Microbiology - Prokaryotes

Prokaryotes Overview

Prokaryotes are the oldest and structurally simplest life forms, representing the earliest forms of cellular life on Earth. They dominated life for over a billion years before the emergence and diversification of eukaryotes, playing crucial roles in shaping Earth's early atmosphere and biogeochemical cycles. They consist of two fundamental domains: Bacteria and Archaea. Despite their ubiquitous presence, an estimated 90-99% of prokaryotic species remain unknown and uncharacterized, highlighting the vast hidden biodiversity.

General Characteristics

Prokaryotes are exclusively unicellular and predominantly single-celled organisms, though some may form colonies or filaments. Their sizes are typically very small, ranging from 0.2 to 10 \mu m, making them microscopic. A defining feature is the absence of a membrane-bound nucleus; instead, their genetic material is located in an irregularly shaped region called the nucleoid, which contains a single, circular chromosome. In addition to the main chromosome, many prokaryotes frequently possess smaller, extrachromosomal DNA molecules known as plasmids, which can carry genes for advantageous traits like antibiotic resistance or virulence factors. Most prokaryotes reproduce asexually through binary fission, a rapid process of cell division that can lead to exponential population growth. They also actively engage in horizontal gene transfer (HGT), which allows for the exchange of genetic material between unrelated organisms, significantly contributing to their genetic diversity and evolutionary adaptation.

Definitions and Terminology

Key terms are essential for understanding prokaryotic biology:

• Extremophiles: Organisms that thrive and survive in extreme environments, often uninhabitable for most other life forms. Examples include:

  • Thermophiles: Live in extremely hot environments (45-122 \text{°C}).

  • Halophiles: Live in highly saline conditions.

  • Acidophiles/Alkaliphiles: Live in very acidic or alkaline environments.

• Chemolithotrophic: Refers to organisms that obtain energy by oxidizing inorganic molecules such as ammonia (NH3), hydrogen sulfide (H2S), ferrous iron (Fe^{2+}), or nitrites (NO_2^-). This process is vital for many biogeochemical cycles.

• Trophic strategies: Describe how organisms obtain energy and carbon.

  • Heterotrophs: Obtain carbon from organic compounds produced by other organisms.

  • Autotrophs: Produce their own organic carbon from inorganic sources, typically CO_2.

An understanding of these terms helps decode prokaryotic nutritional and survival mechanisms.

Prokaryotic Cell Structure

Prokaryotic cells fundamentally lack membrane-bound organelles such as mitochondria, chloroplasts, and an endoplasmic reticulum. Instead, essential metabolic processes often occur on the plasma membrane or within the cytoplasm.

• Plasma Membrane: A selectively permeable barrier that regulates the passage of substances into and out of the cell. It also plays crucial roles in energy generation (e.g., electron transport chain, ATP synthesis) and nutrient transport.

• Internal Infoldings: In some prokaryotes (e.g., photosynthetic bacteria), the plasma membrane can form extensive internal infoldings or mesosomes, which increase surface area for metabolic activities like respiration or photosynthesis.

• Flagella: Long, whip-like appendages responsible for motility, allowing the cell to move towards or away from stimuli (chemotaxis, phototaxis). Bacterial flagella are composed of the protein flagellin and rotate like a propeller, driven by a proton motive force.

• Pili (Fimbriae): Shorter, hair-like appendages involved in attachment to surfaces (adhesion) and to other cells. Sex pili are specifically involved in conjugation, facilitating genetic exchange.

• Cell Wall: A rigid layer outside the plasma membrane that provides structural support, maintains cell shape, and protects against osmotic lysis.

  • Bacteria: Possess a cell wall primarily composed of peptidoglycan (murein), a polymer of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) linked by short polypeptide chains. This structure is targeted by many antibiotics. Bacteria are classified as Gram-positive (thick peptidoglycan layer, no outer membrane) or Gram-negative (thin peptidoglycan layer, presence of an outer membrane containing lipopolysaccharide, LPS).

  • Archaea: Have cell walls composed of various materials, but never peptidoglycan. Common components include pseudopeptidoglycan (pseudomurein), surface-layer (S-layer) proteins, glycoproteins, or other polysaccharides.

