Chapter 11: The Diversity of Prokaryotic Organisms

1. Chapter 11:The Diversity ofProkaryoticOrganisms

2. Important Point: If you are having trouble understanding lecture material: Try reading your text before attending lectures. And take the time to read it well!

3. “Although a million species of prokaryotes are thought to exist, only approximately 6,000 of these, grouped into 850 genera,have been actually described and classified.” • “Traditional culture and isolation techniques have not supported the growth, and subsequent study, of the vast majority.” • “Not surprisingly, most effort has been put into the study of microbes intimately associated with the human population, especially those causing disease, and these have been most extensively described.” • “The phylogenic relationships being elucidated by the ribosomal RNA studies… are causing significant upheaval in prokaryotic classification schemes.” Prokaryotic Diversity

4. “Some organisms, once grouped together based on their phenotypic similarities, have now been split into different taxonomic units based on their ribosomal RNA differences.” • We will consider the following categories (not necessarily monophyletic)of bacteria: • Anaerobic chemotrophs • Oxygenic phototrophs • Aerobic chemotrophs • Notable terrestrial bacteria • Notable aquatic bacteria • Notable animal-symbiotic bacteria • Archaea that thrive in extreme conditions Prokaryotic Diversity

5. The earliest life forms likely were anaerobic chemotrophs since early Earth lacked O2 while photosynthesis requires significant metabolic sophistication. • Anaerobic (no O2) habitats are still in abundance. • These occur from combinations of poor diffusion and mixing along with presence of facultative anaerobes which serve as O2 scavengers. • Often these are poorly mixed wet environments since water slows diffusion while simultaneously supports facultative organisms (i.e., unlike very dry habitats). • Even well-mixed environments can become anaerobic if they become tooeutrophic(nutrient rich). • Basically, by not having to support aerobic metabolisms, non-facultative anaerobes can be more efficient growers and therefore better competitors in anaerobic environments than facultative anaerobes. Anaerobic Chemotrophs

6. Chemolithotrophs obtain their energy from inorganic, reduced chemicals such as hydrogen gas (H2). • Anaerobic chemolithotrophs are anaerobic respirers rather than fermenters (without glucose, where would the pyruvate come from, after all?). • Most anaerobic chemolithotrophs are Archaeans. • The most important are the Methanogens: • 4 H2 + CO2 CH4 + H2O (CH4 = methane) • Feel free to memorize the above as “Hydrogen gas plus Carbon Dioxide go in while Methane comes out.” • Methane is an important component of swamp gas. • Methane also is an important component of cow flatulence (since methanogens are found in ruminent intestines). • Methane is an important greenhouse gas. Anaerobic Chemolithotrophs

7. Chemoorganotrophs obtain their energy from organic compounds such as glucose. • Anaerobically respiring chemoorganotrophs generally use sulfur compounds instead of O2 as their terminal electron acceptor. • Generally their metabolism creates Hydrogen Sulfide (H2S) which has a smell of rotten eggs. • H2S also reacts with ironwhich is corrosive and forms a black product (iron sulfide). • Anaerobic chemoorganotrophs consequently are responsible for significant iron corrosion under anaerobic conditions (e.g., of iron pipes). • H2S reacting with iron also turns anaerobic environments black, such as mud. Anaerobic Chemoorganotrophs

8. Fermenting chemoorganotrophs are anaerobes which lack an electron transport chain and therefore are obligate fermenters. • The Clostridium spp. are endospore-forming, Gram-positive rods that are common soil dwellers and which generally are poisoned by O2 (i.e., they are strict anaerobes). • Common species include: • C. botulinum which causes botulism. • C. tetani which causes tetanus. • C. perfringens which causes gas gangrene. • C. difficile which causes antibiotic-associated colitis(i.e., C. difficile superinfections). Chemoorganotrophic Fermenters

9. Lactic Acid Bacteria (LAB) are another important group of fermenting chemoorganotrophs. • LAB are defined by their production of lactic acid rather than by evolutionary (genetic) relatedness. • They are Gram positive, don’t form endospores, and typically are aerotolerant anaerobes. • Important genera include: • Streptococcus spp.-- strep throat, etc. • Enterococcus spp. -- urinary tract infections • Lactococcus spp. -- sour-milk products such as yogurt • Lactobacillus spp. -- vaginal, etc. normal flora plus sour-milk products(like Lactococcus spp.) • Leuconostoc spp. -- sauerkeaut, food spoilage • Propionibacterium spp. are non-LABs involved in Swiss cheese production as well as acne. Chemoorganotrophic Fermenters

