MBIO 3282 Quiz 1.pdf

Topic 1: Intro/Overview What is the importance of microbes in nature? - Diversity of metabolism o With the help of microorganisms, they can recycle elements (C, O, NA etc.) that make up most living systems and are essenHal for degradaHon of dead organisms...

Topic 1: Intro/Overview What is the importance of microbes in nature? - Diversity of metabolism o With the help of microorganisms, they can recycle elements (C, O, NA etc.) that make up most living systems and are essenHal for degradaHon of dead organisms o Some can use anaerobic respiraHon, chemolithotrophy, nitrogen fixaHon and degradaHon of xenobioHc compounds (any foreign substance that the organism can’t produce itself). - Widespread distribuHon/Abundance/Adaptable o They can be easily dispersed via animals (with animal behaviour such as migraHon), the air, and bodies of water; and are immensely diverse. They are also small in size but large in number. They are capable of adapHng to their environment through molecular regulaHon which also depends on their growth rate. - Survival o Can live long periods of Hme with a minimal energy requirement and survive in extreme environments via mechanisms such as spore sporulaHon where the dominant spore can survive unHl its condiHons are more ideal and can be converted back into a vegetaHve cell. What is the difference between a microbial physiologist and a microbial ecologist? - To study and observe how microbes interact with their environment. Then idenHfying the species and characterizing them physiologically. As well as determining the specific funcHons or acHviHes of those different microbes and characterizing the environment that they are in. - Microbial ecology is important because microorganisms live in all ecosystems and the acHviHes/interacHons they carry out are unique and cannot be done by other organisms and are essenHal for life on earth. Microorganisms are said to have formed the first ecosystems and biosphere. TOPIC 2: HISTORY OF MICROBIAL ECOLOGY Describe how the field of microbial ecology came to be? How is the field guided and how do discoveries get made? - Microbial ecology starts and conHnues to develop as philosophical and technological advances are driven by research quesHons. Advances in technology lead to looking at the world in a different light. Different perspecHves have allowed quesHons to be answered as new quesHons to be asked leading to the development of the field. What were the first quesHons asked in the field of microbiology (and Microbial Ecology) that really boosted the field? - The first quesHon that really spearheaded the field and research in the field was the quesHon how do we know microbes exist? As you know, microbes are invisible to the naked eye, so how can we say that they are there? - This quesHon led to the development of the first microscope, which was revoluHonary for its Hme, but also is criHcal for modern microbial analysis. In the mid 17th century, the first microscope was developed by Antoine Van Leeuwenhoek. Although this microscope was incredibly primiHve in comparison to modern microscopes, he was able to be the first to describe microbes, including bacteria. - The microscope he designed only used a single lens and was incredibly small. - With the development of the first microscope, Antoine was able to describe the first microbes, using wastewater and was able to invesHgate different microbes from their environments. His drawings of the first microbes are sHll today in a museum as well as his original microscope. With the first microscope, the field of microbiology (and eventually microbial ecology) was able to start as scienHsts could see what microbes were which opened the door for the study. What was the second quesHon asked in the field of microbiology and microbial ecology? Who spearheaded the research? - The second quesHon that was asked which helped develop the field of microbiology and microbial ecology is how we get rid of microbes or stop their acHvity. This research was spearheaded by Louis Pasteur. A wine and beer merchant came to Pasteur and asked him to determine why their products kept spoiling. When it was originally prepared, the wine and beer tasted wonderful, but during transport it would get a sour taste. The process of fermentaHon was known, but they didn't know that it was due to microbes. Pasteur discovered that yeast was responsible for fermentaHon, and that the reason the food was spoiling was due to the fermentaHon process conHnuing and bacterial death occurring during transport. - Once this was discovered. in collaboraHon with John Tyndall, they determined that microbial eradicaHon (ge`ng rid of all the microbes in a sample is possible because there is no spontaneous generaHon. Previously to this point it was common belief that microbes could arise, and become living through solely non-living material, but they disproved this theory. Knowing that spontaneous generaHon was false, Pasteur developed the process of sterilizaHon and pasteurizaHon to eliminate