• 1970's: 16rRNA shows divisions between bacteria, archaea, and eukarya
• 1980's: Woese proposes 12 bacterial kingdoms
• 1990's: ~30 kingdoms discovered/proposed
• 2000s: ~50 phyla thought to exist, about half of which are candidate lineages based on DNA

1. Proteobacteria
2. Firmicutes
3. Actinobacteria
4. Cyanobacteria & prochlorophytes
5. Chloroflexi (green nonsulfur bacteria)
6. Deinococcus-Thermus clade
7. Chlorobi
8. Bacteriodetes
9. Spirochetes
10. Chlamydia-Plantomycetes-Verrumicrobia
11. Aquifex and relatives

• Proteo = "changing"
• 5 groups: alpha, beta, gamma, delta, and epsilon
  • beta and gamma groups very similar
• ALL have gram negative cell wall (LPS)
• Sometimes called "purple bacteria"
  
  • Named because of purple nonsulfur bacteria in this group
  • Term not really used anymore

Alpha-Proteobacteria

(4 Important Groups)

1) Acetic acid bacteria

2) Rhodobacteria

3) Rhizobium

4) Rickettsia

• e.g. Acetobacter
• produce acetic acid
• grow on alcohols
  • often found in spoiled alcohol (i.e. spoiled wine, beer, etc)
• Industrial uses: vinegar (acetic acid), vitamin C production
• Produces cellulose pellicle
  • causes it to float
  • new medical use as "organic" wound dressing
  • (Doesn't cause disease)

• Found in soil, associated with legumes
• Important in nitrogen fixation
  
  • N₂ -> NH₃ -> Organic N
  • Nitrogenase, inhibited by O₂
• Symbiosis with plants
  • Bacteria gets sugars, plant gets organic N
  • Form nodules on plants
    • Nodules provide thick wall which reduce O₂ diffusion
    • Plant produces leghemoglobin
      • Pink/red protein which sequesters O₂

• Purple, nonsulfur bacteria
• found in well lit, anoxic mud
• Anoxygenic photosynthesizers
• Don't make much NADH and don't need a lot of H₂S.
• Typically use light rxns of photosynthesis to produce energy (ATP) and then heterotrophically acquire organic building material

• Intracellular pathogens
• 2 important species
  • R. rickettsii
    • carried by ticks
    • causes Rocky Mt Spotted Fever
      • Headaches, fever, spotted rash
      • treated with tetracycline
        • 30% fatality w/o treatment, 5% with treatment
  • R. prowazeki
    • carried by lice
    • causes "Typhus," "worse" form of Rocky Mt Spotted Fever
      • Headaches, high fever, rash
      • Used to be common in crowded unsanitary places
        • Ships, armies, prisons, WWII concentration camps
• 16S rRNA very similar to eukaryotic mitochondrial rRNA, thought to be origin of mitochondria.

Major Beta-Proteobacteria

4 Major Groups

1. Nitrosomonas and relatives
2. Sheathed proteobacteria
3. Burkholderia and relatives
4. Neisseria

Beta-Proteobacteria General Characteristics

• Generally aerobic bacteria
• Diverse metabolisms
  • Aerobic respiration
  • Chemoautotrophs
  • Photosynthetic purple nonsulfur bacteria
• A few pathogens

• Common in soil and water
• Chemoautotrophs that oxidize reduced nitrogen (NH₃) to generate energy (ATP); NH₃ is electron donor with O2 as acceptor
• Carry out nitrosification; nitrifiers a different group
• First chemoautotrophs to be discovered (Sergei Winogradsky, 1890s)

• Found in flowing water with lots of organic material (e.g. polluted streams)
• Aerobic heterotrophs that form filaments of rod shaped cells surrounded by a tubular sheath
• Under unfavorable conditions form flagellated "swarmer" cells that are realeased and swim to new environments.
• Some can oxidize iron (e.g. Leptothrix)

• Aerobic rod shaped heterotrophs (most obligate)
• Common in soil and water; others opportunistic pathogens
• Burkholderia cepacia
  
  • causes pneumonia opportunistically with other lung diseases (such as cystic fibrosis)
• Bordetella pertussis
  
  • causes pertussis (whooping cough)
    • life threatening if not treated
    • more common in 3rd world
    • easily prevented by vaccines/antibiotics
      • DPT

• Aerobic cocci (diplococcic)
• Ferment sugars to produce acids
  • usually identified by sugar tests
• Some commensal, but two important pathogens:
  • N. gonorrhoea
    • Causes gonorrhoea
    • 2nd most common STD
    • Yellow discharge, pain in urination, can lead to PID and subsequent infertility in women
    • Can be asymptomatic
  • N. meningitidis
    • main cause of bacterial meningitis
      
      • inflammation of meninges
        • headaches, more serious brain problems
        • Very easily spread

