Module 2 Microbes in Our Daily Lives PDF

Module 2 Microbes in Our Daily Lives  What are Microbes? organisms that individually are too small to be seen by the naked eye https://www.slideshare.net/verna1206/mcb-1-class-policies-and-lab-safety-procedures What is Microbiology? Area of biology tha...

Module 2 Microbes in Our Daily Lives  What are Microbes? organisms that individually are too small to be seen by the naked eye https://www.slideshare.net/verna1206/mcb-1-class-policies-and-lab-safety-procedures What is Microbiology? Area of biology that study forms of life that are not visible to naked eye. “microscopic” Cannot see without the aid of a microscope “microorganisms/microbes” General public use the term “germs” or “bugs” The Microbial World and You Microbes in Our Lives How do microbes affect our lives? Microbes can cause diseases in other living organisms like humans, animals, fish and plants but… Only a small minority of microorganisms on the planet are pathogenic (disease causing) Most microorganisms are non-pathogenic and actually are beneficial and/or essential to our existence How are microorganisms essential to our existence? The earth 3.5 billion years ago was a toxic wasteland without atmospheric O2 Stromatolites in Shark Bay, Western Australia  Fossilized Cyanobacteria Live Cyanobacteria  Cyanobacteria can perform photosynthesis GLUCOSE H2O + + O2 CO2 + H2O THANK YOU MICROBES! Microbes are critical in many biogeochemical cycles Biogeochemical cycles = recycling of chemical elements by between living organisms and their nonliving environment Living organisms The Carbon Cycle chemical chemical The Nitrogen Cycle element element The Sulfur Cycle The Oxygen Cycle The Phosphorous Cycle The Hydrogen Cycle Nonliving environment (water, earth, atmosphere) https://eschooltoday.com/learn/what-is-the-carbon-cycle/  Not just plants!! Microbes like ALGAE and BACTERIA (e.g., Cyanobacteria) also do this! Not just animals!! Microbes like FUNGI and BACTERIA in the soil or MARINE MICROBES also do this! https://eschooltoday.com/learn/what-is-the-carbon-cycle/  CO2 + H2O BIODEGRADATION PHOTOSYNTHESIS (respiration & fermentation) (carbon fixation) Glucose + O2 + H2O  The Food Chain Tertiary CONSUMERS Secondary CONSUMERS Primary CONSUMERS PRODUCERS  Microbes and the Food Chain When consumers die… Microbes like BACTERIA and FUNGI are DECOMPOSERS! Not just plants!! Photosynthetic microbes like ALGAE and BACTERIA (e.g., Cyanobacteria) also are PRODUCERS! What’s in “fresh air”? 78% of the earth’s atmosphere is made up of… Nitrogen gas (N2) Nitrogen is an element required by all living things So what’s the problem? Animals and plants cannot use nitrogen in the form of N2 gas https://www.cartoonstock.com/directory/c/clean_air.asp The Nitrogen Cycle 1. Nitrogen Fixation N2 gas NH3 (ammonia) Industrial man-made processes (fertilizers) The Nitrogen Cycle 1. Nitrogen Fixation N2 gas NH3 (ammonia) Free-living Nitrogen-fixing bacteria Heterocysts  specialized cells in Cyanobacteria that can convert N2 gas to usable ammonia Cyanobacteria The Nitrogen Cycle 1. Nitrogen Fixation N2 gas NH3 (ammonia) Free-living Nitrogen-fixing bacteria Azotobacter A common soil bacteria The Nitrogen Cycle 1. Nitrogen Fixation N2 gas NH3 (ammonia) Industrial Free-living Symbiotic processes Nitrogen-fixing Nitrogen-fixing (fertilizers) bacteria bacteria The Nitrogen Cycle 1. Nitrogen Fixation N2 gas NH3 (ammonia) A pea plant whose roots are “infected” with the bacteria Rhizobium Symbiotic Nitrogen-fixing bacteria The Nitrogen Cycle 1. Nitrogen Fixation N2 gas NH3 (ammonia) Symbiotic Nitrogen-fixing bacteria Root nodules of a pea plant “infected” with Rhizobium  Symbiotic relationship = both partners benefit Bacteria provides plant with a usable source of nitrogen (ammonia) Plant supplies bacteria with the environmental conditions it needs in order to grow The Nitrogen Cycle 1. Nitrogen Fixation (convert N2 gas to ammonia) Second way to produce ammonia using different microbes… Microbial Decomposition & Ammonification Proteins from dead cells decomposition Amino acids and waste products soil bacteria & fungi ammonification Amino acids soil bacteria & fungi Ammonia (NH3)  Ammonia (NH3) is a gas that rapidly disappears from dry soil (poor nitrogen source for plants) If soil is moist ammonia (NH3) converted to ammonium ions (NH4+) that can be used by other microbes as well as plants NH3 + H2O NH4+ + OH- The Nitrogen