202 General Microbiology II

Microbial Evolution and Systematics Lecture Outline

Physical Evolution of Earth

• Big Bang

• Patchy condensation

• Planet Earth formed
  • geology
    • inner core (0-1227km)

    • outer core (1227-3486km)

    • mantle (3486-6350km)

    • crust (6350km-surface)
      • oceanic crust

      • continental crust

  • primitive atmosphere
    • reducing

    • mildly oxidizing

  • liquid water

Origin of Life on Earth

• Primordial soup (solution) theory
  • chemical reactions

  • accumulation

  • spontaneous aggregation

  • anaerobic thermophilic fermenters

• Surface theories
  • pyrite theory

  • clay theory

  • thermophilic anaerobic lithotrophs

Early Evolution of Organisms with Increasing Complexity

• Fossils

• Mutations
  • Anoxygenic photosynthesizers

  • Oxygenic photosynthesizers

Atmosphere Evolved as Microbes Produced Oxygen ~2.5 Ba

• Oxygen content slowly increased

• Ozone layer formed as UV light energy was absorbed by oxygen

Atmospheric Oxygen Availability Led to Increasing Diversity

• Microbial diversity increased ~0.5 billion years after oxygen generation began

• "Modern" eukaryotes evolved ~1.3 Ba (1.2 billion years after oxygen generation began)
  • eukaryotic diversity increased

  • metazoans evolved

Broad Evolutionary Picture

• Original organism

• Universal ancestor

• Universal Tree of Life ... Bacterial, Archaeal, Eukaryal Domains

Classification

• Phylogeny vs. Taxonomy

• Binomial nomenclature

Molecular Approaches to Phylogeny

• Attributes of acceptable molecules
  • universally distributed

  • functionally homologous

  • alignable

  • slow rate of sequence changes

• Molecules used
  • proteins

  • 5S rRNA

  • ATP synthase

  • 16S rRNA (18S rRNA in eukaryotes)
    • determine primary rRNA structure

    • analyze rRNA sequence homology
      • cataloging (80%) - signature sequences

      • distance matrix (20%) - ED calculated

  • Ef-Tu and Ef-G (used to "root" 3-domain tree)

Phylogeny of Bacteria, Archaea and Eukarya

• Bacterial Phylogeny
  • Proteobacteria (Kingdom I)
    • Purple Sulfur Bacteria - Chromatium, Halorhodospira, Thiocapsa, Thiococcus, Thiopedia,Thiospirillum

  • Purple Nonsulfur Bacteria - Rhodobacter, Rhodocyclus, Rhodobacter Rhodopseudomonas, Rhodophila

  • Nitrifying Bacteria - Nitrobacter, Nitrosomonas

  • Sulfur- and Iron-Oxidizing Bacteria - Thiobacillus, Beggiatoa, Thioploca, Thiothrix

  • Hydrogen-Oxidizing Bacteria - Alcaligenes

  • Methanotrophs and Methyltrophs - Methlyosinus, Methylcoccus

  • Pseudomonas and the Pseudomonads - Pseudomonas, Agrobacterium, Rhizobium, Zymomonas

  • Acetic Acid Bacteria (Acetobacteraceae) - Acetobacter, Gluconobacter

  • Free-Living Aerobic Nitrogen-Fixing Bacteria - Azotobacter, Azomonas

  • Neisseria, Chromobacterium, and Relatives - Neisseria, Chromobacterium

  • Enteric Bacteria - Escherichia, Salmonella, Proteus, Enterobacter

  • Vibrio and Photobacterium - Vibrio, Photobacterium

  • Rickettsias

  • Spirilla - Spirilum, Bdellovibrio, Campylobacter

  • Sheathed Proteobacteria - Sphaerotilus, Leptothrix

  • Budding and Prosthecate/Stalked Bacteria - Hyphomicrobium, Caulobacter

  • Gliding Myxoacteria - Myxococcus, Stigmatella

  • Sulfate- and Sulfur-Reducing Proteobacteria - Desulfovibrio, Desulfobacter, Desulfuromonas