Gamma-Proteobacteria

5 Major Groups

1. Enteric bacteria
   1. Mixed-acid fermentors
   2. Butanediol fermentors
2. Pseudomonads
3. Vibrio and Photobacterium
4. Purple sulfur bacteria
5. Sulfure oxidizing bacteria

• VERY similar to beta-proteobacteria (based on 16s rRNA
• Metabolically diverse
  
  • Aerobic and anaerobic respiration
  • Fermentation
  • Photosynthesis
  • Chemoautotrophy

• All genera are similar: short facultative aerobic rods
• Some nonmotile; some peritrichous
• Distinguished from pseudomonads and vibrios bc catalase positive but oxidase negative
• Common in intestines of mammals/birds, some pathogens
• Two main groups sorted by waste product
  
  • Mixed-acid fermentors
  • Butanediol fermentors

• Escherichia native to intestine
• produces vitamin K
• Some strains pathogenic
  • E. Coli O157:H7 (Enterohemmorhagic)
    
    • ingested in undercooked meal
    • causes bloody diarrhea and renal/neurological damage
      • up to 50% fatality in elderly and young (subfunction immune systems)
  • Salmonella
    • 30-50 strains, possibly related
    • usually pathogenic
    • e.g. S. typhii
      • typhoid fever, fecal-oral transmission, fever and diarrhea for up to a month, ~30 million cases a year globabally, 500,000 deaths
    • e.g. S.  enterica
      • food poisoning

• Group of opportunistic pathogens
• Important genera
  • Enterobacter (E. aerogenes)--Native to intestinal tract, common in sewage.
  • Klebsiella common in soil and water but also opportunistic (K. pneumoniae)
  • Serratia marcescens -- red/pink
    • pink scum in bathrooms (uses detergents as if they were lipids)
    • Operation Sea Spray: 1950s in San Francisco. Navy experiment to explore transmission of bacterium in biological attack.  Later found to be pathogenic (raise in UTIs)

• loose "group": sort of an "other" category in early microbiology taxonomy. Reorganized into various genera, some outside of Gamma-proteobacteria.
• Definition: aerobic heterotrophic rods with polar flagella (single or clumped).  Cannot carry out fermentation (some can carry out anaerobic respiration w/ NO₃
• All catalase and oxidase positive
• Most use simple sugars
• Common in soil and water; some opportunistic pathogens:  CF!!!
• e.g. Pseudomonas aeruginosa

• Closely related genera: curved rods with polar flagella
• Facultative aerobes
• All catalase positive/oxidase positive
• Most are aquatic, some pathogenic
• Vibrio cholerae secretes enterotoxin that causes extremely watery diarrhea and subsequent dehydration. Death within a few hours to days.
• Vibrio parahaemolyticus, Vibrio vulnificus: cause food poisoning from seafood (infected wounds too)
• Some genera bioluminescent, symbiotic within deep sea fish; only at high densities --> quorum sensing.
  
  • When bacteria release autoinducers; causes change in gene expression at specific concentration
  • e.g. Vibrio fischeri symbiotic with some squid; light thought to protect squid from predators

• e.g. Chromatium
• found in lit, anoxic mud
• use H₂S to replenish electron given to NADH
  • (separates from purple nonsulfur bacteria)

• Chemoautotrophs that use reduced sulfur compounds as electron donor
• Waste products acidify environment
• Two well studied groups:
  • Acidithiobacillus: A. thiooxidans and A. ferrooxidans. Former oxidizes sulfur; latter iron. Used to release iron and metals during mining; can acidify rivers
  • Beggiatoa: oxidizes H₂S for energy but uses organic C instead of fixing CO₂ (mixotrophy); found in
    
    • rhizosphere of wetlands, thought to be beneficial b/c removes H₂S
    • rotting seaweed (filamentous, white)
    • sewage

Delta-Proteobacteria

3 Major Groups

1. Dissimilatory sulfate reducing bacteria
2. Bdellovibrio
3. Myxobacteria

• e.g. Desulfo-: Desulfobacter, Desulfovibrio
• Many are obligate anaerobes (O₂ toxic)
• Widespread in anoxic environments with decomposing organic matter: waterlogged soils, wetlands, salt marshes) & sulfur rich hot springs
• All generate ATP through respiration using SO₄^2- or S as terminal electron acceptor.
• e.g. Desulfurella and others oxidize acetate and simple organics using S as e acceptor.
• Fairly inefficient phylum

• predators
• small, comma-shaped (slightly spiral) cells w/ polar flagella; highly motile
• prey on other gram negative bacteria by colliding at high speeds and penetrating into periplasm. Parasitize from within.

• Common in neutral or alkaline soils
• Aerobic heterotrophs that exist in rod shaped individual cells in favorable conditions; motile by gliding and "feed in packs," showing intercellular communication
• In poor conditions cells swarm together to form fruiting bodies; some cells differentiate to form myxospores (resting stages) that are dispersed
• Myxobacteria show most complex behavior and development of all prokaryotes; very genetically complex (large chromosomes, 2x E. Coli)
• e.g. Myxococcus xanthus, model organism for development/evolution; also produces chemicals with possible medical use.

