ENVIRONMENT & MICROORGANISMS

1. ENVIRONMENT & MICROORGANISMS Doç.Dr.Hrisi BAHAR

2. MICROORGANISMS The 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.

3. Microorganisms 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

4. Microorganisms 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.

5. Microorganisms (microbes) • Microbiologyis the study of microorganismsalso 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.

6. Medical microbiology • Medical 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.

7. Mıcroorganisms Microorganisms are similar to more complex organisms in that they need a variety of materials from their environment to function and accomplishtwo primary goals . 1-Tosupply enough energy to manage their processes 2-To extractbuilding blocksto repairthemselves or procreate.

8. Environmental factorsaffecting the growth of microorganisms Mıcroorganisms have • Physical Requirements • Chemical Requirements from the environment where they live.

9. Physical Requirements 1.Temperature: Microbes are loosely classified into several groups based on their preferred temperature ranges.

10. Physical 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 temperaturefood spoilage.

11. Physical Requirements- Temperature - B.Mesophiles: “Middle loving”. Most bacteria. • Include most pathogens and common spoilage organisms. • Best growth between 25 to 40oC. • Optimum temperature commonly 37oC. • Many have adapted to live in the bodies of animals.

13. Physical 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. • ExtremeThermophiles(Hyperthermophiles): Optimum growth at 80oC or higher. Archaebacteria. Most live in volcanic and ocean vents.

14. Physical Requirements- pH - • Most bacteriaprefer neutralpH (6.5-7.5). • Moldsandyeastgrow in wider pH range, but prefer pHbetween 5 and 6. • Acidityinhibits most microbial growth and is used frequently for food preservation (e.g.: pickling). • Alkalinityinhibits microbial growth, but not commonly used for food preservation. • Acidic products of bacterial metabolism interfere with growth. Buffers can be used to stabilize pH.

15. Physical 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 mild acidity. 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 faecalis optimal pH 9. • Soil bacterium Agrobacterium grows at pH 12.

16. Physical 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.

18. Physical 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 Sea • Facultative Halophiles: Do not require high salt concentrations for growth, but tolerate 2% salt or more.

19. Chemical 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.

20. Chemical 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.

21. Chemical Requirements- Other Elements & Trace Elements - Other Elements Potassium, magnesium, and calcium are often required as enzyme cofactors. Calcium is required for cell wall synthesis in Gram positive bacteria Trace Elements Many are used as enzyme cofactors. Commonly found in tap water. • Iron • Copper • Molybdenum • Zinc

22. Chemical 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.

23. Chemical 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.

24. Chemical 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

26. Toxic Forms ofOxygen 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: SOD O2-. + O2-. + 2H+-----> H2O2 + O2 Superoxide Hydrogen free radicals peroxide

27. Chemical 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

28. Chemical Requirements -Hydrogen Peroxide- Catalase 2 H2O2----------> 2H2O + O2 Hydrogen Gas peroxide Bubbles Peroxidase H2O2 + 2H+----------> H2O Hydrogen peroxide

29. Microbial 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

31. Stress response in pathogens • Human pathogens infecting humans respond to stress situations encountered during transition from natural environment to the host. 1-Temperature stress The 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 http://www.ias.ac.in/jarch/jbiosci/21/149-160.pdf

32. Stress response in pathogens 2-Oxygen stress The expression of adherence and invasion factors of several pathogenic bacteria is regulated by oxygen concentration. High oxygen usually represses whereas low oxygen induces invasiveness Response:Induction and repression of some genes . One regulatory network is the Fnr (fumerate-nitrate reductase)-dependent control in response to anaerobiosis

33. Stress response in pathogens 3-Osmotic stress • For a pathogenic bacterium which passes from environmental waters to the human body 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.

34. Stress response in pathogens 4-Metal ion stress Iron is an essential element for bacterial growth and many pathogenic bacteria have 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.

35. Stress response in pathogens 5-Presence of Antibiotic as a stress for bacteria • An 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

36. Stress response in pathogens ACTIVE DRUG Minutes STRESS RESPONSE ACTIVE DRUG Days GROWTH INHIBITION (CELL DIVISION)

37. Bacterial response to environment • Rapid response crucial for survival • Simultaneous transcription and translation • Coordinate regulation in operons and regulons • Global genetic control through modulons • Bacteria respond to • Change from aerobic to anaerobic • Presence/absence of glucose • Amount of nutrients in general • Presence of specific nutrients • Population size

38. Quorum 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 requirements • A signaling molecule that increases in concentration as the population increases; LMW • A receptor; activation of a set of genes

39. Quorum Sensing • New peptide communication factor enabling bacteria to 'talk to each other' discovered http://phys.org/news112885276.html

40. Chemotaxis and other taxes • Movement in response to environmental stimulus • Positive chemotaxis, attraction towards nutrients • Negative: away from harmful chemicals • Aerotaxis: motility in response to oxygen • Phototaxis: motility to certain wavelengths of light • Magnetotaxis: response to magnetic fields • Taxis is movement • Includes swimming through liquid using flagella • Swarming over surfaces with flagella • Gliding motility, requiring a surface to move over

41. Starvation Responses • Bacteria frequently on the bord of starvation • Rapid utilization of nutrients by community keeps nutrient supply low • Normal life typical of stationary phase • Bacteria monitor nutritional status and adjust through global genetic mechanisms • Types of responses • Lower metabolic rates, smaller size . • Release of extracellular enzymes, scavenging molecules • Production of resting cells, spores.

42. Microganisms leaving a stressful environment