Chapter 5: Environmental Influences and Control of Microbial Growth PDF

9/17/24 Chapter 5 Environmental Influences and Control of Microbial Growth 1 Learning Objectives Know the basic classifications used to describe microbes based on their growth under various conditions and how that relates to their environment...

9/17/24 Chapter 5 Environmental Influences and Control of Microbial Growth 1 Learning Objectives Know the basic classifications used to describe microbes based on their growth under various conditions and how that relates to their environment Explain how microbes tolerate variations or extremes in temperature, pH, levels of oxygen and osmotic stress Highlight some of different ways humans use stress to control or eliminate microbes The survival and growth of any microorganism in a given environment depends on its metabolic characteristics. 2 1  9/17/24 Introduction § Microbes have both the fastest and the slowest growth rates of known organisms. - Some hot-springs bacteria can double in as little as 10 minutes, whereas deep-sea sediment microbes may take as long as 1000 years. § These differences are determined by the intrinsic properties of the organisms that live in these places as well as nutrition and niche-specific physical parameters like temperature and pH. 3 5.1 Environmental Limits on Growth § The “normal” growth conditions are: - Temperature 20oC–40oC - Neutral pH 3700 Humanbody - Ample nutrients PH blood § Any ecological niche outside this window is called “extreme,” and organisms inhabiting them are called extremophiles. Yore Exreme organisms 4 2  9/17/24 The environmental habitat (such as high salt or low pH) that a species inhabits is based on one main criterion: The tolerance of that organism’s proteins and other macromolecular structures to the physical conditions within that niche Provide insight into the workings of extraterrestrial microbes we may one day encounter. Astrobiology howlife mightsurvive in different planets 5 § Microbes are commonly classified by their environmental niche. 6 3  9/17/24 Adaptation to Temperature § A bacterial cell’s temperature matches that of its immediate environment. § Growth rate roughly doubles for every 10oC rise in temperature. cannotchange its owntemperature everyorganism has an optimal growth temperature 7 bacon fat 8 4  9/17/24 9 Microbial Classification by Growth Temperature § Microorganisms can be classified by their growth temperature: - Psychrophiles: ~ 0oC–20oC - Mesophiles: ~ 15oC–45oC - Thermophiles: ~ 40oC–80oC - Hyperthermophiles: ~ 65oC–121oC § All of these organisms have membranes and proteins best suited for their temperatures. 10 5  9/17/24 The Heat-Shock Response § Rapid temperature changes experienced during growth activates batches of stress response trytorefold genes. - Resulting in the heat-shock response denature § The protein products of the genes of the heat proteins shock response § include chaperones that maintain protein shape § enzymes that change membrane lipid composition. § This type of response has been documented in all living organisms examined so far. 11 Osmolarity halophiles handling low aw § Water is critical to life, but environments differ in highsalts the amount of water actually available to growing organisms. § Water activity (aw) is a measure of how much water is available for use. 1 - Higher solutes= decreased water activity lowsolutes high wateractivity mostcells need 0.95 12 bacteria fungi 0.86 moredry 6  extremehalophiles 0 75 10times saltierthan ocean 9/17/24 Osmotic Stress § Osmolarity is a measure of the number of solute molecules in a solution and is inversely related to aw. paanaporing osmolarity water activity 13 it making Cells Minimize Osmotic Stress so that not § In addition to moving water, microbes have at there is water on least two mechanisms to minimize osmotic stress: more the § Compatible Solutes outside § Mechanosensitive inside in salty water Channels 14 I instant Pot allowspressure to escape 7  9/17/24 Halophiles Require High Salt § Halophiles require high salt concentrations. - From 2 to 4 M NaCl (10%–20% NaCl) 15 Adaptation to pH § The concentration of hydrogen ions (H+)—also has a direct effect on the cell’s macromolecular structures. to told chane inthe Of H ions 16 8  9/17/24 Neutralophiles, Acidophiles, and Alkaliphiles § Three classes of organisms are differentiated by the pH of their growth range: - Neutralophiles grow at pH 5–8. - Acidophiles grow at pH 0–5. - Alkaliphiles grow at pH 9–11. 