Epsilon-Proteobacteria

2 Major Groups

1. Campylobacter jejuni
2. Helicobacter pylori
   

• Least studied subdivision; fewest cultured representatives
• Best studied epsilon-Proteobacteria are spiral shaped, motile bacteria that are pathogens or symbionts
• Two major genera:
  1. Campylobacter jejuni--microaerophilic (O₂ toxic). Common in water and digestive tract of birds. Cause of severe bloody diarrhea in undercooked chicken, mostly affect 15-29 years olds.
  2. Helicobacter pylori--closely related to C. jejuni, but infects stomach lining. First linked in 1980's by Barry Marshall; explains why bismuth compounds help stomach ulcers.

• Originally grouped together as the Gram Positive bacteria
• Originally subdivided based on GC content
  • High GC (>50%) = Actinobacteria
  • Low GC (<50%) = Firmicutes
• Now recognized to be two separate phyla based on rRNA, but happen to fit GC categories well.

• All have <50% GC content of their DNA; most have a Gram positive cell wall
• Subdivided into three groups:
  1. Spore-forming firmicutes
  2. Non-spore forming firmicutes
  3. Mollicutes

• Mainly heterotrophic rods that are common in soil; includes some pathogens
• Metabolism varies: aerobic, fermentation, photoheterotrophic
• All form endospores
• 3 Major Groups
  1. Bacillus
  2. Clostridium
  3. Heliobacteria

• Use aerobic respiration (some facultative)
• Often digest complex substrates by extracellular enzymes
• Many also produce antibiotics/secondary chemicals (B. thuringiensis)
• e.g. Bacillus thuringiensis: produces insecticides during sporulation; insectiside genes copied into plants
• e.g. Bacillus anthracis: causes anthrax, first bacterium linked to disease (Koch, 1870s)
• e.g. Bacillus cereus: causes food poisoning in leftover rice

• Strictly anaerobic bacteria that use fermentation
• Some can ferment proteins/amino acids (putrefying meat/flesh)
• Anoxic parts of soil, some native to intestinal tract
• e.g. Clostridium difficile infects large intestine after antibiotic use
• e.g. Clostridium botulinum causes botulism, present in improperly canned food, BOTOX
• e.g. Clostridium tetani infect wounds and cause tetanus
• e.g. Clostridium perfringens can infect wounds and cause gas gangrene and hemolysis

• Unusual group, different cell walls than firmicutes (not Gram +), related to clostridia
• Produce ATP through anoxygenic photosynthesis, use organic C through fermentations:  photoheterotrophs
• Found in waterlogged soils (rice paddy fields); carry out nitrogen fixation

• Usually cocci, often staphlo- or strepto-
• Many fairly resistant to drying and can tolerate high salt concentrations
• Some important industrially others are pathogens
• 2 Major Groups:
  1. Staphylococcus
  2. Lactic Acid Bacteria

• Facultative aerobes (can ferment some sugars)
• Cocci are in staphylo-; often pigmented
• Tolerate salt to 7.5%, which can select for them: Mannitol Salt Agar
• Common on the skin but can become pathogenic
• e.g. Staphylococcus aureus pathogen that causes boils and pimple, but can cause pneumonia, meningitis, etc.; 20% population are carriers;Very common nosocomially, some strains antibiotic resistant (MRSA)
• e.g. Staphylococcus epidermis is non-pathogenic and very common on skin, mucous membranes, thought to be more benign, but can cause infection
• e.g. Staphylococcus saprophyticus -- UTIs (15-20% of the time caused by this bacterium, most of the time by enteric bacteria like E. Coli)

• Produce lactic acid as waste product from sugar fermentation, most aerotolerant
• Rods or cocci; most tolerate low pH
• Minimal biosynthesis capability, so generally require many a.a.'s and vitamins for growth
• Can be divided phenotypically based on waste products
  1. Homofermentative - only produce lactic acid
  2. Heterofermenative - produce lactic acid + ethanol & CO₂
• e.g. Streptococcus: homofermentative with cocci in chains. S. pyogenes causes strep throat S. mutans found in mouth and contributes to tooth decay.
• e.g. Lactococcus: related to Streptococcus, dairy industry uses to produce buttermilk, cheese
• e.g. Lactobacillus also used in food industry (yogurt, sauerkraut); some species common in vagina or intestinal tract; L. brevis cause of spoilage in beer
• e.g. Listeria common in environment but can cause food poisoning (listeriosis); grow at refrigerated temps. Recent idea to use L. specific bacteriophages to ctrl.