microbes in a sample. PasteurizaHon is the gradual heaHng of the sample just enough to kill microbes but maintain the natural components of the sample, and sterilizaHon is the rapid and hot treatment of a product to eliminate the microorganisms present in the sample. Finally, Pasteur was able to describe endospores and their survival and disseminaHon by air to new environments. What was the third quesHon that was asked in the development of the field of microbiology and microbial ecology? - At this point, science knew that not all microbes present in the environment were bad and they knew that not all microbes caused infecHon, but there was sHll a lidle bit of difficulty determining which microbes were good, such as that that ferments wine, or that were pathogenic. There was also the discussion of what individual microbes do in the environment. - Due to these quesHons Robert Koch decided to grow microbes and try to obtain pure cultures of microbes using solid media. This way you can determine which microbes are present in infecHon, and what is present in many (or all humans). - Koch iniHally used slices of potatoes but then later versions of his culHvaHon used gelaHne and agar to make solid media for isolaHon. Agar is the media of choice as gelaHne is liquid at room temperature as well as can be broken down by microbes creaHng soup basically that is hard to obtain pure cultures. - Using solid media, John Lister, Koch and Fannie Hesse were able to conclude that specific disease is caused by specific bacteria, as well as they were able to discover and define the monomorphism of bacteria. What was the fourth quesHon that was asked in the development of the field of microbiology and microbial ecology? - The fourth quesHon that was asked was what are the microbes capabiliHes? This is where the ecology aspect of microbiology really started to thrive. At this point we know that there are microbes everywhere, but at this point the quesHons about what they were able to do in these environments started to come up. - Sergei Winogradsky and MarHnus Beikernick were the founders of microbial ecology and they studied the relaHonship between environmental condiHons and the corresponding microbes. Through this, they developed the concept of selecHvity of environments which is the idea that the environment selects for what bacteria can grow. They were the first microbiologists to connect the relaHonship between the environment and the microbes present in those environments. - Winogradsky and Beikernick developed the first enrichment culture techniques where the imitaHon of natural environments in culture condiHons allows them to expand the number and diversity of known microbes and their microbial condiHons. This allowed them to study what condiHons were required for certain species of microbes to grow, what condiHons prevented them from growing, and when we switch condiHons how does it affect the overall growth of bacteria. - Winogradsky developed something called the Winogradsky column, which is used in growing phototrophic, anaerobic and microaerophilic soil bacteria. The Winogradsky column worked by simulaHng the condiHons in which bacteria normally grew in the soil. Due to the column, he was able to isolate and grow anaerobes which are unable to be cultured using previous standard culture techniques. Using the Winogradsky  column, it allowed for the discovery of sulphate reducing bacteria. This conclusively demonstrated chemoautotrophy. The Winogradsky column can be described as an arHficial microbe ecosystem, where ½ of the contained is full of organically rich sulphide containing mud with carbon substrates, a buffer to keep the pH stable, and Cas04 as a sulphate source. The mud was covered with environmental water. Once the column is placed near the light it allows for phototrophic bacteria to grow. Due to all these condiHons, a diverse community is eventually able to develop. - In the top of the column, it is under aerobic condiHons and at the bodom of the column there are anaerobic condiHons. The column creates a gradient of oxygen, and then from there you can decide which bacteria you want to work with. The column might change colours depending on the presence of algae and cyanobacteria and the soil might turn purple or green depending on the presence of purple sulphur bacteria or green sulphur bacteria. - What was the 5th quesHon asked in the development of microbial ecology? - The 5th quesHon asked in the development of microbial ecology was how a microbe grows in its environment. AJ Kluver, CB van Niel, H Schlegal and the delk school of microbiology has done a lot of work and focus on microbial ecology. All the previous persons menHoned were followers of Beiiernck. They developed comparaHve and ecological microbial physiology and biochemistry. - They related how organisms to environmental condiHons, isolated phototrophs and chemolithotrophs and reported their physiological diversity. They applied thermodynamics and energy calculaHons to microbial physiology and then