregation is not well understood  Unlike eukaryotic cells, lack mitotic spindle to separate replicated chromosome.  Segregation does involve specialized chromosomal-associated proteins to ensure accurate chromosomal segregation.  It involves the synthesis of a partition, or septum that separates the mother cell into two genetically identical daughter cells. 2.1.3.2. Sexual reproduction There are 3 ways bacteria reproduce sexually, these are: 1. Transformation 2. Transduction 3. Conjugation Type of Sexual Description Mechanism Examples Reproduction Uptake of free DNA from the 1. Natural competence or Streptococcus environment by a bacterial cell, Transformation artificial methods pneumoniae leading to genetic changes. Transfer of genetic material from Generalized or Escherichia coli, 2. Transduction one bacterium to another via a specialized Salmonella spp. bacteriophage (virus). transduction Direct transfer of DNA between F plasmids and sex F-factor plasmid 3. Conjugation two bacterial cells through a pilus, pilus in E. coli often involving plasmids. A. Conjugation  In conjugation, genetic material is transferred from one to the other through pilus.  In contrast to transformation and transduction, conjugation involves body contact between two cells.  Bacteria that show conjugation are dimorphic, meaning that they have two types of cells. o Male (F+) or donor cell and o Female (F-) or recipient cell.  The male or donor cell possesses 1 to 4 sex pili on the surface and fertility factor (transfer factor, sex factor) in its plasmid. Eg. antibiotics resistance gene and other characteristics needed for gene transfer. B. Transduction  In this type of sexual reproduction of bacteria, foreign genes are transferred into a bacterial cell with the help of a virus.   These viruses are called bacteriophages and they are not virulent. C. Transformation  In transformation, a bacterium takes up DNA from its environment and often DNA that’s been shed by another bacteria. Common Bacteria Disease 2.2. Archaea  Species in the domain archaea known as archaeans, are unicellular, microscopic, live as producers or decomposers  General Characteristics o Prokaryotic single celled. o Lack membrane bound organelles and nucleus.  o Lack true peptidoglycan, but they have pseudo peptidoglycan in their cell wall. o Their cell membrane lipids have branched hydrocarbon chains o Many are found in extreme environment. o Based on physiological characteristics there are three major groups of Archaea.  Methanogens (they generate methane)  Extreme halophiles and  Extreme thermophile o This classification is not phylogenetic or evolutionary classification. 1. The Methanogens  Strictly anaerobic  They are isolated from divergent/different anaerobic environments such as: Waterlogged soil, lake sediments, Marshes, Marine Sediments, and gastrointestinal tracts of animals including human.  They degrade organic molecule to methane. 2. Extreme halophiles  Grow in highly saline environment such as the Great Salt Lake, the Dead Sea, salt evaporation ponds and the surfaces of salt preserved foods  Unlike the Methanogens, generally obligate aerobes. 3. Extreme Thermophiles/hyperthermophiles  Found near volcanic vents, fissures that release sulfurous gases and other hot vapor.  With optimum temperatures usually in excess of 80ºc, they may be either obligate aerobes, facultative aerobes, or obligate anaerobes 4. Thermophilic Extreme Acidophiles:  Member of two genera, Thermoplasma and Picrophilus, are notable for growing in extremely acidic hot environment. Archaea share other common features that distinguish them from bacteria:  Lack true peptidoglycan  Their cell membrane lipids have branched hydrocarbon chain.  The initial amino acid in their polypeptide chains, coded by the AUG start codon, is methionine (as in eukaryote and in contrast to the N-formylmethionine used by bacteria). Archaea Reorduce by:  Binary fission  Budding  Fragmentation or other mechanisms Nutritional mode of Archaea  They are either aerobic, facultative anaerobic or strictly anaerobic,  Chemolithoautotrophs to organotrophs. Characteristic Chemolithoautotrophs Organotrophs Inorganic compounds (e.g., hydrogen, sulfur, Organic compounds (e.g., Energy Source iron) carbohydrates, fats, proteins) Carbon Source Carbon dioxide (CO₂) Organic compounds Rely on the breakdown of Utilize oxidation of inorganic substances for Metabolic Pathways organic compounds for energy energy Certain bacteria (e.g., Sulfolobus, Most animals, fungi, and Examples Nitrosomonas) many bacteria (e.g., E. coli)  Important in biogeochemical cycles (e.g., Decomposers, consumers in Ecological Role nitrogen, sulfur) food webs 2.2.1. Beneficial aspect of Archaea B/c of their tolerance to high temperatures Archaea become the source of enzyme that: 1. That usually added to detergent in order to help it maintain its activity even at higher temp. 2. Proteases and lipases derived from alkaliphilic bacteria are being used as detergent additive to increase their stain removal ability. 3. Some Archaea also bear the potential for bioremediation or help in cleaning contaminated site. 4. Archaean has become the source of the enzyme harnessed as the basis for amplification of the DNA in a technique called PCR. Eg. Thermophilic Archaea, Thermus aquaticus ( a species of bacteria that can tolerate high temperature). 2.2.2. Physical factors that affecting microbial growth  The major physical factors which affect microbial growth are solutes and water activity, pH, temperature, oxygen level, pressure and radiation. 1. Temperature  Includes three groups preferring  Cold temperature  Psychrophiles_15ºC  Psychrotrophs_25ºC  Warm temperature  Mesophiles_37ºC  Hot temperature  Thermophiles_60ºC  Hyperthermophiles_95ºC 2. Oxygen  Aerobic – microbes using oxygen  Obligate aerobes-microbes require oxygen  Microaerophiles- requiring reduced level of oxygen.  Facultative- microbes growing with or without oxygen  Anaerobic- microbes not using oxygen  Aerotolerant- microbes tolerating oxygen  Obligate anaerobes- microbes sensitive to oxygen 3. pH  Acidophiles _microbes growing below pH 6 4. Osmotic condition  Halotolerant  Tolerating NaCl  Nonhalophiles  Not tolerating NaCl  Microbes requiring NaCl  Halophiles_up to 15%   Extreme halophiles_up to 15-30% 2.3. Fungi (Sing. Fungus)  Latin fungus, mushroom to describe eukaryotic organisms those are: o Spore-bearing o Have absorptive nutrition o Lack chlorophyll and o Reproduce sexually and asexually.  Mycology is scientific discipline devoted to fungi  Mycologists are scientists who study fungi.  Mycotoxicology is the study of fungal toxins and their effects.  