  • Gram-Positive Bacteria (Kingdom II)
    • Nonsporulating, Low GC, Gram-Positive Bacteria (plus Lactic Acid Bacteria) - Staphylococcus, Micrococcus, Streptococcus, Lactobacillus
    • Endospore-Forming, Low GC, Gram-Positive Bacteria (plus Homoacetogenic Bacteria and Heliobacteria) - Bacillus, Clostridium, Sporosarcina, Heliobacterium
    • Cell Wall-Less, Low GC, Gram-Positive Bacteria: The Mycoplasmas - Mycoplasma, Spiroplasma
    • High GC, Gram-Positive Bacteria: Coryneform and Propionic Acid Bacteria - Corynebacterium, Arthrobacter, Propionibacterium

  • High GC, Gram-Positive Bacteria: Mycobacterium

  • Filamentous, High GC, Gram-Positive Bacteria: The Actinomycetes - Streptomyces, Actinomyces
    • Nocardioforms
    • Actinomycetes with Multilocular Sporangia
    • Actinoplanetes
    • Streptomyces and Related Genera
    • Maduromycetes
    • Thermonospora and Related Genera
    • Thermoactinomycetes
    • Other Genera

• Cyanobacteria, Prochlorophytes, and Chloroplasts (Kingdom III)
  • Cyanobacteria - Synechococcus, Oscillatoria, Nostoc

  • Prochlorophytes and Chloroplasts - Prochloron, Prochlorothrix

  • Chlamydia (Kingdom IV) - Chlamydia
  • Planctomyces/Pirella (Kingdom V) - Planctomyces, Pirella
  • Bacteroides/Flavobacteria (Kingdom VI) - Bacteroides, Cytophaga
  • Green Sulfur Bacteria (Kingdom VII) - Chlorobium, Prosthechloris, Chlorochromatium
  • Tightly Coiled Bacteria: The Spirochetes (Kingdom VIII) - Spirochaeta, Treponema, Cristispira, Leptospira, Borrelia
  • Deinococcus (Kingdom IX) - Dienococcus, Thermus 
  • Green Nonsulfur Bacteria (Kingdom X) - Chloroflexus, Thermomicrobium 
  • Thermotoga (Kingdom XI)
  • Thermodesulfobacterium (Kingdom XII)
  • Aquifex and Relatives (Kingdom XIII)

• Archaeal Phylogeny
  • Korarchaeota (Kingdom) ... newly discovered extreme thermophiles; most primitive life forms discovered to date

  • Crenarchaeota (Kingdom) ... includes extreme thermophiles and marine cryophiles such as Thermofilum, Thermoproteus, Pyrodictium, Desulfurococcus, Sulfolobus in addition to a number of as yet unidentified marine Crenarchaeotes

  • Euryarchaeota (Kingdom) ... includes methanogens, sulfur utilizers, extreme thermophiles and extreme halophiles Methanopyrus, Thermococcus, Methanococcus, Archaeoglobus, Thermoplasma, Methanothermus, Methanobacterium, Methanospirillum, Haloferax, Halococcus, Halobacterium
    • Extreme Halophiles
    • Methanogens
    • Extreme Thermophiles
    • Sulfate Reducers
    • Wall-Less Archaea

      

• Eukaryal Phylogeny
  • Protozoa (Kingdom)
  • Fungi (Kingdom)
    • Chytridiomycota
    • Oomycota
    • Zygomycota
    • Ascomycota
    • Basidiomycota
    • Deuteromycota

  • Plants (Kingdom)
  • Animals (Kingdom)

• Endosymbiotic theory of eukaryotic organelle origin and evolution 
  • evidence
  • endosymbiosis has been proposed as the mechanism underlying the origin and evolution of mitochondria and chloroplasts in Eukarya
  • endosymbiotic theory proposes that ...
  • evidence supporting the endosymbiotic theory includes the facts that mitochondria and chloroplasts:
  • analysis of rRNA sequences of a large number of mitochondria and chloroplasts has shown that:
  • proposed, but not well-supported, hypotheses include the ideas that: