Introduction to Microbiology PDF

LESSON 1: INTRODUCTION TO many organisms like bacteria. It is called culturing. MICROBIOLOGY Found everywhere...

LESSON 1: INTRODUCTION TO many organisms like bacteria. It is called culturing. MICROBIOLOGY Found everywhere - It is accessible because you I. The Main Themes of Microbiology can literally found them a. The Scope of Microbiology everywhere b. Naming and classifying of microorganism Functioning of the biosphere c. A brief history of Microbiology - The nitrogen cycle or nitrogen fixation Microbiology Source of nutrients - The scientific study of microscopic - It is beneficial to agriculture organisms and viruses, and their especially to the soil roles in human disease as well as Body digestion and vitamins beneficial processes. - Vitamins like A&B and insulin - Study of microorganism Application of modern biotechnology Microorganisms - Genetic engineering - Are minute living things that Harmful impacts individually are usually too small to - Discuss that can harm be seen with the unaided eye human - Size of a typical bacterium(1μm) - Ubiquitous FIELDS and OCCUPATIONS Public Health Microbiology and Epidemiology - Monitor and control the spread of diseases Environmental Microbiology - Study of microorganism and their ecological relationship in their natural habitats Biotechnology Immunology Genetic Engineering and Recombinant DNA Technology 3 Domain of life Agricultural Microbiology Archaea Food Microbiology Bacteria Eukarya Branches of Microbiology Microbial physiology IMPORTANCE - Study of structure-function Number of mass - structure - function - They reproduce. In the field relationships in microbes, of research, it is easier to especially how microbes utilize because there are  responds to their Origin of Microorganisms environment Microbial Morphology - Study of structure,shape,size of microbes Parasitology - Scientific discipline concerned with the study of biology of parasites and parasitic diseases Protozoology - The study of protozoans Microbial ecology - Scientific investigation of how microorganisms interact with their environment, each other and their hosts Molecular biology - Studies the molecular basis of biological activity Phycology or Algology - The study of algae Microbial taxonomy - Comprises the identification Prokaryotes of isolates into known - The genetic materials are not species the classification of located in the nucleus because they new isolates ( creation of don't have nucleus. new taxa) and nomenclature - They are scattered in the cytoplasm Bacteriology particularly the region of “nucleoid” - Study of bacteria Mycology Eukaryotes - Study of fungi - The genetic material is found inside Virology the nucleus. - Study of biological viruses Microbial genetics - Relatedness or genetics of microbes NAMING AND CLASSIFYING OF Fungi MICROORGANISMS - (singular: fungus) - eukaryotes - cell wall (chitin) - multicellular (mushroom, molds) - unicellular ( yeast) Ex. Mushroom- 2 factors/ nitrogen gas convert nitrate. Can be biological or atmospheric Protozoa - singular: protozoan - unicellular GENERAL CHARACTERISTICS OF - eukaryotic MICROORGANISMS - some are photosynthetic; others feed on organic MAJOR GROUPS OF MICROBES material: free-living; parasitic Bacteria Ex. Amoeba - unicellular that has the ability - singular: bacterium to change its shape - relatively simple, unicellular Paramecium- can move one place to organisms another, slipper-like, they have “cilia” - Prokaryotes; do not have Algae true nucleus - singular: alga - cell wall (peptidoglycan) - photosynthetic - either photosynthetic or non - eukaryotes photosynthetic - both sexual and asexual - Differ in shapes reproductive forms - They reproduce mitotically - Can be either unicellular or (asexual/binary fission) multicellular Archaea - cell walls ( cellulose) - consist of prokaryotic cells, - photosynthetic but if they have cell walls, the Ex. Dinoflagellates walls lack peptidoglycan - Known as “Red tides” - found in extreme - The production of toxins environments Virus Three Main Groups of Archaeans - acellular, structurally simple a. Methanogens- can degrade CO2 - Have genetic material & into methane protein but cannot use it both b. extreme Halophiles- high salt at the same time concentration - Cannot grow w/o their host c. extreme Thermophiles- heat loving - simple archaea Multicellular