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Bacteria - General Bacteria (Procaryotes) tremendous physiological diversity can do photosynthesis and respiration in 100’s of ways versus animals and plants which have only one type of photosynthesis and two types of respiration. can metabolize virtually any natural or manmade product of major importance in biogeochemical cycles dominate the biosphere in terms of numbers (outnumber all eucaryotes combined) more in handful of dirt than all people who have every lived more in mouth than all people in NYC widest tolerances for temperature, pH, salt, etc than any other kingdom of organisms only about 15,000 species known; estimates up to 4 million species possible all are procaryotes very small 1-5µm (vs eucaryotes 10-100µ long) but Epulopiscium fishelsoni from the gut of a surgeon fish is larger than most eucaryotic cells (500µ) rarely occur in isolation, but form part of heterogenous microbial community individually are invisible but can form large multicellular aggregations when nutrients are plentiful – then are easily visible soil crumbs microbial mats sewage flocks biofilms bacterial blooms tend to be embedded in matrix of water and organic molecules (glycoproteins and polysaccharides) in some ways these microbial communities take on characteristics of multicellular organisms lots of interactions and symbioses advantages of aggregations: provide more stable environment protect cells from UV and heat minimize effects of rapid changes in environment may offer protection from predators highly effective in trapping nutrients however, most environments are nutrient scarce Bacterial Structure no organelles – much less efficient design but they make up for this with rapid reproductive rate and wide tolerance for environmental conditions Cell Wall almost all have cell wall surrounding the cell membrane cell wall varies from species to species also varies for each kingdom in most Eubacteria the cell wall contains the carbohydrate = peptidoglycan, not cellulose as in plants and some algae. the actual composition of the cell wall varies among the different bacterial groups: eg Gram + and Gram – bacteria G+ => lots of peptidoglycan simpler structure G- => less peptidoglycan lots more lipids often more pathogenic lipids are often toxic protect them from body defenses more resistant to some antibiotics (antibiotics inhibit synthesis of peptidoglycan layers) the cell wall produces the three basic shapes of bacterial cells: cocci bacilli (rods) spirals Capsule some produce a capsule – a gelatinous, sticky layer that allows bacteria to: attach to substrates and glues “colonies” together; also increases pathogenic bacteria’s resistence to host’s defenses Pili some bacteria have pili used for attachment and for bacterial conjugation in which genes are exchanged between two different bacterial cells (a type of primitive sexual reproduction) Motility – about half of all bacterial species are motile can move up to 50µm/sec [~100x’s body length/sec] ability to move and orient produces simple behavors = “taxes” or movements toward or away from stimuli such as light, food, oxygen, gravity, etc. eg. + & - chemotaxes have specific receptor molecules on cell surface to detect chemicals movement by: flagella slime trail helical filaments Flagella flagellum is whiplike rod that rotates like propeller to move bacteria along Magnetic particles – some bacteria contain rows of magnetic particles that allow them to orient toward the earth’s magnetic field Endospores some bacteria can form endospores to withstand desiccation and harsh conditions very resistant to destruction not for reproduction Chromosome not enclosed in membrane of nucleus or associated with proteins DNA is in form of one large circular chromosome and one or few small circular plasmids Physiology: Growth growth in bacteria is measured as ability to reproduce to reproduce all bacteria must be able to synthesize the proteins, carbos anf fats and nucleic acids they need also must have energy source the kinds of raw materials bacteria use to accomplish this depend on the species All life has nutrient “limiting factors” => those nutrients in shortest supply that prevent or limit growth and reproduction eg. plants => usually N and P eg. humans => sometimes Fe, Ca, Vitamins, etc Most bacteria are heterotrophs => need organic food for both nutrients and energy nutrition at most basic level requires simple elements and an energy source of these nutrients often the most critical is Carbon In some aquatic environments, P or N often become a problem other specific nutrients needed varies greatly: eg. E. coli – glucose is ONLY organic nutrient needed Lactobacillus – needs all 20 amino acids, several vitamins other organic compounds even when nutrients are in short supply most bacteria do not die => they can enter a dormant state (=anabiotic) bacterial rates of growth and reproduction are also greatly affected by various environmental factors: temperature pH water availability light (for photosynthetic bacteria) every type of nutrition found in eucaryotes