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    The First Organisms

    Prokaryotic organisms are pre-nuclear.

    • They lack a membrane-bounded nucleus.
    • They lack membrane-bounded organelles.
    • They have ribosomes and internal membrane systems.

    There are two distinct lineages of prokaryotic organisms:
    • Domain Archaea (archaeans)
    • Domain Bacteria (bacteria)

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    Three Domains

    The Three Domain system was introduced by Carl Woese, et al. in 1977.
    It is based upon synapomorphic rRNA sequences.

    Woese was also the first to hypothesize that RNA, not DNA,
    was the first nucleic acid to evolve (1967).

    His model was the inspriation for the RNA World Hypothesis.

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(source: Wikimedia Commons)

    Domain Archaea: Earliest Life on Earth

    Earth's earliest inhabitants spent their first 2 billion years
    as the only life on earth.

    Although Archaeans share some similarities
    with both bacteria and eukaryotes,
    they have many characters unique to Archaea.

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(click on pic for source)

    Archaea: Bacterial Similarities

    Archaeans share some similarities with bacteria:
    • They have one circular DNA chromosome
    • They are haploid
    • They reproduce via binary fission (asexual)
    • Their shapes can be superficially similar to those of bacteria

    The archaean genome ranges widely in size among different species.
    It may be anywhere from ~500,000 - 6,000,000bp (base pairs). long

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(modified from Cshirc1, Wikimedia Commons)

    Archaean Synapomorphies

      Shared characteristics unique to Archaea include

      • a cell wall composed of material unique to Archaeans

      • flagella composed flagellin proteins unique to Archaeans

      • unique tRNAs

      • cell membrane structure/composition unique to Archaeans

      • ribosomes more similar to eukaryote ribosomes
        than to bacterial ribosomes

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(click on pic for source)

    Extremophiles

    Archaeans can withstand more extreme environments
    than almost any other life form.

    Classifications based on metabolic strategies
    may not necessarily indicate homology.

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(click on pic for source)


(click on pic for source)

    Halophiles

    Halophiles thrive in extremely salty environments.
    They grow profusely in evaporation ponds
    and very salty water (e.g., Great Salt Lake)

    They generally have an unpleasant smell.

    They owe their salt tolerance to

    • high lipid content of the plasma membrane
    • protective gel capsule outside the membrane
    • high internal salt concentration

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    Methanogens

    Methanogens are anaerobic, thriving in oxygen-free environments.

    Methanogens produce methane as a metabolic by-product of CO2 reduction.

    They are commonly found in the intestinal tracts of many vertebrates.

    They are important symbionts in the intestines of most animals,
    including ruminants and humans.

    (Don't blame the beans.)
    (Blame the beef.)

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(click on pic for source)


(click on pic for source)

    Thermophiles

    Thermophiles thrive in extremely hot environments.

    They are found in

    • sulfur hotsprings
    • deep sea thermal vents

    The closest living relatives of Eukaryota are thermophile archaeans.

    New research from the laboratory of Nick Lane at University College London
    provides evidence that deep sea vents could have provided a biochemical environment
    conducive to forming protocells, a necessary step in the origin of life.

    Thermal vent protocells may have given rise to the first thermophilic archaeans.

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Vortex Blue (P. vortex), by Eshel Ben-Jacob
(click on pic for source)

    Domain Bacteria

    Bacteria are arguably the most successful life form on the planet.

    They diverged from their common ancestor so long ago
    that their true evolutionary relationships may never be fully known.

    But they are vital components of every ecosystem on earth.

    • ubiquitous
    • diverse
    • economically important
    • ecologically vital

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Paenibacillus dendritiformis colony, by Eshel Ben-Jacob
(click on pic for source)

    Bacterial Basics

    The bacterial genome is contained in a single, circular chromosome.
    • Like archaeans, bacteria are haploid.
    • The average bacterial genome has about 1000 genes.

