🦠Microbiology Unit 4 – Prokaryotic Diversity

Key Concepts and Definitions

• Prokaryotes are single-celled organisms that lack a membrane-bound nucleus and other membrane-bound organelles
• Prokaryotic cells are generally smaller and simpler than eukaryotic cells, typically ranging from 0.1 to 5.0 micrometers in diameter
• Prokaryotes are divided into two domains: Bacteria and Archaea, which differ in their cell wall composition, membrane lipids, and other cellular features
• Prokaryotic genomes are typically circular DNA molecules located in the cytoplasm, called the nucleoid
• Prokaryotes reproduce asexually through binary fission, where the cell divides into two identical daughter cells
• Horizontal gene transfer allows prokaryotes to exchange genetic material between individuals through mechanisms such as conjugation, transformation, and transduction

Prokaryotic Cell Structure

• Prokaryotic cells have a cell wall composed of peptidoglycan (in bacteria) or pseudopeptidoglycan (in archaea) that provides structural support and protection
• The cell membrane of prokaryotes is a phospholipid bilayer that serves as a selective barrier and contains essential proteins for various cellular functions
  • Bacterial membranes contain phospholipids with ester-linked fatty acids, while archaeal membranes have ether-linked isoprenoid lipids
• Prokaryotic cells may possess additional surface structures such as capsules, slime layers, or S-layers that provide protection and aid in attachment to surfaces
• Prokaryotic cells often have appendages such as flagella for motility, pili for attachment and DNA transfer, and fimbriae for adhesion to surfaces
• Ribosomes in prokaryotes are smaller (70S) than those in eukaryotes and are the sites of protein synthesis
• Some prokaryotes have specialized structures such as gas vesicles (for buoyancy), magnetosomes (containing magnetic particles), or carboxysomes (for carbon fixation)

Classification and Taxonomy

• Prokaryotes are classified based on various characteristics, including morphology, physiology, genetics, and molecular phylogeny
• The three-domain system, proposed by Carl Woese, divides life into Bacteria, Archaea, and Eukarya based on differences in ribosomal RNA sequences
• Within the domains Bacteria and Archaea, prokaryotes are further classified into phyla, classes, orders, families, genera, and species
• Bacterial nomenclature follows the binomial system, with the genus name capitalized and the species name lowercase (e.g., Escherichia coli)
• Prokaryotic species are defined based on DNA-DNA hybridization, 16S rRNA gene sequence similarity, and average nucleotide identity (ANI)
  • Strains within a species typically share >70% DNA-DNA hybridization, >97% 16S rRNA gene sequence similarity, and >95% ANI
• Bergey's Manual of Systematic Bacteriology is a widely used reference for the classification and identification of prokaryotes

Metabolic Diversity

• Prokaryotes exhibit a wide range of metabolic capabilities, allowing them to thrive in diverse environments
• Prokaryotes can be classified based on their energy source (phototrophs or chemotrophs) and carbon source (autotrophs or heterotrophs)
  • Phototrophs obtain energy from light, while chemotrophs obtain energy from chemical compounds
  • Autotrophs fix carbon dioxide into organic compounds, while heterotrophs rely on organic compounds as their carbon source
• Prokaryotes can be further classified based on their electron donors (lithotrophs or organotrophs) and electron acceptors (aerobic or anaerobic respiration, fermentation)
• Some prokaryotes are obligate aerobes (require oxygen), while others are obligate anaerobes (cannot tolerate oxygen) or facultative anaerobes (can grow with or without oxygen)
• Prokaryotes play crucial roles in biogeochemical cycles, such as the carbon, nitrogen, and sulfur cycles, through their diverse metabolic activities
• Extremophilic prokaryotes have adapted to thrive in extreme environments, such as high temperatures (thermophiles), low temperatures (psychrophiles), high salinity (halophiles), or extreme pH (acidophiles or alkaliphiles)

