2MICROORGANISMSThe word microorganism is used to describe an organism that is so small that can not be seen without the use of a microscope.Viruses, bacteria, fungi, protozoa and some algae are all included in this category.
3Microorganisms are responsible for many of the changes observed in organic and inorganic matter (e.g., fermentation and the carbon, nitrogen and sulfur cycles that occurred in nature).Microorganisms in our lives► Microorganisms as Disease Agents► Microorganisms and Agriculture► Microorganisms and the Food Industry► Microorganisms, Energy, and the Environment► Microorganisms and the Future
4Microorganisms in our lives They generate at least half the oxygen we breathe.They are roots of life's family tree. An understanding of their genomes will help us understand how more complex genomes developed.
5Microorganisms (microbes) Microbiology is the study of microorganisms also known as microbes.Microbes are single-celled microorganisms that can perform the basic functions of life: metabolism, reproduction, and adaptation.Except viruses. Viruses can’t metabolize nutrients, can’t produce and excrete wastes, can’t move around on their own, or even can’t reproduce unless they are inside another organism’s cells.
6Medical microbiologyMedical microbiology is both a branch of medicine and microbiology which deals with the study of microorganisms including bacteria, viruses, fungi and parasites which are of medical importance and are capable of causing infectious diseases in human beings.
7MıcroorganismsMicroorganisms are similar to more complex organisms in that they need a variety of materials from their environment to function and accomplish two primary goals .1-To supply enough energy to manage their processes2-To extract building blocks to repair themselves or procreate.
8Environmental factors affecting the growth of microorganisms Mıcroorganisms havePhysical RequirementsChemical Requirementsfrom the environment where they live.
9Physical Requirements 1. Temperature: Microbes are loosely classified into several groups based on their preferred temperature ranges.
10Physical Requirements -Temperature - A-Psychrophiles: “Cold-loving”. Can grow at 0oC.Two groups:True Psychrophiles: Sensitive to temperatures over 20oC. Optimum growth at 15oC or below.Found in very cold environments (North pole, ocean depths). Seldom cause disease or food spoilage.Psychrotrophs: Optimum growth at 20 to 30oC. Responsible for most low temperature food spoilage.
11Physical Requirements - Temperature - B. Mesophiles: “Middle loving”. Most bacteria.Include most pathogens and commonspoilage organisms.Best growth between 25 to 40oC.Optimum temperature commonly 37oC.Many have adapted to live in the bodies of animals.
13Physical Requirements - Temperature - C- Thermophiles: “Heat loving”.Optimum growth between 50 to 60oC.Many cannot grow below 45oC.Adapted to live in sunlit soil, compost piles, and hot springs.Some thermophiles form extremely heat resistant endospores.Extreme Thermophiles (Hyperthermophiles): Optimum growth at 80oC or higher. Archaebacteria. Most live in volcanic and ocean vents.
14Physical Requirements - pH - Most bacteria prefer neutral pH ( ).Molds and yeast grow in wider pH range, but prefer pH between 5 and 6.Acidity inhibits most microbial growth and is used frequently for food preservation (e.g.: pickling).Alkalinity inhibits microbial growth, but not commonly used for food preservation.Acidic products of bacterial metabolism interfere with growth. Buffers can be used to stabilize pH.
15Physical Requirements - pH - Organisms can be classified as:A. Acidophiles: “Acid loving”.Grow at very low pH (0.1 to 5.4)Lactobacillus produces lactic acid, tolerates mildacidity.B. Neutrophiles:Grow at pH 5.4 to 8.5.Includes most human pathogens.C. Alkaliphiles: “Alkali loving”.Grow at alkaline or high pH (7 to 12 or higher)Vibrio cholerae and Alkaligenes faecalisoptimal pH 9.Soil bacterium Agrobacterium grows at pH 12.