Mycoses (Sing. Mycosis) is disease caused by fungi in animals. 2.3.1. General Characteristics of True Fungi 1. All are eukaryotic (cell with nuclei and cytoplasmic organelles). 2. Most are filamentous.  Composed of individual microscopic filaments called hyphae, which exhibit apical growth and.  Which branch to form a network of hyphae called a mycelium.  Some have septate hyphae and the other has nonseptate (coenocytic hyphae). o Coenocytic hyphae that contains many nuclei not separated by cell walls. 3. Some are unicellular e.g. Yeasts 4. Protoplasm of hypha or cell is surrounded by rigid wall.  Composed primarily of chitin and glucans, although the walls of some species contain cellulose  5. Many reproduce both sexually and asexually  Both often result in the production of spore. 6. Their nuclei are typically haploid and hyphal compartments are often multinucleate  Oomycota and some yeasts possess diploid nuclei. 7. All are achlorophyllous  Lack chlorophyll pigments and are incapable of photosynthesis. 8. All are chemoheterotrophic (chemoorganotrophic)  Utilize pre-existing organic sources of carbon in their environment and the energy from chemical reaction to synthesize the organic compounds they require for growth and energy. 9. Posses characteristic range of storage compounds. e.g. trehalose, glycogen, sugar alcohols and lipids 10. Nutritionally categorized into three (saprophytic, parasitic, and symbiotic). 2.3.2. Ecology of Fungi  Colonized nearly all environments on Earth.  But frequently/on many occasion/ found in cool, dark, moist place with supply of decaying.  Fungi are saprobes/feed on decay/ that decompose organic matter.  Many successful mutualistic relationships involve a fungus and another organism. o Mycorrhizal association  Fungus with plant roots o Lichens  Symbiotic relationship between a fungus and a photosynthetic organism.  Photosynthetic organism provides energy derived from light and carbohydrates.  Fungus supplies minerals and protection. 2.3.3. Classification of Fungi Many mycologists currently recognize five major groups of fungi. 1. Chytridomycota  Zoospore (spore capable of independent movement) producing fungi. Eg. Allomyces and water molds  The simplest and most primitive Eumycota or true fungi.  Like all fungi, chytrids have chitin in their cell walls.  The Chytrids are the only fungi that have retained flagella.   They produce both gametes and diploid zoospores that swim with the help of a single flagellum.  An unusual feature of the chytrids is that both male and female gametes are flagellated.  Allomyces produces diploid or haploid flagellated zoospores in a sporangium. 2. Glomeromycota_ Eg. Mycorrhizal fungi  Newly established phylum that comprises about 230 species, all of which are involved in close associations with the roots of trees.  Plants supply the carbon source and energy in the form of carbohydrates to the fungus, and the fungus supplies essential minerals from the soil to the plant.  The exception is Geosiphon pyriformis, which hosts the cyanobacterium Nostoc as an Endosymbiont.  Do not reproduce sexually and do not survive without the presence of plant roots.  Although they have coenocytic hyphae like the zygomycetes, they do not form zygospores. DNA analysis shows that all glomeromycetes probably descended from a common ancestor, making them a monophyletic lineage. 3. Zygomycota- sporangial fungi E.g. rhizopus and mucor  They include the familiar bread mold, Rhizopus stolonifer, which rapidly propagates on the surfaces of breads, fruits, and vegetables.  Most species are saprobes, living off decaying organic material; a few are parasites, particularly of insects.  The fungi usually reproduce asexually by producing sporangiospores.  The black tips of bread mold are the swollen sporangia packed with black spores.  When spores land on a suitable substrate, they germinate and produce a new mycelium. 4. Ascomycota. Ascospore(spore produced sexually inside membrenous spore case ascus) producing fungi Eg. Saccharomyces cerviciae 5. Basidomycota. Basidia producing fungi E.g. rusts and smuts  Recent genomic evidence indicates that the chytrids and zygomycetes are paraphyletic. 2.3.4. Reproduction in Fungi  Sporulation is the processs of spore formation.  It usually occurs in fruiting bodies (Part of a fungus in which spores are formed).  These structures may be: o Asexual and invisible to the naked eye, or o Sexual structures, such as the microscopic mushrooms. A. Asexual reproduction  Asexual reproductive structures develop at the end of specialized hyphae  Asexually thousands of genetically identical spores are produced through mitotic division in sporangia (sing., sporangium; angio= “vessel). The spore is called sporangiospore. o Sporangia is a sacs or vessels where spore develop. o Eg. Common bread mold Rhizopus  The other fungi produce unprotected dust-like spores on supportive structure called conidiophores. These unprotected dust-like spores is called canidia.  In other fungi spore is formed simply by fragmentation of hyphae. These type of spore is called arthrospore. Eg. Fungi that cause athlete’s foot.  Fungal spores are extremely light and are blown about in huge numbers by wind currents.  Budding  Many yeasts reproduce asexually by budding.  In this process the cell becomes swollen at one edge, and a new cell called a blastospore develops.  Eventually, the plastospore breaks free to live independently and the parent cell can continue to produce additional blastospore. B. Sexual reproduction  Many fungi produce spore by sexual reproduction  In the process opposite mating types come together and fuse.  B/c the nuclei are genetically different in each mating type, the fusion cell represents a heterokaryon (hetro=different; karyo=nucleus); that is, a cell with genetically dissimilar nuclei existing for some length of time in a common dikaryotic cytoplasm.  Eventually the nuclei fuse and diploid cell if formed  Chromosome soon halved by meiosis, returning the cell or organism to a haploid condition. Eg. Mushroom 2.3.5. Economic importance of fungi Beneficial aspects of fungi 1. Recycling of carbon and other elements in the environment b/c fungi exist either saprobes or parasites 2. Important sources of food. Eg. Edible wild or domesticated variets of mushrooms (Basidiomycetes). 3. Industrial processes involving fermentation Eg. Yeasts 4. For preparation of traditional food cheeses, soy sauce and sufu, Enjera, Tela, Tej, Bulla, etc and many organic acids (citric, gallic) certain drugs. 5. For production of citric, oxalic, gluconic and itaconic acid. Eg. Molds such as Aspergillus species.  