17 pH Optima, Minima, and Maxima § All enzymes exhibit activity optima, minima, and maxima with regard to pH. 18 9  9/17/24 pH Homeostasis and Acid Tolerance § When cells are at pH below the optimum, protons can enter the cell and lower internal pH to lethal levels. § Microbes can prevent the unwanted influx of protons by exchanging extracellular K+ for intracellular H+ when the internal pH becomes too low. use antiporters toswap w Ktions § Under extremely alkaline conditions, the cells can use the Na+/H+ antiporter to bring protons into the cell in exchange for expelling Na+. § Many, if not all, microbes also possess an emergency global response system referred to as acid tolerance or acid resistance. 19 Bacteria regulate internal pH. 20 10  9/17/24 5. Oxygen and Other Electron Acceptors § Many microorganisms can grow in the presence of molecular oxygen (O2). § Many organisms are killed instantly by O2. § Some even use oxygen as a terminal electron acceptor (TEA) in the electron transport chain. 21 Aerobes, Anaerobes, and More § Strict aerobes can only grow in oxygen. § Microaerophiles grow only at lower O2 levels. § Strict anaerobes die in the least bit of oxygen. § Aerotolerant anaerobes grow in oxygen while retaining a fermentation-based metabolism. § Facultative anaerobes can live with or without oxygen. - They possess both the ability for fermentative metabolism and respiration (anaerobic and aerobic). 22 11  9/17/24 Oxygen Has Benefits and Risks § Oxygen is a benefit to aerobes, organisms that can use it as a TEA to extract energy from nutrients. § Oxygen is toxic to all cells that do not have enzymes capable of efficiently destroying the reactive oxygen species (ROS)—for example, anaerobes. § For example, catalase enzyme. § Oxygen rich atmosphere is lethal to many organisms!!! 23 Culturing Anaerobes in the Lab § Three oxygen-removing techniques are used today: 1. Special reducing agents (thioglycolate) or enzyme systems (Oxyrase) can be added to ordinary liquid media 2. An anaerobe jar - O 2 is removed by a reaction catalyzed by palladium 3. An anaerobic chamber with glove ports - O 2 is removed by vacuum and replaced with N 2 and CO 2 24 12  9/17/24 25 5.5 Nutrient Deprivation and Starvation § Starvation is a stress that can elicit a “starvation response” in many microbes. Enzymes are produced to increase the efficiency of nutrient gathering and to protect cell macromolecules from damage. § The response is usually triggered by the accumulation of small signal molecules such as cAMP or guanosine tetraphosphate, which globally transform gene expression. These highly soluble, small molecules can quickly diffuse throughout the cell, promoting a fast response. 26 26 13  9/17/24 Microbes Encounter Multiple Stresses in Real Life § Bacterial stress responses have traditionally been studied in terms of individual stresses. § In the world outside of the laboratory, environmental situations can be quite complex, involving multiple, not just single, stresses. For example, an organism could simultaneously undergo carbon starvation in a high-salt, low-pH environment. 27 27 Physical Agents That Kill Microbes § High temperature Moist heat is more effective than dry heat. Boiling water (100°C) kills most cells. Killing spores and thermophiles usually requires a combination of high pressure and temperature. At high pressure, the boiling point of water rises to a temperature rarely experienced by microbes. – Even endospores quickly die under these conditions. § Chemical Agents § Ethanol or Iodine or Chlorine (bleach) 28 14  9/22/24 Bacteria regulate internal pH. 1 5. Oxygen and Other Electron Acceptors § Many microorganisms can grow in the presence of molecular oxygen (O2). § Many organisms are killed instantly by O2. § Some even use oxygen as a terminal electron acceptor (TEA) in the electron transport chain. 2 1  9/22/24 Oxygen Has Benefits and Risks § Oxygen is a benefit to aerobes, organisms that can use it as a TEA to extract energy from nutrients. species catalase § Oxygen is toxic todetoxifying reactive all cells that do not haveoxygen enzymes capable of efficiently destroying the reactive oxygen species (ROS)—for example, anaerobes. § For example, catalase enzyme. not in 99 85 § Oxygen rich atmosphere is lethal to many organisms!!! 3 Aerobes, Anaerobes, and More § Strict aerobes can only grow in oxygen. humans § Microaerophiles grow only at lower O2 levels. § Strict anaerobes die in the least bit of oxygen. § Aerotolerant anaerobes grow in oxygen while retaining a fermentation-based metabolism. § Facultative anaerobes can live with or without oxygen. - They possess both the ability for fermentative metabolism and respiration (anaerobic and aerobic). 