• Unusual group that does not have cell wall; 16S rRNA shows members of Firmicutes. Consequences:
  • Penicillin won't work
  • No shape...: "pleiomorphic"
• Very small genome: 580 kb, ~1/10 of E. Coli at 5 Mb
• Pathogens:
  • e.g. Mycoplasma genitalium can cause urethral infections; 
  • Mycoplasma pneumonia can cause pneumonia; 
  • Spiroplasma infects plants
• M. genitalium first genome artifically synthesized
• Future plans to create whole artificial species: M.laboratorium

Phylum III: The Actinobacteria

General Overview and 5 Major Groups

• All have >50% GC content in their DNA and are Gram +
• Morphology is generally rods or filamentous
• Aerobic Respiration most common, some carry out fermentation
• Many common in soils; some important pathogens
• 5 groups:
  • Arthrobacter
  • Propionic acid bacteria
  • Corynebacterium
  • Mycobacterium
  • Filamentous Actinobacteria (Actinomycetes)

• Most common in soil
• Most obligate aerobes
• Cell morphology changes from rods to cocci, young to old
• Divide by "snapping division": V-shaped splitting
• Decomposers

• Aerotolerant anaerboes that produce propionic acid and CO₂ as waste
• Ferments lactic acid; called "secondary fermentation", often found with lactic acid fermentors
• e.g. Propionibacterium freudenreichii used in dairy industry where it is involved in production of Swiss cheese (acid adds to the flavor, CO₂ holes
• e.g. Propionibacterium acnes found in pores of skin (where it ferments fatty acids); overgrowth can lead to acne (often treated with antibiotics)

• Facultative aerobes common in soil, some pathogens
• Cells often club-shaped (one end appears swollen)
• e.g. Corynebacterium diphtheriae  causes diphtheria
  
  • Growth of membranous sheath in upper respiratory tract
  • Only strains infected by lysogenic phase (produces toxin)
  • Not a big deal in West, all vaccinated
  • Some resurgence in USSR states

• Related to Corynebacterium; two serious pathogens
• Aerobic rods, some form fragile filaments
• Unique waxy lipids in cell wall (mycolic acids); specific stains identify
• e.g. Mycobacterium tuberculosis
  
  • Infects lungs mainly but other systems
  • once responsible for 1 in 7 deaths historically
  • now 1.5 mil deaths/yr, 1/3 world pop infected
  • Some aymptomatic but latent infects can become active
  • Easily transmitted (airborne)
  • Strains becoming increasingly resistant (MDR, XDR)
• e.g. Mycobacterium leprae - Hansen's Disease (leprosy); results in skin lesions and loss of motor function; treated w/ rifampicin

• Often grouped as the Actinomycetes but really a number of different, unrelated Actionbacteria
• All common in soil (especially well drained,alkaline soils) and form networks of branching filaments (mycelia) similar to fungi (thinner cells)
• All aerobic (some facultative)
• e.g. Frankiacarries out N₂ fixation and froms symbiotic associations with some roots (e.g. alder)
• e.g. Streptomyces most well characterized genus with over 500 species
  • Produce geosmins (earth smells)
  • Many other secondary metabolites
    • some antibiotics: streptomycin, tetracycline, erythromycin, chloramphenicol; over 60 common antibiotics are dervied from this genus)
    • many also capable of using complex organic polymers for energy through the production of extracellular enzymes

Phylum IV: The Cyanobacteria and Prochlorophytes

General Overview

• Oxygenic phototrophs (use Photosystems I and II; H₂O as source of electrons
• Widespread in water
• Prochlorophytes subgroup of cyanobacteria, related to chloroplasts of eukaryotes
• Originally classified as type of unusual algae ("blue-green algae); however clearly prokaryotes and loosely related to Firmicutes (but they have a Gram - cell wall)

• Morphology varies; unicellular and filamentous
• All photosynthetic and contain chlorophyll a and phycobilins usually in thylakoid membranes
• Planktonic species may also have gas vesicles for buoyancy
• Filamentous forms (e.g. Nostoc, Anabaena) may have heterocysts
• Geosmins and toxins:  neurotoxins, hepatotoxins (e.g. Microcystis)
  • Usually the culprit when a dog goes swimming and turns up dead
• Cyanobacterial blooms  major problems: nutrients result in rapid growth, followed by death and decomposition--> depletion of O₂; responsible for fish kills often

• Use chlorophyll a and chlorophyll b
• Very similar to eukaryotic chloroplasts
• Many very small cells, most abundant bacteria in open ocean (e.g. Prochlorococcus)
• Some symbiotic with marine invertebrates (e.g. Prochloron inside sea squirts)

• Related to Deinococcus-Thermus phylum
• Originally found to be filaments of green cells found in hot springs
  • Anoxygenic photosynthesis using H₂S or H₂ as electron donor
  • Photoheterotrophys
  • e.g. Chloroflexus
• Many of this group probably don't do photosynthesis, however
• More recently, other Chloroflexi have been found which are mesophilic heterotrophs, so the group is metabolically diverse
• e.g. Herpetosiphon is an aerobic heterotroph composed of flexible filaments of rod-shaped cells; common in sewage. "Snake-like"
• e.g. Dehalococcoides ethenogenes anaerobic heterotroph that dechlorinates dry cleaning solvents --> bioremediation. 