6. Important source of antibiotics Actinomycetes_Penicillin _AmphotericinB _Adriamycin and bleomycin 7. Useful tools for studying complex eukaryotic events, such as cancer and aging within a simple cell. Harmful aspects of fungi 1. Cause disease of plants, animals and humans.  Plants are vulnerable to fungal disease b/c invade leaves through their stomata. Over 5,000 species attack economically valuable crops. 2. Molds can cause deterioration of fabrics, leather, electrical insulation and other manufactured goods. 3. Spoil agricultural products if improperly stored. 4. Mycotoxicoses A. Aflatoxis_  Aspergillus flavus and Aspergillus parasiticus, produce mycotoxins called aflatoxin.  Aflatoxin are deposited in agricultural products such as peanuts, grains, cereals, sweet potatoes, corn, rice and animal feed.  When these foods ingested by humans where they are thought to be carcinogenic, especially in the liver.  Contaminated meat and dairy products are also source of the toxin B. Ergotism_  Caused by Claviceps purpurea, an ascomycete fungus producing a powerful toxin.  C. purpurea grows as hyphae on kernels of rye, wheat and barley and consume the substance of the grain dense tissue harden into a purple body called sclerotium. o Sclerotium produce alkaloid (a group of peptide) and deposited in the grain as a substance called ergot.  Products such as bread made from rye grain may cause ergot rye disease or ergotism. C. Mushroom poisoning or mycetism, From mushrooms that produce mycotoxin that affect human body 5. Superficial Fungal infections (dermatophytosis)  Superficial mycoses are fungal infection of the outermost area of the human body: o Hair o Fingernails o Toenails and o The dead , outermost layers of the skin.  These disease caused by genera o Trichophyton o Epidermophyton and o Microsporum  The various forms of dermatophytosis (fungal infection of skin, hair and nail) are referred to as tineas or ringworm Clinically, the tineas are classified according to the anatomical site or structure affected. 1. Tinea corporis(ringworm): Affects hairless skin.  Caused by Microsporum canis and Trichophyton mentagrophytes.  2. Tinea pedis (athletes foot): Affects mainly the lower legs.  Caused by T. rubrum, T. mentagrophytes, and Epidermophyton floccosum. 3. Tinea capitis: Affects the scalp, eyebrows, and eyelashes.  Caused by T. tonsurans and M. canis. 4. Tinea barbae: affecting the beard area, leading to red, itchy patches and hair loss.  T. rubrum and T. mentagrophytes.  Beard ringworm. 5. Tinea unguium (onychomycosis): Affect the nail  Caused by T. rubrum, T. mentagrophytes and E. floccosum. Mode of transmission Directly  Human contact  Animal_human contact Indirectly  From inanimate objects o Clothes, carpets (floor covering), moisture, and dust in showers, swimming pools wardrobes, gyms. Prevention  Regular disinfection of showers and wardrobes Summary of some fungal disease 1. Dermatophytosis o Causative agents__Epidermophyton, Microsporum, Trichophyton o Sign and symptoms__Blister-like lesions o Transmission__Fragments of skin on skin floors or surface o Prevention and control__ Keeping skin dry, not sharing person items 2. Candidiasis o Causative agents__ Candida albicans o Sign and symptoms__ Itching, burning pains, “cheesy discharge” discharge o Transmission__Sexually o Prevention and control__ Avoiding baths hot and tubs, Avoiding douches 3. Thrush o Causative agents__ Candida albicans o Sign and symptoms__ White flecks on mucous membranes o Transmission__Passage through the birth canal o Prevention and control__practicing good oral hygiene, limiting sugar intake  4. Aspergillosis o Causative agents__Aspergillus fumigatus o Sign and symptoms__ Bloody cough, chest pain, wheezing shortness of breath o Transmission__Air borne spores o Prevention and control__ staying away from sources of mold. 2.4. Protozoa  The term protozoa(sing., protozoan; Greek protos, first, and zoon, animal).  Traditionally referred to chemoorganotrophic protists.  Protozoology refers to the study of protozoa.  General characteristics o Unicellular and lack cell wall. o Free living or parasitic o Aerobic o Eukaryotes o Mostly microscopic, although some are large enough to be seen with the unaided eyes. o Locomotion by pseudopodia, flagella, cilia, and direct cell movements; some sessile. o Nutrition of all types:  Autotrophs_(photosynthesis)  Heterotrophic_(depending on other plants and animals)  Saprozoic_(using nutrients dissolved in the surrounding medium) o Aquatic or terrestrial habitat: as free living or symbiotic mode of life.  Reproduction:  Asexually: fission, budding and cyst  Sexually: conjugation or by syngamy (union of male and female gamate to form zygote Classification of protozoa 1. Ciliates  Means of movement Cilia  Method of reproduction: o Asexually: Transverse fission o Sexually: Conjugation  Representatives: Balantidium coli, Paramecium, Stentot, Tetrechymena, Vorticella 2. Amebae (amebas)  Means of movement: Pseudopodia (false feet)  Method of reproduction o Asexually: Binary fission o Sexually: When present, involves flagellated sex cell  Representatives: Ameoba, Naegieria, Entamoeba histolytica 3. Flagellates  Means of movement: Flagella  Method of reproduction: o Asexually: Binary fission o Sexually: None  Representatives: Chlamydomonas, Giardia lamblia, Trichomonas, Trypanasoma 4. Sporozoa  Means of movement: Non motile except for certain sex cells   Method of reproduction o Asexually: multiple fission (nucleus divided into many nucleus, before cell divided, and then the cell divided into many part) o Sexually: involves flagellated sex cells  Representatives__Plasmodium, Toxoplasmangondii, Cryptosporidium Reproduction in protozoa Most protozoa are asexual and reproduce in one of three ways. These are: 1. Fission: cell divides evenly to form two new cells. 2. Budding: cell divides unevenly. 3. Multiple fission (schizogony): when the nucleus of the cell divides multiple times before the rest of the cell divides and each nuclei separate into a daughter cell. Types of Binary Fission  Binary fission has four types according to how the cell divides: (1) irregular, (2) transverse, (3) longitudinal, and (4) oblique. 1. Irregular  In irregular binary fission, the cell divides at any plane. However, it is mostly in a manner perpendicular to where the nuclear division (karyokinesis) occurred. 