is found in bacteria and them some more metabolic diversity than all other kingdoms combined can be autotrophs - derive all nutrients from inorganic sources; eg CO2, NH3, etc - any carbon source for nutrient - must build and store organic molecules for later breakdown and energy production – does not require organic carbon source for energy, can be photoautotrophs - use sunlight as energy source or chemoautotrophs – oxidizes inorganic compounds for energy eg. H2S; NH3; Fe++, etc or heterotrophs - derive at least some of nutrients from complex organic molecules - use these same organic molecules for energy production also – needs organic carbon for energy and nutrient can be chemoheterotrophs – extract both Carbon and energy from organic molecules eg. aerobic respiration (eg animals) eg. saprobes, parasites eg. fermentation or photoheterotrophs – extract carbon from organic molecules but energy from sunlight most bacteria are [chemo] heterotrophs – need organic foods nitrogen is essential for proteins and nucleic acids other kingdoms are fairly limited in the sources they can use: NH3, NO2, NO3, Proteins, Nucleic Acids bacteria can metabolize many forms of nitrogen both organic and inorganic some bacteria can fix nitrogen gas – only organisms that can do this; (N gas makes up 80% of atmosphere but unuseable by all but bacteria) some of these form symbiotic root nodules with plant roots and allow these plants to grow in poorer soil bacteria have various requirements for oxygen: obligate aerobes (strict aerobes) – die without oxygen gas obligate anaerobes (strict anaerobes) – die in the presence of oxygen gas facultative anaerobes – can use oxygen when available, and do anaerobicmetabolism when its not some (but not all!) bacteria can be grown on artificial media: selective media – prevents the growth of certain bacteria while allowing others to grow enrichment media – has special nutrients that enhance the growth of the desired bacteria differential media – contains a specific nutrient and an indicator the show whether the species is able to use that nutrient variations in the rate of growth and reproduction are greatly affected by environment temperature pH light - cyanobacteria water lack of organelles makes procaryotes much less efficient at metabolism but they compensate for this by rapid reproductive rate, metabolic diversity, and ability to withstand adverse conditions Reproduction bacteria reproduce by asexual binary fission most bacterial reproduction is asexual the single chromosome duplicates cytoplasm splits into equal halves time between divisions = generation time generation time varies considerably: Staph aureus 30 min M. tuberculosis 18 hrs T. pallidum 33 hrs E coli 20 min eg. E. coli: one cell at 8:00 am, no limiting factors: => 36 hrs later => 1 foot over surface of earth Bacterial Growth curve: lag: transferred to new environment log: maximum rate of reproduction stationary: nutrients and space and env variables become limiting and slow rate of reproduction death: population decline, nutrients gone, build up of toxins no true sexual reproduction but due to rapid life cycles, natural mutations are the main source of genetic variations but can exchange genetic material in several ways: transformation conjugation transduction How did bacteria, which reproduce primarily asexually evolve and diversify so quickly? bacteria can trade genes at a rapid pace their DNA is loose inside cells they often have spare strands of DNA (extra genes) these genes can be easily traded, absorbed from the environment or moved by viruses in early earth, UV radiation may have increased the rate of this exchange the typical distinction between species does not apply to bacteria “create a huge planetary gene pool that gives rise to temporarily classifiable bacterial ‘types’ or ‘strains’ which radically and quickly change, keeping up with the environmental conditions” -Margulis and Sagan, 1995 Classification of Bacteria: two procaryote kingdoms: Archaebacteria + Eubacteria Archaebacteria: earliest fossils of living organisms most primitive most are single, simple cells highly unusual morphologies most have rigid cell wall but no peptidoglycan in cell walls tend to live in extreme environments some heterotrophs some autotrophs unique chemical composition, structure, metabolism and DNA unique lipids in cell membranes unique kind of ribosomes three groups: 1. Methanogens: thrive in swamps, sewage, stock yards, animal guts strict anaerobes use H2 to reduce CO2 produce methane as end product of energy production: H2 + CO2 ->CH4 + energy gut bacteria produce 2B tons of methane/yr affect global carbon cycle methane collected from garbage and dung used as renewable energy source 2. Halophiles (salt lovers) brackish ponds, salt lakes, near deep ocean hydrothermal vents most are aerobic colonies often purple or red eg. Halobacterium 3. Thermophiles (heat lovers) highly acidic soil, hot springs, coal mine wastes, deep ocean hydrothermal vents autotrophs (but chemoautotrophs not photo) use H2S as hydrogen (electron) source to make energy (instead of