taxonomy of microorganisims

1. Major characteristics used in taxonomy
Classical characteristics
Molecular characteristics

2. Classical characteristics
Morphological characteristics
Physiological and metabolic characteristics
Ecological characteristics
Genetic analysis

3. Molecular characteristics
Comparison of proteins
Nucleic acid composition
Nucleic acid hybridization
Nucleic acid sequencing

4. Comparison of proteins
Protein amino acid sequence reflects gene sequence
DNA  mRNA  protein
Comparison of proteins from different organisms can be used for
taxonomical classification

5. Comparison of proteins
Amino acid sequencing
Comparison of electrophoretic mobility
Immunological techniques
Comparison of enzymatic properties

6. Nucleic acid composition
Usually expressed as the G + C content (% G + C)
G + C = (G + C / G + C + A + T) x 100
Can be determined in a number of ways
Hydrolysis of DNA and analysis of of bases using HPLC
Measurement of melting point (Tm)

7. Measuring the Tm of DNA
GC pairs connected by 3 H bonds
AT pairs connected by 2 H bonds
Higher GC content  higher Tm

8. Measuring the Tm of DNA
Absorbance of 260 nM light (UV)
by DNA increases during strand
separation
Absorbance reaches plateau at
maximum strand separation
Midpoint of rising curve is the Tm

9. Nucleic acid composition

10. Nucleic acid hybridization
Measure of sequence homology
DNA heated above Tm to form single stranded DNA
ssDNA incubated with radioactive ssDNA from other organism

11. Nucleic acid hybridization
dsDNA heated to form ssDNA
ssDNA bound to nitrocellulose
membrane
Membrane incubated with
radioactive ssDNA from different
organism

12. Nucleic acid hybridization
Filter incubated at temp lower than
Tm
Filter washed and amount of
bound DNA measured

13. Nucleic acid hybridization
Percent DNA bound indicates
relatedness of organisms
DNA-rRNA hybridization can be
used on more distantly related
organisms

14. Nucleic acid hybridization

15. Nucleic acid sequencing
Sequencing of nucleic acid only way to provide direct
comparison of genomes
Sequence of 16 S rRNA gene often used to compare organisms
16 S rRNA gene amplified by PCR
PCR product sequenced and sequence compared with that of
known organism

16. Phylogenetic trees
Graphs that indicate
phylogenetic (evolutionary)
relationships
Made up of nodes connected
by branches
Nodes represent taxonomical
units e.g. species

17. Phylogenetic trees
Trees can be rooted or
unrooted
Rooted trees show the
evolutionary path of the
organisms

18. Indicators of phylogeny
Different cell constituents can be used as indicators of phylogeny
Sometimes referred to as molecular chronometers
Include:
Ribosomal RNA (rRNA)
DNA
Proteins

19. Ribosomal RNA (rRNA)
Has changed very little over time and can serve as an indicator of
evolutionary relatedness

20. Ribosomal RNA (rRNA)
16S rRNA contains oligonucleotide
signature sequences specific for
members of a particular
phylogenetic group
Sequence is absent in other groups
of organisms

21. Domains
All organisms are divided into one of three domains based on
rRNA studies conducted by Carl Woese and others
Archaea
Bacteria
Eukaryotes

22. Domains

23. Domains

24. Domains
Different theories exist regarding
the evolution of the three domains
The currently accepted theory is (b)

25. Domains
Widespread gene transfer between
the different domains has occurred
This creates difficulties in
constructing phylogenetic trees
Gene transfers were/are most likely
virus-mediated

26. Kingdoms
Some biologists prefer the kingdom classification system
Simplest system includes the kingdoms;
Monera
Protista
Fungi
Plantae
Animalia

27. Kingdoms

28. Kingdoms

29. Bergey’s Manuals
Bergey’s Manual of Determinative Bacteriology (in 9th edition)
Classification of bacteria used for identification
Bergey’s Manual of Systematic Bacteriology
Contains detailed descriptions of each organism
2nd edition is in 5 volumes (currently being published)

30. Phylogeny of bacteria
Bacteria divided into 23 phyla,
including:
Proteobacteria
Low G+C gram +’s (Firmicutes)
High G+C gram +’s (Actinobacteria)
Cyanobacteria
Bacteriodetes
Spirochaetes

31. Phylogeny of archaea
Archaea divided into 2 phyla
Euryarchaeaota
Crenarchaeaota

32. Major archaeal groups

33. Crenarchaeota
Thought to resemble the
ancestor of archaea
Divided into 1 class 3 orders
and 5 families

34. Crenarchaeota
Most are thermophiles or
hyperthermophiles
Many grow
chemolithoautotrophically
by reducing sulfur to sulfate

35. Crenarchaeota
Most are strict anaerobes
Are often found in
geothermally heated water
and soils (e.g. Yellowstone
National Park)

36. Euryarchaeota
A very diverse phylum with many
classes orders and families
Will focus on the 5 major groups

37. Euryarchaeota
Methanogens
Anaerobes that obtain energy by
converting compounds to methane
(and CO2)
Halobacteria
Growth is dependent on a high
concentration of salt (at least 1 M)

38. Euryarchaeota
Thermoplasms
Thermoacidophiles that lack cell
walls
Thermophilic S0-reducers
Anaerobes that can reduce sulfur
to sulfide

39. Euryarchaeota
Sulfate-reducing archaea
Extract electrons from various
molecules and reduces sulfate,
sulfite or thiosulfate to sulfide
Cannot use S0 as an electron
acceptor