2. Transverse  In transverse-type, cell division occurs along the transverse axis, hence the name. 3. Longitudinal  In longitudinal binary fission, the cell divides longitudinally/long axis of the body. 4. Oblique  In oblique binary fission, cell division occurs obliquely, which may either by left or right oblique. Sexual reproduction (conjugation)  A distinctive feature of ciliates is the presence of two types of nuclei: Tiny micronuclei o Genetic variation results from conjugation, a sexual process in which two individuals exchange haploid micronuclei but do not reproduce. Gene found in micronucleus used for gamete formation (Responsible for the inheritance of genetic material). Large macronuclei o Genes in the macronucleus control the everyday functions of the cell, such as feeding, waste removal, and maintaining water balance.  A cell has one or more nuclei of each type  Ciliates generally reproduce asexually by binary fission, during which the existing macronucleus disintegrates and a new one is form from the cell’s micronuclei Stages of conjugation in Paramecium caudatum 1. Compatible mating strains meet and partly fuse 2. The micronuclei undergo meiosis, producing four haploid micronuclei per cell. 3. Three of these micronuclei disintegrate. The fourth undergoes mitosis. 4. The two cells exchange a micronucleus. 5. The cells then separate. 6. The micronuclei in each cell fuse, forming a diploid micronucleus. 7. Mitosis occurs three times, giving rise to eight micronuclei. 8. Four of the new micronuclei transform into macronuclei, and the old macronucleus disintegrates. 9. Binary fission occurs twice, yielding four identical daughter cells. Nutrition in Protozoans  Heterotrophic and can grow in both aerobic and anaerobic environments. Eg protista that live in the intestine of animals.  Some protista, such as Euglena, photosynthetic. Obtain nutrients from organic matter and through photosynthesis b/c they contain chlorophyll. Euglena are considere both algae and protozo.  Most Protists obtain (take) food in one of three ways: o Absorption (Saprozoic): food is absorbed across the protist’s plasma membrane. o Ingestion: cilia outside the protist create a wave-like motion to move food into a mouth-like opening in the protist called a cytosome. o Engulf: Pseudopods (false feet) engulf food, and then pull it into the cell using a process called phagocytosis. Eg. Amoeba.  After food enters into the cell, digestion occurs in the cell vacuole.   Waste material is occurred in the cell removed by exocytosis. 2.4.1. Common diseses caused by protozoa  Most protozoas are not harmful.  Many types are even beneficial in the environment because: o They help make it more productive. o Improve water quality by eating bacteria and other particles.  There are few protozoa that cause disease to human. Disease Cusative Organ Transmission/Vetor Clinical features agents affected Amoebiasis Entamoeba Intestine,  Fecally contaminated  Multiplication and tissue destruction histolytica liver food or water; abscesses(Pus-filled cavity).  Disease associated with  Irritating of cell lining the intestine resu poverty, homosexual and amebic dysentery (bloody diarr men and migrant ulceration). worker, Giardiasis Giardia Intestine  Fecally contaminated  Ingested cyst survive stomach passage: lamblia water,  trophozoites emerge from the cysts in th  Person to person in day *Some-attach to epithelium care centers. *Other move freely  Mucosal function impaired by adher immune response. Trichomoniasis Trichomonas Urogenit  Sexual contact  Vaginal discharge, odor and edema or e vaginalis al organ African Trypanosoma Blood,  Tsetse fly (Glossina) Initial haemolytic phase (fever, joint pains f sleeping brucei brain disorder, somnolence) sickness Somnolence_sleep inducing(making some b Leishmaniasis Leishmania WBC,  Sand fly(Phlemotomus)  Skin ulcers donovani Skin,  Mucocutaneous complication and intestine  Visceral diseases (hepatosplenomegaly) Malaria Plasmodium Liver,  Mosquito (Anopheles  Fever, shivering, cough, respiratory dis spp. RBC headache, watery diarrhea, vomiting, co Toxoplasmosis Toxoplasma Blood,  Domestic cats, food  Blindness and mental retardation – i gondii Eye children  In immunosuppressed patients_mor splenomegaly, polymyositis, dermato myccarditis, pneumonitis, hepatitis multisystem organ failure. 2.5. Viruses Viruses are:  Small, obligate, intracellular particle, ultramicroscopic particle.  Most can be seen only with the electron microscope.  They must infect and take over a host cell in order to replicate. This is b/c they lack the chemical machinery for generating energy and synthesizing large molecule. as a result cause disease. 2.5.1. Characteristics of viruses  Have inner core of nucleic acid surrounded by protein coat known as an capsid.  Cannot be grown on artificial cell free media (however, grow in animals, eggs or tissue culture).  Do not have cellular organization. They do not have, o Cell wall  o Cell membrane o Cellular organelle including ribosomes.  They do not free live in nature but act as obligate intracellular parasite.  They lack the enzymes necessary for protein and nucleic acid synthesis and are dependent for replication on the synthetic machinery of host cells.  They are not affected by antibacterial antibiotics.  Occupy a space in between living and non-living, b/c they are crystallizable and non- living outside the body of host.  Obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants and animals.  Ultramicroscopic size, ranging from 20-450nm (diameter).  Do not independently fulfill the characteristics of life.  Inactive macromolecules outside the host cell and only active inside host cell.  Basic structure consists of protein shell (capsid) surrounding nucleic acid core and viral genome (either DNA or RNA but, not both).  Molecule on virus surface impart/giving high quality/ high specificity for attachment to the host cell.  Multiply by taking control of host cell’s genetic material and regulating the synthesis and assembly of new viruses.  Lack machinery for synthesizing proteins. Structure of Viruses  A basic structure of virusis: o Nucleic acid core (DNA or RNA but not both)- this is called genome o Capsid- a protein coat surrounds nucleic acid core. o An envelope made up of glycoprotein and phospholipid bilayer is present outside the capsid. o Enzyme (lysozyme or and polymerase) The basic structural components of a virus are: 1. Core-the genomic material o Either DNA or RNA o DNA or RNA may be single stranded or double stranded 2. Capsid- A protective coat of protein surrounding the core. 3. Nucleocapsid- the combined structure formed by the core and capsid 4. Envelope o Afew viruses have an additional lipoprotein layer around the capsid derived from the cell surface membrane of the host cell. 5. Capsomeres o Capsids are often built up of identical repeating subunits called capsomeres. 