• Related to the Chloroflexi
• Two small groups closely related to each other, both tend to be found in extreme environments
• Thermus are aerobic heterotrophs that are common in hot springs (water heaters)
  
  • rod-shaped, sometimes filamentous
  • Gram (-) cell walls;
  • Produces Taq polymerase
• Deinococcus are aerobic heterotrophs sometimes found in dry soils or dust
  
  • rods or cocci with complex, multi-layered cell wall (Gram pos, but not really)
  • Very resistant to freezing, drying and radiation.
    • e.g. Deinococcus radiodurans tolerates up to 15,000 grays (20 grays fatal to humans, 60 fatal to E. Coli; found in nuclear reactors, irradiated food.
      
  • Radiation damages chromosome, but has effect DNA repair systems
  • Resistance to radiation probably against drying out, not radation

• All anoxygenic phototrophs carrying out photosynthesis using H₂S
• Fix CO₂ using reverse CAC pathway; most are photoheterotrophs
• Anoygenic photosynthesis produces S as a waste product, deposited outside cell, unlike purple sulfur bacteria which deposit inside periplasm
• Cell shape varies from cocci and rods (Chlorobium) to gliding filaments (Chloroherpeton)
• Contain chlorosomes:  light harvesting structures that transfer light energy on one molecules, allowing cell to grow at low illumination levels than other photosynthetic cells (i.e. purple sulfur bacteria)
• Usually found deeper in anoxic mud than purple sulfur bacteria (less light, more H₂S

• Diverse phylum distantly related to Chlorobi
• Sometimes called CFB group: Cytophaga-Flavobacterium-Bacteroides
• All heterotrophs but metabolism varies from aerobic to fermentation; cells typically rod shaped (some in filaments)
• Three groups:
  1. Bacteroides ferment polysaccharides (cellulose) and sugars. Most abundant in intestines; some opportunistic pathogens (e.g. Bacteroides fragilis)
  2. Flavobacterium are aerobic rods that move by gliding; notable for aquaculture pathogenicity: e.g. F. psychrophilum causes fish disease in trout; F. columnare infects catfish gills
  3. Cytophaga also move by gliding mixed metabolism.  common on decaying plant material. E.g. Cytophaga hutchinsoniidegrades cellulose, notable for possible use in production of bioethanol.

• Sprial (wavy)
• Find in soil, mud, e.g. Spirochaeta
• Flagella stays in periplasm, never goes out of cell wall: "endoflagellum" (sometimes called axial filament)
  • Gives them jerking movement rather than gliding.
• Major pathogen: Tryponema pallidum
  • causes syphillis, get usually through urinary tract
  • Three stages
    1. Chancre (days to months) -- painless "sore"
    2. Rash in a very different place from where you got the infection.  not everyone develops 
    3. Decades later: 10-20 years. Internal damage, neurological, cardiac, massive damage, can be fatal.
  • Easily treatable; rememeber Ehrlich and first antimicrobial, salvarsan. Very treatable by penicillin.
  • Disease on the rise in US.
• Other pathogen:  Borellia burgdorferi, etc.
  • linear chromosome
  • causes Lyme Disease (named after Lyme, CT)
    
    • transmitted by Ixodes tick.
    • bull's eye rash
    • fatigue, fever, organ damage, arthritis

• Intracellular pathogens
• Morphology: small, inert "elementary" bodies
• Taken into host cell, froms an "inclusion body"
• Inside, elementary --> "reticulate body" (becomes active, grows, and divides using host's resources).  Break out and lyse host.
• Infects some amoeba
• Human pathogen:  Chlamydia trachomatis, most common STD. The "silent epidemic"
  • Males tend to have painful urination, but many females don't realize anything. May have painful urination. Women can get pelvic inflammatory disease and sterility. Also causes blindness
  • Also can have disease called "trachoma," very common form of blindness in developing countries.  (eye infection)

• Very strange group of bacteria:
  
  • some planctomycetes have a stalk (Pirellula)
  • some have internal compartments, membranes around nucleoid,  (Gemmata)
  • Unusual metabolism:  anaerobic ammonium oxidation (Anammox reaction) e.g. [image]Brocadia
    • Many bacteria take NH₄ and give electrons to oxygen making NO_2/3
    • These bacteria do this but not with oxygen, electrons go to nitrite (NO_2^-).  Products N₂ and H₂O.
    • Beginning to be thought major player in nitrogen cycle. x

• named because the look like they have warts on them (Verruco --> "wart").
• They seem to be very common, but extremely hard to culture
• e.g. Verrucomicrobium spinosum
• May also have internal membranes

• Branches close to "original split" --> primitive
• Non cause diseases so far as we know.
• Aquifex, Hydrogenobacter
  • Chemoautotrophs that oxidize hydrogen, produce water.
  • Hyperthermophilic (up to 95 degrees C)
  • Simple genome (1/3 size of E. Coli)
• Thermotoga
  • rod-shaped cells enclosed by sheath "toga"
  • Thermophilic
  • Some genes are archaean
• Thermodesulfobacterium
  • Thermophilic sulfate reducers--uses sulfate as electron acceptor
  • Cell membranes has ether linkages.

