Topic_3_Archaea_students
Page 1: Topic 3 Archaea
Page 2: Topic Overview
Distinctive properties of Archaea
Archaeal cell structure
Diversity of the Archaea
Page 3: Distinctive Properties of Archaea
Archaea visually resemble bacteria but are genetically distinct.
Many archaea thrive in extreme environments, among the most hostile on Earth.
Figure 4.1: Illustrates the various bizarre shapes of some archaea.
There are currently no known archaeal pathogens that affect humans.
Page 4: Reference Information
Wessner, Dupont, Charles, Neufeld. Microbiology, 3rd Edition. Wiley.
Page 5: Phylogeny of Archaea
Genetic comparisons using rRNA sequences establish phylogenetic relationships.
Research began in the 1970s, led by Woese and Fox; archaea were initially termed "Archaebacteria."
The first archaea discovered were methanogens, known for producing methane.
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Figure 1.8: Three domains of life illustrated: Bacteria, Archaea, and Eukarya.
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Discusses new views of the tree of life and the dramatic expansion of genome numbers.
Metagenomics and genomics have significantly improved our understanding of life's diversity by enabling the classification of uncultured organisms.
Published in Nature Microbiology; highlights the inadequacies of earlier methods of classification.
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Lists various bacterial phyla and their classifications, including many archaea with their distinct features.
Page 9: Selected Archaeons and Their Growth Requirements
Table 4.1: Lists organisms like Halobacterium and Pyrococcus furiosus, along with their habitat and specific growth requirements.
Page 10: Morphology and Structure
Archaeal cell size typically ranges from 0.5 to 5 μm in diameter but can vary significantly.
Example: N. equitans at 0.4 μm, Thermoproteus spp. can reach lengths of 100 μm.
Page 11: Cell Shape
Archaeal shapes include:
Rods
Cocci
Spirals
Irregular shapes (e.g., Sulfolobus spp.)
Rectangular shapes (e.g., Thermoproteus spp.)
Squares (e.g., Haloquadratum walsbyi)
Page 12: Visual Representation
Visual shows examples of archaeal cell sizes, highlighting a 5 μm specimen.
Page 13: Cytoplasm
Cytoplasm of Archaea contains molecules similar to bacteria, microcompartments/inclusion bodies (e.g., carbon storage, gas vacuoles).
Archaeal chromosomes are typically circular and lack a membrane-bound nucleus.
DNA replication enzymes in Archaea share similarities with those in Eukarya.
Histones have evolved as early transitions in the evolution of Archaea and Eukarya.
Page 14: Histone Structure
Displays the differing structural lengths of histone proteins in Eukaryotic versus Archaeal nucleosomes.
Page 15: Cytoskeleton
Cytoskeletal homologues identified in Archaea, some more similar to bacterial structures.
Example: Actin homolog Ta0583 resembling eukaryal actin.
Page 16: Cell Envelope
All archaea possess a plasma membrane; many have cell walls differing from bacterial structures.
Page 17: Plasma Membrane Structure
Unique bilayer composition differing from bacteria:
Glycerol-1-phosphate
Phytanyl side chains (isoprene units) with ether linkages contributing to stability in extreme environments.
Page 18: Monolayers
Some archaea possess lipid monolayers, particularly advantageous in high-temperature habitats.
Page 19: Lipid Representation
Chemical structure of archaeal membrane lipids showcased.
Page 20: Ignicoccus
Unique archaeon with outer membrane resembling Gram-negative cells. ATP synthase housed in the outer membrane.
Page 21: Cell Wall Composition
Composed of pseudomurein, similar to peptidoglycan but with notable differences, including β-1,3 linkages that resist lysozyme degradation.
Page 22: Cell Surface Structures
Archaeal cells often feature an S-layer for protection against predators and viruses, including cannulae that connect cells in networks.
Page 23: Flagellum vs. Archaellum
Comparison of bacterial flagellum (grows from tip) with archaeal flagellum (grows from base) and distinctive structural features.
Page 24: Classification of Archaea
Classification remains fluid, but four superphyla are proposed:
Euryarchaeota
TACK
DPANN
Asgard
Page 25: Diversity of Archaea
Describes four major phyla:
Euryarchaeota
Crenarchaeota
Thaumarchaeota (formerly Crenarchaeota, oxidizing ammonia)
Nanoarchaeota
Additional proposed phyla include Korarchaeota and Aigarchaeota.
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No additional notes provided.
Page 27: Crenarchaeota Temperature Preferences
Focus on thermophilic and hyperthermophilic crenarchaeotes, including examples and temperature ranges.
Page 28: Survival in Extreme Conditions
Discusses adaptations of some archaea, including:
Acidophiles (thrive at low pH)
Barophiles (thrive under high pressure).
Page 29: Adaptations for Survival
Notable adaptations for high temperatures include modified proteins, stronger chaperone complexes, and thermostable DNA-binding proteins.
Page 30: Structural Representations
Structural representations of helices and sheets in extremophilic proteins.
Page 31: Electrostatic Interactions
Depicts interactions that stabilize protein structures under extreme conditions.
Page 32: Euryarchaeota (Halophiles)
Characterization of halophilic archaea, their salt requirements, and living conditions.
Page 33: Halophilic Environments
Discusses habitats such as the Great Salt Lake and Dead Sea that have extreme salinity.
Page 34: Evaporating Ponds
Visual representation from San Francisco showcasing saline environments for halophiles.
Page 35: Osmotic Balance in Halobacterium
Illustrates inbound and outbound water dynamics in various solution types affecting halophiles.