4 2  9/22/24 Culturing Anaerobes in the Lab § Three oxygen-removing techniques are used today: 1. Special reducing agents (thioglycolate) or enzyme systems (Oxyrase) can be added to ordinary liquid media 2. An anaerobe jar Plasticcontainer - O2 is removed by a reaction catalyzed by palladium 3. An anaerobic chamber with glove ports - O2 is removed by vacuum and replaced with N2 and CO2 gascylinders flush 0 out ofenvironment 5 5.5 Nutrient Deprivation and Starvation § Starvation is a stress that can elicit a “starvation response” in many microbes. waysto recognize lackof nutrients Enzymes are produced to increase the efficiency of nutrient gathering and to protect cell macromolecules from damage. § The response is usually triggered by the accumulation of small signal molecules such as cAMP or guanosine tetraphosphate, which globally transform gene expression. These highly soluble, small molecules can quickly diffuse throughout the cell, promoting a fast response. 6 6 3  9/22/24 Microbes Encounter Multiple Stresses in Real Life § Bacterial stress responses have traditionally been studied in terms of individual stresses. § In the world outside of the laboratory, environmental situations can be quite complex, involving multiple, not just single, stresses. For example, an organism could simultaneously undergo carbon starvation in a high-salt, low-pH environment. need to deal w multiple stresses at once 7 7 Physical Agents That Kill Microbes extrahotsteamlethal § High temperature to allorganisms autoclave Putwaterin Moist heat is more effective than dry heat. Boiling water (100°C) kills most cells. turn Killing spores and thermophiles usually requires a combination of high pressure and temperature. At high pressure, the boiling point of water rises to a temperature rarely experienced by microbes. underpressur – water boiling Even endospores quickly die under these conditions. § Chemical Agents Point higher § Ethanol or Iodine or Chlorine (bleach) 8 4  9/22/24 Chapter 6: Virus Structure and Function! 9 What Is a Virus? § A virus is a non-cellular particle that must infect a host cell in order to reproduce. DNARNA § The virus particle (virion), consists of a single nucleic acid (can be DNA or RNA) contained within a protective protein capsid. § Only discovered in 1892!! sameasbasketball RNADNA caps 10 5  9/22/24 Introduction § All life-forms can be infected by viruses. § Some viruses can be infected by viruses! § From dengue fever to influenza to AIDS to COVID- 19. § In research, viruses have provided both tools and model systems in molecular biology. 11 Kitahara bacteriadish Places Figure 6.3 wplaques batter off no In single bacterialcells thatwereused open byviruses h pe miniurus Passthroughmembrane giant virus throughbudding 12 viral Phage virusesthat Insecoverumsest 6  9/22/24 Viruses come in different sizes § Small viruses § Large viruses may commonly have a have more than small genome, 100 genes encoding under giantviruses ten genes - Mimivirus dontknowwhatgenesareimportantfor encodes over research - The genes may 1,000 genes Pandora2500 actually overlap in sequence borderingsizeof small bacteria 13 Viruses have varying levels of lethality Marburg Virus- The mortality rate was more than 80% in the 1998-2000 outbreak in the Democratic Republic of Congo. One strain of Ebola (Reston), doesn't even make people sick. But the Bundibugyo strain is up to 50% and it is up to 71% for the Sudan strain Somestrainsdont kill Rabies- 100% lethal if you don’t get treatment SARS-CoV-2 Could Influenza flu 14 7  9/22/24 Viral Ecology § Viruses exist with host organisms in complex ecosystems. facilitatesgenetransferto onevirus § Huge #’s in the environment! toanotherthroughhostDNA § Viruses fill important niches in all ecosystems. sins- Limiting host population density hostrange certaincentres to gron - Selecting for host diversity theycaninfect moreviruses in ocean thanthere are stars B 15 killwinnerhypothesismorelikelyto kill organismto passinfectionfromonehost to another § Virus-to-bacteria ratios range from 10:1 in marine and smalltish aquatic environments, to 1,000:1 in soils. § On a global scale, viruses play a significant role in the carbon zooplanoffuses balance. carbonpasses up thefood chain Et 16 8  9/22/24 § In the oceans, viruses are extremely numerous and genetically diverse. - The number of bacteriophages and algal viruses can reach 107 (10 million) per milliliter. Makeshiftsdielianbeseen § When marine algae inspace overgrow, viruses play a decisive