Microbial Taxonomy naming and classifying

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Microbial Taxonomy- naming and classifying

• Dr. William Stafford
• wstafford_at_uwc.ac.za

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BTY227 Environmental Microbiology and
BiotechnologyDetails available on
http//www.biotechnology.uwc.ac.za/teaching/BTY227
/

• TEACHING SCHEDULE 2006
• Lecture no. Title
• 10 Tuesday 12 00 08 Aug Microbial Taxonomy
• Thursday 0830 10 Aug Test 1
• 11 Tuesday 0830 15 Aug Archaea
• 12 Tuesday 12 00 15 Aug Microbial Applications
• 13 Thursday 0830 17 Aug Biofuels
• 14 Tuesday 0830 22 Aug Bioremediation
• 15 Tuesday 12 00 22 Aug Biomining
• 16 Thursday 0830 24 Aug GM 1
• 17 Tuesday 0830 29 Aug GM 2 impact/monitorin
• Tuesday 12 00 29 Aug Tutorial
• Thursday 0830 31 Aug TEST 2

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• Environmental Biotechnology- Scragg
• Microbiology- Prestcott
• Biology of microorganisms -Brock
• Microbial ecology -Atlas

Recommended texts
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Why taxonomy?

• To predict the properties of organisms based on
  the properties of its relatives. Understanding an
  organisms relationships to other species is the
  key to understanding it's properties.
• To prevent inappropriate comparisons based on
  nonexistant relationships. For example, Euglena
  was used for years as model system to study
  photosynthesis, but Euglena isn't related to
  plants, but to the trypanosomes.
• To understand how individuals interact in complex
  ways and contribute to the functioning of the
  ecosystem
• To know what is available as an untapped
  resource-Bioprospecting for Biotechnology

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Taxonomic ranks

• Organisms are ranked
• A category in any rank unites groups in the level
  below it, based on shared properties
• Domain Bacteria
• Phylum Proteobacteria
• Class g- Proteobacteria
• Order Enterobacteriales
• Family Enterobacteriaceae
• Genus Shigella
• Species dysenteriae

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What do taxa define?

• Members of lower level taxa (e.g., species) are
  more similar to each other than are members of
  higher level taxa (e.g., kingdoms or domain)
• Members of specific taxa are more similar to each
  other than any are to members of different
  specific taxa found at the same hierarchical
  level
• When you know two organisms are members of the
  same taxon, you can infer certain similarities
  between the two organisms (e.g., all members of
  Family Enterobacteriaceae are facultatively
  anaerobic, Gram-negative rods)

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Hierarchical Classical taxonomy
The higher eukaryotes and the lower
prokaryotes
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The species

• Species- basic fine resolution taxonomic rank.
• What IS a species?
• For higher organisms the biological species is
  used interbreeding groups of natural populations
  that are reproductively isolated from other
  groups.
• For microorganisms this fails- they dont
  reproduce sexually!

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How can we classify microorganisms?

• Phenotype The functional characteristics.
• Observation by microscopy (eg. Morphology,
  structure) or biochemical analysis (Metabolic
  diversity) or habitat (ecological diversity)
• Genotype The genetic characteristics. If a DNA
  marker is used then we can trace evolutionary
  relationships

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Phylogeny

• Phylogeny understands the connections between all
  groups of organisms by ancestor/descendant
  relationships (family tree).
• A molecular marker is used to explore the
  evolutionary history between microorganisms.

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Molecular DNA markers

• The evolutionary history can be found by
  constructing a phylogenetic tree using an
  appropriate DNA marker.
• E.g.
• Ef-Tu and Ef-G, HSP
• 5S rRNA or ITS region
• ATP synthase
• rRNA gene

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Desirable attributes of a phylogenetic marker?

• Universally distributed
• Functionally conserved
• Constant rate of change (mutation)- a molecular
  clock
• Not subject to lateral gene transfer

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How long ago did organism A and organism B last
have a common ancestor?

• The number of nucleic acid or amino acid
  differences between two organisms is proportional
  to the time since they diverged from a common
  ancestor.

1 2 3
1 AAGGCTA 2 AAGGGTA 3 AAGGATG Example
Rate of Evolution 1bp per 100 years
100years
200 years
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rRNA gene as a molecular marker

• Ribosomes are ribonucleoprotein particles
  consisting of LSU and SSU.
• The rRNA are transcribed from rnn operon

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What makes the rRNA gene a good choice for a
phylogenetic marker?

• It is present in all cells where is has the same
  function
• Sufficient sequence information 1500-2000
  residues
• Well conserved enough in sequence structure for
  alignment
• It contains both rapidly slowly evolving
  regions - the fast regions are useful for
  determining closely-related species, and slow
  regions are useful for determining distant
  relationships.
• Horizontal transfer of rRNA genes apparently does
  not occur
• There is a large growng database (about 10,000)
  of aligned sequences available eg. NCBI

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A long time for evolution

• Origin of Life on Earth
• Primitive organisms capable metabolism and
  reproduction appeared 3.6 Billion years ago, and
  were most likely thermophilic anaerobes
• Universal ancestor was the result of considerable
  evolution of the original life form and gave rise
  to three domains of living things Bacteria,
  Archaea and Eukarya
• The Eukaryotes are thoughts to have arisen
  through the endosymbiosis of prokaryotes
  (nucleus, mitochondria and chloroplasts)

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The modern molecular Tree of life-Three domains
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Modern Molecular Tree of life

• All previous trees were subjective qualitative.
  This tree is quantitative and objective, based on
  statistical analysis of gene sequences, in this
  case small subunit ribosomal RNA.
• The tips of all the branches are modern
  organisms. Each node within the tree represents a
  common ancestor.
• There is no ranking of above (superior) or below
  (inferior) in the tree. Evolutionary distance
  (divergence) is measured along the lengths of the
  branches connecting species.
• Multicellular eukaryotes are a very small portion
  of evolutionary diversity - just the tip of one
  branch of the eukaryotes
• Prokaryotes fill 2/3rds of the tree (bacteria and
  archaea).
• The tree also offers final proof of the
  endosymbiont theory for the origin of
  mitochondria and chloroplasts since these
  organelles have their own DNA genes. The
  mitochondria are related to the purple Bacteria,
  and the chloroplasts are related to
  cyanobacteria.

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Millions or billions of microbial species?!

• The microbial diversity is the UNSEEN MAJORITY of
  life on earth!
• 1000 species/ gram soil
• 100 species/L sea water

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What was the universal ancestor?
BACTERIA
EUKARYOTES
ARCHAEA
Was is like an Archaea?...
The progenote