Bacteria and Archaea: Diversity, Structure, and Ecological Roles

Bacteria and Archaea: Diversity, Structure, and Ecological Roles

Overview of the Three Domains of Life

The three domains of life—Bacteria, Archaea, and Eukarya—represent the major evolutionary lineages on Earth. Bacteria and Archaea are both prokaryotic, lacking a nucleus, while Eukarya includes all eukaryotic organisms.

• Bacteria: Single-celled prokaryotes, highly diverse, found in nearly all environments.

• Archaea: Single-celled prokaryotes, often extremophiles, more closely related to Eukarya than to Bacteria.

• Eukarya: Organisms with a true nucleus and membrane-bound organelles.

• Evolutionary Relationships: Archaea and Eukarya share features such as histones and similar ribosomal proteins, indicating a closer evolutionary relationship.

Prokaryotic Cell Structure and Diversity

Prokaryotes are characterized by their small size (1-5 μm), simple cell structure, and rapid cell division. They exhibit a wide variety of shapes and arrangements.

• Major Shapes:

  • Coccus: Spherical

  • Bacillus: Rod-shaped

  • Spiral: Includes spirochaetes (flexible) and spirilli (rigid)

• Cell Wall Types:

  • Gram-positive: Thick peptidoglycan wall, stains purple, sensitive to penicillin.

  • Gram-negative: Thin peptidoglycan wall, resistant to penicillin.

• Membrane Linkages: Archaea have ether linkages, making their membranes more resistant to extreme conditions.

Extremophiles and Specialized Prokaryotes

Many Archaea and some Bacteria are extremophiles, thriving in environments with extreme temperature, salinity, or acidity.

• Halophiles: Thrive in high-salt environments.

• Thermophiles: Thrive in high-temperature environments.

• Methanogens: Produce methane as a metabolic byproduct.

Ecological Roles of Prokaryotes

Prokaryotes play essential roles in ecosystems as decomposers, producers, nitrogen fixers, and in various symbiotic relationships.

• Decomposers: Break down dead organic matter, releasing minerals for reuse.

• Producers: Cyanobacteria and other photosynthetic bacteria generate organic compounds and oxygen.

• Nitrogen Fixers: Convert atmospheric nitrogen ($N_2$) into ammonia ($NH_3$), making nitrogen available to plants.

• Pathogens: Some bacteria cause diseases such as cholera, leprosy, and pneumonia.

• Symbioses: Prokaryotes form mutualistic, commensal, and parasitic relationships with other organisms.

Horizontal Gene Transfer in Prokaryotes

Horizontal gene transfer (HGT) is a process by which prokaryotes acquire genetic material from other organisms, contributing to genetic diversity and evolution.

• Transformation: Uptake of free DNA from the environment.

• Conjugation: Direct transfer of DNA between cells via cell-to-cell contact.

• Transduction: Transfer of DNA via viral vectors (bacteriophages).

• Significance: HGT is widespread; up to 80% of prokaryotic genes have been involved in HGT.

Prokaryotic Reproduction

Prokaryotes reproduce primarily by binary fission, a simple form of asexual reproduction.

• Binary Fission: One cell divides into two genetically identical daughter cells.

• Colony Formation: Used in laboratory methods to detect and count bacteria.

Classification by Nutritional Type

Prokaryotes are classified based on their energy and carbon sources.

• Photoautotrophs: Use light energy and CO2 as a carbon source.

• Photoheterotrophs: Use light energy and organic compounds as a carbon source.

• Chemoautotrophs: Use inorganic chemicals for energy and CO2 as a carbon source.

• Chemoheterotrophs: Use organic compounds for both energy and carbon.

Classification by Oxygen Response

Prokaryotes differ in their requirements and tolerance for oxygen.

• Obligate Aerobes: Require oxygen for survival.

• Facultative Aerobes: Can use oxygen but can also survive without it.

• Obligate Anaerobes: Cannot tolerate oxygen.

• Aerotolerant Anaerobes: Do not use oxygen but are not harmed by its presence.

Major Bacterial Groups

Bacteria are classified into many phyla, with Proteobacteria and Cyanobacteria being especially important.

• Proteobacteria: Diverse group, includes many nitrogen-fixing and pathogenic species.

• Cyanobacteria: Photosynthetic bacteria, generate oxygen, gave rise to plastids in eukaryotes.

• Nitrifying Bacteria: Convert ammonia ($NH_3$) to nitrites ($NO_2^-$) and nitrates ($NO_3^-$), critical for plant growth.

Symbiotic Relationships

Prokaryotes engage in various symbiotic relationships with other organisms.

• Mutualism: Both partners benefit (e.g., bioluminescent bacteria in squid).

• Commensalism: One partner benefits, the other is unaffected.

• Parasitism: One partner benefits at the expense of the other (e.g., pathogenic bacteria).

Prokaryotes in the Global Carbon Cycle

Prokaryotes are crucial in the cycling of carbon and other elements in ecosystems.

• Producers: Cyanobacteria contribute to atmospheric oxygen and organic carbon production.

• Decomposers: Break down deaFlashcardsd organisms, releasing nutrients.

• Microbial Loop: Heterotrophic bacteria increase trophic efficiency in oceanic food webs.

Applications and Environmental Impact

Prokaryotes have significant impacts on human health and the environment.

• Pathogens: Cause diseases such as cholera, leprosy, and tooth decay.

• Bioremediation: Bacteria can break down pollutants, such as oil spills and plastics.

• Human Microbiome: Bacteria in the human body outnumber human cells and provide essential services.

Key Terms and Definitions

• Halophile: Organism that thrives in high-salt environments.

• Extremophile: Organism that lives in extreme environmental conditions.

• Thermophile: Organism that thrives at high temperatures.

• Methanogen: Archaea that produce methane.

• Decomposer: Organism that breaks down dead organic matter.

• Nitrogen Fixation: Conversion of atmospheric nitrogen ($N_2$) to ammonia ($NH_3$).

• Aerobic: Requires oxygen.

• Anaerobic: Does not require oxygen.

• Photoautotroph: Uses light energy and CO2 for growth.

• Photoheterotroph: Uses light energy and organic compounds.

• Chemoautotroph: Uses inorganic chemicals and CO2.

• Chemoheterotroph: Uses organic chemicals for energy and carbon.

• Transformation: Uptake of free DNA from the environment.

• Transduction: DNA transfer via viruses.

• Conjugation: DNA transfer via direct cell contact.

• Mutualism: Both partners benefit.

• Commensalism: One benefits, the other is unaffected.

• Parasitism: One benefits at the expense of the other.

Table: Comparison of Bacteria, Archaea, and Eukarya

Feature	Bacteria	Archaea	Eukarya
Cell Type	Prokaryotic	Prokaryotic	Eukaryotic
Membrane Lipids	Ester-linked	Ether-linked	Ester-linked
Cell Wall	Peptidoglycan	No peptidoglycan	Cellulose/chitin (if present)
Histones	Absent	Present	Present
Extremophiles	Some	Many	Few

Example: Cyanobacteria and Nitrogen Fixation

• Cyanobacteria: The only prokaryotes that generate oxygen via photosynthesis. They played a key role in the evolution of eukaryotic algae and plants by giving rise to plastids.

• Nitrogen Fixation Equation: $N_2 + 8H^+ + 8e^- + 16ATP \rightarrow 2NH_3 + H_2 + 16ADP + 16P_i$

Additional info:

• Prochlorococcus sp. is responsible for about 20% of atmospheric oxygen production.

• Plastic-eating bacteria have been discovered that can break down PET, offering solutions to environmental pollution.