compared different organisms, revealing unifying metabolism in the microbial world developing the unity of biochemistry concept. Topic 3: Physiology and Habitat List the physical and chemical effects of an environment on physiology - The environmental condiHons are a key player in how and which bacteria grow in said environment. Structure is closely related to funcHon, therefore, as the microbes that grow in a certain environment are going to have specific physical characterisHcs so that they can survive and thrive. Some of the main physical and chemical effects of the environment on physiology include: o 1. Temperature o 2. pH o 3. Light (radiaHon) o 4. Water acHvity o 5. Redox potenHal o 6. Oxygen concentraHon Define what a habitat is. A habitat refers to the specific environment or locaHon where a microbial community resides and thrives. A habitat provides the physical, chemical and biological condiHons that are required for a microbe to live, grow and reproduce. Microbial habitats can range from extreme environments like hot springs and deep-sea vents, to more common areas like soil, freshwater, ocean water and even the human body. Each habitat supports different types of microbes that have adapted to its specific condiHons. SubsecHon 1: Temperature Describe the minimum temperature, opHmal temperature and maximum temperatures. - Minimal temperature is the LOWEST temperature at which a microorganism can grow and carry out metabolic acHviHes. Below this temperature, the cell's enzymaHc funcHon slows down significantly or it stops all together prevenHng the microbe from dividing or sustaining growth. - OpHmal temperature is the range in which a microorganism displays its fastest growth rate and highest metabolic efficiency. It can also be called the ideal temperature for enzyme acHvity, membrane fluidity and cellular processes. Different microorganisms have different opHmal temperatures based on their adaptaHons - Maximum temperature is the highest temperature at which a microbe can grow and carry out metabolic acHviHes. Beyond this temperature, criHcal processes such as protein structure, enzyme funcHon and membrane integrity begin to break down leading to cell death or dormancy. Classify microbes based on their opHmal temperature growth temperatures. - As menHoned above, microorganisms have an opHmal growth temperature where they grow and thrive. Based on these opHmal temperatures we can classify microorganisms, which allows us to organise them. - Psychrophiles: Microorganisms that thrive at cold temperatures, their minimal temperature typically sits around 0°C (and can even be lower than this) and they have an opHmal range between 10°C and 15°C. Their maximum growth temperature typically is below 20°C. - Mesophiles: Microorganisms that grow best IN moderate temperatures, with a minimal temperature typically between 10°C and 15°C and an opHmal range of around 20°C and 45°C. The maximum temperature is around 45°C to 50°C. Mesophiles are any bacteria that we say is "convenHonal" temperatures. - Thermophiles: microorganisms that are found in higher temperature environments. Their minimal temperature is typically around 40°C and they thrive at temperatures between 50°C and 70°C. Their maximum temperatures are usually between 70°C and 80°C. - Hyperthermophiles: Microorganisms that grow in extreme heat with a minimal temperature of above 60°C. Their opHmal growth temperatures are above - 80°C and their maximum growth temperature is 121°C  - Typically, bacteria and archaea have the greatest range of opHmum growth, whereas eukaryotes tend to fall in the mesophiles (someHmes thermophiles) category. Individual microbes can have growth ranges from -20°C to 40°C, but each individual bacteria are going to have a different ability to tolerate temperature fluctuaHons. Some species can beder adapt to the extreme condiHons. In thermophiles and mesophiles, when bacteria grow at higher temperature, they display higher metabolic acHviHes. This is not the case in hyperthermophiles, even if they can withstand higher temperatures, they display less metabolic acHvity than thermophiles and mesophiles. What are some of the key traits of hyperthermophiles? List some examples of hyperthermophiles? - Hyperthermophiles are bacteria that have an opHmal growth temperature of around 80°C. Environments that display such high temperatures tend to be hot springs and underwater vents. These extreme environments tend to not only be extreme in the sense of temperature, but also other condiHons. - Hyperthermophiles tend to be anaerobic and chemolithotrophic. Hyperthermophiles are never phototrophic as the organelles and membranes that perform phototrophic acHvity are sensiHve to heat, and under high temperatures they denature, or are damaged. Phototrophic eukaryotes cannot grow at temperatures greater than 60°C and cyanobacteria (prokaryoHc phototrophs) cannot grow at temperatures greater than 73°C. - Most known hyperthermophiles are archaea, but a few are prokaryoHc bacteria. The archaeal