An Overview of Microbial Life

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An Overview of Microbial Life

• Chapter 2

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Elements of Cell and Viral Structures

• 3 Domains Archae, Eubacteria, Eukaryota
• Two structural types of cells are recognized the
  prokaryote and the eukaryote.
• Prokaryotic cells have a simpler internal
  structure than eukaryotic cells, lacking
  membrane-enclosed organelles.
• Viruses
• Viruses are not cells but depend on cells for
  their replication.

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Cells from each domain
Eukarya
Bacteria
Archae
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The basic components..

• All microbial cells share certain basic
  structures in common, such as cytoplasm, a
  cytoplasmic membrane, ribosomes, and (usually) a
  cell wall.
• Note Animal cells typically do not have a cell
  wall
• The major components dissolved in the cytoplasm
  include
• Macromolecules
• Inorganic ions

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Eukaryotic Cells

• Larger and structurally more complex
• Euk. microorganisms include algae, fungi and
  protozoa
• Membrane enclosed organelles
• Nucleus
• Mitochondria
• Chloroplasts (photosynthetic cells only)

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Prokaryotic Cells

• Lack membrane enclosed organelles
• Include Bacteria and Archae
• Smaller than eukaryotic cells (Typically 1-5 um
  long and 1um in width)
• However, can vary greatly in size

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Viruses

• Not cells
• Static structures which rely on cells for
  replication and biosynthetic machinery
• Many cause disease and can have profound effects
  on the cells they infect
• Cancer, HIV
• However, can alter genetic material and improve
  the cell

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Arrangement of DNA in Microbial Cells

• Genes govern the properties of cells, and a
  cell's complement of genes is called its genome.
• DNA is arranged in cells to form chromosomes.
• In prokaryotes, there is usually a single
  circular chromosome whereas in eukaryotes,
  several linear chromosomes exist.

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Nucleus vs. Nucleoid

• Nucleus a membrane-enclosed structure that
  contains the chromosomes in eukaryotic cells.
• Nucleoid aggregated mass of DNA that constitutes
  the chromosome of cells of Bacteria and Archaea

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Prokaryotic DNA

• Most DNA is circular
• Most have only a single chromosome
• Single copy of genes
• Haploid
• Many also contain plasmids

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Plasmids

• Plasmids are circular extrachromosomal genetic
  elements (DNA), nonessential for growth, found in
  prokaryotes.
• Typically contain genes that confer special
  properties (ie unique metabolic properties)
• Useful in biotechnology

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Eukaryotic DNA

• Organized into linear molecules
• Packaged into chromosomes
• Number varies
• Typically contain two copies of each gene
• Diploid

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Genes, genomes, and proteins

• E.coli genome a single circular chromosome of
  4.68 million base pairs
• of genes 4,300
• A single cell contains
• 1,900 different proteins
• 2.4 million protein molecules
• Abundance of proteins varies

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Genome size, complexity, and the C-value paradox

• Genome size does not necessarily correlate with
  organismal complexity

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In actuality.
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The Tree of Life

• Evolution change in allelic frequencies over
  generations
• The evolutionary relationships between life forms
  are the subject of the science of phylogeny.
• Phylogenetic relationships are deduced by
  comparing ribosomal sequences

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The three domains of life

• Comparative ribosomal RNA sequencing has defined
  the three domains of life Bacteria, Archaea, and
  Eukarya.

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What has this sequencing revealed??

• Molecular sequencing has shown that the major
  organelles of Eukarya have evolutionary roots in
  the Bacteria
• Mitochondria and chloroplasts were once
  free-living cells that established stable
  residency in cells of Eukarya eons ago.
• The process by which this stable arrangement
  developed is known as endosymbiosis.

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What has this sequencing revealed?? Cont.

• Although species of Bacteria and Archaea share a
  prokaryotic cell structure, they differ
  dramatically in their evolutionary history.
• Archae are more closely related to eukaryotes
  than are species of bacteria

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Molecular sequencing and microbiology

• Overall rRNA sequencing technology has helped
  reveal the overall evolutionary connections
  between all cells
• In particular prokaryotes
• Impacted subdispiciplines
• Microbial classification and ecology
• Clinical diagnostics
• Can identify organisms without having to culture
  them

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Microbial Diversity

• Cell size and morphology
• Metabolic strategies (physiology)
• Motility
• Mechanisms of cell division
• Pathogenesis
• Developmental biology
• Adaptation to environmental extremes
• And many more

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Physiological Diversity of Microorganisms

• All cells need carbon and energy sources
• Energy can be obtained in 3 ways
• Organic chemicals
• Inorganic chemicals
• Light
• Types of physiological diversity
• Chemoorganotrophs
• Chemolithotrophs
• Phototrophs
• Heterotrophs and Autotrophs
• Habitats and Extreme environments

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Chemoorganotrophs

• Chemoorganotrophs obtain their energy from the
  oxidation of organic compounds.
• Energy conserved as ATP
• All natural and even synthetic organic compounds
  can be used as an energy source
• Aerobes
• Anaerobes
• Most microorganisms that have been cultured are
  chemoorganotrophs

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Chemolithotrophs

• Chemolithotrophs obtain their energy from the
  oxidation of inorganic compounds.
• Found only in prokaryotes
• Can use a broad spectrum of inorganic compounds
• Advantageous because can utilize waste products
  of chemoorganotrophs

