Prokaryotic Diversity Lecture Notes (October 15, 2024) PDF

10/14/24 Class 14 Prokaryotic Diversity October 15, 2024 1 Diversity of Prokaryotes Scientists just beginning to...

10/14/24 Class 14 Prokaryotic Diversity October 15, 2024 1 Diversity of Prokaryotes Scientists just beginning to understand vast diversity of microbial life Only a fraction of over a million species of prokaryotes described Vast majority have not been isolated New molecular techniques aiding in discovery, characterization Goal of this class Heather Davies/Science Photo Library/Getty Images Provide a high-level overview of diversity of characteristics and habitats While focusing on the areas where we see prokaryotes of medical importance 2 1  10/14/24 Anaerobic Chemotrophs Atmosphere anoxic for first approximately 1.5 billion years that prokaryotes inhabited Earth Early chemotrophs likely used anaerobic respiration Terminal electron acceptors such as Sulfur Anaerobic Photosynthesis increased life on the surface After Glucose standardized as an energy molecule, other species likely used fermentation Passed electrons to organic molecule like pyruvate, Producing ethanol, CO2, etc. Then came Cyanobacter... 3 Cyanobacter and Two-stage Photosynthesis Introduced large amounts of oxygen to atmosphere Poison for obligate anaerobes on the surface of the planet! But anaerobic habitats remain common, even today Mud, tightly packed soil limit diffusion of gases Aquatic environments can become limiting Any area of limited Oxygen replenishment Human and animal bodies – Especially intestinal tract! Also, anaerobic microenvironments in skin, oral cavity Facultative Aerobes contribute by depleting Oxygen and maintaining anaerobic conditions 4 2  10/14/24 Anaerobic Chemolithotrophs Oxidize inorganic chemicals for energy Anaerobes use alternative electron acceptor such as sulfur Most in domain Archaea Methanogens are one group No major medical agents 5 Anaerobic Chemoorganotrophs -- Anaerobic Respiration Chemoorganotrophs oxidize organic compounds (for example, glucose) to obtain energy Anaerobes often use sulfur, sulfate as electron acceptor Sulfur and Sulfate Reducing Bacteria Produce hydrogen sulfide (rotten-egg smell) H2S is corrosive to metals Important in sulfur cycle At least a dozen recognized genera Desulfovibrio most studied; Gram-negative curved rods Also, some archaea No major medical agents. 6 3  10/14/24 Anaerobic Chemoorganotrophs -- Fermentation Numerous current day anaerobic bacteria ferment! ATP via substrate-level phosphorylation (Glycolysis!) Many different organic energy sources, end products The genera Clostridium and Clostridioides are in this group! Normally inhabit soil environments (where facultative anaerobes keep oxygen down) Endospore formers – which can survive long exposure to oxygen. (And heat, drying, chemicals, radiation….) Some are commensals (peaceful inhabitants of the intestinal track) Others are trouble 7 Medically Important Clostridia Clostridium tetani Ubiquitous in rich (e.g., manure fertilized) soils Common in many animal intestine (incidental in human) Classic infection by deep puncture wound (anaerobic!) Has a plasmid encoded neurotoxin – “tetanospasmin” Two protein combination First protein chain binds to membranes of neurons Second protein internalized by active neurons and blocks release of Inhibitory neurotransmitters (transmitters that stop a neuron from firing) Once muscles contract, cannot relax Toxin is irreversible – the neuron must grow new axons… Treatment complicated by symptoms Currently controlled by vaccination against the toxin! (not the organism) 8 4  10/14/24 Medically Important Clostridia Clostridium botulinum Ubiquitous in rich (e.g., manure fertilized) soils Low levels in human gut controlled by competition with normal gut flora But infants with poorly developed gut flora can be susceptible Classic disease in US is foodborne Improper canning – if spores not killed, grows happily in airtight environments. Any strain has one or more of a set of neurotoxins that block excitatory neurons. takes days from exposure to be symptomatic Headache, blurred vision, drymouth (nerves in head stop working) Weakness descends bilaterally. When hits diaphragm, breathing issues! Toxin is irreversible. Recovery requires regrowth of nerves and can take months/years. Can be treated with antitoxin, ventilation support Focus on prevention of food poisoning 9 Medically Important Clostridia Clostridioides difficile Commonly isolated from intestinal flora. Usually growth kept limited by normal flora in intestine. Problem is when antibiotic treatment destroys normal flora in intestine! Mild disease often resolved by discontinuing(!) antibiotics. Severe disease treated with different, high dose antibiotics. Side note– Alexander Flemming and Penicillin. Tested in mice. Cured infections! If had tested in guinea pigs, all would have died from C. difficile! 