role in controlling the algal bloom. calcium plates oytoplankton 17 green CalorumPlates 18 released organisms by dying fromviral 9 infections  I got algae 9/22/24 Emergence of Viral Pathogens § Certain human-infecting viruses are well known to persist in the wild, such as Rabies virus and West Nile virus. use otheranimals as reservoirs § But how does a seemingly “new” virus emerge to sicken humans? Sars Cov 2 encountering animals that we havent moving ontounknownjungle 19 viruses can gothroughmutations to infecthosts Virus Structure § The viral capsid is composed of repeated protein subunits. § The capsid packages the viral genome and delivers it into the host cell. § Different viruses make different capsid forms. 20 10  9/22/24 Symmetrical Viruses § Icosahedral viruses - Are polyhedral with 20 identical triangular faces - Have a structure that exhibits rotational symmetry 21 § In some icosahedral viruses, the capsid is enclosed in an envelope, formed from the host cell membrane. - The envelope contains glycoprotein spikes, which are encoded by the virus. 22 11  9/22/24 §Filamentous viruses - The capsid consists of a long tube of protein, with the genome coiled inside - Vary in length, depending on genome size - Filamentous viruses show helical symmetry A 23 Tailed Viruses § These have complex multipart structures § T4 bacteriophages - Have an icosahedral “head” and helical “neck” 24 12  9/22/24 Viral Genomes and Classification § Viral genomes can be: - DNA or RNA - Single- or double-stranded (ss or ds) - Linear or circular § Include genes encoding viral proteins - Capsid - Envelope proteins (if needed) - Any polymerase not found in host cell 25 Bacteriophage Replication § All viruses require a host cell for reproduction. - Thus, they all face the same needs for host infection: - Host recognition and attachment - Genome entry - Assembly of virions - Exit and transmission 26 13  9/22/24 Bacteriophages Infect a Bacterial Host 27 Bacteriophages Infect a Bacterial Host § Most bacteriophages (phages) inject only their genome into a cell through the cell envelope. - The phage capsid (now termed “ghost”) remains outside, attached to the cell surface. 28 14  9/22/24 § All bacteriophages can undergo one life cycle - 1. Lytic cycle Some bacteria can undergo a second lifecycle - 2. Lysogenic cycle § The “decision” between the two cycles is dictated by environmental cues. - In general, events that threaten host cell survival trigger a lytic burst. 29 § The lytic replication cycle requires these steps: - Host recognition and attachment - Genome entry - Assembly of phages - Exit and transmission § In a lytic cycle, when a phage particle injects its genome into a cell, it immediately reproduces as many progeny phage particles as possible. 30 15  9/24/24 Virus Structure § The viral capsid is composed of repeated protein subunits. § The capsid packages the viral genome and delivers it into the host cell. § Different viruses make different capsid forms. 1 Symmetrical Viruses § Icosahedral viruses - Are polyhedral with 20 identical triangular faces - Have a structure that exhibits rotational symmetry Sidesare made up of same Proteins 2 1  9/24/24 § In some icosahedral viruses, the capsid is enclosed in an envelope, formed from the host cell membrane. - The envelope contains glycoprotein spikes, which are encoded by the virus. 3 §Filamentous viruses - The capsid consists of a long tube of protein, with the genome coiled inside - Vary in length, depending on genome size - Filamentous viruses show helical symmetry ebolavirus A 4 2  9/24/24 Tailed Viruses § These have complex multipart structures § T4 bacteriophages - Have an icosahedral “head” and helical “neck” Combination of both 5 Viral Genomes and Classification § Viral genomes can be: - DNA or RNA - Single- or double-stranded (ss or ds) - Linear or circular § Include genes encoding viral proteins - Capsid - Envelope proteins (if needed) - Any polymerase not found in host cell 6 3  9/24/24 Bacteriophage Replication § All viruses require a host cell for reproduction. - Thus, they all face the same needs for host infection: - Host recognition and attachment - Genome entry - Assembly of virions - Exit and transmission 7 Attachment of Bacteriophages evolved to attach to onespecificreceptor site LPs layer attachedto outermembrane gram bacteria 8 4  9/24/24 Bacteriophages Infect a Bacterial Host § Most bacteriophages (phages) inject only their genome into a cell through the cell envelope. - The phage capsid (now termed “ghost”) remains outside, attached to the cell surface. paves deck contracts 9 Virus Replication/ Life Cycle § 2 general “life cycles” for bacteriophage § All viruses can undergo one life cycle - 1. Lytic cycle Some bacteria can undergo a second lifecycle - 2. Lysogenic cycle § The “decision” between the two cycles is dictated by environmental cues. - In general, events that threaten host cell survival trigger a lytic burst. 