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Phototrophs

• Phototrophs contain pigments that allow them to
  use light as an energy source.
• ATP generated from light energy
• Cells are colored
• Oxygenic photosynthesis
• O2 involved
• Cyanobacteria and relatives
• Anoxygenic photosynthesis
• No O2
• Purple and green bacteria

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Autotrophs and Heterotrophs

• All cells require carbon as a major nutrient
• Microbial cells are either
• Autotrophs use carbon dioxide as their carbon
  source, whereas heterotrophs use organic carbon
  from one or more organic compounds.
• Autotrophs considered primary producers
• Synthesize organic matter from CO2 for themselves
  and that of chemoorganotrophs
• All organic matter on earth has been synthesized
  from primary producers

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Habitats and Extreme Environments

• Microorganisms are everywhere on Earth that can
  support life
• Extremophiles organisms inhabiting extreme
  environments
• Boiling hot springs,
• Within ice, extreme pH, salinity, pressure

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Examples of Extremophiles
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Prokaryotic Diversity

• Several lineages are present in the domains
  Bacteria and Archaea
• An enormous diversity of cell morphologies and
  physiologies are represented
• rRNA analysis has shown dramatic differences in
  phenotypic characteristics within a given
  phylogenetic group

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Bacteria
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Proteobacteria

• The Proteobacteria is the largest division
  (called a phylum) of Bacteria
• A major lineage of bacteria that contains a large
  number of gram(-) rods and cocci
• Represent majority of known gram(-) medical,
  industrial, and agricultural bacteria of
  significance
• Extreme metabolic diversity
• Chemorganotrophs E.coli
• Photoautotrophs Purple sulfur bacterium
• Chemolithotrophs Pseudomonas, Aztobacter
• Pathogens Salmonella, Rickettsia, Neisseria

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Proteobacteria examples
Chemolithotrophic sulfur-oxidizing bacteria
Achromatium
Neisseria gonorrhoeae
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Gram-positive bacteria

• United by a common cell wall structure
• Examples
• Spore forming
• Clostridium, Bacillus
• Antibiotic producing
• Streptomyces
• Lactic acid bacteria
• Streptococcus
• Lactobacillus
• Mycoplasmas
• Lack cell wall
• Small genomes
• Often pathogenic

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Cyanobacteria

• The Cyanobacteria are phylogenetic relatives of
  gram-positive bacteria and are oxygenic
  phototrophs.
• First oxygenic phototrophs to have evolved on
  Earth

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Planctomyces

• Characterized by distinct cells with stalks that
  allow for attachment to solid surfaces
• Aquatic

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Spirochetes

• Helical shaped
• Morphologically and phylogenetically distinct
• Widespread in nature and some cause disease
• Most notable sp cause Syphilis and Lyme Disease

Spirochaeta zuelzerae
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Green sulfur and non-sulfur bacteria

• Contain similar photosynthetic pigments
• Can grow as autotrophs
• Chloroflexus
• Inhabits hot springs and shallow marine bays
• Dominant organism in stratified microbial mats
• Important link in the evolution of photosynthesis

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Chlamydia

• Most species are pathogens
• Obligate intracellular parasites
• How would this affect an immune response?

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Deinococcus

• Contain sp with unusual cell walls and high level
  of resistance to radiation
• Cells usually exist in pairs or tetrads
• Can reassemble its chromosome after high radiation

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Aquifex, Thermotoga, Env-OP2

• Sp that branch early on the tree
• Unified in that they grow at very high temps
  hyperthermophily
• Inhabitats of hot springs

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Archaea

• There are two lineages of Archaea the
  Euryarchaeota and the Crenarchaeota
• Many are extremophiles
• All are chemotrophic
• Many using organic carbon
• While others are chemolithotrophs

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Euryarchaeota Crenarchaeota

• Physiologically diverse groups
• Many inhabit extreme environments
• From extreme pH, temperature, salinity

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Limitations of Phylogenetic analyses

• Not all Archaea are extremophiles
• Difficult to culture
• Based on molecular microbial ecology, the extent
  of diversity is much greater than once thought

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Eukaryotic Microorganisms

• Collectively, microbial eukaryotes are known as
  the Protista.
• Microbial eukaryotes are a diverse group that
  includes algae, protozoa, fungi, and slime molds
• Cells of algae and fungi have cell walls, whereas
  the protozoa do not.
• The early-branching Eukarya are structurally
  simple eukaryotes lacking mitochondria and other
  organelles
• Ex Giardia

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Eukaryotic microbial diversity
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Eukaryotic microbial diversity

• Diplomonads flagellates, many are parasitic
• Ex Giardia lamblia (synonymous with Lamblia
  intestinalis and Giardia duodenalis) is a
  flagellated protozoan parasite flagellated
  protozoan parasite
• Trichomonads anaerobic protist, many are
  pathogenic
• Ex. Trichomonas vaginalis
• Flagellates all protozoa in this group utilize
  flagella for motility, free-living, and
  pathogenic
• Ex. Trypanosomes
• Slime molds resemble fungi and protozoa
• Ex. Dictyostelium discoideum

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Fungi
Protozoa
Algae
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Lichens

• Some algae and fungi have developed mutualistic
  associations called lichens.