3.3 Classification of Prokaryotes  In the 5K system all prokaryotes were placed in the Kingdom Monera because they have prokaryotic cells  Until the late 20 th century, prokaryotic taxonomy was based on phenotypic characters such as shape, motility, Gram stain, and nutritional mode  Starting in the 1970s, a molecular systematics approach using SSU-rRNA DNA sequences as a marker for evolutionary relationships revealed some startling results The genetic diversity of prokaryotes is immense Horizontal gene transfer is is important in the evolution of prokaryotes

Major Findings from Molecular Systematics There are two distinct evolutionary lineages of prokaryotes, the Archaea and the Bacteria  Kingdom Monera is therefore obselete, and Archaea and Bacteria are both domains in the 3D system  Archaea is actually more closely related to Eukarya than to Bacteria and shares many characteristics with it.

Major Findings from Molecular Systematics Most traditional groupings do not hold up  Eg. Gram-negative bacteria are not one lineage  Cyanobacteria is a monophyletic group Figure A tentative phylogeny of some of the major taxa of prokaryotes

Major Groups of Bacteria

Diversity Within the Archaea  The “extremophiles” - including the thermophiles, the halophiles and the methanogens  The thermophiles thrive in very hot environments  The halophiles live in highly saline environments  The methanogens are strict anaerobes that use CO 2 to oxidize H 2 as a source of energy, releasing CH 4 as a waste product  All of the halophiles and methanogens, and some of the thermophiles, are in the Kingdom Euryarchaeota  Most of the thermophiles are in the Kingdom Crenarchaeota

Methanogens Some methanogens inhabit the anaerobic guts of animals and aid in their digestion… Others live in swamps and marshes and produce “marsh gas”!

Extreme Halophiles These critters tolerate or even require a high salt environment  15-20% salinity found in evaporating ponds of San Francisco Bay  The colour is due to bacteriorhodopsin - a photosynthetic pigment Halobacterium halobium (A photoheterotroph!)

Extreme Thermophiles These little guys tolerate temperatures up to about 113 o C, although the optimal temperature is usually o C They tend to inhabit hot springs  Eg. Sulfolobus solfataricus lives in sulfur-rich volcanic springs, and obtains energy by using CO 2 to oxidize sulfur

3.4 Example of A Heterotrophic Bacterium Escherichia coli Domain Bacteria, Kingdom Gamma Proteobacteria A colony-forming bacillus (rod-shaped) bacterium Gram-negative A nutritional generalist - requires only a single monosaccharide (eg. glucose) as a carbon & energy source Part of the human intestinal fauna Normally beneficial, but certain strains can cause food poisoning E. coli photo gallery

3.5 Example of An Autotrophic Bacterium Nostoc sp. Domain Bacteria, Kingdom Cyanobacteria A filamentous spherical (coccus) species Filaments are also called trichomes Trichomes form gelatinous colonies Contains the pigment chlorophyll for oxygenic photosynthesis Demonstrates “metabolic cooperation” Most cells perform photosynthesis Specialized cells called heterocysts perform nitrogen fixation The conversion of atmospheric N 2 to NH 3 O 2 deactivates enzymes for nitrogen fixation A very independent organism Needs only light energy from its environment, makes everything else

Nostoc sp. Photo Gallery