Cycle Nitrogen Fixation and/or Microbial Decomposition & Ammonification Symbiotic Soil bacteria & Nitrogen-fixing fungi bacteria Nitrogen NH4+ Fixation (ammonium ions) Free-living Decomposition & Now what?? Nitrogen-fixing Ammonification bacteria The Nitrogen Cycle 1. Nitrogen Fixation 2. Microbial Decomposition & Ammonification 3. Nitrification (a two step process) Step #1 Nitrosomonas bacteria Ammonium ion (NH4+) Nitrite ion (NO2–) The Nitrogen Cycle 1. Nitrogen Fixation 2. Microbial Decomposition & Ammonification 3. Nitrification (a two step process) Step #2 Nitrobacter bacteria Nitrite ion (NO2–) Nitrate ion (NO3–) Both compounds are produced with the help of soil microbes and are essential for plant growth The Nitrogen Cycle But how do you complete the cycle?? Symbiotic Soil bacteria & Nitrogen-fixing fungi bacteria Nitrogen Fixation Free-living Decomposition & Nitrifying soil Nitrogen-fixing Ammonification bacteria Nitrification bacteria NH4+  NO2-  NO3- The Nitrogen Cycle 1. Nitrogen Fixation 2. Microbial Decomposition & Ammonification 3. Nitrification (a two step process) 4. Denitrification Bacteria such as Pseudomonas Nitrate ion (NO3–) N2 (gas) The Nitrogen Cycle Denitrification NO3-  N2 gas Denitrifying soil bacteria Symbiotic Soil bacteria & Nitrogen-fixing fungi bacteria Nitrogen Fixation Free-living Decomposition & Nitrifying soil Nitrogen-fixing Ammonification bacteria Nitrification bacteria NH4+  NO2-  NO3- Review What is a microorganism. Explain how microorganism transformed the earth from a toxic wasteland 3.5 billion years ago and what is the name of one microbe we have to thank for this transformation? What is a biogeochemical cycle and explain how microorganisms are an important part of the carbon cycle. What are the two general types of bacteria that can convert nitrogen gas to ammonia? What is the name of this process and why is it so important to animals and plants? Rhizobium is a nitrogen-fixing bacterium that has a symbiotic relationship with plants. What does this mean and explain how this relationship works. Microorganisms can also produce ammonia from waste products and dead cells in a process that involves which two chemical steps? With respect to microbiology, explain why watering the soil is beneficial to plants. Review What are the two steps in the process of nitrification and name the general type of bacteria that are required for these steps. What chemical conversion occurs during the denitrification step in the nitrogen cycle and what general type of bacteria can carry this process out. Additional information on the carbon and nitrogen cycles can be found in Chapter 8.7 “Biogeochemical Cycles” in the OpenStax Microbiology textbook. How are microbes involved? In the past (before population expansion) or in less industrialized communities: Simple “discharge” of raw sewage into well-oxygenated rivers or streams Unfortunately, discharging raw sewage into bodies of water causes pollution and health hazards!! Overall Goals of Wastewater Treatment: To release to the environment water that has significantly reduced levels of: 1. Microorganisms 2. Biologically degradable organic (carbon) material The amount of biologically degradable organic matter in water is measured by: Biochemical Oxygen Demand (BOD)  Oxygen put into the water by photosynthetic organisms (including microbes!) Oxygen removed from the water by organisms (including microbes!) through respiration  Organic matter More organic material present for microorganisms to breakdown… More O2 required by microorganisms in order to perform the breakdown… Eutrophication = Addition of organic matter and subsequent removal of O2 from a body of water Sewage Treatment Raw sewage/wastewater is piped to a wastewater treatment plant for a 3 STEP treatment process Step #1 termed Primary sewage treatment is a PHYSICAL process that consists of two stages Stage 1: Sewage is passed through a series of SCREENS to remove large debris, rocks and grit  Step #1 termed Primary sewage treatment is a PHYSICAL process that consists of two stages Stage 2: The wastewater is moved into SEDIMENTATION or SETTLING tanks. Solids still in the water will settle to the bottom of the tank and can then be removed. A settling or sedimentation tank used in primary sewage treatment After primary treatment: 1. Primary sludge (solid) 2. Primary effluent (liquid) After primary sewage treatment… 25-35% of BOD removed Primary