hyperthermophiles tend to belong to the crenarchaeota genera, but a few are found in the euryarchaeota. Their names oken have a prefix or a suffix that you can tell means they grow at high temperature. Some common prefixes or suffixes are thermo -, pyro-, and -thermus. Although some hyperthermophiles don't have them, some examples include sulfolobus or archaeoglobus. Describe the bacteria with the highest known opHmal temperature. - For a while, Pyrolobus fumari was the record holder for the highest opHmal temperature of 110°C - 115°C, but in 2003, a new species of archaea was discovered which can grow at an opHmal temperature of 121°C. This new Archaea was called Geogemma barosii, also called strain 121 (due to the temperature at which it can grow), and is an iron reducer. It has a maximum growth temperature of 130°C. - Due to its ability to withstand high temperatures, G. barosii can withstand and survive the autoclaving process, which has led to the development of alternaHve autoclaves that can go to higher temperature, although G. barosii is uncommon in nature due to its growth requirement therefore many labs don't have an autoclave that can kill it. What is the upper limit (temperature) for growth in nature? Why is this temperature significant? - The upper limit temperature for growth in nature is believed to be around 150°C, although hyperthermophiles that grow at the known highest temperature are 130°C. This temperature is hypothesised to be the upper limit due to the structure of ATP, which is the energy source of the cell. - ATP denatures at around 150°C, and therefore, life as we know it cannot be supported above 150°C. It is possible that one day in the future, some form of life will be discovered that can grow at higher temperatures but this is not currently the case. Describe the changes in protein, DNA and lipid structure that allow different microbes to behave as hyperthermophiles/Thermophiles. - There are many ways in which a hyperthermophile and a thermophile adapted its protein, DNA, and lipid structure to allow it to thrive at higher temperatures that are considered inhospitable. There is not one single adaptaHon (or mix of adaptaHons) that is found in all hyperthermophiles, and therefore the following list is a hypothesis of what might affect their opHmal temperature. o Proteins: proteins are specifically vulnerable to high heats as when they are exposed to high temperatures, they denature, and unfold, therefore affecHng their funcHon. One thing that might allow hyperthermophiles and thermophiles to withstand high temperature is small changes in the amino acids of the protein; these small changes allowing an increase in ionic and hydrophobic bonds allows the protein to maintain its acHvity level even under higher temperature. Hyperthermophiles and thermophiles tend to also possess many chaperonins, which is a class of enzymes that assists with protein folding. They are released by the cell when it is subjected to higher temperature, but also can be used when the proteins are first synthesised. o DNA: DNA, which is the blueprint for life and cellular funcHon denatures at a temperature of around 100°C, therefore thermophiles and hyperthermophiles need to come up with an alternaHve way to ensure that their DNA remains structurally sound. Some hyperthermophile archaea have a special DNA gyrase enzyme that performs posiHve supercoils (opposite direcHon than normal DNA gyrase enzymes), and this posiHve coiled DNA is more thermally stable than the negaHvely supercoiled DNA. Some species of hyperthermophile bacteria have addiHonal DNA binding proteins called histones that protect the DNA from denaturaHon. Other species have extra magnesium which also helps protect them from damage due to high temperatures o Lipids: remember from earlier level microbiology course, we learn that bacterial membranes are arranged in lipid bilayers. In these lipid bilayers, the hydrophilic head faces outwards, whereas the hydrophobic tails face inward. Membranes also contain a variety of proteins, polysaccharides and peripheral membrane proteins that affect the funcHon of the membrane. Thermophilic  and hyperthermophilic bacteria, to counteract the effects of extreme temperatures, adjust their lipid bilayer. o Oken, they increase the length and decrease the unsaturaHon (presence of double bonds in the FA). Some hypothermic bacteria such as theAquifex species have ether linked linear chains rather than isoprenoids. o Thermophilic and hyperthermophiles archaea contain biphytanyl diglycerol tetraether lipids that span their membranes. o This basically looks like one long fady acid with two heads, and the tails are connected in the middle, and is more of a monolayer than a bilaver membrane. Understand what an endospore is and relate its formaHon to temperature and other habitat condiHons. Endospores are basically bacteria seeds that are resistant to heat, drying and freezing and other extreme environments. When extreme condiHons occur, the bacteria such as Bacillus, Clostridium, and