10. These are oxygen-producing photosynthetic bacteria. • A number of eukaryotic organisms are also oxygenic phototrophs (e.g., plants) though all are so because they harbor oxygenic phototrophic bacteria in their cytoplasms (e.g., chloroplasts). • Cyanobacteria are the most common non-endosymbiotic bacterial oxygenic phototrophs. • Cyanobacteria are Gram negative. Many are nitrogen fixers. • Oxygenic phototrophs are the most important primary producers, getting their energy from the sun and fixing carbon, thereby making organic carbon (and associated energy) available to chemoheterotrophs such as us. • Oxygenic phototrophs, as carbon fixers, are also key players in the carbon cycle, so important in these days of global warming (which is important regardless of whether humans are at fault). Oxygenic Phototrophs

11. So far as this course is concerned, Aerobic Chemoorganotrophs are the most important of bacteria. • This is in part a bias of culturing techniques, which tend to favor the growth of organisms that grow on organic food-type stuff under aerobic conditions, and our own biases towards aerobic environments and organic materials as food. • Many pathogens are aerobic chemooganotrophs. • We are aerobic chemoorganotrophs! • We can divide aerobic chemoorganotrophs, based on their oxygen requirements, into: • Obligate aerobes • Facultative anaerobes • Because of their breadth and importance we will consider them genera by genera. Aerobic Chemoorganogtrophs

12. Mycobacterium spp. includes both soil-adapted saprophytes (eaters of dead and decaying organisms) and important pathogens. • Members of Mycobacterium spp. are often described as mycobacteria, which is neither italicized nor the name of their genus. • Mycobacteria are obligately aerobic, acid-fast, pleiomorphic rods, that don’t form endospores but do have waxy cell envelopes. • Mycobacteria are more disinfectant resistant than most other bacteria (endospores excepted). • Medically important Mycobacteria include: • Mycobacterium tuberculosis which causes tuberculosis. • Mycobacterium leprae which causes leprosy (Hansen’s disease). Genus Mycobacterium

13. Members of Pseudomonas spp. are also described as pseudomonads, which is neither italicized nor the name of their genus. • Pseudomonads are Gram-negative, motile rods some of which are strict aerobes while others can respire anaerobically (and none of which can ferment). • Pseudomonads are notable for their diversity(their genus probably is poly- or paraphyletic)including metabolic diversity. • Pseudomonads are ubiquitous, inhabiting waters and soils, including highly nutrient-poor habitats, and are resistant to certain disinfectants. • Pseudomonas aeruginosa is an opportunistic pathogen, meaning that it is a pathogen of individuals who already suffer from medical conditions. Genus Pseudomonas

14. Corynebacterium diphtheriae is a Gram-positive, pleomorphic, rod-shaped, facultatively anaerobic bacterium. • C. diphtheriae is most notable as the cause of diphtheria, a respiratory disease associated with the diphtheria toxin. • Vaccination against diphtheria is actually vaccination against diphtheria toxin and as a consequence of vaccination this once dreaded disease is now quite rare where vaccination is common. • Non-C. diphtheriae members of genus Corynebacterium serve as harmless members of the throat normal flora. Genus Corynebacterium

15. Members of family Enterobacteriaceae, otherwise known as enterics or enterobacteria, are facultatively anaerobic, Gram-negative, Glucose-fermenting rods. • Most that we are concerned with live in the large intestine, where many serve as pathogens; others serve as plant pathogens and soil bacteria (e.g., Erwinia spp.) • Important gastrointestinal genera or species include Enterobacter, Escherichiacoli, Klebsiella, Proteus, Salmonella, and Shigella. • Klebsiella pneumoniae causes pneumonia. • Escherichia and Proteus cause urinary-tract infections. • Yersinia pestis is the bubonic plague bacillus. Family Enterobacteriaceae

16. “Bacillus and Clostridium are common Gram-positive rod-shaped bacteria that form endospores.” • “Bacillus species may be either obligate aerobes or facultative anaerobes.” • “Bacillus anthracis causes the disease anthrax, which can be acquired from contacting its endospores in soil or in animal hides or wool.” (though only if those materials are B. anthracis contaminated, of course) • B. anthracis endospores can enter the body either through inhalation or through a break in the skin. • The B. anthracis niche, apparently, is to grow in or on animals, produce large quantities of endospores, and then, by killing their host animal, disseminate those spores back to the soil and thereby to other animals. • Other Bacillus spp. simply are soil-dwelling species with endospores allowing survival during hot, dry spells. Genus Bacillus

