Introduction Microbes are a diverse group of organisms that can be divided into the viruses, unicellular groups (Archaea,

Eubacteria, protista, some fungi and some chlorophyta) and a small number of organisms with a simple multicellular structure (the large fungi and chlorophyta). Microbiology: the science (logos) of small (micro) life (bios). The study of living things so small that they cannot be seen with the naked eye. The three-domain system is a biological classification introduced by Carl Woese that divides cellular life forms into archaea, bacteria, and eukaryote domains. In particular, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria (now Bacteria) and Archaebacteria (now Archaea). Microorganisms were first visualized by Antoni van Leeuwenhoek (16321723), a Dutch cloth merchant and an expert lens grinder. The first proof of the involvement of bacteria in disease and the definitive proof of the germ theory of disease came from the German Robert Koch. Kochs postulates: 1, The microorganism must be present in every instance of the disease and absent from healthy individuals. 2, The microorganism must be capable of being isolated and grown in pure culture. 3 ,When the microorganism is inoculated into a healthy host, the same disease condition must result. 4, The same microorganism must be re-isolated from the experimentally infected host. Chapter one Fungi include yeasts, molds, and mushrooms. Viruses are noncellular organisms; they are intra-cellular parasites of animals, plants, or bacteria. 1, The Prokaryotes can be divided into two kingdoms, Bacteria and Archaea. The classification was first proposed by Woese based on the differences in 16S rRNA sequence. 2, Prokaryotic microorganism : It is an single-celled organism which doesnt have a nuclear membrane outside the cell nucleus and only has the bare DNA called as the nuclear area. 3, Many bacteria are shaped like long rods twisted into spirals or helices; they are called spirilla if rigid and spirochetes ( ) when flexible. 4, Capsules ( ) and slime layers ( ) usually are composed of polysaccharides ( ), but they may be constructed of other materials. 5, Gram staining procedure() In the first step of the Gram-staining procedure, the smear is stained with the basic dye crystal violet, the primary stain. It is followed by treatment with an iodine solution functioning as a mordant. That is, the iodine increases the interaction between the cell and the dye so that the cell is stained more strongly. The smear is next decolorized by washing with ethanol or acetone. This step generates the differential aspect of the Gram stain; gram-positive bacteria retain the crystal violet, whereas gram-negative bacteria lose their crystal violet and become colorless. Finally, the

smear is counterstained with a simple, basic dye different in color from crystal violet. Safranin, the most common counterstain, colors gram-negative bacteria pink to red and leaves gram-positive bacteria dark purple. 6, The Mechanism of Gram Staining Although several explanations have been given for the Gramstain reaction results, it seems likely that the difference between gram-positive and gram-negative bacteria is due to the physical nature of their cell walls. If the cell wall is removed from grampositive bacteria, they become gram negative. The peptidoglycan itself is not stained; instead it seems to act as a permeability barrier preventing loss of crystal violet. During the procedure the bacteria are first stained with crystal violet and next treated with iodine to promote dye retention. When gram-positive bacteria then are decolorized with ethanol, the alcohol is thought to shrink the pores of the thick peptidoglycan. Thus the dye-iodine complex is retained during the short decolorization step and the bacteria remain purple. In contrast, gram-negative peptidoglycan is very thin, not as highly cross-linked, and has larger pores. Alcohol treatment also may extract enough lipid from the gramnegative wall to increase its porosity further. For these reasons, alcohol more readily removes the purple crystal violet-iodine complex from gram-negative bacteria.
G+ G- G+ G- G- G+

1 3 L-lysm-DAP 2 4 -D-Ala 3 -m-DAP

Endospore()

Endospore-forming process ()

flagellum; G- LPSM ; G+ 2 The systemic taxa of mocroorganisms follow the systemic taxa built by Linnaeusincluding seven grades from top to bottom: KingdomPhylum ClassOrderFamilyGenusSpecies All species names of cellular microorganisms obey the Latin binominal nomenclature built by Linnaeus without exception.

Mycoplasma ( )are the procaryotic organism between bacteria () and rickettsia ().