H2O) eg. Sulfolobus: thrives in acaidic sulfur rich hot springs pH optimum = 2 temperature optimum = >70º C Eubacteria: most common bacteria are in this group all human pathogens most bacteria that are used to make food products very diverse array of bactera upper levels of classification (eg. phyla, classes) are just being worked out: typical rods cocci and spirals cyanobacteria other types of photosynthetic forms disease organisms (parasites) many symbionts (eg. Rhizobium) Nannobacteria?? first described in 1996 much smaller than average bacteria 1/10th the size of eubacteria found IN rocks, clay, sand may contribute to most geologic chemistry may make up most of the earth’s biomass some report growing them in lab dish can kill other cells may be found in blood and animal tissues may cause human diseases may exist on mars may not exist at all??? Impacts of Bacteria on the world 1. essential for cycling nutrients (biogeochemical cycles): if they weren’t here, we wouldn’t be either, we would run out of nutrients 2. Deep ocean hydrothermal vents discovered in 70’s at deep ocean ridges hot mineral rich waters flowing out of cracks in the crust, especially rich in hydrogen sulfide whole community of organisms, most are unique species; include large worms and clams, crabs, shrimp, fish, and dense clouds of bacteria bacteria live inside the tissues of some of these animals; the animals absorb hydrogen sulfide from the hot waters, and use hemoglobin to carry this H2S to the bacteria deep in their tissues; the bacteria use the energy in H2S to make sugars which the animals absorb therefore it’s an entire ecosystem that is not based on solar energy for autrotrophic production 3. Bacteria are used to make a wide variety of foods and drinks (see lab): bread, bakery products, cheeses, alcoholic beverages, etc, etc, etc, Cheeses The first step in making most cheeses is to prepare a curd by adding lactic acid bacteria and rennin or bacterial enzymes to milk. The bacteria sour the milk and enzymes coagulate the milk protein, casein, to produce a soft ‘curd’ to make cheese and a liquid ‘whey’ which is a waste product. The amount of whey removed determines the hardness of the cheese. eg. soft cheeses the whey is simply drained away. Harder cheeses are heated and pressurized to remove additional whey from the mixture. After this separation, most cheeses are ripened with inoculations of various species of bacteria and/or fungi. Hard Ripened Cheeses (Cheddar, Swiss, Colby, Edam, gouda, Parmesan) The flavor, smell and taste of these cheeses are produced by fermentations from various species of bacteria including: Streptococcous lactis S. cremoris S. durans Lactobacillus helveticus Proprionibacterium shermanii The longer the incubation time the higher the acidity and the sharper the taste Swiss Cheese The flavor and taste of Swiss cheese is produced by the fermentation by Streptococcus lactis, S. thermophilus and S. helveticus. The addition of Proprionibacterium species to the culture produce various amounts of lactic and proprionic acids and produces carbon dioxide which makes the characteristic “holes” in the cheese. Semisoft Cheeses (eg. Limburger, Muenster, Brick, Roquefort, Blue) The cheese curd is ripened by bacteria and other contaminating organisms growing on the surface including: Streptococcus lactis, S. cremoris, and Brevibacterium linens. Soft Cheeses (eg. Brie, Camembert) The curd is ripened by a variety of microorganisms including Streptococcus lactis, S. cremoris, P. camemberti and P. candidum. In this case the ripening process is aerobic and the cultures are inoculated onto the surface of the cheese and extend hyphae throughout. Soy Sauce Soy sauce is produced by the fermentation of roasted soy beans and wheat using a mixture of various bacteria and fungal species including: bacteria: Pectococcus halophilus Lactobacillus delbrueckii fungi: Aspergillus soyae A. oryzae Saccharomyces rouxii Candida versitilis The starch degrading enzymes produced by the molds produces a sugar that is then fermented by the bacteria. The entire process takes about a year. Yogurt Yogurt is made from milk solids which are concentrated by evaporation. The lactose in the milk is fermented by Lactobacillus bulgaricus and Streptococcus thermophilus to produce lactic acid. The flavor is a result of the sugar and the 2-3% lacatic acid generated by this fermentation. Sauerkraut Sauerkraut is produced by the natural fermentation of layers of shredded cabbage alternating with layers of salt. The salt inhibits undesirable bacteria and draws out the juices of the cabbage. Several species of Leuconostoc including L. mesenteroides and Lactobacillus plantarum are common in the first few days. In two to three months the acids and esters produce the desired aromas and flavor. Memmi Memmi is a product made with soy sauce and used for a simple soup base for noodles. Vinegar Vinegar is a fermented food traditionally made by the spontaneous souring of wine. Industrial Vinegar production begins by inoculating the fruit juice with yeasts which ferment it to an alcohol content of 1020%. Then