Archaeal Diversity

Differences from Bacteria

• Very different DNA
• No peptidoglycan in cell walls
• Ether-linked lipids
• Have only one RNA polymerase but more similar to eukaryote RNA Pol

• Originally thought to be confined to extreme environments (hot springs, acidic areas, etc.)
• More widespread than originally thought; evidence of Archaea (DNA) found in soil, lakes, etc.
• No pathogenic Archaea, but some animal symbionts (methanogens in intestines)

1. Euryarchaeota
2. Crenarchaeota
3. Korarchaeota
4. Nanoarchaeota

Euryarchaeota

Four Major Groups

1. Halophilic Archaea
2. Methanogens
3. Thermoplasmatales
4. Hyperthermophilic Euryarchaeota

• All require high [salt] (most require 35% solution, saturation level, 10x seawater)
  • Dead Sea level
• Maintain positive water balance because of high internal [K⁺]
• Many aerobic heterotrophs or "light-controlled ATP synthesis"
• Have bacteriorhodopsin--acts as proton pump; light causes it to move H⁺ out of the cell and the H⁺ makes ATP via ATPase
  • gives bacteria pink/red color
  • typically occurs under anoxic conditions
  • ultimate protein structure similar to human rhodopsin
• Various cell shapes (rods, cocci, discs); most non-motile
• Most studied is Halobacterium; found in Great Salt Lake, Dead Sea

• Obligate anaerobes that generate CH₄ by reduction of CO₂ or single carbon organic substrates; growth autotrophic if using CO₂ and H₂
• Mesophillic, a few thermophiles
• Common in anoxic areas such as animal intestines, wetlands; also found in deep subsurface
• Diverse group:  e.g. Methanobacterium, Methanococcus

• Acidophiles, often growing at <2; some are also thermophilic
• "-plasma": no cell wall
• e.g. Thermoplasma: thermophilic facultative anaerobes (use O₂ or S as e^- acceptors) that have no cell wall; originally found in coal refuse piles
• e.g. Ferroplasma: chemoautotrophs (use Fe²⁺) as an e^- donor) that have no cell walls; found in mine tailings and oxidize pyrite (FeS) producing acid waste
• e.g. Picrophilus are aerobic heterotrophs that have a cell wall; optimal growth at pH 0.7 (most acidic known) found in acidic hot springs

• Various small, unrelated groups of Euryarchaeota that grow at very high temperature
• All groups branch close to root of archaeal tree
• Pyrococcus furiosus ("furious fireball")
  
  • has optimum growth at 100 degrees C; can tolerate up to 103 degrees C
  • Anaerobic heterotroph (uses S as e acceptor)
  • found in geothermal marine sediments
  • thermostable enzymes have uses in biotechnology (e.g. DNA Pol used instead of Taq pol)

Crenarchaeota

General Characteristics and 2 Major Groups

• Cultured organisms genetically diverse group of hyperthermophiles; DNA data suggests also common in other (nonthermal) environments and may be most abundant Archaea in ocean
• Separated into two groups based on environment:
  1. Terrestrial (typically hot springs)
  2. Submarine (deep sea hydrothermal vents)

• Common in hot springs; various types of metabolism and cell shape
• Sulfolobus one of the most studied
  • found in sulfur-rich acidic hot springs up to 90 degrees C
  • cells roughly spherical with lobes
  • aerobic chemoautotrophs that can use H₂S, S, or Fe²⁺ as e donor
    
    • But can also use organic substrates through aerobic respirations, so easier to culture compared to other Archaea
  • First to find viruses infecting
• Pyrobaculum use either aerobic or anaerobic respiration (S, NO₃^- as e acceptors); rod-shaped cells found in neutral and alkaline hot springs around 100 degrees C

• Includes the most thermophilic of all Archaea; found in and around deep sea hydrothermal vents where high pressure keeps water from boiling at >100 deg C
• Pyrodictum are disc shaped cells that
  
  • grow attached together as a mycelium (branching filaments)
  • obligate anaerobes (use S as e acceptor)
  • Oxidize organic substrates (heterotrophs) or H₂ (chemoautotrophs)
  • optimum growth at 105 deg C
• Staphylothermus 
  • morphologically look like Staphylococcus
  • grow by fermentation of proteins
  • optimal growth of 92 deg C
• Pyrolobus fumarii (chimney)
  
  • most thermophilic organism known
  • grows to 113 deg C and can survive for hours at 121 deg C (autoclave)
  • Chemoautotroph  that uses H₂ as e donor and NO₃^-, thiosulfate, or low levels of O₂ as acceptor
  • Probably one of main sources of production in black smoker hydrothermal vents