Wastewater BOD ~200 Remaining BOD is mostly dissolved organic matter How can the dissolved organic matter be removed? MICROBES TO THE RESCUE! Step #2 termed Secondary sewage treatment is a BIOLOGICAL process that relies on microbes to remove organic material Microbial Respiration: Organic matter In the presence of OXYGEN, AEROBIC microbes can breakdown the dissolved organic matter in the water This process can be done in one of two ways… Secondary sewage treatment is a BIOLOGICAL process that relies on microbes to remove organic material An Activated Sludge System AERATION TANK Settling tank Collects any remaining solids plus microbes = “activated sludge” which can be reused Dissolved organic matter Add Aerobic microbes and bubble tank with O2  Empty An aeration tank used in an activated sludge system Full Aerobic microbes in the activated sludge Secondary sewage treatment is a BIOLOGICAL process that relies on microbes to remove organic material After secondary treatment with an Activated Sludge System 75-95% of BOD removed! Step #2 termed Secondary sewage treatment is a BIOLOGICAL process that relies on microbes to remove organic material Microbial Respiration: Organic matter In the presence of OXYGEN, AEROBIC microbes can breakdown the dissolved organic matter in the water This process can be done in one of two ways… 1. An activated sludge system Secondary sewage treatment is a BIOLOGICAL process that relies on microbes to remove organic material Trickling Filter System Microbes form a biofilm on the rocks or plastic Secondary sewage treatment is a BIOLOGICAL process that relies on microbes to remove organic material After secondary treatment with an Trickling Filter System 80-85% of BOD removed Step #3 termed Tertiary sewage treatment is a CHEMICAL process that involves disinfection of the water To destroy any pathogenic microbes that remain in the water CHLORINE is added Finally, the water is chemically treated to remove residual chlorine (dechlorinated) and then can be released Chlorination Contact Tanks Which can be used for?? With additional Tertiary Treatment… “FROM TOILET TO TAP” Physical and chemical treatments to remove all BOD, nitrogen & phosphorous prior to filtration, disinfection by chlorination and release A settling or sedimentation tank used in primary sewage treatment After primary treatment: NOTHING GOES TO 1. Primary effluent (liquid) WASTE!! 2. Primary sludge (solid) Sludge Digestion Sludge can be “processed” in large tanks almost devoid of oxygen termed anaerobic sludge digesters Under anaerobic conditions a different population of microbes in the sludge can grow and degrade the organic solids into soluble substances and methane gas Key components produced in an anaerobic sludge digester: 1. Methane gas, a biogas that can be used as fuel 1. Stabilized dry sludge, termed biosolids, can be used as fertilizer/soil conditioner BIOREMEDIATION = the use of microbes to detoxify or degrade pollutants March 1989: the oil tanker Exxon Valdez ran aground off of Prince William Sound, Alaska, spilling ~11 million gallons of crude oil across 1,300 miles of coastland March 1989: the oil tanker Exxon Valdez ran aground off of Prince William Sound, Alaska, spilling ~11 million gallons of crude oil across 1,300 miles of coastland  How do you “clean-up” a mess of this magnitude? High pressure hosing with water – not very effective Bioenhancer = compound that allows a specific bacterial population to increase (in this case oil- degrading bacteria) April 2010: the oil rig Deepwater Horizon explodes in the Gulf of Mexico killing 11 people and causing the release of 49 million barrels of crude oil over a 3 month period long hydrocarbons found in oil 2 carbon units long hydrocarbons found in oil 2 carbon units Use of genetically modified microbes for bioremediation Review What two things must wastewater be significantly reduced in before it can be released into the environment? What is BOD and eutrophication? Describe the two steps in primary sewage treatment and what are the two products that result from primary sewage treatment? Describe what occurs during secondary sewage treatment. What is an activated sludge system and what is a trickling filter system? What chemical is added to treated wastewater to destroy pathogenic microbes and what additional steps must be done to allow wastewater to be used as drinking water (toilet to tap)? Explain how sludge from wastewater