Bacteria vs. Archaea

While both are prokaryotes, Bacteria and Archaea exhibit distinct biochemical and genetic differences:

• Cell Wall Composition: Bacteria possess peptidoglycan, which is absent in Archaea. Archaea have diverse cell wall compositions, including pseudopeptidoglycan or S-layers made of proteins/glycoproteins.

• Membrane Structure: This is a major distinguishing feature. Bacterial plasma membranes are composed of ester-linked fatty acids that are unbranched. Archaeal membranes, in contrast, are characterized by ether-linked branched isoprene units, which often form lipid monolayers instead of bilayers, providing increased stability in extreme environments.

• Membrane Lipids: Bacteria use D-glycerol, while Archaea use L-glycerol.

• DNA Replication and Gene Expression: Archaea often share more similarities with eukaryotes in their molecular machinery for DNA replication, transcription, and translation, including the presence of histones in some species and structurally similar RNA polymerases. Bacteria have unique RNA polymerases and do not typically use histones to package their DNA.

• Pathogenicity: All known pathogenic prokaryotes are Bacteria; no known Archaea are human pathogens.

Prokaryotic Genetics

Prokaryotic cells rapidly adapt to changing environments and evolve through both mutation and various mechanisms of horizontal gene transfer (HGT), which allow for the exchange of genetic material between independent organisms without reproduction. Key mechanisms include:

• Transformation: The uptake of naked, foreign DNA from the environment into the bacterial cell. Pioneering work by Frederick Griffith demonstrated this phenomenon. For transformation to occur, cells must be in a state of "competence," meaning they can take up external DNA, either naturally or induced in a laboratory setting (e.g., by chemical treatment or electroporation).

• Transduction: The transfer of bacterial DNA from one bacterium to another via bacteriophages (viruses that infect bacteria). This process can be:

  • Generalized transduction: Any portion of the bacterial genome can be transferred. This occurs when a fragment of host DNA is accidentally packaged into a new phage particle during assembly.

  • Specialized transduction: Only specific genes located near the integration site of a lysogenic phage are transferred. This happens when the prophage excises imprecisely from the host chromosome, carrying adjacent bacterial genes with it.

• Conjugation: Direct cell-to-cell contact through a sex pilus (or conjugation pilus) facilitates the transfer of genetic material, typically a plasmid (e.g., F plasmid, R plasmid) or a portion of the bacterial chromosome (in Hfr cells) from a donor cell to a recipient cell. This mechanism is crucial for the rapid spread of adaptive traits.

Antibiotic Resistance: A significant consequence of prokaryotic genetics is the widespread development and dissemination of antibiotic resistance. Resistance primarily spreads through:

• R plasmids: Plasmids often carry genes encoding resistance to multiple antibiotics. These can be rapidly transferred between bacteria of the same or different species via conjugation or transformation.

• Mutations: Spontaneous mutations in chromosomal genes can confer resistance by altering drug targets, reducing drug uptake, or enhancing efflux pumps.

• Horizontal Gene Transfer: The various HGT mechanisms (transformation, transduction, conjugation) allow resistance genes to be quickly acquired and shared within bacterial populations, accelerating the evolution of superbugs.

Prokaryotic Metabolism

Prokaryotes exhibit unparalleled metabolic diversity, enabling them to inhabit virtually every environment on Earth. Their nutritional strategies define how they acquire carbon and energy. They transform energy either through chemical oxidation of electron donors or by capturing light.

Five primary nutritional types based on energy source (chemo-/photo-) and carbon source (auto-/hetero-):

1. Chemoorganoheterotrophs (Chemohetrotrophs):

   • Energy Source: Organic compounds (e.g., sugars, lipids, proteins).

   • Carbon Source: Organic compounds (from other organisms).

   • Examples: Most pathogenic bacteria, decomposers (e.g., Escherichia coli, many soil bacteria).

2. Chemolithoheterotrophs:

   • Energy Source: Inorganic compounds (e.g., H2S, NH3).

   • Carbon Source: Organic compounds.

   • Examples: Some archaea and bacteria in anoxic environments.

3. Chemolithoautotrophs (Chemoautotrophs):

   • Energy Source: Inorganic compounds (e.g., H2S, NH3, Fe^{2+}, NO_2^-).