16Physical Requirements - Osmotic pressure - Cells are 80 to 90% water.A. Hypertonic solutions: High osmotic pressure removes water from cell, causing shrinkage of cell membrane (plasmolysis).Used to control spoilage and microbial growth.Sugar in jelly.Salt on meat.B. Hypotonic solutions: Low osmotic pressure causes water to enter the cell. In most cases cell wall prevents excessive entry of water. Microbe may lyse or burst if cell wall is weak.
18Physical Requirements - Osmotic pressure- Halophiles: Require moderate to large salt concentrations. Ocean water contains 3.5% salt.Most bacteria in oceans.Extreme or Obligate Halophiles: Require very high salt concentrations (20 to 30%).Bacteria in Dead SeaFacultative Halophiles: Do not require high salt concentrations for growth, but tolerate 2% salt or more.
19Chemical Requirements -Carbon- Makes up 50% of dry weight of cell.Structural backbone of all organic compounds.Chemoheterotrophs: Obtain carbon from their energy source: lipids, proteins, and carbohydrates.Chemoautotrophs and Photoautotrophs: Obtain carbon from carbon dioxide.
20Chemical Requirements - Nitrogen, Sulfur, and Phosphorus - ► Nitrogen: Makes up 14% of dry cell weight. Used to form amino acids, DNA, and RNA.► Sulfur: Used to form proteins and some vitamins (thiamin and biotin).► Phosphorus: Used to form DNA, RNA, ATP, and phospholipids.
21Chemical Requirements - Other Elements & Trace Elements - Potassium, magnesium, and calcium are often required as enzyme cofactors. Calcium is required for cell wall synthesis in Gram positive bacteriaTrace ElementsMany are used as enzyme cofactors.Commonly found in tap water.IronCopperMolybdenumZinc
22Chemical Requirements -Oxygen- Organisms that use molecular oxygen (O2), produce more energy from nutrients than anaerobes.Microorganisms can be classified based on their oxygen requirements:A.Obligate Aerobes: Require oxygen to live. Disadvantage: Oxygen dissolves poorly in water.Example: Pseudomonas, common nosocomial pathogen.
23Chemical Requirements -Oxygen- B. Facultative Anaerobes: Can use oxygen, but can grow in its absence. Have complex set of enzymes.Examples: E. coli, Staphylococcus, yeasts, and many intestinal bacteria.C. Obligate Anaerobes: Cannot use oxygen and are harmed by the presence of toxic forms of oxygen.Examples: Clostridium bacteria that cause tetanus and botulism.
24Chemical Requirements -Oxygen- D. Aerotolerant Anaerobes: Can’t use oxygen, but tolerate its presence. Can break down toxic forms of oxygen.Example: Lactobacillus carries out fermentation regardless of oxygen presence.E. Microaerophiles: Require oxygen, but at low concentrations. Sensitive to toxic forms of oxygen.Example: Campylobacter
26Toxic Forms of Oxygen Superoxide Hydrogen 1. Singlet Oxygen: Extremely reactive form of oxygen, present in phagocytic cells.2. Superoxide Free Radicals (O2-.): Extremely toxic and reactive form of oxygen. All organisms growing in atmospheric oxygen must produce an enzyme superoxide dismutase (SOD), to get rid of them. SOD is made by aerobes, facultative anaerobes, and aerotolerant anaerobes, but not by anaerobes or microaerophiles.Reaction: SODO2-. + O H > H2O2 + O2Superoxide Hydrogenfree radicals peroxide
27Chemical Requirements -Hydrogen Peroxide- Hydrogen Peroxide (H2O2): Peroxide ion is toxic and the active ingredient of several antimicrobials (e.g.: benzoyl peroxide). There are two different enzymes that break down hydrogen peroxide:A. Catalase: Breaks hydrogen peroxide into water and O2. Common. Produced by humans, as well as many bacteria.B. Peroxidase: Converts hydrogen peroxide into water
29Microbial Stress Response A changing environment creates conditions that can be stressful for microorganisms.Microbes have physiological acclimation mechanisms to survive and remain active in the face of stress.They have to appropriately respond to numerous adverse conditions in order to proliferate or at least survive