6. Enzymes  o Some virus contains enzymes which play central role during infection process. o Eg. o Some bacteriophage contains an enzyme lysozyme which makes small hole in bacterial cell that allows nucleic acid to get in. o Retrovirus contain RNA dependent DNA polymerase called reverse transcriptase. RNA virus replicate inside host cell as DNA intermediate. 2.5.2. Viral Symmetry 1. Helical symmetry  These viruses consist of identical protein subunit or protomers which assembled in a helical structure around the genome.  This type of protein subunits generally forms a rigid nucleocapsid.  Also provide flexibility to the filaments Eg. Tobacco mosaic virus and Sendai virus 2. Icosahedral symmetry  A type of polyhedron with 20 equilateral triangular faces and 12 vertices.  Rigid structure provide protection to genome. Eg. Papova virus, Picorana virus, adenovirus, Togavirus. 3. Complex Symmmetry  Do not come under the above mentioned groups.  Consist complex structural components. Eg. Pox virus Difference between DNA and RNA Viruses DNA Viruses  DNA as their genetic material where as RNA their genetic material as RNA.  DNA mostly double stranded   is slower rate of mutation than RNA RNA Viruses  RNA as their genetic material  RNA mostly single stranded  higher rate of mutation than DNA  Retroviruses: is an RNA virus that converts its genetic information from RNA to DNA after it infects the host cell.  Viruses infect all cellular life forms: Eukaryotes and Prokaryotes.  HIV is a virus that attacks the body’s immune system. If HIV is not treated, it can lead to AIDS 2.5.3. Classification of Viruses Today, the primary criteria for delineating (describing)the main viral taxa are: 1. The type and character of the viral genome 2. The strategy of viral replication 3. The types of organisms they infect Viral Replication Viruses go through the following five steps in their replication cycles to produce more virions. 1. Adsorption_ attachment of viruses to host cells. 2. Penetration _ the entry of virions (Or their genome) into host cells. 3. Synthesis_synthesis of new nucleic acid molecule, capsis proteins, and other viral componenets within host cells while using the metabolic machinery of those cells. 4. Maturation_assembly of newly synthesized viral components into virions. 5. Release-the departure of new virions from host cells. Bacteriophages/Phage  The viruses that infect prokaryotes.  They are obligate intracellular parasites that multiply inside bacteria by making use of some or all of the host biosynthesis machinery.  Bacteriophage structure o Genome_ carries the genetic information necessary for repllication of new phage particles. o Tail sheath_ retracts so that the genome can move from the head into the host cell’s cytoplasm. o Plate and tail fibers_attach phage to specific receptor sites on the cell wall of host. Phages exhibits two different types of life cycle Lytic cycle/Virulent cycle  Intracellular multiplication of the phage results in the lysis of host bacteria, resulting in release of progeny virions.   Viral genome replication is independent of host cell.  Lysozyme breaks down the cell wall, allowing viruses to escape.  In the process the bacterial host cell is lysed (destroyed).  Cell lysis releases new phage particles that can infect more bacteria. Eg. T4 Lysogenic Cycle  Unlike virulent phage (w/c cause cell lysis), some phages(such as temperate phage) integrate into the genome of bacterial chromosome without causing any lysis (without destroy).  The integrated phage nucleic is known as the prophage.  Viral genome replicated by integrated with host cell.  Prophage behaves like a segment of host chromosome and multiplies synchronously(happening at the same time) with it.  The bacterium that carries a prophage within its genome is called lysogenic bacterium such phage are called lysogenic or temperate. Key Differences  Lytic cycle need stage: attachment, Entry/ adsorption/ penetration, Replication, Assembly and Lysis (release).  Lysogenic cycle need stage: attachment, Entry/ adsorption/ penetration, integration, Replication, Assembly and Lysis (release).  Outcome for Host: The lytic cycle results in the death of the host cell, while the lysogenic cycle allows the host cell to survive and replicate.  Replication Timing: The lytic cycle replicates the virus immediately, whereas the lysogenic cycle involves a dormant phase before replication. Lytic vs Lysogenic Cycle Lytic Cycle Lysogenic Cycle The DNA of the virus doesn’t integrate into The DNA of the virus integrates into the host the host DNA DNA Host DNA hydrolyzed Host DNA not hydrolyzed Absence of prophage stage Presence of prophage stage DNA replication of virus takes place DNA replication of virus takes place along independently from the host DNA replication with the host DNA replication Occurs within a short period of time Takes time Symptoms of viral replication are evident Symptom of viral replication not evident Genetic recombination in the host bacterium Genetic recombination in the host bacterium not allowed allowed Te cellular mechanism of the host cell is totally The cellular mechanism of the host cell is undertaken by the viral genome somewhat disturbed by the viral genme. Common Viral Disease in Ethiopia Disease Causative agent Sign and Symptoms Transmission P C Mumps Mumps virus  Swollen and painfull protid Person to person in infected V glands. saliva  Pain on chewing and swallowing Measles Measles Virus  Caugh, nasal discharge, eye Droplet contact V (rubeola) redness and high fever Rabies Rabies Virus  Tingling, burning, coldness at Bite from rabid animals A bite site, Fever, headache, a increased muscle tension, w Paralysis and hydrophobia (fear a of fluid) v n Polio Polio Virus  Often no sign and symptoms Fecal- Oral- route P p Common Cold Rhino viruses  Sneezing, sore throat, runny and Respiratory droplets P (rhinitis) Adeno viruses and stuffy nose, hacking cough h other viruses Chicken pox Varicella Zoster  Fever, headache, Droplet contact C Virus Malaise(discomfort) with red,itchy rash on face, scalp, chest, and back 2.6. Normal Microbiota Normal Microbiota  Population of microorganisms growing on the body of healthy individuals.  There are two types of normal microbiota Resident microbiota Transient microbiota Feature Resident Microbiota Transient Microbiota Microorganisms that permanently inhabit a Microorganisms that are temporarily Definition specific environment within the host, present in a host but do not establish establishing a stable population. long-term residence. Long-term presence; can persist for a Short-term presence; may be present Duration lifetime, often adapting to the host's for hours to weeks but eventually environment. eliminated by host defenses. Play essential roles in host metabolism, Generally do not provide benefits; may Function immunity, and protection against be pathogenic or non-pathogenic and pathogens; contribute to overall health. can be cleared by the immune system. Relatively stable in composition; can Highly variable; composition changes fluctuate with changes in health, diet, and Stability frequently based on environmental environmental conditions, but core exposure and individual activities. members remain.  