Phylogenetic Diversity of Microorganisms: Bacteria, Archaea, and Eukarya

Phylogenetic Diversity of Bacteria

Phylum: Bacteroidota

The phylum Bacteroidota (formerly known as Bacteroidetes) is a major group of Gram-negative bacteria found in diverse environments. Members of this phylum play important roles in the degradation of complex organic materials and are prominent in the human gut microbiome.

• Gram-negative: These bacteria possess a thin peptidoglycan layer and an outer membrane containing lipopolysaccharides.

• Non-sporulating: They do not form spores.

• Metabolism: Most are obligately anaerobic or fermentative, meaning they thrive in environments without oxygen and obtain energy by fermentation.

• Distribution: Found everywhere in nature, including soil, water, and animal intestines.

Example: Bacteroides species are dominant in the human gut and are essential for the digestion of complex polysaccharides.

Order: Cytophagales

Cytophagales are Gram-negative rods known for their gliding motility and ability to degrade cellulose.

• Habitat: Found in toxic soils and freshwater environments.

• Role: Major contributors to cellulose digestion in nature.

• Pathogenicity: Some species can affect stressed fish in polluted waters (e.g., Cytophaga psychrophila).

Order: Flavobacteriales

Flavobacteriales are Gram-negative bacteria that degrade complex polysaccharides and are common in marine and polar environments.

• Metabolism: Many are psychrophilic (cold-loving) or psychrotolerant.

• Role: Agents of food spoilage due to their ability to break down organic matter.

Order: Sphingobacteriales

Sphingobacteriales are similar to Flavobacteriales but are distinguished by their ability to degrade a wider range of complex polysaccharides.

Phylogenetic Diversity of Archaea

Archaea are a domain of single-celled microorganisms distinct from Bacteria and Eukarya. They are known for their ability to thrive in extreme environments and possess unique biochemical traits.

Main Archaeal Phyla

• Euryarchaeota: Includes methanogens, halophiles, and thermophiles. Most cultured archaeal species belong to this phylum.

• Thaumarchaeota: Contains ammonia-oxidizing archaea important in nitrogen cycling.

• Crenarchaeota: Includes many thermophilic and acidophilic species.

• Asgard Archaea: Recently discovered group, important for understanding the evolution of eukaryotes.

Key Archaeal Traits

• Membrane Lipids: Archaeal membranes contain ether-linked lipids, which are more stable in extreme conditions.

• Cell Wall: Lack peptidoglycan; some have pseudopeptidoglycan or protein-based cell walls.

• Polymerases: Archaeal DNA polymerases resemble those found in Eukarya.

• Extremophily: Many archaea are adapted to high temperatures, salinity, or acidity.

Methanogenic Archaea

Methanogens are archaea that produce methane ($CH_4$) as a metabolic byproduct in anaerobic conditions.

• Habitats: Sediments, wetlands, rice paddies, wastewater treatment plants, and animal digestive tracts.

• Orders: Includes Methanobacteriales, Methanococcales, Methanomicrobiales, and others.

• Metabolism: Use substrates such as carbon dioxide ($CO_2$) and hydrogen ($H_2$) to produce methane.

Equation for Methanogenesis:

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

Halophilic Archaea

Halophiles are archaea that require high salt concentrations for growth.

• Minimum Salt Requirement: At least 9% NaCl (seawater is ~2.5%).

• Habitats: Salt lakes, marine salterns.

• Adaptations: Produce pigments for UV protection and have specialized proteins for osmotic balance.

Thermophilic and Acidophilic Archaea

Some archaea thrive at temperatures above 80°C and/or at very low pH.

• Examples: Thermoplasma (lacks cell wall, grows at pH below 1), Ferroplasma (acidophilic, iron-oxidizing).

• Habitats: Self-heating refuse piles, acidic mine drainage.

Phylogenetic Diversity of Eukarya

Eukarya is the domain that includes all organisms with complex cells containing a nucleus and organelles. Eukaryotic diversity is organized into several major clades.

Major Eukaryotic Groups

• Stramenopiles: Includes diatoms, brown algae, and oomycetes.

• Alveolata: Includes ciliates, dinoflagellates, and apicomplexans.

• Rhizaria: Includes foraminifera and radiolarians.

• Excavates: Includes diplomonads and parabasalids.

• Amoebozoa: Includes amoebae and slime molds.

• Opisthokonta: Includes animals, fungi, and related protists.

Note: These are not strict taxonomic ranks but clusters of related phyla.

Excavates: Diplomonads and Parabasalids

Excavates are a diverse group of unicellular eukaryotes, many of which are anaerobic and lack typical mitochondria.

• Diplomonads: Have two nuclei of equal size and reduced mitochondria (mitosomes). Example: Giardia intestinalis, a common cause of intestinal disease.

• Parabasalids: Possess a hydrogenosome, an organelle that produces ATP via fermentation and releases hydrogen gas. Example: Trichomonas vaginalis, causes the sexually transmitted disease trichomoniasis.

Additional info: Hydrogenosomes are thought to have evolved from mitochondria and are found in anaerobic eukaryotes.

Structural Features of Eukaryotes

• Golgi Apparatus: Provides structural support and is involved in protein modification and sorting.

• Mitochondria: Organelles responsible for aerobic respiration and energy production.

• Cellular Organization: Eukaryotes can be unicellular or multicellular. Example: Brown algae form kelp forests.