Chapter 2: Characteristics and Classification of Microorganisms PDF

A. To describe the classification of microorganisms B. To describe the characteristics of different microorganisms including bacteria, fungi, yeasts and viruses. ¡ Prokaryotic cells are characterized by having § No nucleus § DNA in an unbound region called the nucleoi...

A. To describe the classification of microorganisms B. To describe the characteristics of different microorganisms including bacteria, fungi, yeasts and viruses. ¡ Prokaryotic cells are characterized by having § No nucleus § DNA in an unbound region called the nucleoid § No membrane-bound organelles § Cytoplasm bound by the plasma membrane  Fimbriae Nucleoid Ribosomes Plasma membrane Bacterial Cell wall chromosome Capsule 0.5 µm (a) A typical Flagella (b) A thin section rod-shaped through the bacterium bacterium Bacillus coagulans (TEM)  Eukaryotic cells are characterized by having § DNA in a nucleus that is bounded by a membranous nuclear envelope § Membrane-bound organelles § Cytoplasm in the region between the plasma membrane and nucleus ¡ Eukaryotic cells are generally much larger than prokaryotic cells Taxonomic Hierarchy DOMAIN "Dear King Philip Come Over For Good Soup" Kingdom Phylum Class Order Genus Family Species 9 5 Kingdoms Classification Animalia - multicellular Protista - Simple eukaryote Monera (Prokaryotae) -all bacteria Plantae - multicellular, photosynthesis Fungi -grow by spores or fermentation of hypae 11 12 Scientific name or binomial name = Genus + species All organisms have a scientific name : genus name + species name The scientific name is always italicized or underlined (in the case of hand writing). Genus name is capitalized at the beginning. Species name is not capitalized at the beginning. Scientific names can be abbreviated/ shortened by using the capital letter of the genus and a period: Example. M.koenigii Correct examples: Genus: Species: Murraya koenigii Murraya koenigii M. koenigii Murraya koenigii M. koenigii 13 Scientific names can : Ø Describe an organism ¡ e.g: Staphylococcus aureus ¡ staphylo - describes clustered arrangement of the cells. ¡ coccus - point out that they’re sphere shaped. ¡ aureus - Latin for golden, the colour of many colonies of this bacteria. Ø Honour a researcher ¡ e.g: Escherischia coli ¡ Escherichia named after a scientist: Theodor Escherich. Ø Identify the habitat of a species ¡ coli from E. coli reminds us that it live in the colon or large intestines. 14 For new isolated organism To achieve formal taxonomic standing as a new genus or species, a detailed description of the isolate and proposed name is published and a viable culture of the organism is deposited into international culture collections American Type Culture Collection (ATCC) German Collection for Microorganism (DSMZ) 15  Taxonomy (REVIEW) Science of classifying organisms Provides universal names for organisms Provides a reference for identifying organisms  ¡ Prokaryotes Cells that lack a membrane-enclosed nucleus. Smaller than eukaryotic cells. 2 groups of prokaryotes: bacteria and archaea Have higher growth rate and higher metabolic activity than eukaryotes. WHY? 19  1. Archaea Consist of prokaryotic cells. If have cell walls, will lack peptidoglycan. Often found in extreme environment. They’re not known to cause disease to humans. Divided into 3 main groups: Methanogens : Øproduce methane as waste product from respiration. Extreme halophiles : ØLive in extremely salty environments like the Dead Sea or Great Salt Lake. Extreme thermophiles : ØLive in hot sulfurous water like hot springs at Yellowstone National Park. 20 ¡ The smallest and most common microorganisms are prokaryotes—unicellular organisms that lack a nucleus. ¡ Contains an enormous variety of prokaryotes. ¡ There is a large variety of morphologies and physiologies in this domain. 21 ¡ are identified by characteristics such as: ▪ shape ▪ the chemical nature of their cell walls ▪ the way they move ▪ the way they obtain energy Cell morphologies 1. Cell morphology 24 In General procaryotic cells are smaller than eukaryotic : Being small is important! They have more surface area relative to cell volume -> Better nutrient exchange and faster growth In General procaryotic cells are smaller than eukaryotic : Being small is important! They have more surface area relative to cell volume -> Better nutrient exchange and faster growth Staphylococus Escherichia aureus coli 1. Phospholipid layer of cytoplasmic membrane 2. A rigid layer called peptidoglycan of cell wall 3. Gram-Positive bacteria : 90% of peptidoglycan and teichoic acid embedded. 4. Gram negative bacteria : contain outer membrane called LPS (Lipopolysacchride) 1. Relate the cell wall structure to Gram staining! 2. How and why?  Safranine Gram Staining Technique Cell wall of Gram +ve bacteria ØThicklayer of peptidoglycan, attached to the outer surface of the membrane. Ø60-90% of the cell wall is peptidoglycan and only contain little protein. ØIf peptidoglycan is digested, Gram +ve bacteria become protoplasts (cells with a cell membrane but without a cell wall) ØProtoplasts will shrivel or burst unless they’re kept in an isotonic solution (solution that has the same pressure as that inside of the cell). ØLack both an outer membrane & periplasmic space. 