Specific to certain anatomical sites, such Can be found in various locations Location as the gut, skin, mouth, and respiratory depending on exposure, but do not tract; often unique to the individual. establish a permanent niche. Typically commensal or mutualistic; Often neutral or opportunistic; may Host contribute to the host's health and help cause infections if the host's immune Interaction prevent infections by outcompeting system is compromised but typically do pathogens. not harm healthy hosts. Bacteroides species in the gut, Escherichia coli (certain strains), Example Staphylococcus epidermidis on the skin, Staphylococcus aureus, or other Organisms and various Lactobacillus species in the transient pathogens acquired from the vaginal microbiota. environment. Reasons to acquire knowledge of the normal human microbiota 1. An understanding of the different microorganisms at particular location provides greater insight into the possible infections that might result from injury to these body sites. 2. A knowledge of the normal microbiota helps the physician investigator understand that cause and consequence of colonization and growth by microorganisms normally absent at specific body site. 3. An increased awareness of the role that these normal microbiota play in stimulating the host immune response can be gained. This awareness is important because the immune system provides protection against potential pathogens. One of the most significant contribution of the normal microbiota to health is protection against pathogens. They excludes pathogens by; 1. Covering binding sites. 2. Consume available nutrients 3. Produce compounds toxic to other bacteria. 4. Stimulate the adaptive immune system When members of the normal microbiota are killed or their growth suppressed, as can happen during antibiotic treatment,  Pathogens may colonize and cause disease Eg. Oral antibiotics_ can inhibit members of the normal intestinal microbiota, allowing the overgrowth of toxin-producing strain of Clostridium difficile that cause antibiotic- associated diarrhea and colitis(inflammation of Colon). Normal microbionta of the human body 1. Upper respiratory tract(Nose, nasopharynx, propharynx) Bacterial Genera  Streptococcus, Neisserie, Haemophilus, Staphylococcus Fungal Genera  Candida 2. Oral Cavity  Dense and diverse microbial population  Streptococcus, Treponema, Neisseria, Haemophilus, Lactobacillus, Staphylococcus, Propionibacterium 3. Skin Bacterial genera  Populated with primarly gram +ve bacterial genera   Staphylococcus, streptococcus, Corynebacterium, Propionibacterium, Micrococcus Fungal genera  Candida 4. Female reproductive tract The vagina can be densely populated with: Bacterial genera  Lactobacillus, Staphylococcus, Corynebacterium, Streptococcus, Entrococcus Fungal genera  Candida 5. Urinary tract Female urethra may contain:  Lactobacillus, Corynebacterium, Streptococcus, Bacteroides Male urethra may contain:  Corynebacterium, Streptococcus 6. Intestine Small  Lactobacillus, Corynebacterium, Streptococcus, Bacteroides Large  Dense and diverse microbial population Germ theory of Disease and Koch’s Postulates  In order to prove whether or not disease are caused by microorganisms:  He used mice as experimental animal.  Koch’s postulates state the following: If the disease is caused by microorganism (infectious disease): 1. Disease- causing organism (pathogen) must always be present in infected animals but absent in healthy animals. 2. The organisms must be cultivated in a pure culture media away from the animal body. 3. The isolated organism must cause the disease when inoculated into healthy susceptible animals. 4. The organism must be isolated from the newly infected animals and cultured again in the laboratory, after which it should be seen to be the same as the original organism. Proteins/Prion diseases  Prion diseases are a group of neurodegenerative disorders caused by misfolded proteins in brain known as prions.  Prions are infectious agents composed primarily of protein.  They lack nucleic acids (DNA or RNA).  Which is resistant to proteolytic degradation.  It can affect both human and animals  Transmission  Sporadic Cases: cases occur without any known cause.  Inherited Cases: Certain prion diseases can be inherited due to mutations in the gene coding for the prion protein.  Consumption of contaminated meat,  Contaminated surgical instruments,  Blood transfusions from infected donors. Symptoms: behavioral changes, ataxia, and visual disturbances. Prevention: Avoiding Contaminated Food  Screening donors blood  Strict sterilization protocols for surgical instruments and prevent cross-contamination. vCJD(Variant Creutzfeldt-Jakob Diseases)  Variant Creutzfeldt-Jakob Disease (vCJD) is a rare and fatal neurodegenerative disorder that affects the brain.  It is one of the types of prion diseases, characterized by the accumulation of misfolded prion proteins, leading to brain damage.  Caused by the ingestion of prions. Transmission Pathway: is primarily associated with the consumption of contaminated beef `` products. Initial Symptoms: Early symptoms may include psychiatric changes such as depression, anxiety, or personality changes. Neurological Symptoms: As the disease progresses, patients may experience:  Memory problems and cognitive decline  Ataxia (loss of coordination)  Visual disturbances, including blurred vision or blindness  Muscle stiffness and involuntary movements Chagas disease-caused by protozoan parasite known as Trypanosoma cruzi, transmitted by blood sucking insect (that feed on human and animals) and cause heart feilur and digestion complication and prevented Vector Control. 2.7. Mode of disease transmission and ways of prevention  Microorganisms are transmitted in health care setting by four main routes: o Contact o Droplet o Airborne o Comon Vehicle  Methods of How transmission route works Example of disea transmission Droplet infection  Many of these are respiratory disease-disease affect the Common cold, flu, pneumonia airways of the lungs.  The infectious microbes are carried in tiny droplet when an infected person sneeze or cough. Drinking  The micro-organisms transmitted in this way often Cholera, typhoid fever contaminatd water infect regions of the gut.  