Introduction to Prokaryotes and Eukaryotes

Early Taxonomy and Classification of Life

  • Early taxonomists classified all species simply as plants or animals.

  • Recently, the three-domain system has been adopted, categorizing life into:

    • Bacteria

    • Archaea

    • Eukarya

  • Out of these, there are two domains of prokaryotes:

    • Bacteria

    • Archaea

  • There is one domain of eukaryotes, which includes the kingdoms:

    • Fungi

    • Plantae

    • Animalia

  • The Tree of Life suggests that eukaryotes and archaea are more closely related to one another than to bacteria.

  • The tree is largely based on rRNA genes; however, using genes other than rRNA can reveal different relationships.

Horizontal Gene Transfer

  • Horizontal Gene Transfer (HGT) plays a significant role in evolution, defined as the movement of genes between organisms across different species.

    • It occurs through various methods:

    • Exchange of transposable elements and plasmids.

    • Viral infection.

    • Fusion of organisms.

    • Transformation.

  • HGT has been implicated in the evolution of both prokaryotes and eukaryotes.

  • An example of HGT is seen in Bdelloid Rotifers, which do not reproduce sexually, possibly using HGT as a replacement for sexual reproduction.

  • The alga Galdieria sulphuraria exemplified this by acquiring about 5% of its genes from bacterial and archaeal sources.

  • Some biologists argue that early life should be depicted as a tangled network of connected branches due to the prevalence of HGT.

Prokaryotic Diversity and Importance

  • Prokaryotes are incredibly diverse and widespread, largely microscopic, yet numerically abundant:

    • There are more prokaryotes in a handful of fertile soil than the number of humans who have ever lived.

    • They comprise more than 10 times the biomass of all eukaryotes.

    • Prokaryotes thrive in extreme conditions, such as very hot, cold, salty, acidic, or alkaline environments.

  • The colorful appearances in rocks are often due to colonies of prokaryotes.

  • Prokaryotes are essential for various ecological functions:

    • Recycling essential nutrients like carbon, nitrogen, and other chemical elements.

    • The bacteria in and on the human body are crucial for producing vitamins and protecting against disease.

  • Currently, about 10,000 prokaryotes have been adequately described, but millions remain unnamed.

  • The two major branches of prokaryote evolution are:

    • Bacteria

    • Archaea, which differ significantly in structural, biochemical, and physiological characteristics.

Current Taxonomy of Prokaryotes

  • Taxonomy now classifies prokaryotes into two domains:

    • Domain Bacteria

    • Domain Archaea

  • Bacteria and Archaea diverged early in life and exhibit fundamental differences.

  • Both domains are classified as prokaryotic due to the absence of a membrane-bound nucleus; however, many microbiologists prefer to avoid the term "prokaryote" due to its limitations.

Characteristics of Prokaryotic Cells

  • Morphology:

    • Most prokaryotes are unicellular; some species can aggregate temporarily.

    • Common shapes include:

    • Cocci (spherical)

    • Bacilli (rod-shaped)

    • Spirilla (helical)

    • Prokaryotic cells typically range from 0.5 to 5 μm in diameter, with the largest being a sulfur-metabolizing bacterium measuring 0.75 mm.

  • Cell Wall Composition:

    • Gram Stain:

    • A valuable tool for classifying bacteria based on cell wall composition.

    • Gram-positive bacteria have simpler and thicker cell walls with large amounts of peptidoglycan.

    • Gram-negative bacteria have complex outer membranes and less peptidoglycan.

    • Differences in wall composition affect susceptibility to antibiotics, as antibiotics may target peptidoglycan synthesis.

Surface Structures of Prokaryotic Cells

  • The capsule, sheath, or glycocalyx is a sticky layer of polysaccharides or proteins that helps adhere prokaryotes to surfaces and other cells, improving colonization and resistance to host defenses.

  • Fimbriae or pili are appendages that allow prokaryotes to adhere to other cells or surfaces and can be involved in genetic transfer through conjugation.

  • Mobility:

    • Approximately half of prokaryotes are capable of directional movement, typically using flagella.

    • The structure of bacterial flagella consists of chains of proteins in a spiral, with rotation driven by proton movement across the membrane.

Prokaryotic Genetics and Reproduction

  • Genomic Structure:

    • Prokaryotic cells have a simpler organization, lacking membrane-bound organelles and typically having a single, circular chromosome.

    • The nucleoid region contains a concentrated mass of DNA and may also include plasmids, which can harbor genes that confer resistance to antibiotics.

  • Genetic Diversity Mechanisms:

    • Prokaryotes exhibit diversity through rapid reproduction, genetic recombination, and mutation:

    • Transformation: Uptake of foreign DNA from the environment.

    • Transduction: Gene transfer mediated by bacteriophages.

    • Conjugation: Direct transfer of DNA between cells via a pilus.

Growth and Population Dynamics

  • Prokaryotes reproduce asexually via binary fission, capable of rapid population growth rates under optimal conditions (as short as 20 minutes).

  • The combination of rapid reproduction and genetic variation allows prokaryotes to adapt quickly to environmental changes.

  • E. coli experiments have shown that mutations can arise frequently within short generation times, leading to significant phenotypic changes through natural selection.

Nitrogen Cycle and Prokaryotic Contributions

  • Prokaryotes play a critical role in the nitrogen cycle:

    • Nitrogen-fixing bacteria, such as Rhizobium, convert atmospheric nitrogen (N2) to usable ammonium (NH4+).

    • Nitrifying bacteria convert ammonium to nitrite (NO2-) and nitrate (NO3-).

    • Bacterial activity is essential for plant nitrogen uptake, making atmospheric nitrogen accessible to other organisms.

  • The overall nitrogen fixation equation can be summarized as follows:
    N2 + 8e^- + 8H^+ + 16ATP → 2NH3 + H_2 + 16ADP + 16Pi

Environmental and Ecological Roles of Prokaryotes

  • Bioremediation: Certain prokaryotes, particularly anaerobic bacteria, are effective in decomposing organic pollutants, playing a crucial role in environmental clean-up efforts.

  • Prokaryotes can also significantly affect the oxygen levels in their environment through varied metabolic pathways:

    • Obligate aerobes require oxygen (e.g., nitrifying bacteria).

    • Facultative anaerobes can function with or without oxygen (e.g., E. coli).

    • Obligate anaerobes are poisoned by oxygen (e.g., Clostridium).

  • Prokaryotic processes such as nitrogen fixation and decomposition are vital for maintaining ecosystem balance and environmental integrity.

Pathogenic Prokaryotes

  • Pathogenic prokaryotes can cause infections through the release of exotoxins or endotoxins:

    • Exotoxins can cause illness even if the organism is not present in the body (e.g., botulinum toxin).

    • Endotoxins are released when bacteria die, often associated with the bacterial cell wall (e.g., Salmonella).

  • Pathogenic bacteria are responsible for a significant portion of human diseases; they are also potential agents of bioterrorism.

  • The Great Plate Count Anomaly highlights the disparity between the number of prokaryotes detected via culture methods and those found through molecular techniques, emphasizing the prevalence of unculturable prokaryotes in various environments.

  • Discovery and understanding of bacterial roles in human health lead to applications like bacteriotherapy, where fecal transplants are used to restore beneficial gut microbiota after antibiotic-induced dysbiosis.