10 5  10/14/24 Aerotolerant Fermenters – Lactic Acid Bacteria Gram-positive bacteria that produce lactic acid as a product of fermentation Most can grow in aerobic environments; lack catalase so they only ferment Medical Important genera Lactobacillus are part of healthy, normal flora (e.g., vaginal flora). Some Streptococcus inhabit oral cavity; normal microbiota But others, like β-hemolytic S. pyogenes (Group A Strep) are pathogens Suite of toxins and enzymes dissolve red and white blood cells “Strep Throat”, Scarlet fever, Necrotizing fasciitis, and more… Also, systemic disease, heart valve injury, internal prosthetic contamination. Treatment – Penicillin still first line of defense. 11 Intervening Prokaryotic types (from book) (Environmental impact!) 11.2 Anoxygenic Phototrophs Purple Bacteria (Sulfur and non-sulfur) Green Bacteria Filamentous Anoxygenic Phototrophic Bacteria 11.3 Oxygenic Phototrophs Cyanobacteria 11.4 Aerobic Chemolithotrophs Sulfur Oxidizing Bacteria Nitrifiers Hydrogen-Oxygen Bacteria 12 6  10/14/24 Aerobic Chemoorganotrophs Oxidize organic compounds for energy Use Oxygen as terminal electron receptor Obligate Aerobes -- Cannot ferment! 13 Mycobacterium Additional components to cell wall Covering of mycolic acids (long chain fatty acids) Help survive in dry environments Protect against chemical attack Survive in harsh environments Identify by “acid fast staining” Most species are environmental But two key medical agents M. tuberculosis – scheduled for case study. M. leprae 14 7  10/14/24 Pseudomonas Wide range of degradative activities (as a group) Metablolize complex molecules (plastics!) Also, unusual sugars, amino acids Widespread in soil and water Medically important MOs P. aeruginosa Grows in a nutrient poor environment Can contaminate what you would think is “just water” Resistant to many standard disinfectant procedures Opportunistic infection in hospital environment 15 Side bar: Scientific interest Thermus Grows at high temperatures Heat stable enzymes Deinococcus Extremely radiation resistant Multiple genomes and active DNA repair mechanisms. 16 8  10/14/24 Facultative Anaerobes Preferentially use Aerobic respiration But can ferment if oxygen limited. Major role in maintaining anaerobic environments Example: as air comes into digestive tract, they rapidly use all available oxygen. Keeps environment safe for obligate anaerobes. We know a lot about them because isolated from various (anaerobic) nooks and crannies on humans (both commensal and disease causing), but can readily grow in laboratory. Environmental indicators of fecal contamination! 17 Medically Important Family: Enterobacteriaceae Common intestinal residents in humans and other animals Normal flora in their evolved niche Can cause disease if out of that niche Genera include: Enterobacter, Klebsiella, Proteus, Escherichia Others cause intestinal or systemic disease Salmonella – normal flora in other animals (chicken, reptiles), but enteric disease in humans (food poisoning). Also, systemic infection (S. typhi) in humans. Shigella (plus O157 variant of E. coli) cause severe intestinal infection Yersinia pestis – both bubonic and pneumonic plague 18 9  10/14/24 Other Medically Important Genera Corynebacterium Common genera on skin and mucosal membranes C. diphtheria okay until infected with phage carrying toxin gene… Toxin gets into bloodstream and is distributed around the the body with systemic symptoms. As was the case for tetanus, the vaccine targets the toxin, not the bacteria. Vibrio Require some sodium ions for growth. Medical example: V. cholerae. Free living in high saline water. But if ingested, some survive stomach and adhere to intestine wall Secretes a toxin that triggers export of water from body into