    Bacteria may be
    • unicellular (individual, independent cells) (primitive)
    • aggregate (associated/adhered cells)
    • colonial (some division of labor) (derived)

    A bacterial colony that has grown to form a field or mat is called a lawn.

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(source: Getty Images)

    Bacterial Anatomy

    Bacteria (1-5 μm) are smaller than most eukaryotic cells (100-1000 μm).

    Double-stranded DNA is organized as the nucleoid.

    Cytoplasm is enclosed (from inner to outer layer):

    • fluid plasma membrane
    • tough cell wall
    • protective gel capsule (some species)

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(source: Dreamstime.com)

    Bacterial Shapes

    Bacteria may be categorized (not necessarily classified) by shape:
    • spherical
    • rod-shaped
    • helical
    • variants of the above

    Bacterial shapes do not necessarily reflect phylogenetic relationships.

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(click on pic for source)

    Aggregate Bacteria

    Clustering bacteria may be given the prefix staphyl
    • Greek for "a cluster" or "bunch of grapes"
    • as in Staphylococcus spp.

    Link-forming bacteria may be given the prefix strept

    • Greek for "bent; pliable"
    • as in Streptococcus spp.


(click on pic for source)

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Many bacterial species have fimbriae (singular = fimbria extending from the cell surface that allow them to attach to substrates or to other bacteria.

    Fimbriae

    A Fimbria (plural = fimbriae) is a threadlike extension
    from the bacterial surface.

    A pilus (plural = pili) is a specialized, tubular fimbria
    that is used during conjugation to transfer DNA from
    a donor bacterium to a recipient bacterium.

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A pilus (plural = pili) is a type of fimbria used to exchange genetic material during conjugation.

Fimbriae are thinner and shorter than flagella.

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(By Spaully; click on pic for source)

    Plasmids

    Some bacteria contain plasmids:
    • small, circular pieces of autonomously replicating DNA
    • usually contain only a few genes
    • are not considered part of bacterium's genome
    • but may confer phenotypic traits such as

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    Bacterial Movement

    Most bacteria are motile, meaning they can move.
    Mode of locomotion be used in bacterial identification.

    Gliding
    • bacteria slide on a secreted slime trail
    Swimming
    • bacteria rotate one or more flagella

    Note the differences between the prokaryotic and eukaryotic flagella:
    • different protein composition (flagellins vs. tubulins)
    • different mechanism of action (rotating vs. waving)
    • different ultrastructure (see illustration)

    Taxis means "movement".
    Bacteria exhibit positive or negative taxis in response to environmental stimuli.
    Responses to various stimuli differ among species.

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(click on pic for source)

    Peptidoglycan

    The bacterial cell wall contains peptidoglycan,
    a lattice of amino acids cross-linking two sugars
    • N-acetyl glucosamine (NAG)
    • N-acetyl muramic acid (NAM) (unique to bacterial cell walls)

    Peptidoglycan forms a thick, rigid layer in the cell wall.
    The layer varies in location and thickness among species.

    Cell wall composition can serve as a diagnostic character
    in bacterial identification.

    (Exception: mycoplasmas, intracellular parasites, lack a cell wall.)

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(source: picfair)

    Gram Staining

    Two cell wall types can be distinguished
    by means of Gram Staining.

    • Gram Positive (G+) bacteria
      • thick peptidoglycan layer
      • stains dark purple with gram stain

    • Gram Negative (G-) bacteria
      • thinner peptidoglycan layer
      • lies between inner and outer plasma membranes
      • does not stain dark purple with gram stain
      • stains pink with safranin counterstain

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(source: picfair)

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    Gram + and Gram - Bacteria

    Gram stain can sometimes identify pathogens.
    G - bacteria often have a gel capsule that
    • prevents gram stain uptake
    • protects bacterium from a host immune system
    • protects bacterium from peptidoglycan-targeting antibiotics

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Bacterial Reproduction

Bacteria can reproduce either asexually or "sexually" (i.e., with genetic recombination)

(click on pic for source)

    The Ecological Importance of Prokaryotes

    Bacteria are the most numerous organisms on the planet.
    Their ecological impact cannot be understated.