31 Cell wall of Gram -ve bacteria üThinner but more complex than Gram +ve bacteria. üOnly 10-20% is peptidoglycan, the remainder consists of various polysaccharides, proteins, & lipids. üContains an outer membrane. üThe inner surface of the cell wall is separated from the cell membrane by a wide periplasmic space. üToxins & enzymes remain in the periplasmic space to help destroy substance that might harm the bacterium, but they don’t harm the organism that produce them. üIf the cell wall is digested away, Gram –ve bacteria become spheroplasts (cells that have both a cell membrane & most of the outer membrane). 32 ¡ Also called endotoxin. ¡ Important part of the outer membrane and can be used to identify Gram negative bacteria. ¡ An integral part of the cell wall & is not released until the cell walls of dead bacteria are broken down ¡ LPS consists of polysaccharides and lipid A ¡ Lipid A is toxic which make any Gram negative infection a potentially serious medical problem 34 oLipid A causes fever & dilates blood vessels so the blood pressure drops precipitously oBecause bacteria release endotoxin mainly when they’re dying, killing them will increase the concentration of this toxic substance. oThus, antibiotics given late in an infection may cause a worsening of symptoms, or even death. 35  Cell wall of Acid-Fast Bacteria (the Mycobacteria) üAlthough the cell wall is thick like Gram +ve bacteria, 60% of it is lipid & contain less peptidoglycan. üThe lipids make acid-fast organisms impermeable to most stains & protect them from acids & alkalis. üThe organisms grow slowly because the lipids impede/block entry of nutrients into cells, & the cells must expend/use large quantities of energy to synthesize lipids. üAcid-fast cells can be stained by the Ziehl-Neelsen Stain üCan also be stained via Gram stain method : they stain as Gram +ve üExample of acid-fast bacteria: Mycobacterium tuberculosis and Mycobacterium leprae. 36  Visualization of Mycobacterium tuberculosis (an Acid-Fast bacteria) using the Ziehl-Neelsen Stain. 37 The life cycle of an endospore-forming bacterium. (Clostridium pascui) Vegetative cell Developing spore Germination Sporulating cell Mature spore § In unfavorable conditions, many bacteria form spores. ▪ An endospore forms when a bacterium produces a thick internal wall that encloses its DNA and some of its cytoplasm. ▪Spores can remain dormant for months or years, allowing bacteria to survive harsh conditions.  Endospore Formation and Germination Certain species of bacteria produce structures Exosporium called endospores during sporulation Extremely resistant to heat, harsh chemicals, Spore coat and radiation. Function as survival structures and enable the Core wall organism to endure unfavorable growth Cortex conditions Life cycle: vegetative cell – endospore- DNA vegetative cell. Commonly found in soil, and species of Bacillus are the best-studied representatives.  Bacterial flagella are long, thin appendages free at one end and attached to the cell at the other end The filament of a bacterial flagellum is composed of many copies of a protein called flagellin. Moves by rotation, much like a propeller of a boat motor. Gliding allows a cell to exploit new resources and to interact with other cells.  Chemotaxis (a) No attractant present: (b) Attractant present: Directed Random movement movement  Phototaxis Light 0 1 2 Time (h) Phototaxis of an entire colony of the purple phototrophic bacterium Rhodospirillum centenum. ¡ Growth and Reproduction ▪ Most prokaryotes reproduce by binary fission. ▪ Some prokaryotes take part in conjugation. ▪ Other prokaryotes produce spores. § Binary Fission ▪Binary fission is a type of asexual reproduction in which an organism replicates its DNA and divides in half, producing two identical daughter cells. Binary Fission  Fungi Mycology: the study of fungi Chemoheterotrophs Decompose organic matter Aerobic or facultative anaerobic Absorptive heterotrophs Cell walls made of chitin  Nutritional Adaptations Grow better at pH of 5 Grow in high sugar and salt concentration; resistant to osmotic pressure Can grow in low moisture content Can metabolize complex carbohydrates Table 12.1 Selected Features of Fungi and Bacteria Compared Fungal Hyphae Hyphae Thread of cells One cell thick High surface area to volume ratio Fungal Hyphae Hyphae Absorb water, ions, nutrients Gas exchange Waste disposal Figure 12.2 Characteristics of fungal hyphae. Cell wall Pore Nuclei Spore Septum Septate hypha Coenocytic hypha Growth of a hypha from a spore Figure 12.3 Aerial and vegetative hyphae. Aerial hyphae Vegetative hyphae Aerial hyphae Aspergillus niger A. niger on agar Fungal Body Mycelium Loosely woven mat of hyphae Feeding structure Reproductive Structures Make spores, either by mitosis or meiosis Some are called “fruiting bodies” Yeasts EUKARYOTIC, classified as members of the fungus kingdom. Single-celled budding organisms. Often isolated from sugar rich materials. They DO NOT produce mycelia. The colonies are visible on agar plate in 24 hours. Their soft and moist colonies resemble bacterial cultures rather than molds. By fermentation, yeast species such as Saccharomyces cerevisiae converts carbohydrates to carbon dioxide and alcohol. IMPORTANT! Bacteria Yeasts Fungi  Economic Importance of Fungi Saccharomyces cerevisiae (YEAST): bread, wine, hepatitis B