• Originally described solely from 16S rRNA sequences found in Obsidian Pool (Yellowstone National Park);
• Appear to branch very closely to base of Archaea, so may be similar to ancient life
• No clearly isolated species but some have been grown in mixed cultures

• Appear to be tiny parasitic cells inside some thermophilic Crenarchaeota (Ignicoccus)
• Nanoarchaeum equitans is only named species
  
  • Very small cocci (1/100 the size of E. Coli)
  • Unknown metabolism (never cultured outside of host cell)
  • Very small genome (likely smaller than the Mycoplasmas), may be lacking many basic genes.
  • Debate over whether species or just self-enclosed folding of some Crenarchaeota.

• Genetic elements (DNA, RNA) that cannot replicate without a host
• Nucleic acid (+protein? +lipids? --DNA or RNA
• Also must be independent of host chromosome
• Plasmids--not stable outside of host, (also typic beneficial to host)

• The extracellular form--the "virion"--nucleic acid + protein coat (capsid)
  • "Nucleocapsid"
    • e.g. Rhinoviruses, bacteriophages
  • Some virions have lipid membrane called an "Envelope"
    • e.g. HIV
    • More common in animal viruses than bacteriophages
• Intracellular formin mainly just the virus genome.
• The capsid = repeated proteins (CAPSOMERS)
  • Only takes a few protein types = few genomes
  • Small genomes = 5-200 kb
  • Size is <0.3 um (think 0.2 um)

• "circular" = icosahedral (20 sides), pretty common
• "rod" = really more helical
• "complex" = Bacteriophage T4 (E. Coli)
  • icosahedron + helical tail + tail fibers

• Generally inactive in extracellular form, but can contain enzymes
  •  
    • Lysozyme = breaks down peptidoglycan (often in bacteriophages)
    • NA Pols = viruses at some point have to copy their NA
      • RNA -> DNA Viruses = Reverse transcriptase
        • "retroviruses"

1. Attachment -- Virion must first attach to cell wall/membrane
2. Penetration -- Has got to get in.
3. Nucelic acid and protein synthesis -- Must use cell machinery to make copies of
4. Assembly
5. Release of mature virions

• Viruses are very specific to their host and even tissues within a host (immune system)
• Virion recognize specific surface receptors and attach to those receptors. If receptors aren't present or are different., nothing happens

• Whole? (with/w/o any envelope)
• Just the nucleic acid.  e.g. T4 see fig 16.3
  • Helical protein can contract to inject genetic elements

• Viral NA --> viral mRNA --> "Early proteins"
  •  
    • enzymes that are used to replicate NA
• Next, another round of viral mRNA --> "Late proteins"
  •  
    • structural proteins that make up capsomers

• Capsomers --> Spontaneously enclose capsids
• Cell membrane (host) --> envelope

• Lysis -- destroys cell releasing a good bit at once
• "Shed" -- steadily releases new viruses

• Bacteriophages (well studied b/c easy to work with...enteric, E. Coli)
• Animal virus (human importance)
• Baltimore Classification System
  • based on nucleic acid in their genome (extracellular form)
  • 7 types
    1. Double stranded DNA--e.g. T4, lambda virus
    2. Single stranded DNA
    3. Double stranded RNA
    4. Single stranded (+) RNA (one that can directly make mRNA)
    5. Single stranded (-) RNA (one that must be copied to make mRNA)
    6. Retroviruses (RNA --> DNA) (+)
    7. Retroviruses (RNA --> DNA) (-)

• Lysis--standard cycle: infect cell, make viruses, break out
• Lysogenic -- temperate life cycle: infects cell, viral DNA integrates into host DNA. So long as bacteria copies, virus DNA copied with it. At some point, something changes, triggers lysogenic phage to go into lytic cycle.
  • e.g. Corynebacterium diptheria: only produces diptheria toxin when lysogenically infected.

• RNA or DNA genomes
  • Mammalian typically RNA: HIV, rhinovirus, rabies
• Most enveloped (from cell membrane)
• Bacteriophages --> Lytic or lysogenic
• Animals --> 
  • lytic --> cell lyses e.g. adenovirus not really common
    
    • mild respiratory infection
  • "persistent infection"-> virus infects cell --> replication NO LYSIS
    • typically just shed from cell without lysis
    • e.g. Influenza
  • latent --> infection --> replication -->-->-->--> later release
    
    • e.g. Herpes simplex (cold sores)

• Single stranded RNA (Type IV & V)
  • Rhinovirus, influenza, rabies
  • Polio
• Double stranded RNA (III)
  • Rotaviruses (diarrhea in little kids)
• DNA
  
  • Herpes simplex
  • Chicken pox (Varicella)

• RNA genome -->
  
  • e.g. HIV
  • replicate through DNA intermediate --> RNA genome
  • key enzyme = reverse transcriptase
  • inside capsid typically have two single RNA + reverse transcriptase
  • Rous sarcoma virus, first virus shown to cause cancer

Huma-Microbial Interactions

Introduction

• 90% of "body's" cells are microbial.
  • most harmless/beneficiala
  • some are opportunistic pathogens,
    
    • if out of control or
    • more virulent (chance of causing disease...NOT INFECTION, you already are). How many cells are needed to cause a disease?