When unclean water containing infectious microbe is drunk, they colonise a suitable area of the gut and reproduce.  They are passed out with faeces and find their way back into the water. Eating contaminated  Most of food poisoning is bacterial, but some viruses are  Salmonellosis (food poisoning cause GI food transmitted this way.  Typhoid fever  The organism initially infect region of the gut.  Listeriosis ( a disease of the nervous meningitis (stiff neck), miscarriage or pre  Botulism- toxin affects nervous system difficulty in breathing and even death). Direct contact  Many skin infection transmitted this way when direct Athlete’s foot, ringworm contact with an infected person or contact with surface carrying the organism. Sexual intercourse  Organisms infecting the sex organs can be passed from  Candidiasis (thrush). one sexual partner to another during intercourse.  AIDS virus o Some are transmitted by direct body contact.  Syphilis o Others are transmitted in semen or vaginal secretions. o Some can be transmitted in saliva. Blood-to-blood  Many of STD can also be transmitted by this route. AIDS, hepatitis B contact Animal vector  Many diseases are spread through the bites of insects. Malaria, Sleeping sickness o Mosquitoes spread malaria and tsetse flies spread sleeping sickness.  Disease causing organism is transmitted when the insect bites humans in order to suck blood.  Flies can carry micro-organisms from faeces onto food. 2.8. Use of Microorganisma A. Agriculture  Help in organic matter decomposition, humus formation.  Help in nitrogen fixation  phosphate solubilization  Potassium mobilization  Antagonism (oposition) towards pathogens, pests.  Responsible for converting these elements into form that plants and animals can use. A. Sewage treatment  Anaerobic bacteria are used in waste water treatment on a normal base  Reduce the volume of sludge/solid waste and produce methane gas from it.  Phosphorus removal from wastewater. B. Bioremediation  Bioremediation is the use of microoganisms and/or their derivatives (enzymes or spent biomass) to clean-up environmental contaminant.  Pollutants in the different environmental compartment always come into contact with microrganisms.   Microbes transform/ break down pollutants via their inherent metabolic processes wit h or without slight pathway modification to allow the pollutant to be channeled into the normal microbial metabolic pathway for degradation and biotransformation. C. Food production and processing  A group of lactic acid bacteria produce lactic acid.  These bacteria-including species of Lactobacillus, Lactococcus, Streptococcus, Leuconostoc and Pediococcus are obligate fermenters.  This lactic acid provide tart test to yoghurt, pickles, sharp cheeses, and some sausages.  Some also produce flavorful and aromatic compounds that contribute to the overall quality of fermented foods. D. Medicine  Microorganisms have made it possible to make medicine which when enter the body, target defected genes and make healthy changes in them and they become functional again.  Now it is possible to synthesize insulin in microorganism and yeast.  Microorganisms are inserted in the body in the form of vectors and cure the defected genes  Scientists have made use of them for making many medicines and drugs and also used them for durg delivery. E. Health  Human contain ten times more microorganisms than the body cells.  These microorganisms are useful. Example o Release components which help in the digestion of food---E.coli o Used to fight against harmful bacteria. o Helps in synthesizing the vitamins like:  Biotin(V. B7)_related to the utilization of fats, carbohydrates, and amino acids.  Vitamin K _used in blood cloting  Folic acid(V.B9)_Folate (vitamin B-9) is important in red blood cell formation and for healthy cell growth and function F. Biotechnology  Field which has made use of microorganisms most.  By using the techniques of biotechnology, scientists have succeeded in o Developing human insulin o Growth hormone o Use microorganisms for the drug delivery in the form of vectors and plasmids The role of bacteria in recycling mineral through ecosystem Decomposers  Many bacteria are decomposers.  Break down complex molecule in dead body part of an organisms into simpler molecules.  Use some for metabolism  They release some minerals in various forms.   Almost 90% of living organisms are made up of C, O,N and H and these substance are limited in their availability.  In order for life to continue the substances should be recycled. This is done by decomposers. The carbon cycle  All organisms are composed of organic molecules such as, carbohydrates, proteins and lipids.  The carbon travels through the food chain. Primary producers→Primary consumers→Secondary consumers  Decomposers use the remains of primary producers and consumers. Carbon fixation  Carbon fixation is a fundamental aspect of the carbon cycle, the defining characteristics of primary producer.  Fermentation and respiration in hetrotrophs consume organic material and produce CO2 during synthesis of ATP.  In rapidly multiplying bacteria often the oxygen supply has a strong influence on the carbon cycle.  Oxygen not only allows degradation of certain compounds such as lignin, it also helps determine the type of carbon containing gases produced o When organic material degrade aerobically, a great deal CO2 is produced. o When oxygen level is low, however as in the case in marshes, swamps, and manure piles the degradation is incomplete, generating some CO 2 and variety of other products. Methanogenesis and Methane oxidation  In anaerobic environments,  CO2 is used by Methanogens.  Methanogens obtain energy by oxidizing hydrogen gas, using CO 2 as a terminal electron acceptor, generating methane(CH4).  In aerobic respiration, organic matter such as glucose is oxidized to CO 2, and O2 is reduced to H2O. In contrast, during hydrogenotrophic methanogenesis, H2 is oxidized to H+, and CO2 is reduced to CH4  Methane that enters the atmosphere is oxidized by UV light and chemical ions, forming carbon monoxide (CO) and CO2.  Methylotrophs(a group of microorganisms) use methane as an energy source, oxidizing it to produce CO2. The Nitrogen Cycle  Nitrogen cycle - Atmospheric nitrogen is converted into chemical forms by bacteria and brought back into the atmosphere is called the nitrogen cycle. The major steps involved in the nitrogen cycle are:- 1. Nitrogen fixation- In this step atmospheric nitrogen is fixed by nitrogen fixation bacteria like Anabaena, Nostoc, and, Rhizobium and conversion of nitrogen into ammonia takes place. N2 to NH3. 