Prokaryotic Diversity and Phylogeny: Bacteria and Archaea

Prokaryotic Diversity and Phylogeny

Introduction to Prokaryotic Domains

Prokaryotes are divided into two major domains: Bacteria and Archaea. Molecular systematics, especially the analysis of small-subunit ribosomal RNA, revealed that Archaea are genetically more closely related to Eukaryotes than to Bacteria. This division is fundamental to understanding the evolutionary relationships among all life forms.

• Bacteria: One of the two prokaryotic domains, characterized by unique cell wall structures and metabolic diversity.

• Archaea: The other prokaryotic domain, sharing some traits with Bacteria and others with Eukaryotes, but also possessing unique features due to billions of years of divergence.

• Eukarya: The domain containing all eukaryotic organisms, genetically closer to Archaea than to Bacteria.

Example: The phylogenetic tree based on ribosomal RNA sequences shows the evolutionary relationships among Bacteria, Archaea, and Eukarya.

Comparison of Characters Among Domains

Key Cellular and Molecular Features

Distinctive characteristics separate Bacteria, Archaea, and Eukarya. These include cell structure, membrane composition, genetic machinery, and environmental adaptations.

Characteristic	Bacteria	Archaea	Eukarya
Nuclear envelope	Absent	Absent	Present
Membrane-enclosed organelles	Absent	Absent	Present
Peptidoglycan in cell wall	Present	Absent	Absent
Membrane lipids	Unbranched hydrocarbons	Some branched hydrocarbons	Unbranched hydrocarbons
RNA polymerase	One kind	Several kinds	Several kinds
Initiator amino acid for protein synthesis	Formyl-methionine	Methionine	Methionine
Introns in genes	Rare	Present in some genes	Present
Growth at >100°C	No	Some species	No

Archaea

Unique Features and Evolutionary Relationships

Archaea share traits with both Bacteria and Eukaryotes, but also possess unique characteristics due to extensive evolutionary divergence. The Lokiarchaeota group, part of the TACK supergroup, is considered closely related to eukaryotes.

• Lokiarchaeota: Paraphyletic group close to the origin of eukaryotes.

• Archaea have unique membrane lipids and genetic machinery.

Example: Prometheoarchaeum syntrophicum is a member of Lokiarchaeota, providing clues to the origin of eukaryotes.

Extremophiles

Many archaea are extremophiles, thriving in environments with extreme conditions.

• Extreme halophiles: Live in highly saline environments (e.g., Halobacterium).

• Extreme thermophiles: Thrive in very hot environments (e.g., Pyrococcus furiosus, Sulfolobus).

Example: Hydrothermal vents and geothermal pools are habitats for thermophilic archaea.

Methanogens

Methanogens are archaea that use carbon dioxide to oxidize hydrogen, producing methane as a metabolic waste product.

• Strict anaerobes, poisoned by oxygen.

• Found in swamps, marshes, and animal guts (e.g., cattle, termites).

• Play a role as decomposers in sewage treatment.

Equation:

$CO_2 + 4H_2 \rightarrow CH_4 + 2H_2O$

Example: Methanobrevibacter smithii is a common methanogen in the human gut.

Bacteria

Overview and Major Groups

Bacteria exhibit a wide range of nutritional and metabolic modes. Most species remain undiscovered, but five major groups are recognized:

• Proteobacteria

• Chlamydias

• Spirochetes

• Cyanobacteria

• Gram-positive bacteria

Example: The phylogenetic tree of bacteria shows their evolutionary relationships and major clades.

Proteobacteria

General Features

Proteobacteria are a diverse clade of gram-negative bacteria, including photoautotrophs, chemoautotrophs, and heterotrophs. They are subdivided into five subgroups: Alpha, Beta, Gamma, Delta, and Epsilon.

Alpha Proteobacteria

• Closely associated with eukaryotic hosts.

• Rhizobium: Forms nodules in legume roots, fixing atmospheric nitrogen ($N_2$) into ammonia ($NH_3$).

• Likely gave rise to mitochondria via endosymbiosis.

Example: Pelagibacter ubique is a living relative of the ancestor that shared a common ancestor with mitochondria.

Beta Proteobacteria

• Nitrosomonas: Soil bacterium that increases nitrogen bioavailability by converting ammonium ($NH_4^+$) to nitrite ($NO_2^-$).

Equation:

$NH_4^+ \rightarrow NO_2^-$

Gamma Proteobacteria

• Includes sulfur bacteria such as Thiomargarita, which oxidize hydrogen sulfide to sulfur for ATP production.

• Contains pathogens: Legionella, Salmonella, Vibrio cholerae.

• Escherichia coli: Common in mammalian intestines, usually non-pathogenic.

Delta Proteobacteria

• Slime-secreting myxobacteria with large genomes (10-16 million nucleotides).

• Useful in antibiotic production.

• Travel in swarms to increase feeding efficiency.

Epsilon Proteobacteria

• Contains many pathogens, including Campylobacter (causes blood poisoning) and Helicobacter pylori (causes stomach ulcers).

Chlamydias

Parasitic Bacteria

Chlamydias are obligate parasites that live within animal cells. Chlamydia trachomatis causes blindness and nongonococcal urethritis (STD).

Spirochetes

Helical Heterotrophs

Spirochetes are helical-shaped bacteria, many of which are parasites.

• Treponema pallidum: Causes syphilis.

• Borrelia burgdorferi: Causes Lyme disease.

Cyanobacteria

Photoautotrophic Bacteria

Cyanobacteria are photoautotrophs that generate oxygen. They are the group from which plant chloroplasts likely evolved via endosymbiosis.

• Oscillatoria: Filamentous cyanobacterium.

Gram-Positive Bacteria

Diversity and Importance

Gram-positive bacteria include many important decomposers and pathogens.

• Actinomycetes: Decomposers in soil.

• Bacillus anthracis: Causes anthrax.

• Clostridium botulinum: Causes botulism.

• Staphylococcus and Streptococcus: Can be pathogenic.

• Mycoplasmas: Smallest known cells, lack cell walls.

• Streptomyces: Source of many antibiotics.

Example: Streptomyces produces antibiotics used in medicine.

Summary Table: Major Bacterial Groups

Group	Main Features	Examples
Proteobacteria	Gram-negative, diverse metabolism	Rhizobium, Escherichia coli, Salmonella
Chlamydias	Obligate intracellular parasites	Chlamydia trachomatis
Spirochetes	Helical, motile, some are pathogens	Treponema pallidum, Borrelia burgdorferi
Cyanobacteria	Photoautotrophs, oxygenic photosynthesis	Oscillatoria
Gram-positive bacteria	Thick cell wall, many are decomposers or pathogens	Bacillus anthracis, Streptomyces

Additional info: These notes expand on the original slides by providing definitions, examples, and context for each major group and concept. The tables have been recreated and summarized for clarity.