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Lecture Overview

This document outlines key concepts discussed in Lecture 13 of BIO104 Cellular and Microbial Biology at Swansea University, specifically focusing on "Archaeal Diversity" as presented by Dr. Eva Sonnenschein.

Introduction to Archaeal Diversity

The lecture covers similarities and differences between archaea, bacteria, and eukaryotes, as well as the composition and classification of archaeal organisms. Notable examples, such as thermoacidophilic archaea found in acidic pools at Yellowstone Park, are highlighted to illustrate the unique characteristics of archaea.

1. Differences and Similarities between Domains

1.1. Cellular Structure

Archaea vs. Bacteria vs. Eukaryotes: Under the microscope, archaeal and bacterial cells appear very similar. However, distinct genetic and biochemical features differentiate them.
Carl R. Woese (1928-2012): Pioneered the classification of life into domains through 16S rRNA sequencing, revealing that archaea are fundamentally distinct from bacteria, leading him to refer to them initially as "archaeabacteria," which he later deemed a misnomer.
LUCA (Last Universal Common Ancestor): Bacteria and archaea descended from this common ancestor but diverged significantly enough to occupy separate evolutionary pathways.

1.2. Characteristics of Archaea and Bacteria

Both groups are typically unicellular and lack a nucleus or membrane-bound organelles.
Both contain 70S ribosomes, comprising 50S and 30S subunits.

1.3. Archaea and Eukaryotes Similarities

Genetic and Biochemical Insights: Archaea share key molecular mechanisms with eukaryotes, such as similar DNA polymerases and RNA polymerases. Their RNA polymerase (RNAP) is structurally similar to RNAPII in eukaryotes.
Distinctive Traits of Archaea:
- None of the known archaeal species are pathogenic to plants or animals.
- Their unique cell envelope structure distinguishes them from eukaryotes and bacteria.

2. The Archaeal Cell Envelope

2.1. Structure of the Cell Envelope

Archaea Cell Envelope vs. Bacterial Cell Envelope:
- Bacterial cells possess a phospholipid bilayer, wherein a glycerol phosphate head is attached to two fatty acids.
- Archaeal cells may have either a phospholipid bilayer or, in some instances, a phospholipid monolayer, featuring long isoprenoid chains connected to glycerol phosphate heads at both ends.
Stability: Archaeal membranes, both bilayers and monolayers, exhibit heightened stability under extreme conditions, such as low pH, elevated temperatures, and high salinity, which are necessary for survival in extreme environments.

2.2. Cell Wall Composition

Walled Archaea: Some possess cell walls made from polysaccharides or pseudomurein, a compound made up of N-acetylglucosamine and N-acetyltalosaminuric acid linked by β(1-3) glycosidic bonds, rendering them resistant to lysozyme.
Wall-less Archaea: Others lack these walls and instead utilize a protein/glycoprotein S-layer, creating a protective lattice around their cell membranes.

3. Archaeal Taxonomy

3.1. Historical Context

Early classifications recognized only two phyla of archaea: Crenarchaeota (extremophiles) and Euryarchaeota (methanogens and extremophiles).

3.2. Contemporary Revisions

The discovery of new archaeal species via environmental DNA (eDNA) sequencing has led to the classification of archaea into four superphyla as per Spang et al. in their 2017 publication.
It is proposed that eukaryotes emerged from the Asgard superphylum of archaea, specifically from the lineage dubbed "Loki" (identified in 2010).

4. Archaeal Diversity and Habitats

4.1. Ecosystem Roles

Archaea manifest a remarkable diversity and abundance, capable of thriving in extreme environments but also commonly found in soil, freshwater, and marine habitats.

4.2. Notable Archaeal Groups

4.2.1. Thermoacidophiles

These archaea flourish at temperatures exceeding 70 ºC and at pH levels as low as 2.

4.2.2. Extreme Halophiles (Haloarchaea)

Require high salt concentrations (4M) for optimal growth; otherwise, they experience cell lysis.
Found in salt evaporation ponds where they produce carotenoid pigments that impart a bright red hue.
Adaptations include the use of bacteriorhodopsin, which acts as a light-driven proton pump that establishes a transmembrane proton gradient, enabling ATP synthesis via ATP synthase.

4.2.3. Methanogens

Methanogenic archaea perform a critical role in the digestive systems of ruminants, assisting in energy extraction from plant matter. They contribute significantly to global methane production, producing 10-20% of the atmospheric methane.
The anaerobic metabolism of methanogens converts carbon dioxide (CO2) to methane (CH4) with the reaction: ext{4 H}2 + ext{CO}2
ightarrow ext{CH}4 + 2 ext{H}2 ext{O}.
Methanogens are prevalent in landfills, where they contribute to methane production after solid waste deposition, comprising around 50% of gases generated, which can be captured for use as natural gas, thereby curbing greenhouse gas emission and decreasing reliance on fossil fuels.

5. Practical Laboratory Applications and Experimentation

5.1. Microbiology Lab Practical

Experiment focus: The effect of oxygen availability on bacterial nutrition and growth with observations focused on specific bacterial cultures such as E. coli and Bacillus subtilis under varied conditions.[Details omit for brevity]
Students are instructed to conduct comparative analysis and reflect on results concerning expected growth patterns under different conditions.