the juice in inoculated with the bacterium, Acetobacter aceti, which convert the alcohol to acetic acid. Coffee After coffee beans are picked they are soaked in water containing natural cultures of Erwinia dissolvens and Saccharomyces spp. to loosen the berry skins before roasting. Some fermentation occurs which is believed to produce some of the unique flavors of various varieties of coffee. Cocoa Microbial fermentation by Candida krusei and Geotrichum spp. is used to help remove the cocoa beans from the pulp covering them in the pod. The products of this fermentation contribute to the flavor of the cocoa. Cured (Fermented) Beef or Pork Sausages eg. Pepperoni, Salami, Thuringer, Polsa These are generally produced by adding seasoning agents to the ground meats, stuffing the meat into casings and incubating them at warm temperatures. Mixed acids produced from the fermentation of carbohydrates by such bacteria as Pedicoccus cerevisiae and Micrococcus spp. in the meat give the sausage its unique flavor and aroma. Pickles Pickles are made by fermenting cucumbers in a mixture of bacteria normally found growing on them including Lactobacillus plantarum and Pedicoccus cerevisiae. Butter Butter is produced by inoculating pasteurized cream or milk with a lactic starter culture which includes Streptococcus cremoris, S. diacetylactis and S. lactis. and allowing the fermentation to proceed until the required amount of acidity is obtained. The acidified cream is churned until the thick butter forms. It is then worked to remove excess liquid, washed, salted, and packaged. The characteristic aroma and taste of butter result from the compound diacetyl, which is formed by bacteria such as Streptococcus diacetylactis and other microorganisms. Buttermilk Buttermilk is the liquid remaining after cream is churned for butter production. It can also be prepared by inoculating skim milk with a starter culture of Streptococcus cremoris, S. diacetylactis or S. lactis which produce lactic acid making the sour taste and curdling the milk. Leuconostoc citrovorum and L. dextranicum help to create the desired odors. Sour Cream Cultured sour cream is prepared by fermenting pasteurized light cream with a lactic starter with the same organisms as for making buttermilk; including Streptococcus cremoris, S. diacetylactis or S. lactis. Acidophilus Milk Lactobacillus acidophilus is added to milk to produce an acidity of 2-3% lactic acid. Sourdough Bread Wheat flour is fermented using S. exiguus and Lactobacillus sanfrancisco to produce the tart, acidy flavor Spirulina Spirulina is a cyanobacterium that is used as a protein supplement in various dishes and soups Green Olives Fermented by Leuconostoc mesenteroides and Lacrtobacillus plantarum Kimchi Made from shredded cabbage fermented with lactic acid bacteria 4. Industrial microbiology: uses large cultures of bacteria and other microorganisms to produce various industrial chemicals such as amino acids, citric acid, enzymes, pharmaceuticals, etc 5. Some bacteria are used for energy (methane) production 6. Genetically engineered bacteria are increasing the variety of products we can produce from bacteria 7. Some bacteria are pathogens: A. Tuberculosis (Mycobacterium tuberculosis) an ancient disease also called consumption has been called the worlds most neglected epidemic kills more people worldwide than any other infectious disease about half of the worlds population is infected, with 8-10 million new cases each year about 2-3 million people die each year from the disease no longer a major disease in US, esp in urban poor, homeless, and AIDS folks easily combated if caught early, difficult to get rid of in advanced cases slow growing pathogen – respiratory disease infection in lungs causes formation of ‘tubercles’ 90% of infected people remain infected for life but never develop symptoms of the disease = asymptomatic two new strains have appeared: a fast growing form and a completely antibiotic resistant form B. Anthrax (Bacillus anthracis) common soil organism produces spores that can persist for years is a zoonosis – animal disease that people can catch preferred biowarfare agent since it lasts long and can be relatively easily dispersed need pretty high exposure to spores to actually get the disease C. Syphilis (Treponema pallidum) STD once more abundant than it is today in US first recognized in 1500’s. thought it may have been a disease picked up by Native Americans and spread to Europeans, new evidence doubts this, it was in Europe before contact with Americas easily treated in early stages, difficult to treat in advanced stages progresses through three major stages: 1st – after sexual contact, the bacteria produce open sores in genital area they persist for several weeks 2nd – several months later the bacteria have spread throughout the body, fever, headaches, sore throat, rash, etc. symptoms disappear in a few weeks 3rd – latent period lasts up to 20 years, about 30% of patients untreated will show severe pathology, rupture of blood vessels, heart damage, blindness, derangement, convulsions, brain damage, death.