Characterizing and Classifying Prokaryotes: Structure, Diversity, and Taxonomy

General Characteristics of Prokaryotic Organisms

Morphology of Prokaryotic Cells

Prokaryotic cells are the most diverse group of cellular microbes, thriving in a wide range of habitats. Only a small subset is capable of colonizing humans and causing disease. Prokaryotes exhibit a variety of shapes, which are important for identification and classification.

• Coccus: Spherical-shaped cells

• Bacillus: Rod-shaped cells

• Spirillum: Spiral-shaped cells

• Spirochete: Flexible, corkscrew-shaped cells

• Vibrio: Comma-shaped cells

• Pleomorphic: Cells that vary in shape

• Star-shaped: Rare, star-like morphology

Endospores

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

Reproduction of Prokaryotic Cells

All prokaryotes reproduce asexually, primarily through three main methods:

• Binary fission: The most common method, involving the replication of DNA, elongation of the cell, and division into two daughter cells.

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

• Budding: A process where a new cell develops from the surface of an existing cell.

Some prokaryotes, such as actinomycetes, produce spores for reproduction and dispersal.

Viviparity in Prokaryotes

Members of the genus Epulopiscium and its relatives exhibit a unique reproductive strategy called viviparity, where live offspring emerge from the body of the dead mother cell. This is the first noted case of viviparous behavior in the prokaryotic world.

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:

• Diplococci: Pairs of cocci

• Streptococci: Chains of cocci

• Tetrads: Groups of four cocci

• Sarcinae: Cuboidal packets of eight or more cocci

• Staphylococci: Irregular clusters of cocci

Modern Prokaryotic Classification

Three Domains of Life

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

• Archaea

• Bacteria

• Eukarya

Survey of Archaea

General Features of Archaea

Archaea are prokaryotes that lack true peptidoglycan in their cell walls, have unique branched hydrocarbon chains in their membrane lipids, and use methionine as the start amino acid for protein synthesis. They reproduce by binary fission, budding, or fragmentation and display a variety of shapes. Archaea are not known to cause disease in humans, plants, or animals.

Extremophiles

Many archaea are extremophiles, requiring extreme conditions such as high temperature, acidity, or salinity to survive.

• Thermophiles: Require temperatures above 45°C; hyperthermophiles thrive above 80°C. Examples include Thermococcus and Pyrodictium.

• Halophiles: Inhabit highly saline environments, requiring over 9% NaCl. Many produce red or orange pigments for protection from sunlight. Halobacterium salinarium is a well-studied example.

Methanogens

Methanogens are archaea that produce methane gas from carbon dioxide, hydrogen, and organic acids. They play a significant role in the carbon cycle and are a primary source of environmental methane, especially in sediments and the digestive tracts of animals.

Survey of Bacteria

Deeply Branching and Phototrophic Bacteria

Deeply branching bacteria are considered similar to the earliest forms of life, often autotrophic and found in extreme environments. Phototrophic bacteria perform photosynthesis and are divided into groups based on pigments and electron donors:

• Cyanobacteria: Oxygenic photosynthesis, Gram-negative, some fix nitrogen, thought to have contributed to the oxygenation of Earth's atmosphere.

• Green sulfur bacteria: Anoxygenic photosynthesis, use H2S as electron donor.

• Green nonsulfur bacteria: Anoxygenic, use organic compounds as electron donors.

• Purple sulfur bacteria: Anoxygenic, deposit sulfur inside cells.

• Purple nonsulfur bacteria: Anoxygenic, use organic compounds as electron donors.

Phylum/Class	Common Name(s)	Major Photosynthetic Pigments	Types of Photosynthesis	Electron Donor	Sulfur Deposition	Nitrogen Fixation	Motility
Cyanobacteria	Blue-green bacteria	Chlorophyll a	Oxygenic	H2O	None	Some species	Nonmotile or gliding
Chlorobi	Green sulfur bacteria	Bacteriochlorophyll a, c, d, or e	Anoxygenic	H2, H2S, or S	Outside cell	None	Nonmotile
Chloroflexi	Green nonsulfur bacteria	Bacteriochlorophyll a and c	Anoxygenic	Organic compounds	None	None	Gliding
Proteobacteria (Gamma)	Purple sulfur bacteria	Bacteriochlorophyll a or b	Anoxygenic	H2, H2S, or S	Inside cell	None	Motile with polar or peritrichous flagella
Proteobacteria (Alpha/Beta)	Purple nonsulfur bacteria	Bacteriochlorophyll a or b	Anoxygenic	Organic compounds	None	None	Nonmotile or motile with polar flagella

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, endospore-forming rods, cause diseases such as tetanus, botulism, and gangrene.

• Mycoplasmas: Lack cell walls, smallest free-living cells, colonize mucous membranes, cause pneumonia and urinary tract infections.

