Characterizing and Classifying Prokaryotes: Structure, Diversity, and Taxonomy

General Characteristics of Prokaryotic Organisms

Morphology of Prokaryotic Cells

Prokaryotes are the most diverse group of cellular microbes, thriving in a wide range of habitats. Although only a small fraction colonize humans and cause disease, their morphological diversity is immense. Prokaryotic cells exhibit a variety of shapes, which are important for identification and classification.

• Coccus: Spherical-shaped cells.

• Bacillus: Rod-shaped cells.

• Spirillum: Rigid, spiral-shaped cells.

• Spirochete: Flexible, spiral-shaped cells.

• Vibrio: Comma-shaped cells.

• Coccobacillus: Short, oval rods.

• Pleomorphic: Cells that vary in shape.

• Star-shaped: Rare, star-like morphology.

Additional info: Morphological diversity aids in adaptation to various environments and can influence pathogenicity.

Endospores

Endospores are highly resistant, dormant structures formed by certain Gram-positive bacteria, such as Bacillus and Clostridium. Each vegetative cell forms one endospore, which can later germinate into a new cell. Endospores serve as a defensive strategy against unfavorable conditions and are of significant concern in food safety and healthcare due to their resilience.

• Formation: Triggered by nutrient depletion or environmental stress.

• Resistance: Withstand heat, desiccation, chemicals, and radiation.

• Significance: Endospores are difficult to eradicate and can cause persistent contamination.

Reproduction of Prokaryotic Cells

All prokaryotes reproduce asexually, primarily through three main methods:

• Binary Fission: The most common method, involving DNA replication, elongation, and division into two identical cells.

• Snapping Division: A variation of binary fission where the inner cell wall layer forms a cross wall, and the outer layer snaps, separating the cells.

• Budding: A new cell develops from a bud on the parent cell, inheriting a copy of the DNA.

Additional info: Some actinomycetes reproduce by forming spores, which are not true endospores but serve for dispersal and survival.

Viviparity in Prokaryotes

Some prokaryotes, such as Epulopiscium, exhibit viviparity, where live offspring emerge from the mother cell. This is a unique reproductive strategy among prokaryotes and resembles early stages of endospore formation.

Arrangements of Prokaryotic Cells

The arrangement of prokaryotic cells results from the planes in which cells divide and whether daughter cells remain attached. Common arrangements include:

• Cocci: Diplococci, streptococci, tetrads, sarcinae, staphylococci.

• Bacilli: Single, diplobacilli, streptobacilli, palisade, V-shape.

Modern Prokaryotic Classification

Three Domains of Life

Modern classification of prokaryotes is based on genetic relatedness, particularly rRNA sequences. The three domains are:

• Archaea

• Bacteria

• Eukarya

Additional info: This classification reflects evolutionary relationships and molecular similarities.

Survey of Archaea

General Features

Archaea are prokaryotes distinct from bacteria. They lack true peptidoglycan, have unique membrane lipids with branched hydrocarbons, and use methionine as the start codon for protein synthesis. The two most studied phyla are Crenarchaeota and Euryarchaeota. Archaea reproduce by binary fission, budding, or fragmentation and are not known to cause disease.

Extremophiles

Many archaea are extremophiles, requiring extreme conditions such as high temperature, acidity, or salinity. Prominent groups include thermophiles and halophiles.

Thermophiles

• Grow optimally above 45°C; hyperthermophiles require temperatures over 80°C.

• Examples: Thermococcus, Pyrodictium.

Halophiles

• Inhabit environments with >9% NaCl.

• Produce red or orange pigments for protection from sunlight.

• Example: Halobacterium salinarium.

Methanogens

Methanogens are archaea that produce methane from carbon dioxide, hydrogen, and organic acids. They are important in the carbon cycle and are a major source of environmental methane, including that found in the digestive tracts of animals and in ocean sediments.

Survey of Bacteria

Deeply Branching and Phototrophic Bacteria

Deeply branching bacteria are considered among the earliest forms of life, thriving in extreme environments similar to early Earth. Phototrophic bacteria perform photosynthesis and are divided into groups based on pigments and electron donors.