   • Carbon Source: CO_2 (fix their own carbon).

   • Examples: Nitrifying bacteria, sulfur-oxidizing bacteria, deep-sea vent communities (e.g., Nitrosomonas spp.).

4. Photolithoautotrophs (Photoautotrophs):

   • Energy Source: Light.

   • Carbon Source: CO2 (fix their own carbon, using inorganic electron donors like H2O or H_2S).

   • Examples: Cyanobacteria, purple sulfur bacteria, green sulfur bacteria (e.g., Anabaena spp.).

5. Photoorganoheterotrophs:

   • Energy Source: Light.

   • Carbon Source: Organic compounds.

   • Examples: Some non-sulfur purple bacteria (e.g., Rhodospirillum spp.).

Beyond these, prokaryotes are central to global biogeochemical cycles, including:

• Nitrogen Fixation: Conversion of atmospheric nitrogen (N2) into ammonia (NH3), a form usable by plants.

• Nitrification: Oxidation of ammonia to nitrites and then to nitrates.

• Denitrification: Reduction of nitrates to nitrogen gas (N_2).

• Sulfur Cycle: Oxidation and reduction of various sulfur compounds.

They achieve energy transformation through processes like fermentation, aerobic respiration, and anaerobic respiration, each optimized for specific environmental conditions and electron acceptors.

Human Bacterial Diseases

Pathogenic bacteria are a significant cause of human diseases. Their ability to cause illness, or pathogenicity, involves several key steps:

1. Adherence: Pathogens attach to host cells or tissues using adhesins located on pili, fimbriae, capsules, or other surface structures.

2. Invasion: The pathogen penetrates host tissues, often by producing enzymes that degrade host cell components or by inducing host cells to internalize them.

3. Colonization: The pathogen establishes and multiplies in the host, often competing with the host's normal microbiota for nutrients and space.

4. Evasion of Immune Response: Bacteria employ various strategies to avoid destruction by the host immune system, such as forming capsules, producing proteases to degrade antibodies, varying surface antigens, or living intracellularly.

5. Damage/Disease: Pathogens cause damage to the host through several mechanisms:

   • Toxin Production:

     • Exotoxins: Proteins secreted by bacteria that can act locally or systemically (e.g., neurotoxins, enterotoxins, cytotoxins). Examples include tetanus toxin, botulinum toxin, cholera toxin.

     • Endotoxins: Lipopolysaccharide (LPS) components of the outer membrane of Gram-negative bacteria, released upon bacterial lysis. They can trigger a strong inflammatory response, leading to fever, shock, and DIC (disseminated intravascular coagulation).

   • Direct Tissue Damage: Caused by bacterial enzymes (e.g., collagenases, hyaluronidases) or host inflammatory responses.

Notable Diseases: Historically and currently, many significant human diseases are bacterial in origin:

• Tuberculosis (TB): Caused by Mycobacterium tuberculosis, primarily affecting the lungs but can disseminate. Spread via airborne droplets. Incidence is exacerbated by poor living conditions and compromised immune systems.

• Anthrax: Caused by Bacillus anthracis, a spore-forming bacterium. Can manifest as cutaneous, inhalational, or gastrointestinal forms, with inhalational anthrax being the most lethal. Primarily a disease of livestock, transmissibility to humans usually involves direct contact with infected animals or products.

• Sexually Transmitted Infections (STIs):

  • Gonorrhea: Caused by Neisseria gonorrhoeae. Can lead to pelvic inflammatory disease (PID), infertility, and systemic infections if untreated.

  • Chlamydia: Caused by Chlamydia trachomatis. Often asymptomatic, but can cause PID, infertility, and ectopic pregnancy. Both are highly prevalent globally.

Key Factors in Disease Outbreak and Prevalence:

• Sanitation: Proper hygiene, safe water, and waste management are critical in preventing the transmission of many bacterial diseases, especially enteric infections.

• Antibiotic Resistance: The increasing prevalence of antibiotic-resistant strains makes treatment challenging and contributes to higher mortality rates and prolonged illness, complicating efforts to control bacterial diseases globally.

• Vaccination: Vaccines are available for some bacterial diseases (e.g., tetanus, diphtheria, pertussis, some forms of meningitis) and are crucial for prevention.