intestine! If cannot prevent dehydration, patient will die. (Note: following book presentation. List not comprehensive) 19 Note on Environmental factors A few prokaryotes have evolved to live on and in the human body. have learned to take advantage of what we can offer. Generally, see an advantage in not killing too many of us. Orders of magnitude more prokaryotes have evolved to live in various ecological niches To most we are an inhospitable niche where they would never try to grow. To a very few, we accidentally provide what looks like a great new home but we turn out to be a dead end for the bacteria. Sometime us as well! If evolution not possible (i.e., dead end), cannot evolve balance 20 10  10/14/24 Out of Balance -- Terrestrial environments Prime examples are Clostridia spp mentioned earlier in this class. Aquatic environments Example - Legionella Gram negative bacteria – happily growing in wide range of aquatic environments. Add human engineering that creates aerosol droplets (e.g., air conditioning, humidifiers). Allows humans to breathe in bacteria Bacteria in the lung are immediately ingested by macrophages. Kills most bacteria, but these trains have evolved to fight back (past attacks by free living amoebae?) and kill the macrophages instead! Normal human human immune system will eventually win But people with decreased cellular immunity (elderly) at high risk 21 Animals as Habitats Will look at three habitats Skin Strong barrier, if not cut or punctured Dry, salty. Aerobic/anaerobic conditions Mucous Membranes Moist Anaerobic/aerobic Rely on innate and adaptive immune responses to control infections. Intracellular environments Very specialized! 22 11  10/14/24 Skin Staphylococcus epidermidis and aureus Facultative anaerobe, low water/high salt (different biochemistry from Streptococcus) Commensal (even protective) on skin surface But pathogen if gets past the skin (injury) 23 Mucous Membranes: respiratory, genitourinary, and intestinal tracts Already met some of key players Streptococcus – respiratory tract; Lactobacillus – vagina; Enterobacteriaceae – intestinal tract. Other Medical… Digestive tract Helicobacter -- stomach Uniquely adapted to survive the stomach Primary cause of stomach ulcers Campylobacter – small intestine normal flora in intestine of other animals (chickens) Can easily contaminate uncooked food Reportable diarrhea in humans Bacteroides – large intestine strict anaerobe, commensal (in right place) 30% of bacteria in feces! But not easy to culture. 24 12  10/14/24 Other mucosal: Respiratory Respiratory -- Mycoplasma Unique bacteria – NO CELL WALL (membrane and cholesterol) Among smallest size and genome of the bacteria Hard to see (cultures not cloudy!) Specific glycoprotein binds at base of cilia in lung -- interferes with normal clearance of airways! Also acts as “superantigen” – causing inflammation. Causes a mild pneumonia (“walking pneumonia?”) with persistent cough. 25 Other Mucosal -- Genetourinary Neisseria gonorrhoeae – STI/STD Gram negative, but with different outer membrane – no O antigen. Pili stick to mucosal membrane – avoid clearance Needs Iron! Has proteins that specially bind iron ions. Has enzymes that attach penicillin and some antibodies. Only infects Humans (no animal or environmental reservoir). Transmitted by sexual intercourse Asymptomatic carriage is common (50% of infected women, essentially all (after initial symptoms) men. Treponema pallidum – STI/STD Does not grow well in laboratory – not well characterized Three stages of disease. Primary Syphilis transmitted as STI/STD. Does include brief bacteremia (congenital transfer) Secondary Syphilis – disseminated disease, body rash (which is highly infectious) Tertiary or Late Syphilis – systemic disease, organ damage (including brain) Humans are only natural hosts. 26 13  10/14/24 Obligate Intracellular Bacteria Bacteria that cannot replicate outside of a host cell. Multiple Advantages Lots of available food and building blocks Relatively consistent environmental factors (water, temp, salinity, etc) Disadvantage – have to get into and out of cells to infect Example: Chlamydia Small, no peptide glycan Invades epithelial cells of mucous membranes One variant can invade or survive in white blood cells Range of infections, including STI First thought to be a virus 27 Questions? 28 14