treatment is processed and the two key components that result from this process. Define bioremediation, bioenhancer and bioaugmentation. Additional information on bioremediation can be found in Chapter 8.7 “Biogeochemical Cycles” in the OpenStax Microbiology textbook. What does this have to do with microbiology? Baker’s Yeast = Saccharomyces cerevisiae  Causes the dough to rise Evaporates FERMENTATION during baking Only a small amount of ethanol and much more CO2 is made when fermentation occurs in the presence of oxygen  Rennin = an enzyme found in the stomach of cows that causes milk to clot Curds (solid) & Milk Whey (liquid) Lactic Acid Bacteria Produce lactic acid that… flavors the cheese  Curds are allowed to ripen/age During ripening/aging process: moisture lost curds are compressed (firmness) bacteria make acids that affect the taste The longer the cheese is ripened/aged, the more acids are produced by the bacteria  Propionibacterium Produces acids & CO2, Lactococcus which… lactis Blue Cheese Ripened not by a bacterium but instead by a MOLD! Sugar FERMENTATION FERMENTATION When fermentation occurs in the absence of oxygen a large amount of ethanol and less CO2 is made  Starch Sugar Problem: Yeast cannot break down starch into sugar on their own Malting = Grains are allowed to germinate and during this process starch degrading enzymes are produced that break down starch into sugars Starch Sugar GRAINS MALTS BEER Brewer’s Yeast = Saccharomyces cerevisiae Sugar FERMENTATION The Wine Making Process Grapes = sugar source Yeast added In the absence of O2 Yeast removed  WINE VINEGAR Acetobacter species In the presence of O2 can ETHANOL ferment/break down the ACETIC ACID ethanol to produce… Review Sacchromyces cerevisiae is a yeast commonly used in the production of what types of foods? Explain why bread rises. What are the two main components added to milk in order to make cheese and what are their roles in this process? What are curds and whey and what occurs when curd is ripened? Why does Swiss cheese have holes? What are the blue/green clumps in Blue cheese? The fermentation/breakdown of sugar by yeast is key to the making of bread and alcoholic beverages but how is this process different between the making of these products? Why do starch grains need to undergo malting in the process of making beer? Review Why is the malting process not necessary for wine making? Describe how vinegar is produced from wine. What does these have to do with microbiology?  METHANE GAS v Specifically methanogenic bacteria that ferment/break down the garbage to produce… Methanogenic bacteria What does this have to do with microbiology? FEEDSTOCK Genetically Cornstalks engineered bacteria Wood or newly discovered Switchgrass bacteria Other materials that contain cellulose Fermentation Ethanol BIOFUELS Butanol Using algae (photosynthetic microorganisms) to produce biofuel Do NOT need fertile ground! All you need is abundant SUNLIGHT! Review Explain how landfills can be used to produce biogas that subsequently can be converted to electricity? What is the most common biogas produced from landfills? Explain how microorganisms can be used to produce which two common biofuels. What photosynthetic microorganism can also be used to produce biofuels and what is and isn’t required for the microorganism to do this? Fruit tree leafroller Tomato horned caterpillar What do these crop destroying insects have to do with microbiology? European corn borer Bacillus thuringiensis A bacteria that makes a crystalline toxin when it forms a endospore Organic pesticides can contain the bacterial endospores or the crystalline toxin itself  Caterpillars eat the leaves treated with the Bacillus thuringiensis endospores & crystalline toxin Toxin binds to the gut wall of the caterpillar and it stops eating Toxin breaks down the caterpillar’s gut wall Caterpillar dies TOXIN IS SPECIFIC TO INSECTS & NOT HARMFUL TO HUMANS OR ANIMALS Review Explain how the microorganism Bacillus thuringiensis can be used as a potent pesticide and the major advantage of its use? What do these… have to do with these? Why would a microbe want to make a compound that can kill another microbe? Many microbes can make ___________ Many microbes can make antibiotics Why would a microbe want to make a compound that can kill another microbe?  