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