• Skin
• Oral cavity
• Digestive (particularly intestines, not stomaoch)
• Upper respiratory
• Urogenital (bladder pretty clean, urethra often has bacteria)

• Some transient--E. coli, other enterics from feces; Bacteroides will die quickly
• More permanent--have to resist drying, salt--> Staphylococcus can tolerate this
• Acidic pH (not super acidic, but slightly maybe 5)
  • e.g. Proprionibacterium acnes (takes lactic to propionic acid)
  • Typically in sebaceous glands
  • e.g. Corynebacterium

• Moist, warm and contains nutrients
• Saliva dilutes nutrients and contains antimicrobial enzymes like
  • lysozymes (degrades peptidoglycan)
  • lactoperoxidase (generates reactive oxygen)
• Motion (stress by all activity)
• Thus, most bacteria attached to teeth as biofilms
  • Streptococcus mutans, sobrinus
  • Later fusobacterium and borrelia (maybe Treponema), actinomycetes
  • Other microorganisms (including methanogenic Archaea) may invade gums causing gingivitis and periodontal disease

• Stomach- very low pH, kills a lot of bacteria
  • Helicobacter pylori exception, causes stomach ulcers
• Small intestine
  • Duodenum--very few bacteria
  • Jejunum--pH continues to increase,
  • Ileum--bacteria can grow (10^7 bacteria/g content)
    • Lactobacillus
    • Enterococcus
• Large intestine--exponentially increase  10^10
  
  • faculatative (enterics)
  • Obligate anaerobes
    
    • e.g. Bacteroides, Clostridium
    • animals without these bacteria don't last long
    • Human microbiome (changes a lot by life stage, diet)
      • High meat intact, increase in Bacteroides
      • Antibiotics drastically change intestines (C. diff)

• Only found in upper part if healthy
• e.g. Staphylococcus
• e.g. Streptococcus pyogenes
• Ciliated epithelium cells constantly pushing bacteria up and out

• Blood filtered by kidneys
  • bladder sterile
• Urethra
  • Escherichia, Klebsiella, Proteus {Enterics}
• Vagina = Lactobacillus acidophilus (Lactic acid bacteria)
  • lower pH, stops other organisms from growing.

1. increase ability to enter body
2. Increase toxins

1. Hyaluronidase--breaks down hyaluronic acid, part of matrix between cells.
   
   • Connections between epithelial cells
   • Degradation allows bacteria to further infuse body.
   • e.g. S. pyogenes, C. perfringens
   • Body may try to block this by making a clot
2. Streptokinase (S. pyogenes)--breaks down some kinds of clots.
   • also beneficial enzyme used in breaking down clots.
3. Coagulase --forms clots
   • forms fibrous clot around bacterium, protects bacteria from immune system'
   • e.g. S aureus

• some kind of protein produced by pathogenic bacterium

1. Cytolytic --> lyse cells
   
   • hemolysins (RBCs), S. pyogenes
2. A-B exotoxins
   
   • e.g. C. tetani, C. botulinum >block neurotransmitters
   • A-B stands for two parts of protein. B=binding, A=active
3. Superantigens
   • Trigger massive immune response
   • produced by Streptococcus, Staphylococcus

• Toxins that affect the intestines, food poisoning.
• Block water uptake/Trigger water release --> Diarrhea
  • E. coli, Salmonella, B. cereus
  • probably a spreading strategy
• Cholera toxin (V. cholerae)
  • actually an A-B toxin
  • blocks uptake of Na+
  • triggers export of chloride ions into lumen of intestine
  • causes disruption of osmolarity

• part of the bacteria cell
• LPS layer in Gram negative
  • not a problem when intact
  • problem when bacteria lyses, goes into blood stream, trigger a response.
  • Pyrogenic--> fever, inflammation

• First line defenses:  your skin, sebaceous glands --> low pH
• lysozyme (tears, saliva)
• cilia
• Digestives system

• Innate-
  
  • nonspecific,
  • general removal of wrong things from your body.
  • phagocytes
• Adaptive-
  • specific,
  • memory,
  • acquired
  • phagocytes and lymphocytes

• macrophages- destroy antigens/pathogens
  • recognize some antigen in LPS that is Pathogen Associated Molecular Pattern (PAMPs)
  • Has Pattern Recognition Molecules (PRMs)
    • aka Toll-like receptors, found in Drosophila
    • only found in 1980s
    • major things responsible for recognizing PAMPs
  • Usually destroyed by oxidative stress (HOOH)