Desul fotomaculum species produce endospores. Metabolically acHve cells form endospores that can be released when the condiHons are ideal for bacterial growth again, therefore colonies can form once again. What are some bacteria that can grow at low temperatures? What are some limits to this growth? - Psychrophiles are any bacteria that have a minimal temperature of 0°C, an opHmal temperature of 15°C and die at temperatures 20°C and higher. - Some known limits to the growth of bacteria at low temperature are due to the need for liquid water. All forms of life require water for growth, and therefore when you get to certain temperatures, when water is no longer present, growth is unable to occur. - Growth is limited to -17°C but growth at this temperature is quite slow, as metabolism occurs faster at higher temperatures. Metabolism is limited to -25°C, and aker this point you see no metabolic acHvity. Describe the adaptaHons in protein and lipid structure of psychrophilic microbes and how it allows them to thrive at lower temperatures. Just like thermophiles and hyperthermophiles, psychrophiles adapt their structure to allow for them to perform metabolism and other cellular work at colder temperatures. - Protein Structure: the alpha helix secondary structures of proteins tend to be more flexible than the beta sheet domains in secondary protein structure. Therefore, in psychrophilic bacteria they tend to have more alpha helix proteins and less beta sheet proteins. The only downside to this adjustment is that alpha helices are easier to denature. - Protein Structure: the alpha helix secondary structures of proteins tend to be more flexible than the beta sheet domains in secondary protein structure. Therefore, in psychrophilic bacteria they tend to have more alpha helix proteins and less beta  sheet proteins. The only downside to this adjustment is that alpha helices are easier to denature. Can mesophilic bacteria survive at low temperatures? Why can they remain viable? - Some mesophilic bacteria can sHll survive at lower temperatures. Most microbes are tolerant of the cold and they can be stored at low temperatures. When stored at low temperatures they are not metabolically acHve are never found in the exponenHal growth phase. - Mesophiles can be placed in freezers at - 70°C or in liquid nitrogen at -196°C and sHll be viable. They aren't acHvely growing when found in these cold environments, they are not acHvely growing, and when you freeze the cells, you add chemical cryoprotectants such as glycerol to protect the cells from damage by prevenHng the formaHon of crystals that would damage the cell membrane. SubsecHon 2: RadiaHon Define what radiaHon is. What types of radiaHon have the biggest impact on microbial ecology and why do they have this impact? - RadiaHon refers to the emission and transmission of energy in the forms of waves or parHcles through space or material medium. It can occur in several forms such as electromagneHc radiaHon and parHcle radiaHon. - The radiaHon that affects microbial ecology the most is visible light, UV light and gamma rays, but other waves can be influenHal. What are phototrophs? What are two of the main classificaHons of phototrophs? - Phototrophs are organisms that obtain energy from light to produce their food through a process called photosynthesis. They use sunlight as their primary energy source and convert carbon dioxide and water into organic compounds like glucose, releasing oxygen as a byproduct. - Phototrophs can be classified into two main groups, photoautotrophs and photoheterotrophs. Photoautotrophs are organisms that use light energy to convert CO2 into organic compounds and photoheterotrophs are organisms that use light for energy but sHll require organic compounds (rather than CO2) as a carbon source. - Phototrophs play a super important role in ecosystems as primary producers, forming the base of the food chain and supporHng life by producing oxygen and food. There are currently nine known types of bacterial phototrophs (10 if you count the Halobacterium spp), and although there are some similariHes between eukaryoHc photosynthesis and prokaryoHc photosynthesis, the organisaHon of the membrane is completely different. What is some important machinery to photosynthesis in microorganisms? How do they funcHon in photosynthesis? - Bacterial photosynthesis involves a series of proteins, pigment molecules and other machinery to help the process where light energy is converted into chemical energy. Bacteria use a simplified version of photosynthesis, and not all can produce oxygen. Some of the important components of photosynthesis include the following: - Light harvesHng complexes are protein complexes that contain pigment molecules and they funcHon to capture light energy. The pigments molecules bacteria contain include bacteriochlorophylls which are like plant chlorophylls, but they absorb a slightly different wavelength closer to the infrared spectrum. Bacteria also use carotenoids which are accessory pigments