competition for food/nutrients initially all available antibiotics were the metabolic products of microbes microbes make chemical/antibiotics to “take out” the competition What disease effects 9.3% of people in the U.S. (29.1 million people) and is the 7th leading cause of death in the U.S.? What does insulin, the treatment for diabetes, have to do with microbiology? Up until 1982  Biotechnology = Application of microorganisms, cells or cell components to make useful products app Recombinant DNA technology = Generation of genetically modified organism Genetically modified E. 2500 coli that can produce insulin purification 5000 liters = bioreactor Important Bioreactor Parameters to Monitor: 1. Temperature 2. pH of culture broth 3. Amount of aeration (i.e., O2 in the culture broth), which is controlled by air diffusers and rotating impellers/stirrers Why are these children crying and what does this have to do with microbiology? Vaccines not only protect us from infectious diseases but many actually contain microorganisms!  Contains a LIVE but avirulent (i.e., non- disease causing) Protects us against strain of the virus measles  Contains a chemical altered version of the tetanus toxin Protects us against tetanus (i.e., lockjaw) Steps in manufacturing a bacterial-based product: 1. Introduction of raw materials (e.g. the media components and the bacteria) 2. Growth of the bacterial culture in the bioreactor/fermentation tank Steps in manufacturing a bacterial-based product: 3. Downstream processing (e.g. all the further biochemical procedures required to purify the product from waste compounds) 4. Mixing (formulation) and filling of final product Steps in manufacturing a bacterial-based product: 5. Labeling and packaging of the final product Microorganisms have been used to produce: Vaccines Antibiotics Amino acids Enzymes Vitamins Steroids Review Why would it benefit certain microorganisms to produce antibiotics? Define biotechnology and recombinant DNA technology. What is a bioreactor and what three parameters must be monitored when using one? What are the steps involved in manufacturing a bacterial-based product and what types of products have microbes been used to produce?  How are microorganisms essential to our existence? 1 x 1013 1 x 1014 human bacterial cells cells in on/in our our body body Without our normal flora (microbiome) we could NOT lead a healthy existence! Microbes in our gut… Supply us with useful and essential substances like vitamin K Microbes on our skin… Help to prevent the over growth of harmful microorganisms  Only a small percentage of microorganisms cause infectious diseases; however, the effects these microbes have on our society can be devastating MAJORITY of microbes are either neutral or beneficial to humans MINORITY of microbes are pathogens that can cause disease  Only a small percentage of microorganisms cause infectious diseases; however, the effects these microbes have on our society can be devastating “Black Death” – the plague epidemic of the 1340s killed ~50 million people  Only a small percentage of microorganisms cause infectious diseases; however, the effects these microbes have on our society can be devastating The Spanish influenza epidemic of 1918 killed >50 million people  Only a small percentage of microorganisms cause infectious diseases; however, the effects these microbes have on our society can be devastating Currently HIV, which causes AIDS, has killed ~35 million people and the number continues to grow  Only a small percentage of microorganisms cause infectious diseases; however, the effects these microbes have on our society can be devastating The 2014 Ebola outbreak claimed 8,235 lives with 13,224 laboratory-confirmed cases  “It is time to close the book on infectious diseases” Dr. Luther Terry Surgeon General 1967  “It is time to close the book on infectious diseases” Dr. Luther Terry Surgeon General 1967 31 yrs “Infectious diseases a rising peril” What the heck happened? General David Satcher Surgeon General 1998  Increasing lifespan Global Urban travel sprawl Anti- Association vaccine with other movement diseases Association with cancers Bioterrorism Antibiotic resistance Review What outnumbers the amount of human cells in our body and what would happen if this were to disappear? Define normal flora/microbiome and explain how our normal microbiome can be beneficial to us. On earth what are there more of, neutral/beneficial microorganisms or disease-causing microorganisms? Why are infectious diseases still a rising peril?