Animal Parasites( spontaneously from nonliving Helminths) matter - not strictly microorganisms, they are SIMPLE MICROSCOPE of medical importance - Microscope of Anton van - parasitic worms Leeuwenhoek BRIEF HISTORY ANIMALCULES - Leeuwenhoek’s drawing on ROBERT HOOKE (1665) animalcules (bacterial cells) - English natural philosopher - Observed slice of cork ( bark SPONTANEOUS GENERATION from oak tree) - the notion that life can arise from - Noticed tiny boxes in cork nonliving - He called the empty, - Regarding the latter, Leeuwenhoek enclosed spaces cella suggested that maggots did not (small room) -from which arise from wheat grains, but rather today we have the word from tiny eggs laid in the grain that “cell” he could see in his microscope. - Hooke’s discovery marked - Such divergent observation required the beginning of the Cell a new form of investigation – theory— “the theory that all “EXPERIMENTATION” – and a new living things are composed of generation of experimental cells.” naturalists arose. MICROGRAPHIA - This book contained Hooke's FRANCESCO REDI descriptions of microscopes and was - Performed one of history’s filled with stunning hand drawn first biological experiments to illustrations, including the first see if maggots could arise microorganism (a common bread from rotting meat. mold) made from the objects he saw REDI’S EXPERIMENT with his microscope. - The idea of spontaneous generation could produce larger living creatures ANTON VAN LEEUWENHOEK soon subsided. - contemporary of Hooke, was - However, what about the mysterious a successful tradesman and minute animalcules that - cloth merchant appeared to straddle the boundary - Father of Microbiology between the non-living and living - first person to have created world? microscopes to view microbes LOUIS PASTEUR (1859) - first to observed microbes - Disproved the Spontaneous - “animalcules “ Generation through his - “Spontaneous experiment in many years Generation”- life could arise The Theory of Biogenesis grape juice to destroy all the Rudolph Virchow – challenge the evidence of life case for spontaneous generation - PASTEURIZATION- heating with the concept of biogenesis technique to kill the pathogens - “ Living cells arise only from - His experiment demonstrated that pre-existing living cells” yeast and bacterial cells are tiny, living factories in which important SOME EARLY ACCOMPLISHMENTS chemical changes take place. IN MICROBIOLOGY - Infections could cause disease- GERMS ROBERT KOCH - He developed methods of staining bacterial cells and preparing permanent visual records. - In 1877, he accepted an appointment to the Imperial Health Office, and while there, he observed a sliced potato on which small masses of bacterial cells, which he termed “colonies”, were growing and multiplying. - tried adding gelatin to his broth to prepare a solid culture surface in a culture (Petri) dish GOLDEN AGE OF MICROBIOLOGY - inoculated bacterial cells on the surface and set the dish LOUIS PASTEUR aside to incubate - Proved that yeast are the - within 24 hours, visible organisms that are colonies were present on the responsible for the chemical surface process of wine “fermentation” - Germ Theory of Disease- which states that diseases may result from microbial infection. recommended a practical solution for the “wine disease” problem: heat the THE CLASSICAL GOLDEN AGE OF THE CLASSICAL GOLDEN AGE OF MICROBIOLOGY MICROBIOLOGY Vaccination Vaccination - is a biological preparation that improves immunity to a particular disease Immunity- the protection from disease provided by vaccination (or by recovery from the disease itself) Pasteur - developed rabies vaccine Edward Jenner - vaccination for smallpox Chemotherapy - treatment of disease by using chemical substances Antibiotics - chemicals produced naturally by bacteria and fungi that act against other microorganisms Synthetic drugs - chemotherapeutic agents prepared from chemicals in the laboratory Salvarsan - a chemotherapeutic agent; an arsenic derivative effective against syphilis Alexander Flemming - discovered the first antibiotic - penicillin - Penicillium chrysogenum DIVISION OF MICROBIOLOGY LESSON 2: FUNCTIONAL ANATOMY OF PROKARYOTES Binary fission  - Primary method of reproduction of prokaryotic organisms. - An organism duplicates its genetic material (DNA) and then divides into two parts (cytokinesis) with each new organism receiving a copy of DNA. DNA- Directs all genetics and heredity of the cell. Mitosis - The process in which a eukaryotic cell nucleus split in two followed by The Size, Shape, and Arrangement of division of the parent cell into two Bacterial Cells daughter cells. - Somatic cell are involved Meiosis - A process where a single cell divides twice to produce four cells containing, half the original of genetic information - Gametes (Germ cell),sex cell are involved “The shape of a bacterium is determined by heredity.” Monomorphic -they maintain a single shape Pleomorphic -they can have many shape Cell Shapes Most bacteria are classified according to shape: 1. bacillus (pl. bacilli) = rod-shaped 2. coccus(pl. cocci) = spherical 3.spiral shaped a. spirillum(pl. spirilla) = spiral with rigid cell wall, flagella b. spirochete (pl. spirochetes) = spiral with flexible cell wall, axial filament  STRUCTURES EXTERNAL TO THE CELL WALL Structure external to the prokaryotic cell wall 1. Glycocalyx 2. Flagella 3. Axial filaments 4. Fimbriae and Pili 5. S- layers 1. Glycocalyx There are many more shapes beyond those basic ones. A few examples: - a viscous, gelatinous 1. Coccobacilli= elongated coccalform polymer that is external to 2. Filamentous = bacilli that occur in long the cell wall and composed of polysaccharide, threads 3. Vibrios= short, slightly curved rods polypeptide or both. - Capsule, slime layer, - Single polar flagellum 4.Fusiform = bacilli with tapered ends extracellular polymeric substance - Sugar coat,termed used to Arrangement of Cells the substances that surround Bacilli divide along a single axis, cells. seen in pairs or chains. - Made inside the cell and Cocci divide on one or more planes, secreted to the cell surface producing cells in: a. Slime Layer - pairs (diplococci) - The substance(glycocalyx) is - chains (streptococci) unorganized and loosely - cubelike(sarcinae) attached to the call wall - clusters (staphylococci). - Causes bacteria to adhere to solid surface - Glycoproteins loosely associated with the cell wall. - Helps prevent the cell from drying out. Streptococcus - The slime layer of Gram+Streptococcus mutans allows it to accumulate on tooth enamel - Other bacteria in the mouth become trapped in the slime and form a biofilm &  eventually a buildup of Flagellum- specialized appendage attached plaque. to the cell by a basal body. b. Capsule - The substance(glycocalyx) is organized and firmly attached to the cell wall - To determined the capsule in the bacteria used the negative staining - Polysaccharides firmly - Atrichous - without projection attached to the cell wall. - Capsules adhere to solid surfaces and to nutrients in the environment. - Adhesive power of capsules is a major factor in the initiation of some bacterial diseases. - Capsules also protect bacteria from being phagocytized by cells of the 3. Axial filaments (endoflagella) host's immune system. - Bundles of fibrils that arise at the ends of the cell beneath Biofilm- aggregation of microorganism an outer sheath and spiral Virulence- degree to which a pathogens to around the cell cause disease - They are similar to that of Phagocytosis- the ingestion and digestion flagella (endoflagellum) of microorganism - Treponema pallidum - Vibrio cholerae- causative agent of causative agent of syphilis cholera( cause of bacteria) - Borrelia burgdorferi- - They produce glycocalyx, that helps causative agent of lyme attached to small intestine - lyme disease- black legged Bacillus anthracis- the causative agent of anthrax 4. Fimbriae and Pili - They produce capsule which a. Fimbriae (fimbria sing.) protects Bacillus anthracis from - Most Gram-negative bacteria phagocytosis have these short, fine appendages surrounding the 2. Flagella cell - are long filamentous - Gram+ bacteria don’t have appendages that propel - no role in motility bacteria - help bacteria adhere to solid surfaces.  - major factor in virulence. - Fine, hairlike bristles The Cell Wall extending from the cell - a complex, semi rigid structure surface responsible for the shape of the cell. Ex. Gonorrhea- causative agent of - The major function of the cell wall is gonorrhaea to prevent bacterial cells from b. Pili (sing. Pilus) rupturing when the water pressure - tubes that are longer than inside the cell is greater than that fimbriae, usually shorter outside the cell. than flagella. - It surrounds the plasma membrane - Use for movement, like - Serve as point of anchorage of grappling hooks, and also flagella use conjugation pili to - Contribute to the ability of some transfer plasmids species to cause diseases and site - Twitching “motility”- ability of of action of some antibiotics organism to move - If the cell wall is destroyed, the cell - Helps to transfer DNA undergo cell lysis through conjugation. Cell lysis- breaking down of the - Larger than fimbriae in terms membrane of a cell of structure Cell Wall composition and 5. S- layers Characteristics - In bacteria, the S-layer is external to the cell wall. - In some archaea, the S-layer Peptidoglycan consists of a is the only structure outside repeating disaccharide attached by the plasma membrane where polypeptides to form a lattice that it serves as the cell wall. surrounds and protects the entire - are self-assembled cell. paracrystalline protein - Also called murein lattices that cover many bacteria and almost all archaea. - Serve as the plasma membrane in archaea - Helps maintain the shape of bacteria - Helps in the adherence to surfaces BIOLOGICAL ROLES OF S-LAYER - Structural integrity and protection - Resistance to environmental stress Gram-Positive & Gram-Negative - Cell-cell interaction and adhesion  STRUCTURES INTERNAL TO THE CELL WALL Structure internal to the prokaryotic cell wall: 1. Cell membrane 2. Cytoplasm 3. Nucleoid 4. Ribosomes 5. Inclusions 6. Endospores 1. Cell (Cytoplasmic) membrane (Plasma Membrane - In gram-positive the peptidoglycan is above the membrane and it is - separate the cell from its thicker. 90% made of peptidoglycan. environment - phospholipid molecules More treatable with antibiotics because it does not have outer oriented so that hydrophilic ( water-loving head) directed membrane - In gram-negative the peptidoglycan outward and hydrophobic is between the membrane. Hard to (water- fearing tail) directed be treated by antibiotics. Outer inward membrane extra membrane similar - A thin sheet of lipid and to cell membrane protein that surrounds the cytoplasm - proteins are embedded in 2 layers of lipids (lipid bilayer) - Semi -permeable - it allows some ions and other substances to pass through the cell. Atypical Cell Walls Structures: - Prokaryotic cells that have no walls - The phospholipids molecules or have a very little wall material. are arranged in two parallel - Mycoplasma & Halobacterium sp. rows. Acid-Fast Cell Walls - The protein molecules in the - Bacteria of the genus membrane can be arranged Mycobacterium and pathogenic in a variety of ways. species of Nocardia. Functions: - The most important function of the plasma membrane is to serve as a selective barrier through which materials enter and exit the cell.  - Breakdown of nutrients and - It usually contains a single, the production of energy. long, continuous, and - Chromatophores or frequently circularly arranged thylakoids. thread of double-stranded - Mesosomes serve as DNA. compartments of DNA at cell - It can be spherical, division and sporulation and elongated, or dumbbell- are principal sites of shaped. respiratory enzymes.. - Lack pistone & nuclear Destruction: envelope - Plasma membrane is vital to - Cell genetic information the bacterial cell, several required for the cells antimicrobial agents exert structure & function their effect at this site. PLASMIDS - Cellisis- destruction of - Plasmids are circular, plasma membrane double-stranded DNA Two protein in plasma membrane molecules. 1. Integral membrane protein- inserted - Extra elements not to the lipid bilayer. connected to the bacterial 2. Peripheral Protein- are bound to the chromosomes membrane indirectly by protein- - Independently duplicate protein interactions. Transport 4. Ribosomes - Carrier proteins - carry chemicals - The sites of protein across the membrane in both synthesis. directions, down and up the - Several antibiotics work by concentration gradient inhibiting protein synthesis in - Chemical protein- can generate prokaryotic ribosomes. hydrophilic holes in cell membranes - Tiny particles composed of allowing molecules to go down a protein and RNA concentration gradient. 