10 5  9/24/24 § The lytic replication cycle requires these steps: - Host recognition and attachment - Genome entry - Assembly of phages - Exit and transmission § In a lytic cycle, when a phage particle injects its genome into a cell, it immediately reproduces as many progeny phage particles as possible. 11 Lytic all bacteriophage 12 6  9/24/24 Second virus lifestyle found in SOME bacteriophage § “Temperate” phage (aka lysogenic phage), such as phage lambda, can infect and lyse cells like a virulent phage, but it also has an alternative pathway: to integrate its genome as a prophage. integratesitselfinto hostgenome § The phage is said to “lysogenize” the host, leading to a state called lysogeny. - Bacteriophage is quiescent. - Can reactivate to become lytic 13 Lysogenic 14 7  9/24/24 Lytic/ Lysogenic Stressinduced to cellbefore eggyfrom 15 Bacterial Host Defenses § Bacteria have evolved several forms of defense against bacteriophage infection - Genetic resistance imutationsoccurinDNA - Restriction endonucleases - CRISPR integration of phage DNA sequences - Clustered regularly interspaced short palindromic repeats - Kind of bacterial immune saystem geneediting 16 8  9/24/24 Animal and Plant Virus Replication § Animal and plant viruses face problems similar to those faced by bacteriophages: § However, eukaryotic cells have a more complex structure than prokaryotic cells 17 Animal Viruses Show Tropism § Animal viruses bind specific receptor proteins on their host cell. - Receptors determine the viral tropism. - Ebola virus exhibits broad tropism, infecting many kinds of host tissues. - Papillomavirus shows tropism for only epithelial tissues. § Most animal viruses enter host as virions. - Internalized virions undergo uncoating, where genome is released from its capsid. 18 9  9/24/24 Animal Virus Replication Cycles § The primary factor determining the life cycle of an animal virus is the form of its genome. § DNA viruses - Can utilize the host replication machinery § RNA viruses - Use an RNA-dependent RNA-polymerase to transcribe their mRNA § Retroviruses - Use a reverse transcriptase to copy their genomic sequence into DNA for insertion in the host chromosome 19 Animal Virus Replication Cycles § All animal viruses make proteins with host ribosomes. - Translation occurs in the cytoplasm. § Assembly of new virions - Capsid and genome - May occur in the cytoplasm or nucleus - Envelope proteins are inserted into a membrane. - Cell membrane or organelle membrane 20 10  9/24/24 Animal Virus Replication Cycles § Release of progeny viruses from host cell - Lysis of cell - Budding - Virus passes through membrane. - Membrane lipids surround capsid to form envelope. - All enveloped viruses bud from a membrane. - Either plasma membrane or organelle membrane 21 Animal Virus Replication DNA Viruses RNA Viruses RNA Retroviruses 22 11  9/24/24 Oncogenic Viruses § Many human cancers are caused by oncogenic viruses, such as Epstein-Barr virus (which causes lymphomas) and hepatitis C virus (which causes liver cancer). § Oncogenic viruses transform the host cell to become cancerous. § Mechanisms of oncogenesis include: - Insertion of an oncogene into the host genome - Integration of the entire viral genome - Expression of viral proteins that interfere with host cell cycle regulation 23 Plant Virus Replication Cycles § In contrast to animal viruses and bacteriophages, plant viruses infect cells by mechanisms that do not involve specific membrane receptors. § Entry of plant viruses into host cells usually requires mechanical transmission. § Most plant viruses enter by one of three routes: 24 12  9/24/24 § Within a plant, the thick cell walls prevent a lytic burst or budding out of virions. - Instead, plant viruses are transmitted to uninfected cells by plasmodesmata - Membrane channels that connect adjacent plant cells 25 Animal and Plant Host Defenses § Since viruses are ubiquitous, a wide range of defense mechanisms have evolved in animals and plants. - Genetic resistance - Hosts continually experience mutations. - Immune system - “Innate immunity”—interferons - “Adaptive immunity”—antibodies - RNA interference (RNAi) - Widespread among eukaryotes and archaea 26 13