17. The streptomycete, the unitalicized, uncapitalized common name for genus Streptomyces, are Gram-positive rods. • The streptomycete are soil bacteria that make their living much like fungi plus superficially resemble fungi. (They, however, are bacteria, not fungi.) • Like fungi, streptomycete display filamentous forms, called hyphae, that grow into tangled masses called mycelia (sing., mycelium). • Like some fungi, streptomycete disseminate their kind by forming spores called conidia. • Streptomycete give rise to the “’earthy’ odor of soil.” • Members of genus Steptomyces are particularly notable for their production of the common antibioticserythromycin, streptomycin, and tetracycline. Genus Streptomyces

18. The Bdellovibrio are Gram-negative intracellular (intra-periplasmic, actually) parasites of Gram-negative bacteria. Genus Bdellovibrio Don’t worry about the numbers found in this figure.

19. Members of genus Staphylococcus are Gram-positive, facultatively anaerobic cocci that often grow in grape-like clusters called staphylococci. • They thrive in the dry, salty conditions of skin and are distinguishable from other normal flora Gram-positive cocci in that they are catalase positive. • There are a number of normal-flora members of genus Staphylococcus that are not pathogenic. • The notable exception is Staphylococcus aureus which infects wounds, causes food poisoning, and is responsible for one form of Toxic Shock Syndrome. Genus Staphylococcus

20. These are curved (helical), Gram-negative, microaerophilic rods. • Campylobacterjejuniis an important food- and waterborne cause of diarrheal disease. • Helicobacter pylori is the cause of stomach ulcers as well as the development of stomach cancer. Genera Campylobacter & Helicobacter

21. Members of genus Haemophilus are Gram-negative cocobacilli. • Many are respiratory tract normal flora bacteria. • H. influenzae is an important cause of ear and respiratory infections as well as bacterial meningitis. Genus Haemophilus

22. Members of genus Neisseria are Gram-negative cocci, usually diplococci. • They are obligate aerobes and fastidious. • There are a number of Neisseria members of the human normal flora including oral cavity and other mucous membranes. • Most notably, N. gonorrhoeae is the cause of the sexually transmitted disease, Gonorrhea. Genus Neisseria

23. Members of genus Mycoplasma lack cell walls and consequently are pleiomorphic and able to pass through filters that can trap cell-wall containing bacteria. • Mycoplasma pneumoniae is the cause of Walking Pneumoniae. Genus Mycoplasma Note the “fried egg” appearance of Mycoplasma colonies.

24. Spirochetes are Gram-negative helical bacteria that use Axial Filaments, a kind of flagellum (and a.k.a., endoflagella),to display motility. • Axial filaments and their spiral shape allow motility within highly viscous environments, such as mud and mucous. Spirochetes

25. These bacteria are spirochetes: • Borrelia burgdorferi causes Lyme disease. • Treponema pallidum causes Syphilis. Genus Treponema & Borrelia

26. Obligate Intracellular Parasites • Members of genera Chlamydia and Rickettsia are obligate intracellular parasites. • Rickettsia rickettsii causes Rocky Mountain Spotted Fever. • Rickettsia prowazekii causes Epidemic Typhus. • Chlamydia trachomatis cases the sexually transmitted disease, Chlamydia, and is the leading cause of blindness, worldwide. • Chlamydia are unusual in that they lack cell walls.However, unlike mycoplasma which otherwise have Gram-positive-like cell envelopes, Chlamydia have Gram-negative-like cell envelopes.

27. A number of Archaea live in relatively extreme environments. • These include: • Extreme halophiles (Great Salt Lake, Dead Sea) • Extreme thermophiles (Hot Springs, Deep-Sea Vents) • Extreme acidophiles (mine tailings) • It has been postulated that the early Earth, as a consequence of an otherwise absence of life along with periodic extreme meteoric bombardment and volcanism was home originally to extremophiles. • Phenotypic (e.g., current preferences for extreme environments) and genetic evidence (i.e., 16S rRNA) suggests that the ancestors to all of us may have been Archaea. Archaea Exremophiles

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