5. Inclusions - There are reserved deposits 2. Cytoplasm - Common to wide variety of - The substance inside the bacteria plasma membrane. - Stored nutrients such as fat, - Thick, aqueous, phosphate or glycogen. semitransparent, and elastic. a. Metachromatic granules - Major structures found in the - Collectively known a volutin cytoplasm are nucleoid, - large inclusions that take ribosomes, and inclusions. their name from the stain red - Fluid in nature. with certain blue dyes. - Generally grows in 3. Nucleoid (Bacterial phosphate environment chromosomes)  - Also found in algae and f. Gas vacuoles protozoa - Hollow cavities found in - b. Volutin represents a many aquatic prokaryotes, reserve of inorganic including cyanobacteria, an phosphate (polyphosphate) oxygenic photosynthetic that can be used in the bacteria, and halobacteria. synthesis of ATP - Contains buoyancy so that b. Polysaccharide granules bacterial cell will remain at - typically consist of glycogen the depth of water and starch, and their g. Magnetosomes presence can be - inclusions of iron oxide demonstrated when iodine is (Fe304), formed by several applied to the cells. gram- negative bacteria such - If the glycogen is stained is as Magnetospirillum appears reddish-brown magnetotacticum, that act - If the scratch is stained like magnets appears blue - They use magnetosome to move downward until they c. Lipid inclusions reach a suitable attachment - appear in various species of site Mycobacterium, Bacillus, - Eukaryotic cell, peroxisome Azotobacter , Spirillum and is responsible in converting other genera. hydrogen peroxide into water - Sudan dye(fat soluble) is and oxygen used - Protects the bacterial cells d. Sulfur granules from the accumulation of - Consist of tangled mass of H2O2(toxic substance) the branching filaments of actinomyces 6. Endospores e. Carboxysomes - highly durable dehydrated - inclusions that contain the cells with thick walls and enzyme ribulose 1,5 additional layers. diphosphate carboxylase. - The process of endospore Photosynthetic bacteria formation within a vegetative - Make their own food cell takes several hours and - Use carbon dioxide as their sole is known as sporulation or source of carbon and required this sporogenesis enzyme for carbon dioxide fixation - Dormant, tough, non- Theobacilli reproductive structure - Genus of bacteria known for their produced by small numbers ability to oxidize sulfur compounds, of bacteria. particularly sulfide and elemental - The water present in the sulfur as their primary source of forespore cytoplasm is energy eliminated by the time  sporulation is complete, and endospores do not carry out metabolic reactions. - Surrounded with thick protein - Small dormant asexual spore that develops inside the bacterial cell as a means of survival Dormant - Inactive - Dormant body formed within the bacteria Bacillus - Produce endospores in response to harsh environment White blood cell- macrophages “If the environment is no longer harsh, the Actin cytoskeleton- long fibers to proteins endospores will become active.” that encircle the cell Spneumonae- causative agent of pneumonia Treponema pallidum- causative agent of sipilis LESSON 3: Microbial Growth Growth- there is an increase in size. Microbial Growth- increase in the number through binary. “Microbes that are growing are increasing in number” Requirements for Microbial Growth 1.Physical 2.Chemical 1. Physical a. Temperature Minimum growth temperature- lowest temperature at which species will grow. Optimum growth temperature- temperature  at which a species grows - 50-60 degrees optimum best. “ If the temperature is growth but cannot grow above the optimum growth below 45 degrees. temperature the growth IV. Hyperthermophiles or rates drop.” extreme thermophiles- usually Maximum growth members of archaea temperature- highest - 80 degrees or higher temperature at which optimum growth temp. growth is possible. - Live in hot springs associated with volcanic Classification of Microorganisms activity based on their preferred range of - Sulfur is important in their temperature. metabolic activity. I. Psychrophiles- cold loving microbes. b. pH - talks about acidity or - Psychrotrophs (0 degrees basicity. to 30 degrees, spoilage - Bacteria grows best microorganisms) between 6.5-7.5 pH - 15 degrees - optimum I. Acidophiles- they growth are remarkably II. Mesophiles- moderate- tolerant. temperature- loving microbes - Tolerant of acidity - Most common types of bacteria include