Archaeal Diversity

Chapter 19 Part 1: Archaeal Diversity

Chapter Overview

  • Archaeal diversity at a glance

  • TACK Hyperthermophiles: Eat sulfur

  • Thaumarchaeota: Ammonia oxidizers and animal symbionts

  • Euryarchaeota: Methanogens from gut to globe

  • Haloarchaea and other euryarchaeotes: Underground and under ocean

  • DPANN symbionts, Altiarcheales, and Asgard: Possible connection to eukaryotes?

Introduction

  • Archaea are recognized as the most ecologically diverse among the three domains of life, featuring:

    • Psychrophiles: thrive in cold environments

    • Hyperthermophiles: thrive in high-temperature environments

    • Halophiles: thrive in high-salt environments

    • Acidophiles: thrive in acidic environments

    • Methanogens: produce methane as a metabolic byproduct

  • Archaea are also abundant in moderate habitats such as:

    • Open oceans

    • Soil

    • Surface of plant roots

  • Notably, the archaeal domain lacks known human pathogens, but it has notable representatives in the human microbiome.

Archaeal Diversity at a Glance

  • Shared Traits with Other Domains:

    • Archaea share many metabolic features like redox metabolism with bacteria.

    • Core traits of their DNA-RNA machinery and transcription factors are similar to those in eukaryotes.

  • Archaeal Signatures:

    • Unique traits found in Archaea include ether-linked membrane lipids, which differ from structures found in bacteria.

Ether-Linked Isoprenoid Membranes

  • The most distinctive structural feature of Archaea is their ether-linked membrane:

    • Utilization of L-glycerol instead of D-glycerol.

    • Employ ether (R–O–R) linkages rather than ester (R–COO–R) linkages.

    • Constructed from isoprenoid units, with branching occurring at every fourth carbon.

    • Membranes may contain cross-linked lipids such as:

    • Macrocyclic diether

    • Tetraether

    • Potential presence of cyclopentane rings.

Archaeal Gene Structure and Regulation

  • Genomic characteristics:

    • Archaea have genomes that resemble bacterial genomes in size and density, but they share several features with eukaryotes:

    • Certain tRNA genes are interrupted by introns.

    • DNA and RNA polymerases are similar to those in eukaryotes.

    • Presence of histone homologs.

  • Unique genetic traits of Archaea include:

    • The “reverse gyrase” enzyme, prevalent in hyperthermophiles, which maintains positive supercoils at high temperatures.

    • Distinctive modified bases in their tRNA molecules (e.g., Archaeosine, a guanosine analog).

Reverse Gyrase

  • The reverse gyrase performs the following actions: A. Catalyzes DNA strand breakage. B. Passes the complementary strand through the gap, adding one helical turn. C. The broken strand is ligated.

    • The overall reaction expends one molecule of ATP.

Genetic Enzyme Complexes of Archaea versus Eukarya

  • Comparison of RNA polymerase (RNAP) from various domains:

    • Derived from:

    • Bacterium: Escherichia coli (PDB ID: 4YG2)

    • Archaeon: Thermococcus kodakarensis (PDB ID: 4QIW)

    • Eukaryote: Polymerase II from Saccharomyces cerevisiae (PDB ID: 1WCM)

  • Color coding indicates orthologous subunits shared between organisms.

Phylogeny of Archaea

  • DNA sequencing efforts of uncultured organisms are revealing a growing number of previously unknown phylla.

    • Assembly of metagenomes from mixed samples has enabled the construction of “genomic bins” approximating the genomes of uncultured organisms.

    • Sequencing of single-cell genomes has confirmed that the genomes pertain to individual organisms.

  • Phylogenetic trees suggest high similarity between Eukarya and the archaeal phylum Lokiarchaeota.

  • Archaeal genomes are highly “recombinogenic,” often harboring large segments derived from bacteria through horizontal gene transfer.

TACK Superphylum: Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota

  • Characteristics:

    • This superphylum includes major clades of Archaea that thrive at temperatures above 90°C.

    • Common habitats include:

    • Marine hydrothermal vents

    • Hot springs

    • Many within this group metabolize sulfur through:

    • Anaerobic reduction

    • Aerobic oxidation

    • Substantial proportions are mesophilic and contribute significantly to the global carbon cycle through establishment in various environments.