Chlamydia ( )are a genus of minitype Gram-negative prokaryotic organism which obligate parasitize in eukaryotic cells. Spirochaeta are a group of Gram-negative unicellular prokaryotic organism whose configuration and kinesiology are particular. Substrate mycelium Aerial hyphae Sporular hypha Major Characteristics Used in Taxonomy 1Classical Characteristics Morphological Characteristics Physiological and Metabolic Characteristics Ecological Characteristics Genetic Analysis 2, Molecular Characteristics Comparison of Proteins Nucleic Acid Base Composition Nucleic Acid Hybridization Nucleic Acid Sequencing (16S rRNA sequencing) Bacterial colony ( ): A bacterial colony is defined as a visible cluster of organisms growing on the surface of or within a solid medium, theoretically cultured from a single cell. Bacterial lawn ( ): Bacterial lawn is a used by biologists to describe the appearance of bacterial colonies when all the individual colonies on a petridish merge together to form a a field or mat of bacteria. Eukaryotic cell Eukaryotic microorganisms The eukaryotic microorganisms is not a natural monophyletic taxon. They have the nuclear membrane coating a cell nucleus, carry out mitosis, and have mitochondria in the cytoplasm. Eukaryotic microorganisms include : fungi, microalgae and protozoa. Fungi differ from plants in two quite fundamental respects: Plants obtain energy from the sun, fungi do not; Plants utilize CO2 as a carbon source, fungi do not. One of the features that caused taxonomists finally to remove fungi from the plant kingdom was the distinctive chemical nature of the fungal cell wall. Whereas plant and algal cells have walls composed of cellulose, the cell wall of fungi is made up principally of chitin. Fungi This term fungus indicates those organisms that have true nucleus, produce spores by asexual or sexual reproduction, absorb the nourishment material, have no chloroplast. Members of fungi include yeast, mold and mushroom. Major characters of fungi : With a real nucleus; Having no chloroplast and photosynthesis; Vegetative bodies are usually developing filamentous and branched

structure as well as unicell; Typically forming asexual and sexual reproductive spores; Containing chitin in the cell wall; Heterotrophy by absorption; More living adaptively in the land . Some fungi have long, branched, threadlike filaments called hyphae ( ), which aggregate together to form a tangled mycelium (). In some fungi the hyphae have crosswalls called septa( ) separating cells, which may nevertheless be joined by one or more pores, which permit cytoplasmic streaming, a form of internal transport. Fungi are categorized into phyla (divisions) based on the type of structures produced during sexual reproduction. (1) Chytridiomycota (2) Zygomycota (3) Ascomycota (4) Basidiomycota (5) Deuteromycota Ainsworth : PPT PPT rhizoid(); Haustorium

Life cycle of fungi: In general, the life cycle involves the fusion of hyphae from two individuals, forming a mycelium that contains haploid nuclei of both individuals. The fusion of hyphae is called plasmogamy. The fused hyphae containing haploid nuclei from two individuals is heterokaryotic. In some cases, plasmogamy results in cells with one nucleus from each individual. This condition is called dikaryotic. Eventually, two nuclei that originated from different individuals fuse to form a diploid zygote. Meiosis then produces either four haploid nuclei or four haploid cells. Asexual spores ( )are formed by the aerial mycelium of one organism. When these spores germinate, they become organisms that are genetically identical to the parent. Sexual spores ( ) result from the fusion of nuclei from two opposite mating strains of the same species of fungus. Organisms that grow from sexual spores will have genetic characteristics of both parental strains. Virus Virus Viruses are a unique group of tiny infectious particles that are obligate parasites of cells, are not cells but resemble complex molecules composed of DNA or

RNA. Most of them are so small (0.02-0.3m) that an electron microscope is necessary to detect them. Structures of viruses: naked virus (nucleic acid, capsid); enveloped virus (nucleic acid, capsid and envelope). Viral capsids have three different forms: helical symmetry, icosahedral symmetry and complex symmetry. phage) virulent phages 5 ; . Replication cycles of virulent phage(): 1, Adsorption (attachment); 2, Penetration; 3, Replication; 4, Assembly; 5, Release. one-step growth curve 3 . Eclipse period it is the period from the virus penetrating host cell to the releasing of virion . Burst phase During this period, the number of virion increases rapidly with lysis of host cell Platform phage It is the period that all of the host cells are lysated and the valence of virus reaches the apogee. temperate phage

Prion A prion (= proteinaceous infectious particle) is a self-replicating protein responsible for a range of neurodegenerative disorders in humans and mammals. Inclusion bodies Inclusion bodies are nuclear or cytoplasmic aggregates of stainable substances, usually proteins. They typically represent sites of viral multiplication in a bacterium or a eukaryotic cell and usually consist of viral capsid proteins. Types of insect viruses: NPV, CPV GV

Growth factors Organic compounds required because they are essential cell components or precursors of such components and cannot be synthesized by the organism are called growth factors. There are three major classes of growth factors: (1) amino acids, (2) purines and pyrimidines, (3) vitamins.
Nutritional Types of Microorganisms

Microorganisms can be classified as either heterotrophs (or autotrophs with respect to their preferred source of carbon. Phototrophs use light as their energy source; chemotrophs obtain energy from the oxidation of chemical compounds (either organic or inorganic). The large majority of microorganisms thus far studied are either photolithotrophic autotrophs or chemoorganotrophic heterotrophs A substance can be transported across the cell membrane in one of three ways, known as simple diffusionfacilitated diffusion and active transport group translocation Synthetic medium Such a medium in which all components are known is a defined medium or synthetic medium. Complex media Media that contain some ingredients of unknown chemical composition are complex media. Agar is well suited as a solidifying agent because after it has been melted in boiling