    A copiotroph is an organism that lives in a nutrient-rich environment.

    An oligotroph is an organism that lives in a nutrient-poor environment.

    Bacteria of both types play important roles in many ecosystems.

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The dark clusters are nitrogen-fixing bacteria in the root cells
of a legume plant (Pea Family, Fabaceae).

    The Nitrogen Cycle

    The Nitrogen Cycle is essential to life on earth.

    Nitrogen fixation is conversion of atmospheric nitrogen
    to nitrogen compounds plants can take up and assimilate.
    Nitrogen fixation can be performed only by bacteria.
    • free living cyanobacteria and a few genera of heterotrophic bacteria
    • mutualistic Rhizobium bacteria living in legume root nodules

    Denitrification is the decomposition of nitrate-->nitrite-->ammonia-->N2
    Denitrification can be performed only by a few genera of bacteria.
    • Nitrosomonas spp. - convert ammonia to nitrite
    • Pseudomonas spp. - convert nitrite or nitrate into N2 (denitrification)

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(click on pic for source)

    Bacteria as Pathogens

    A pathogen is a disease-causing agent.

    The vast majority of bacteria are non-pathogenic or beneficial.
    However, many can cause disease in plants and animals.

    Many bacterial species are ubiquitous and usually do not cause disease.

    However, in an immunocompromised animal, they can proliferate.
    Many common bacteria can become opportunistic pathogens,
    given a suitable environment.

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(click on pic for source)

    How Do Bacteria Cause Disease?

    Bacteria can cause disease via
    • invading and feeding on tissues

    • producing exotoxins
      • manufactured intracellularly
      • secreted into bacteria's medium
        • Escherichia coli
        • Vibrio cholerae
        • Clostridium spp.

    • producing endotoxins
      • included in the cell's plasma membrane
      • produced primarily by G- bacteria)
      • affect the host when the plasma membrane is lysed
        • Salmonella spp.

    An iatrogenic infection is one that is caused by
    the healer or the place of healing. (Iatros is Greek for "healer".)

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(click on pic for source)

    Koch's Postulates

    In order for a microbe to be confirmed as the cause of a disease,
    four conditions must be met.

    These conditions are Koch's Postulates.

      1. The suspected pathogen must be found in all individuals
      xxsuffering from the disease
      .

      2. The pathogen must be isolated from the diseased host
      xxand grown in pure culture.

      3. The pathogen from the pure culture must cause the disease
      xxwhen it is introduced into a healthy but susceptible host.

      4. The pathogen must be isolated from the inoculated animal
      xxand positively identified as the original pathogen.

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(click on pic for source)

    Antibiotics

    Antibiotics are substances that inhibit the growth of prokaryotic cells.
    They are naturally manufactured by plants, fungi, and bacteria.

    Humans use and modify naturally produced antibiotics as protection against bacteria.

    • A bacteriostatic antibiotic inhibits bacterial growth.

    • A bacteriocidal antibiotic kills bacteria outright.

    Why would bacteria produce antibiotics, if antibiotics kill bacteria?
    DISCUSS

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    Antibiotics: Mechanisms of Action

    Different antibiotics attack different aspects of the bacterial life cycle.
    • inhibition of enzymes involved in peptidoglycan biosynthesis
        (e.g., penicillins)

    • interference with normal nucleic acid (DNA, RNA) function and repair
        (e.g., fluoroquinolones such as ciprofloxacin, enrofloxacin)


    • interference with tRNA function and/or ribosome function
        (e.g., macrolides, chloramphenicol)

    • disruption of the plasma membrane
        (e.g., polymixins; imidazoles)
        • Some of these weakly bind eukaryotic plasma membranes.
        • This limits their use to topical applications (e.g., neosporin).

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    Bacteria World

    Bacteria can be our foes, our competitors, or our allies.

    They form vital, ubiquitous threads in the Web of Life.

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