  • Key features of Thaumarchaeota:

    • Ammonia-oxidizing archaea (AOA) are pivotal in the nitrogen cycle.

    • Metabolism utilizes distinctive pathways based on variants of the Entner-Doudoroff (ED) and Embden-Meyerhof-Parnas (EMP) pathways.

Glucose Catabolism in Archaea

  • Specific metabolic pathways include:

    • Sulfolobus and Thermoplasma species catabolize glucose to pyruvate through a modified ED pathway, yielding no net ATP.

    • Halobacterium species phosphorylate 2-oxo-3-deoxygluconate yielding one net ATP via EMP pathway stage 2.

    • Pyrococcus furiosus oxidizes glyceraldehyde 3-phosphate using ferredoxin instead of NAD+ and avoids phosphorylation.

TACK Hyperthermophiles Eat Sulfur

  • Habitats: Most prevalent in:

    • Hot springs

    • Undersea hydrothermal vents

  • Key features for hyperthermophiles include:

    • Low oxygen content

    • Presence of reduced minerals

    • Acidity

    • Steep temperature gradients

  • Microbial Adaptations:

    • Barophiles at hydrothermal vents must also thrive under high pressure.

Crenarchaeota: Desulfurococcales

  • Characteristics of the order Desulfurococcales:

    • Lack typical cell walls but possess elaborate S-layers.

    • Membranes contain diethers and tetraethers, accommodating higher thermodynamic favorability for sulfur redox reactions.

  • Predominantly hyperthermophiles that are obligate anaerobes and sulfur metabolizers, often discovered in solfataric environments and hydrothermal vents.

  • Key members include:

    • Pyrolobus “Strain 121”:

    • Isolated from hot springs and anaerobically reduces elemental sulfur (S0) to sulfide (HS–).

    • Ignicoccus islandicus:

    • A marine organism with a unique periplasmic space containing membrane vesicles; it acts as a lithotroph by oxidizing hydrogen with sulfur.

Sulfolobales

  • Features of Sulfolobales include:

    • Organisms that oxidize sulfur rather than reducing it as seen in Desulfurococcus.

    • Grow in hot temperatures (80°C–90°C) within volcanic vents.

  • Specific organisms:

    • Sulfolobus solfataricus:

    • A double extremophile thriving at 80°C and pH 2, oxidizes S0 or H2S to produce sulfuric acid.

    • Lacks conventional cell walls, relying solely on an S-layer of glycoprotein composed mainly of tetraethers that may incorporate cyclopentane rings.

  • Archaella:

    • These structures, akin to bacterial flagella, are constructed of helical filaments that gain kinetic propulsion from a motor embedded in the membrane.

Viral Infections in Sulfolobus Species

  • Viral Interactions:

    • Sulfolobus species are susceptible to various archaeal viruses, including turreted icosahedral viruses.

    • Following lysis, the S-layer is typically the remaining intact structure of the ruptured cell.

    • Another virus, fusellovirus, characterized by its spindle shape, is unique to archaea.

    • Provides an example of positive supercoiled DNA, essential in maintaining structural integrity at elevated temperatures.

Barophilic Vent Hyperthermophiles

  • Most extreme hyperthermophiles are barophiles found near hydrothermal vents on the ocean floor.

  • Black smokers as common features:

    • Contribute to high temperatures exceeding 400°C.

    • FeS precipitates from cooling water, fostering microbial growth.

Common Adaptations and Research Methods

  • Specialized equipment is necessary for studying hyperthermophiles from black smoker vents, notably:

    • A robotic system with a collection arm and a pressurized sampling device.

Thermophilic Examples

  • Key members of the Desulfurococcales include:

    • Pyrodictium species, reducing sulfur to H2S either with molecular hydrogen or organic compounds while forming interconnecting cannulae.

Conclusion

  • The diversity of archaea, from hyperthermophiles eating sulfur to ammonia-oxidizing Thaumarchaeota, illustrates their ecological significance and adaptability to extreme conditions.

  • Future studies will continue to reveal the intricate relationships these organisms have with each other and their environments.