that absorb light at addiHonal wavelengths and they also help protect the organism from photo-damage Once these light harvesHng complexes catch the light energy, it is funnelled to something called a reacHon centre. The reacHon centre is the core component of bacterial photosynthesis where light energy is converted into chemical energy. It contains special pigments molecules and proteins that facilitates electron transfers The reacHon centre contains bacteriochlorophylls and bacteriopheophyHn which are involved in light absorpHon and the excitaHon of electrons as well as quinones that facilitate the transfer of electrons from the reacHon centre to other parts of the electron transport chain. The electron transport chain is a series of protein complexes and molecules that shudle electrons leading to the producHon of ATP. In the electron transport chain, cytochromes transfer electrons between different components of the ETC, quinines act as mobile electron carriers transporHng electrons within the membrane and ATP synthase uses the proton gradient generated to synthesise ATP. How to phototrophic bacteria generate energy using sunlight? - Phototrophic bacteria use photons (from light energy) to generate chemical energy that then can be used by the cell. Photons hit antenna molecules found in the membranes of phototrophic bacteria. These antenna molecules contain chlorophyll, which absorbs the light energy and transfers it unHl it reaches the specialised chlorophylls of the reacHon centre. In the reacHon centre, ATP is generated to create energy for the cell. Photosynthesis can occur in two different mechanisms, either cyclic or non-cyclic photosynthesis. - Cyclic photosynthesis in bacteria, is used by many anoxygenic photosyntheHc bacteria such as purple bacteria and green sulphur bacteria. It is called cyclic because the electrons that are excited by light return to the same photosystem, creaHng a closed loop. Some key points you need to know are, no external electron donor is needed like water in oxygenic photosynthesis. No oxygen is produced since water is not split. The primary product is ATP, which the bacteria then use for energy. Also, the cyclic nature of photosynthesis uses the same electrons cycling back to the reacHon centre. The steps of cyclic photosynthesis are as follows: o 1. Light absorpHon: light is absorbed by the bacteriochlorophyll pigments in the reacHon centre of a single photosystem.  o 2. Electron excitaHon: the absorbed light energy exists electrons to a higher energy state. o 3. Electron transport chain (ETC): the high energy electrons are passed through an electron transport chain consisHng of protein like quinones and cytochromes, releasing energy. o 4. Electron transport chain (ETC): the high energy electrons are passed through an electron transport chain consisHng of protein like quinones and cytochromes, releasing energy. o 5. ATP synthesis: the proton gradient drives ATP Synthase which synthesizes ATP as protons flow back into the cell through this enzyme. o 6. Electron recycling: the electrons eventually return to the bacteriochlorophyll in the reacHon center, compleHng the cycle. - Non- cyclic photosynthesis in bacteria involves the one-way flow of electrons leading to the producHon of ATP and reducing power in the form of NADPH. This process is typically used by oxygenic bacteria such as cyanobacteria, or by anoxygenic bacteria when they need both energy and reducing power. Some key points that you need to know are that electron donors are external, where water is used as an electron donor. Non-cyclic photosynthesis produces both ATP and NADPH where they are used for energy and carbon fixaHon. The electrons do not return to the original photosystem, instead they end up reducing NADP to NADHP, requiring a conHnuous supply of new electrons from an external donor. The steps of non-cyclic photosynthesis are as follows: o 1. Light absorpHon: light us absorbed by bacteriochlorophyll pigments in the reacHon center. In cyanobacteria, tow photosystems are involved and in anoxygenic bacteria, only one photosystem is used. o 2. Electron excitaHon: in cyanobacteria (and some anoxygenic bacteria), light excites the electrons in the photosystem, which raises them to a higher energy level. o 3. Electron Transport chain: the higher energy electrons move through an electron transport chain which is coupled to the creaHon of a proton gradient driving ATP synthesis. Electron replacement: in cyanobacteria, the electrons lost from the photosystem are replaced by spli`ng water and producing oxygen. In anoxygenic bacteria, water is not split, instead external electron donors such as hydrogen sulfide are used to replace the electrons. o 4. Transfer to photosystem 1: electrons from the ETC in cyanobacteria are eventually passed to photosystem I, where they are re-excited by light. o 4. NADPH producHon: the excited electrons from photosystem I are based down a second electron chain eventually reducing NADP to form NADPH which is used in carbon fixaHon.