the c. Osmotic pressure common spoilage and - High salt or sugar concentrations disease organisms. draw water out of microbial cells - 24-40 degrees, optimum and prevent their growth. growth - A pressure created by water - Adapted to live in the moving across a membrane bodies of animals usually osmosis have an optimum I. Extreme halophiles temperature close to that II. Obligate halophiles of their host. III. Facultative halophiles - 37 degrees is the optimum IV. Barophiles temperature of pathogenic V. Osmophiles bacteria. III. Thermophiles- heat- loving Tonicity - the concentration of solute in microbes capable of growth at a solution on either side of membrane high temperatures. Concept of tonicity  such as lipids, proteins and carbohydrates II. Chemoautotrophs and photoautotrophs - They derive carbon from carbon dioxide B. Nitrogen, Sulfur and Phosphorus -Elements needed to synthesize materials. - Potassium, magnesium and calcium as cofactors for enzymes. a. Isotonic solution- a solution that NITROGEN- to form amino groups has the same solute of amino acid on proteins concentration as another solution SULFUR- synthesis sulfur containing - There is no net movement amino acid and vitamins of water particles PHOSPHORUS- synthesis nucleic - The membrane remain acids and phospholipids of cell constant membrane and ATP - There is no changes to cell - Nucleic acid- ex. DNA & RNA - Phospholipid- found on the b. Hypertonic solution- a solution surface of plasma membrane that has a higher solute - ATP- adenosine triphosphate concentration than another Ex. 1 NITROGEN & SULFUR Combined solution - They are very important for protein - Water moves out from the synthesis cell “Protein is very important in the cell and - The cell shrink protein is the one distributed into the cell c. Hypotonic solution- a solution either prokaryotes or eukaryotes. They have that has a lower solute specific function” concentration than another solution Ex. 2 NITROGEN & PHOSPHORUS - Very important into the synthesis of - Water moves into the cell DNA,RNA and ATP - The cell expand,swell or will destroy C. Trace Elements - Fe, Cu, Mo, Zn are essential as 2. Chemical cofactors for certain enzymes. A.Carbon- the structural backbone of - Need a cell/bacterium cell in the living matter needed for all the organic small amount only compounds that make up a living cell. - Microbes also required very small I. Chemoheterotroph-They obtain amount of this minerals their carbon as their source of energy from organic molecules D. Oxygen  - Aerobes - need oxygen Bacterial Division - Anaerobes - don't need oxygen a. Binary fission - a single cell divides into two I. Obligate aerobes identical cells - Required oxygen in order to live II. Facultative anaerobes - They use oxygen when it is present but are able to continue growing when oxygen are not available III. Obligate anaerobes b. Budding - They do not use oxygen - the development of a small, - If the oxygen is present they new cell from the surface of will die an existing cell. IV. Aerotolerant anaerobes - Ex. filamentous bacteria - They cannot use oxygen for (Actinomycetes) growth but they tolerate it V. Microaerophiles - They are aerobic and they required oxygen concentration lower than those in air Generation Time E. Organic Growth Factors - the time required for a cell to divide. - Essential organic compounds an - E. coli, doubling occurred every 20 organism is unable to synthesize. minutes. BIOFILM - Communities of microorganisms. - Reside in a matrix made up primarily of polysaccharides, DNA and proteins. - also considered as Hydrogel - Cell to cell communication or quorum sensing Logarithmic Representation of - Biological systems; the bacteria are Bacterial Populations organized into a coordinated, functional community. - Share nutrients, sheltered from harmful factors and transfer genetic information. The Growth of Bacterial Cultures  - The population is decreasing at a logarithmic rate. Phases of Growth Bacterial growth curve - the growth of cell over time - fundamental in understanding population dynamics and control Four basic phases of growth: 1. Lag phase - intense activity preparing for population growth but no increase in population. 2. Log phase - increase in population 3. Stationary phase - During the period of equilibrium, microbial deaths balance production of cells. 4. Death phase