2. Nitrification- In this step, the nitrifying bacteria convert ammonia into nitrates. NH 3 to NO 3. - 3. Assimilation- Nitrogen compounds are now taken up by plants and animals in various forms like NH4+ NH3, NO2- to make proteins. 4. Ammonification- Nitrogen is added back to the soil by plants and animals through waste material and dead bodies. 5. Denitrification- The nitrogen present in the soil break down by the denitrifying bacteria and nitrogen is converted back to the atmospheric nitrogen. The bacteria involved in the steps are: 1. Nitrogen fixation- Anabaena, Nostoc and Rhizobium. 2. Nitrification- Nitrosomes, Nitrosospira, Nitrococcus and Nitrosolobus. 3. Ammonification- Paracoccus denitrificans, and Myxococcota. 4. Denitrification- Serratia, pseudomonas and achromobacter.  The Sulfur Cycle Phosphorus Cycle  Phosphorus occurs in the soil both as organic and inorganic.  It can be found dissolved in the soil solution in very low amounts or associated with soil minerals or organic materials.  Each form of phosphorus in a clay-textured soil being up to ten times greater than in a sandy soil. Organic P in soils  A large number of compounds make up the organic P in soils, with the majority being of microbial origin.  Organic P is held very tightly and is generally not available for plant uptake until the organic material are decomposed and the phosphorus released via mineralization process.  Mineralization is carried out by microbes, and as with nitrogen.  The rate of phosphorus release is affected by: o Soil moisture o Composition of the organic material o Oxygen concentration and pH Inorganic P in soil  The concentration of inorganic P (orthophosphates) in the soil solution at any given time is very small, amounting to less than 1 1b/A.  Phosphorus in the inorganic form occurs mostly as aluminum, iron or calcium compound. 2.9. Controlling Microorganisms Sterilization  A process by which an article, surface, or medium is freed of all living microorganisms either in vegetative or in the spore state.  Any material that has been subjected to this process is said to be sterile.  These terms should be used only in the absolute sense.  An object cannot be slightly sterile or almost sterile; it is either sterile or not sterile  There are no degrees of sterilization  Any material that has been subjected to this process is said to be sterile. A Germicide/microbicidal-  Any chemical agents that kill pathogenic microorganisms.  Can be used on inanimate material or on living tissue.  But it ordinarily cannot kill resistant microbial cells  Any physical or chemical agent that kills “Germs” is said to have germicidal properties. Disinfection  Use of a chemical agent that destroys or removes all pathogenic organisms or organisms capable of giving rise to infection.  Destroys vegetative pathogens but not bacterial Endospore.  Only used on inanimate objects (b/c it is toxic to human and other animal tissue) when used in higher concentration.  Also remove harmful products of microorganisms (toxin) Example a. Applying a solution of 5% bleach to examining table b. Boiling food utensils used by a sick person c. Immersing thermometers in an isopropyl alcohol solution between uses Antiseptics Applied directly to the exposed body surface (skin and mucous membranes), wounds, and surgical incisions to destroy or inhibit vegetative pathogens Example of antisepsis 1. Preparing the skin before surgical incisions with iodine compounds 2. Swabbing an open root canal with hydrogen peroxide 3. Ordinary hand washing with germicidal soap Sanitization Any cleansing technique that mechanically removes microorganisms (along with food debris) to reduce the level of contaminant Preservation  General term for measures taken to prevent microbe caused spoilage of susceptible products (pharmaceuticals, foods). Decontamination  Removal or count reduction of microorganisms contaminating an object. Physical Methods of sterilization and disinfection A. Heat  Heat is a simple, cheap and effective method of killing pathogens  It vary according to the specific application a. Pasteurization  Antimicrobial treatment used for food in liquid form(milk) o Low temp. pasteurization: 61.5ºC, 30 minutes: 71ºC, 15 seconds o High temp Pasteurization: Brief (seconds) of exposure to 80-85ºC in continuous operation o Uperization: Heating to 150ºC for 2.5 seconds in a pressurized container using steam injection. b. Disinfection  Application of temp. below what would be required for sterilization  Boiling medical instruments, needles, syringes, etc  Does not constitute sterilization  Many bacterial spore are not killed by this method c. Dry heat sterilization i. flaming – holding them in the flame of the Bunsen burner till they become red hot Eg. Inoculating loop or wire, the tip of forceps searing spatulas. ii. Incineration_ safely destroying infective material by burning them to ashes  It has many uses  In hospitals and research labs to destroy wastes  Used for complete destruction and disposal of infectious material such as syringes, needles, culture material, dressing, bandages, bedding, animal carcasses, and pathology samples.  Fast and effective for most hospital wastes, but not for metals and heat-resistant glass material iii. Hot air oven  Requires exposure to 160-180ºC for 2 hours and 30 minutes, which ensures through heating of objects and destruction of spores d. Moist heat sterilization  Autoclaves charged with saturated, pressurized steam are used for this purpose  121ºC, 15 minutes, one atmosphere or pressure (total: 202kPa)  134 ºC, three minutes, two atmospheres of pressure(total: 303kPa). Intermittent sterilization  A technique for sterilizing heat-labile substances (eg., Serum, sugar, egg, etc.)  o Serum yellowish fluid obtained upon separating whole blood into its solid and liquid components.  Used for substances cannot withstand the temperature of the autoclave. Tyndallization  Intermittent sterilization  Carried out over a period of 3 days and requires a chamber to hold the materials and a reservoir for boiling water.  Items to be sterilized are kept in the chamber and are exposed to free-flowing steam at 100ºC for 20 minutes, for each of the three consecutive days. 2.10. Bacterial Isolation techniques  Microorganisms can be isolated from food, soil, water or from other materials.  Samples are collected from the desired site  Mos are separated on artificial media by serial dilution method.  Each of the isolates are purified on new media and experimented for  Morphological characteristic like shape, gram nature and arrangement of cells, motility etc.  Enzymatic activities were tested by biochemical characterization.  Molecular techniques are used for further identification.