Page 36: Intracellular K+ Role
Explains how high intracellular K+ concentrations offset high external Na+ and serve as compatible solutes.
Page 37: Protein and DNA Stability
Discusses how high K+ concentrations affect denaturation of proteins and stabilize DNA through higher GC content.
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Image Credit: Matt W. Ford
Page 39: Halobacterium and Light Energy
Describes the phototropic nature of halobacterium through bacteriorhodopsin, which produces a proton motive force (PMF).
Page 40: Chemical Structures
Comparison of retinal configurations (cis and trans) pivotal in light harnessing.
Page 41: Retinal and Metabolism
Discusses the role of retinal in vision and its metabolic use in certain microorganisms.
Page 42: Euryarchaeota (Methanogens)
Key characteristics include reducing CO2 with H2, producing methane as a byproduct.
Page 43: Methanogen Habitats
Figure 4.14: Illustrates habitats where methanogens thrive, including fungi and anaerobic environments.
Page 44: Methanogen Diversity
Highlighting diversity within methanogens due to shared metabolic properties despite differing species.
Page 45: Volta Experiment
Describes Volta's early experiment observing methane production in sediments.
Page 46: Current Research
Discusses ongoing research into greenhouse gas emissions from methane-producing lakes in Arctic regions.
Page 47: Various Habitats of Methanogens
Lists habitats including wetlands, landfills, and digestive tracts where methanogen presence is prevalent.
Page 48: Additional Methanogen Locations
Cover geothermal settings and associations with protozoan and termite guts highlighting microbial symbiosis.
Page 49: Research on Methanogens
Overview of laboratory methodologies involved in studying methanogenic archaea.
Page 50: Other Archaea and Ecological Contexts
General discussion of diversity among archaea and their ecological roles.
Page 51: Phylogeny Review
Summarizes key phyla of Archaea: Euryarchaeota, Crenarchaeota, Thaumarchaeota, and Nanoarchaeota.
Page 52: Marine Phylogenetic Relationships
Describes phylogenetic distribution of marine archaea, including specific examples.
Page 53: Textbook Classification View
Listing of several archaeal genera within main groups depicted in a phylogenetic view.
Page 54: Evolving Classification of Archaea
Updated classification showing ongoing research and adaptations of superphyla within Archaea.
Page 55: Recent Phylogenetic Developments
Discusses valid and provisional phyla per Bacteriological Code, including a comprehensive list of archaea candidates.
Page 56: Discussion on TACK Superphylum
Overview of TACK superphylum, integrating findings from recent research.
Page 57: Classification of Euryarchaeota and Korarchaeota
Illustrates key relationships and characteristics among these diverse groups.
Page 58: Thaumarchaeota Characteristics
Notes key traits of Thaumarchaeota, particularly in nitrogen cycling.
Page 59: Mesophiles and Psychrophiles
Distinguishes between mesophiles (optimal growth at moderate temps) and psychrophiles (growth in cooler temperatures).
Page 60: Emerging Archaeal Phyla
New phyla like Korarchaeota and potential classifications among mesophilic organisms.
Page 61: Ocean Contributions
Quantitative assessments of archaeal and bacterial populations in marine environments highlighting their significance in global cycling.
Page 62: Cultivation Challenges
Complications in cultivating new archaeal species, specific mention of Korarchaeota.
Page 63: Review of Asgard Superphylum
Emergent group bridging prokaryotic and eukaryotic life.
Page 64: DPANN Superphylum
Focus on small archaea with unique genomes and metabolic characteristics.
Page 65: Associated Ultra Small Archaea
Describes ARMAN, illustrating interrelationships with Euryarchaeota.
Page 66: Nanoarchaeota Characteristics
Distinct classification of Nanoarchaeota highlighting size and unique symbiotic relationships.
Page 67: Nanoarchaeum equitans Details
Discusses the discovery of this archaeon’s lifestyle, genome, and metabolic dependencies.
Page 68: Ignicoccus and Relationships
Details interactions between Ignicoccus and its obligate parasite Nanoarchaeum.
Page 69: Cellular Representation of Archaea
Overview illustrating the interactions between various archaeal groups.
Page 70: DPANN Superphylum Overview
Outlines common features of very small archaea, highlighting genomic and metabolic trends.
Page 71: Asgard Superphylum
Discusses cells considered closest evolutionary relatives to eukaryotes.
Page 72: Further Definition of Asgard
Continuation on Asgard’s relationship with eukaryotic cells, emphasizing evolutionary implications.
Page 73: Overview of Key Discoveries
Discusses how certain findings inform our understanding of early eukaryotic evolution.
Page 74: Current Research in Archaeal Genomics
Summarizes recent studies focusing on archaeology of life.
Page 75: Lokiarchaeota Significance
Emphasizes their theoretical importance in understanding the origins of complex cell life within Archaea.
Page 76: Graphical Representation of Evolution
Displays the most recent common ancestor conceptual framework leading from archaea to more complex life forms.
Page 77: Eukaryotes and Archaeal Relationships
Explains the connection between eukaryotic development and archaeal ancestors based on phylogenetic data.
Page 78: Phylogenomics and Eukaryotic Origins
Highlights research supporting a strong link between specific archaeal and eukaryotic lineages.
Page 79: Isolation of Archaeal Species
Covers breakthrough discoveries in isolating archaea thought to be crucial in eukaryotic ancestry.
Page 80: Comparative Genomic Analysis
Examines relatedness among Asgard and eukaryotes and the role of various metabolic traits.