vaccine Trichoderma: cellulase Taxomyces: taxol Entomophaga: biocontrol Coniothyrium minitans: kills fungi on crops Paecilomyces: kills termites  Viruses Particles of nucleic acid, protein, and sometimes lipids Viruses can reproduce only by infecting living cells A typical virus is composed of a core of DNA or RNA surrounded by a protein coat Viruses are very small. They can only be seen with an electron microscope  Capsid A viruses protein coat The capsid proteins of a typical virus bind to receptors on the surface of a cell and “trick” the cell into allowing it inside Once inside, the viral genes are expressed and causes the host cell to make copies of the virus and in the process the host cell is destroyed Because viruses must bind precisely to proteins on the cell surface and then use a hosts genetic system, most viruses are highly specific to the cells they infect  Viral Infection Once the virus is inside the host cell, two different processes may occur  Lytic Infection In a lytic infection, a virus enters a cell, makes copies of itself, and causes the cell to burst  Lysogenic Infection In a lysogenic infection, a virus integrates its DNA into the DNA of the host cell, and the viral genetic information replicates along with the host cells DNA Unlike lytic viruses, lysogenic viruses do not lyse the host cell right away. Instead, a lysogenic virus remains inactive for a period of time Eventually, only one of a number of factors may activate the DNA of a prophage which will then remove itself from the host cell DNA and direct the synthesis of new viruses particles  Viruses and Living Cells Viruses must infect a living cell in order to grow and reproduce They also take advantage of the host’s respiration, nutrition and all the other functions that occur in living things Therefore, viruses are considered to be parasites  Are viruses alive? Cells and Viruses Characteristic Cell Virus Structure Cell membrane, cytoplasm; eukaryotes also contain nucleus and organelles Reproduction Independent cell division either asexually or sexually Genetic Code DNA Growth and Development Yes; in multicellular organisms, cells increase in number and differentiate Obtain and Use Energy yes Response to Environment yes Change Over Time yes  Viral Disease in Humans Like bacteria, viruses produce disease by disrupting the body’s normal equilibrium Unlike bacterial diseases, viruses can’t be treated with antibiotics The best way to protect against most viral diseases lies in prevention by the use of vaccines Covid-19 Parasitology Parasitology is the area of biology that deals with organisms that seek shelter and nourishment on or within other living organism Parasitology is the study of parasites and is traditionally limited to parasitic protozoa, helminths, and arthropods  a. Types of Parasites Parasites Microparasite Macroparasite Small, unicellular & multiplies Large, multicellular and has within its vertebrate host, example no direct reproduction within like protozoa, fungi, bacteria its vertebrate host Ectoparasites- organism which live on the surface of the body eg mites Endoparasites- organism that live within the body of the host are known endoparasites. Source: Contaminated soil Ascaris lumbricoides A major burden of parasitic disease worldwide. Live in the intestine. Ascaris eggs are passed in the feces of infected people. If an infected person defecates outside, or if the feces of an infected person is used as fertilizer, worm eggs are deposited on soil. People with ascariasis often show no symptoms. If symptoms occur they can be light. Symptoms include abdominal discomfort or pain.  Source: Contaminated Water Cryptosporidium A microscopic parasite that causes the diarrheal disease cryptosporidiosis. The parasite is protected by an outer shell that allows it to survive outside the body for long periods of time and makes it very tolerant to chlorine disinfection.  Source: Undercooked meat Taenia saginata (beef tapeworm) Transmitted to humans through a bovine intermediate host, through the consumption of undercooked beef  Portal of Entry Into the Body Skin Kissing- transmitted from peson-to-person Latrogenic infection by kissing Malaria parasites may be transmitted by transfusion of blood Congenital- from the donor whom positive for malaria Infection may be transmitted from mother to foetus Sexual contact transplacentally  Pathogenicity (Various way of damage caused by parasites) Secondary infection- Lytic blood Inflammatory Allergic necrosis infection reaction manifestation -parasites -most - The normal Traumatic releases Neoplasia parasites secretions and damage certain Parasitic provoke excretions of -traumatic enzymes that infection may cellular the growing damage of lyses tissues contribute to the proliferation larvae can pulmonary for the development of capillaries parasite & infiltration cause allergic manifestation new and growth abnormal growth of cells  Protozoa Unicellular eukaryotes Inhabit water and soil Animal-like nutrition Complex life cycles Asexual reproduction is by fission, budding, or schizogony (multiple fission) Sexual reproduction is by conjugation Figure 12.17 Conjugation in the ciliate protozoan Paramecium. Macronucleus Micronucleus Figure 12.19 Amebae. Food vacuole Pseudopods Nucleus Amoeba proteus Red blood cells Nucleus Entamoeba histolytica