Ecological Roles and Habitats

• Prokaryotes are ubiquitous and can be found in virtually every habitat on Earth, from the deep ocean to the human gut
• Prokaryotes play essential roles in ecosystems as primary producers (through photosynthesis or chemosynthesis), decomposers (breaking down organic matter), and symbionts (forming mutually beneficial relationships with other organisms)
• In aquatic environments, prokaryotes are involved in nutrient cycling, organic matter decomposition, and the formation of microbial mats or biofilms
• Soil prokaryotes contribute to soil fertility, plant growth promotion, and the degradation of pollutants
• Prokaryotes are also found in extreme environments, such as hot springs, deep-sea hydrothermal vents, and hypersaline lakes, where they have adapted to harsh conditions
• Many prokaryotes form symbiotic relationships with other organisms, such as nitrogen-fixing bacteria in legume root nodules or the gut microbiome in humans and other animals
• Prokaryotes can also cause diseases in plants, animals, and humans, acting as pathogens or opportunistic pathogens when host defenses are compromised

Prokaryotic Evolution and Adaptation

• Prokaryotes are believed to have originated over 3.5 billion years ago and were the first forms of life on Earth
• The evolution of prokaryotes has been shaped by various mechanisms, including mutation, recombination, and horizontal gene transfer
  • Mutations can introduce genetic variation, while recombination and horizontal gene transfer allow for the exchange of genetic material between individuals or even between different species
• Prokaryotes have a remarkable ability to adapt to changing environments through the acquisition of new genes or the modification of existing ones
• Antibiotic resistance is a prime example of prokaryotic adaptation, where bacteria acquire resistance genes or develop mutations that confer resistance to antibiotics
• Prokaryotic evolution has also been influenced by their interactions with other organisms, such as the development of symbiotic relationships or the co-evolution of pathogens and their hosts
• The study of prokaryotic evolution relies on comparative genomics, phylogenetic analysis, and the identification of conserved and variable genomic regions

Notable Prokaryotic Groups

• Cyanobacteria are photosynthetic bacteria that played a crucial role in the oxygenation of Earth's atmosphere and are important primary producers in aquatic environments
• Proteobacteria are a diverse phylum of Gram-negative bacteria that include many important pathogens (e.g., Escherichia, Salmonella, Vibrio) as well as beneficial symbionts (e.g., Rhizobium)
• Firmicutes are a phylum of Gram-positive bacteria that include notable genera such as Bacillus, Clostridium, and Staphylococcus, which are important in food production, biotechnology, and human health
• Actinobacteria are Gram-positive bacteria known for their ability to produce secondary metabolites, including antibiotics (e.g., Streptomyces), and for their role in soil ecology and plant interactions
• Archaea were initially discovered in extreme environments but are now known to be widespread in various habitats, including the human gut and ocean waters
  • Methanogens are archaeal microorganisms that produce methane as a metabolic byproduct and are important in anaerobic environments and the global carbon cycle
• Chlamydiae are obligate intracellular bacteria that cause diseases such as chlamydia and trachoma in humans and are also found in a wide range of animal hosts
• Spirochetes are a phylum of spiral-shaped bacteria that include the causative agents of Lyme disease (Borrelia), syphilis (Treponema), and leptospirosis (Leptospira)

Applications and Importance in Microbiology

• Prokaryotes are essential in biotechnology, where they are used to produce a wide range of products, such as antibiotics, enzymes, and recombinant proteins
• Genetic engineering techniques allow for the modification of prokaryotic genomes to enhance their production capabilities or to introduce novel functions
• Prokaryotes are used in bioremediation to degrade pollutants and clean up contaminated environments, such as oil spills or heavy metal contamination
• In agriculture, prokaryotes are used as biofertilizers (e.g., nitrogen-fixing bacteria) and biopesticides (e.g., Bacillus thuringiensis) to promote plant growth and control pests
• Probiotics are beneficial prokaryotes that are consumed to improve gut health and boost the immune system, such as Lactobacillus and Bifidobacterium species
• Prokaryotes are crucial in food production, including the fermentation of dairy products (e.g., yogurt, cheese), the production of fermented vegetables (e.g., pickles, sauerkraut), and the brewing of beer and wine
• The study of pathogenic prokaryotes is essential for understanding the mechanisms of infection, developing diagnostic tools, and discovering new antimicrobial agents to combat bacterial diseases
• Prokaryotic research has also contributed to our understanding of fundamental biological processes, such as DNA replication, transcription, translation, and gene regulation, which have implications for all life forms