water, it can be cooled to about 40 to 42C before hardening and will not melt again until the temperature rises to about 80 to 90C. Agar is also an excellent hardening agent because most microorganisms cannot degrade it. Types of Media general purpose media enriched ( media Selective media Differential media. Differential media ()Differential media are media that distinguish between different groups of bacteria and even permit tentative identification of microorganisms based on their biological characteristics. Enriched ( media Blood and other special nutrients may be added to general purpose media to encourage the growth of fastidious heterotrophs. These specially fortified media (e.g., blood agar) are called enriched (media. Pure culture: a population of cells arising from a single cell. Pure cultures are so important that the development of pure culture techniques by the German bacteriologist Robert Koch transformed microbiology. The Growth Curve: When microorganisms are cultivated in liquid medium, they usually are grown in a batch culture ( or closed system. The growth of microorganisms reproducing by binary fission can be plotted as the logarithm of the number of viable cells versus the incubation time, and the resulting curve is called growth curve. The resulting curve has four distinct phases: lag phase, exponential phase, stationary phase and death phase. Measurement of Microbial Growth includes: (1) microbial numbers and (2) microbial masses. Methods for estimating microbial numbers fall into two main categories: (1) those that count total cell numbers; (2) and those that count viable cells only. : Factors affecting microbial growth: Temperature; pH; Oxygen; Osmotic pressure Radiation; sterilization disinfectionantisepsis. transformation) DNA Transformation is the uptake by a cell of a naked DNA molecule or fragment from the

medium. The transformation frequency of very competent cells is around 10-3 for most genera when an excess of DNA is used. Artificial transformation is carried out in the laboratory by a variety of techniques, including treatment of the cells with calcium chloride() TransductionTransduction is the transfer of bacterial genes by viruses. Bacterial genes are incorporated into a phage capsid because of errors made during the virus life cycle. The virus containing these genes then injects them into another bacterium, completing the transfer. There are two very different kinds of transduction: generalized transduction (and specialized transduction Generalized transduction occurs during the lytic cycle of virulent and temperate phages and can transfer any part of the bacterial genome. During the assembly stage, when the viral chromosomes are packaged into protein capsids, random fragments of the partially degraded bacterial chromosome also may be packaged by mistake Transposition The chromosomes of bacteria, viruses, and eucaryotic cells contain pieces of DNA that move around the genome. Such movement is called transposition. Transposable elements DNA segments that carry the genes required for this process and consequently move about chromosomes are transposable elements.

Microbial ecology: Microbial ecology is the study of microbial relationships with other organisms and also with their nonliving environments. Microbial ecology is the study of the behavior and activities of microorganisms in their natural environments. The characteristics of microbial ecosystem 1.microenvironments 2.stability 3.adaptability PPT Biogeochemical cycling Microorganisms, in the course of their growth and metabolism, interact with each other in the cycling of nutrients, including carbon, sulfur, nitrogen, phosphorus, iron, and manganese. This nutrient cycling, called biogeochemical cycling. PPT 3

Mutualism [Latin mutuus, borrowed or reciprocal ] defines the relationship in which some reciprocal benefit accrues to both partners. This is an obligatory relationship in which the mutualist and the host are metabolically dependent on each other. Lichens are excellent example of mutualism. Lichens are the association between specific ascomycetes (the fungus) and certain genera of either green algae or cyanobacteria. Protocooperation Protocooperation is a mutually beneficial relationship, similar to that which occurs in mutualism, but in protocooperation, this relationship is not obligatory. Commensalism [Latin com, together, and mensa, table] is a relationship in which one symbiont, the commensal, benefits while the other (sometimes called the host) is neither harmed nor helped. This is a unidirectional process. (competition) (antagonism) (parasitism) predation rhizosphere): rhizosphere effect: R/S ratio A, B, C, D, A, B, C, infection):

 Infectious disease): Zoonotic disease) : exotoxin)(endotoxin) exotoxin): An exotoxin is a toxin excreted by a microorganism, including bacteria, fungi, algae, and protozoa. An exotoxin can cause damage to the host by destroying cells or disrupting normal cellular metabolism. toxoid)0.3%-0.4% . ~ endotoxin): Immunity(): The function of immune include: () 1immunologic defence); 2immunologic homeostasis); 3 immunologic serveillance) complement) - interferons, IFNs)dsRNA A, B, C central immune organ bone marrow)thymusbursa of Fabricius) immunologically competent cell B K NK N D T immune response) immune response) T B The process of immune response includes: Inductive stage ( Proliferative and

differentiation stage Effective stage. Antigen Substances, such as proteins, nucleoproteins, polysaccharides, and some glycolipids, that elicit an immune response and react with the products of that response are called antigens. Most antigens are large, complex molecules with a molecular weight generally greater than about 10,000. complete antigen): incomplete antigen)hapten) antigenic determinant)epitope) Antibody An antibody is glycoprotein that is made in response to an antigen, and can recognize and bind to the antigen that caused its production. 1962Edelman GIgY IgY HL Igclasses)subclasses)Ig Igtype)subtype) Ig The field of microbiology application: 1, Microorganism as fertilizer; 2, Microorganism as bio-medicine; 3, Microorganism as food; 4, Microorganism in wastewater treatment and bioremediation; 5, Microorganism in the mining industry.