Archea pt2

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  • This lecture presentation and the accompanying PowerPoint slides are the exclusive copyright of Professor Omri.

  • Usage is limited to students enrolled in Introduction to Microbiology (BIOL-2026 E) during Fall term 2025 at Laurentian University.

  • Unauthorized or commercial use, including uploading to external sites, is prohibited.

Course Information

  • Course Code: BIOL-2026EL

  • Course Title: Introduction to Microbiology

  • Term: Fall 2025

  • Chapter Focus: The Archaea - Part II

  • Lecture Dates: September 24-29, 2025

Euryarchaeota: Methanogens

Overview

  • Methanogenesis is a metabolic process crucial to global biogeochemical cycles, particularly carried out by methanogens within the Euryarchaeota phylum.

Key Metabolic Pathways for Methanogens

  • Methanogens produce methane (CH₄) as a metabolic byproduct through several anaerobic reactions:

    • Acetoclastic methanogenesis:

    • Reaction: CH3OOH → CH4 + CO2

    • Process: Splitting acetate into methane and carbon dioxide.

    • Hydrogenotrophic methanogenesis:

    • Reaction: CO2 + 4H2 → CH4 + 2H2O

    • Process: Reducing carbon dioxide with hydrogen gas.

    • Methylotrophic methanogenesis:

    • Process: Utilization of other C1 compounds, such as methanol and methylamines, as substrates for methane production.

Ecological Significance

  • Strict Anaerobes: Methanogens require oxygen-free environments for survival.

  • Ubiquitous Habitats: Commonly found in:

    • Wetland soils

    • Rice paddies

    • Gastrointestinal tracts of humans and animals (notably ruminants like cows)

    • Termite guts, often in association with protozoan symbionts

    • Landfills and marine/lake sediments

Examples of Methanogenic Archaea

Methanobrevibacter smithii

  • Habitat: Human gut; contributes to intestinal gas production and nutrient metabolism.

Methanococcus maripaludis

  • Habitat: Thrives in salt marshes and saline environments; serves as a model organism for studying methanogen physiology.

Historical Context: Discovery of Methane

  • Alessandro Volta's Contributions (1776-1778): He collected “inflammable air” from marshlands around Lake Maggiore

  • Alessandro Volta (1745-1827): His work laid groundwork for understanding methane.

Emerging Archaeal Phyla

Key Examples

  • Thaumarchaeota:

    • Part of the TACK superphylum.

    • Proposed as a separate phylum for mesophilic crenarchaeotes.

  • Korarchaeota:

    • Part of the TACK superphylum.

    • Distinct 16S rRNA sequences obtained from hydrothermal environments; currently no cultivated species.

  • Nanoarchaeota:

    • Part of the DPANN superphylum.

    • Contains the sole member, Nanoarchaeum equitans, possibly one of the smallest living organisms, displaying distinct 16S rRNA sequences.

TACK and DPANN superphyla

  • TACK includes: Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota.

  • DPANN includes: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota.

Nanoarchaeum equitans

  • Discovered in hydrothermal vent north of Iceland.

  • Characteristics:

    • Obligate parasite of the crenarchaeote, Ignicoccus; measures just 0.4 μm (1% of the volume of E. coli).

    • Genome size: 0.49 Mbp.

    • Lacks metabolic genes; only carries genes for replication, transcription, and translation.

Historical Insights on Archaea

Classification Shift

  • Initially, life was divided into two groups: eukaryotes and prokaryotes.

  • Advances in ribosomal RNA sequencing revealed three distinct domains:

    • Eukarya

    • Bacteria

    • Archaea

Evolutionary Relationships

  • Many archaeal DNA replication, transcription, and translation proteins demonstrate similarities to their eukaryotic counterparts.

  • Hypothesis: Archaea and eukaryotes may have evolved from a common bacterial ancestor.

  • Morphological diversity: Archaea present varied shapes, predominantly spherical or rod-shaped, typically ranging from 0.5-5 μm in diameter.

Structural Summary of Archaea

  • Archaea possess a circular chromosome and may utilize histones for DNA packaging.

  • Plasma membranes consist of glycerol 1-phosphate with ether-linked isoprenoids; some have lipid monolayers rather than bilayers.

  • Archaeal cell walls are composed of pseudomurein, distinct from bacterial peptidoglycan, and their flagella consist of unique flagellin proteins.

Introduction to Archaea

  • Archaea represent one of the three domains of life alongside Bacteria and Eukarya.

  • Initially misclassified due to microscopic size and absence of a true nucleus.

  • Carl Woese and George Fox's exploration in the 1970s revealed the archaeal domain using 16S rRNA sequencing.

Discovery and Classification of Archaea

  • Woese and Fox traced phylogenetic relationships among microbes through 16S rRNA gene sequencing, leading to the modern three-domain classification system.

  • First recognized archaeal group: methanogens, microbes that produce methane.

Distinctive Properties of Archaea

  • Archaea are genetically distinct from Bacteria and Eukarya, thriving in extreme environments such as hot springs and deep-sea vents.

  • No known archaeal species are human pathogens.

Phylogeny and Evolutionary Trends

  • It is proposed that Archaea and Eukarya may share a common ancestor, with the first recognized archaea being methanogens, later followed by groups like crenarchaeotes and euryarchaeotes.

  • Horizontal gene transfer has had a significant impact on the evolution and shaping of archaeal genomes.

Morphology and Structure

  • Archaeal cells exhibit a variety of shapes including rods, spheres, and spirals, generally ranging in size from 0.5 to 5 micrometers. Exceptions include Nanoarchaeum equitans and Thermoproteus.

  • Archaea possess histone proteins, akin to those in eukaryotes but display distinct mechanisms for DNA wrapping.

Archaeal Cell Envelope

  • Archaeal plasma membranes can consist of either bilayers or monolayers, adapted for stability in extreme conditions.

  • Unique outer membrane structures in some archaea, such as Ignicoccus, house ATP synthase.

Archaeal Cell Wall and Surface Structures

  • The archaeal cell wall differs from bacterial peptidoglycan; some archaea employ pseudomurein.

  • Structural features like S-layers and cannulae facilitate surface interactions, protection, and adhesion.

Archaeal Flagella

  • Archaeal flagella are thinner than their bacterial equivalents and are composed of multiple flagellin proteins.

  • They are theorized to grow from the base, contrasting with the growth process in bacterial flagella.

Diversity of Archaea

Key Phyla

  • Major Phyla Include:

    • Crenarchaeota: Thermophiles adapted to high temperatures, containing tetraether lipids and often monolayers in their membranes.

    • Euryarchaeota: Contains halophiles (salt-loving) and methanogens (crucial in carbon/nitrogen cycles).

    • Thaumarchaeota: Specializes in ammonia oxidation, contributing significantly to the nitrogen cycle.

    • Korarchaeota and Nanoarchaeota: Remain enigmatic; no cultivated representatives yet identified; determined through 16S rRNA sequences.

Impact and Significance of Archaea

  • Archaea challenge traditional perceptions regarding the evolutionary tree of life.

  • Discoveries in this domain highlight their ecological significance and remarkable adaptability.

Upcoming Content

  • Course Code: BIOL-2026EL

  • Next Chapter: Chapter 3 - Eukaryal Microorganisms

  • Dates: October 01-06, 2025

  • Presented by: A. Omri