31Stress response in pathogens Human pathogens infecting humans respond to stress situations encountered during transition from natural environment to the host.1-Temperature stressThe first signal to an invading bacteria on entry into the host is an increase in temperature from that of the environment to the physiological temperature of the human body (37°C).Response: * Induction of virulence genes* Induction of heat shock genes
32Stress response in pathogens 2-Oxygen stressThe expression of adherence and invasion factors of several pathogenic bacteria isregulated by oxygen concentration.High oxygen usually represses whereas low oxygen induces invasivenessResponse:Induction and repression of some genes .One regulatory network is the Fnr (fumerate-nitrate reductase)-dependent control in response to anaerobiosis
33Stress response in pathogens 3-Osmotic stressFor a pathogenic bacterium which passes from environmental waters to the humanbody for infection, osmolarity is an important criterion to distinguish between the external and host associated environments.Osmolarity of an aqueous environment is thought to be no greater than that equivalent to 0·06 M NaCl while in the intestinal lumen the osmolarity is much higher (equivalent to 0·3 M NaCl) and in the blood stream the bacteria encounters an osmolarity equivalent to about 0·15 M NaCl.Response. Increase in osmolarity is associated with expression of virulence factors in many pathogenic organisms.
34Stress response in pathogens 4-Metal ion stressIron is an essential element for bacterial growth and many pathogenic bacteriahave evolved highly efficient iron scavenging systems which are regulated in response to the iron status of the environment.Response: Ex: Low iron concentration leads to the increased synthesis of virulence determinants in several pathogenic bacteria.
35Stress response in pathogens 5-Presence of Antibiotic as a stress for bacteriaAn untreated microbe maintained under optimal growth conditions will not be stressed.*Similarly, the same cell when exposed to an antibiotic to which it is fully resistant will also not be stressed.*When exposed to a lethal concentration of an antibiotic to which it is susceptible, the cell will be highly stressed in its quest to survive.Response:Antibiotic resistance
36Stress response in pathogens ACTIVEDRUGMinutesSTRESS RESPONSEACTIVEDRUGDaysGROWTHINHIBITION(CELL DIVISION)
37Bacterial response to environment Rapid response crucial for survivalSimultaneous transcription and translationCoordinate regulation in operons and regulonsGlobal genetic control through modulonsBacteria respond toChange from aerobic to anaerobicPresence/absence of glucoseAmount of nutrients in generalPresence of specific nutrientsPopulation size
38Quorum Sensing Bacteria monitor their own population size Pathogenesis: do not produce important molecules too soon to tip off the immune system.Light production: a few bacteria make feeble glow, but ATP cost per cell remains high.Bacteria form spores when in high numbers, avoid competition between each other.System requirementsA signaling molecule that increases in concentration as the population increases; LMWA receptor; activation of a set of genes
39Quorum SensingNew peptide communication factor enabling bacteria to 'talk to each other' discovered
40Chemotaxis and other taxes Movement in response to environmental stimulusPositive chemotaxis, attraction towards nutrientsNegative: away from harmful chemicalsAerotaxis: motility in response to oxygenPhototaxis: motility to certain wavelengths of lightMagnetotaxis: response to magnetic fieldsTaxis is movementIncludes swimming through liquid using flagellaSwarming over surfaces with flagellaGliding motility, requiring a surface to move over
41Starvation Responses Bacteria frequently on the bord of starvation Rapid utilization of nutrients by community keeps nutrient supply lowNormal life typical of stationary phaseBacteria monitor nutritional status and adjust through global genetic mechanismsTypes of responsesLower metabolic rates, smaller size .Release of extracellular enzymes, scavenging moleculesProduction of resting cells, spores.