• Cyanobacteria: Gram-negative phototrophs that contributed to the oxygenation of Earth's atmosphere. Some fix nitrogen.

• Green sulfur bacteria, green non-sulfur bacteria, purple sulfur bacteria, purple non-sulfur bacteria: Differ in pigments and metabolic pathways.

Additional info: Cyanobacteria are thought to be the ancestors of chloroplasts in plants and algae.

Low G + C Gram-Positive Bacteria

These bacteria have a low guanine-cytosine content in their DNA and include several medically and industrially important genera:

• Clostridia: Obligate anaerobes, many form endospores.

• Mycoplasmas: Lack cell walls, smallest free-living cells, colonize mucous membranes.

• Bacillus: Endospore-formers, includes B. thuringiensis (insecticide) and B. anthracis (anthrax).

• Listeria: Can grow at refrigeration temperatures, crosses placenta.

• Lactobacillus: Used in food production, rarely pathogenic.

• Streptococcus, Enterococcus, Staphylococcus: Common pathogens, some are multi-drug resistant.

High G + C Gram-Positive Bacteria

These bacteria have a high guanine-cytosine content in their DNA and include:

• Corynebacterium: Pleomorphic, produce metachromatic granules.

• Mycobacterium: Slow-growing, acid-fast rods due to mycolic acid in cell walls.

• Actinomycetes: Form branching filaments, important in soil ecology and antibiotic production.

Gram-Negative Proteobacteria

Overview

Proteobacteria are the largest and most diverse group of Gram-negative bacteria, divided into six classes: Alpha-, Beta-, Gamma-, Delta-, Epsilon-, and Zetaproteobacteria.

Alphaproteobacteria

• Nitrogen fixers: Azospirillum and Rhizobium associate with plant roots and convert atmospheric nitrogen to ammonia.

• Nitrifying bacteria: Nitrobacter oxidizes nitrogen compounds, important in agriculture.

• Pathogens: Rickettsia (arthropod-borne diseases), Brucella (brucellosis).

• Other genera: Acetobacter, Gluconobacter, Caulobacter.

Betaproteobacteria

• Pathogens: Neisseria (gonorrhea, meningitis), Bordetella pertussis (whooping cough), Burkholderia (opportunistic infections).

• Environmental bacteria: Thiobacillus (sulfur recycling), Zoogloea (sewage treatment), Sphaerotilus (impedes waste flow).

Gammaproteobacteria

• Purple sulfur bacteria: Phototrophic, deposit sulfur internally.

• Intracellular pathogens: Legionella pneumophila (Legionnaire's disease), Coxiella burnetii (Q fever).

• Glycolytic facultative anaerobes: Includes Escherichia coli, Salmonella, Shigella, Proteus, Klebsiella, Yersinia pestis, Vibrio cholerae, Haemophilus influenzae.

• Pseudomonads: Aerobic, flagellated rods, important pathogens and spoilage organisms.

Deltaproteobacteria

• Desulfovibrio: Reduces sulfates, produces hydrogen sulfide.

• Bdellovibrio: Predatory on other Gram-negative bacteria.

• Myxobacteria: Soil bacteria with complex life cycles, decompose organic matter.

Epsilonproteobacteria

• Campylobacter: Causes gastroenteritis and blood poisoning.

• Helicobacter: Causes gastric ulcers and increases risk of stomach cancer.

Zetaproteobacteria

Recently discovered based on DNA sequences, with Mariprofundus ferrooxydans as the only formally named species. Common in ocean environments.

Other Gram-Negative Bacteria

Chlamydias

Obligate intracellular parasites with both DNA and RNA, cytoplasmic membranes, and ribosomes. They reproduce by binary fission and are the most common sexually transmitted bacteria in the U.S. (Chlamydia trachomatis).

Spirochetes

Spiral-shaped bacteria that move via axial filaments. Some are pathogenic, such as Treponema pallidum (syphilis) and Borrelia burgdorferi (Lyme disease).

Bacteroids

Common inhabitants of the digestive tract, aiding in digestion. Some species are pathogenic, causing diarrhea and other symptoms. Cytophaga species degrade polysaccharides in aquatic environments.