• Bacillus: Endospore-forming rods, Bacillus thuringiensis produces insecticidal toxins, Bacillus anthracis causes anthrax.

• Listeria: Contaminates dairy and meat, can reproduce under refrigeration, crosses placenta in pregnant women.

• Lactobacillus: Used in food production, rarely pathogenic.

• Streptococcus and Enterococcus: Cause various diseases, some strains are multi-drug resistant.

• Staphylococcus: Common human inhabitant, produces toxins and enzymes, causes food poisoning and other diseases.

Phylum/Class	G + C %	Representative Genera	Special Characteristics	Diseases
Clostridia	Low (<50%)	Clostridium	Obligate anaerobic rod; endospore former	Tetanus, botulism, gangrene, severe diarrhea
Mollicutes	Low (<50%)	Mycoplasma	Lacks cell walls; pleomorphic; smallest free-living cell	Pneumonia, urinary tract infections
Bacilli	Low (<50%)	Bacillus	Facultative anaerobic rod; endospore former	Anthrax
Bacilli	Low (<50%)	Listeria	Contaminates dairy products	Listeriosis
Bacilli	Low (<50%)	Lactobacillus	Produces yogurt, buttermilk, pickles, sauerkraut	Rare blood infections
Bacilli	Low (<50%)	Streptococcus	Cocci in chains	Strep throat, scarlet fever, and others
Bacilli	Low (<50%)	Staphylococcus	Cocci in clusters	Bacteremia, food poisoning, and others

High G + C Gram-Positive Bacteria

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

• Corynebacterium: Pleomorphic aerobes, produce metachromatic granules, cause diphtheria.

• Mycobacterium: Aerobic rods with waxy cell walls (mycolic acid), slow-growing, cause tuberculosis and leprosy.

• Actinomycetes: Form branching filaments, important for antibiotic production (e.g., Streptomyces), degrade pollutants (Nocardia).

Gram-Negative Proteobacteria

Overview and Classes

Proteobacteria are the largest and most diverse group of Gram-negative bacteria, divided into six classes:

• Alphaproteobacteria

• Betaproteobacteria

• Gammaproteobacteria

• Deltaproteobacteria

• Epsilonproteobacteria

• Zetaproteobacteria

Alphaproteobacteria

• Nitrogen fixers: Azospirillum and Rhizobium associate with plant roots, important for agriculture.

• Nitrifying bacteria: Nitrobacter oxidizes nitrogenous compounds, crucial for nitrogen cycling.

• Purple nonsulfur phototrophs: Grow in aquatic environments.

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

• Other genera: Acetobacter, Gluconobacter, Caulobacter (unique reproductive strategies).

Betaproteobacteria

• Pathogens: Neisseria (various diseases), Bordetella (pertussis), Burkholderia (respiratory infections).

• Environmental bacteria: Thiobacillus (sulfur recycling), Zoogloea (sewage treatment), Sphaerotilus (wastewater flocs).

Gammaproteobacteria

• Purple sulfur bacteria: Anoxygenic phototrophs.

• Intracellular pathogens: Legionella (Legionnaires’ disease), Coxiella (Q fever).

• Methane oxidizers: Use methane as a carbon and energy source.

• Glycolytic facultative anaerobes: Catabolize carbohydrates by glycolysis and pentose phosphate pathway. Includes Escherichia, Salmonella, Shigella, Yersinia, Klebsiella, Vibrio, Haemophilus.

• Pseudomonads: Degrade organic compounds, important pathogens (Pseudomonas).

Family	Special Characteristics	Representative Genera	Typical Human Diseases
Enterobacteriaceae	Straight rods; oxidase negative; peritrichous flagella or nonmotile	Escherichia, Salmonella, Proteus, Shigella, Yersinia, Klebsiella	Gastroenteritis, enteritis, urinary tract infection, shigellosis, plague, pneumonia
Vibrionaceae	Vibrios; oxidase positive; polar flagella	Vibrio	Cholera
Pasteurellaceae	Cocci or straight rods; oxidase positive; nonmotile	Haemophilus	Meningitis, ear infections, pneumonia

Deltaproteobacteria

• Desulfovibrio: Sulfate-reducing bacteria.

• Bdellovibrio: Predatory bacteria that attack other Gram-negative bacteria.

• Myxobacteria: Exhibit complex life cycles and social behavior.

Epsilonproteobacteria

• Campylobacter and Helicobacter: Important human pathogens, associated with gastrointestinal diseases.

Zetaproteobacteria

• Discovered through DNA sequencing, common in oceans, only a few species cultured. Mariprofundus ferrooxydans is a notable example.

Other Gram-Negative Bacteria

• Chlamydias: Intracellular pathogens, some smaller than viruses, cause common sexually transmitted infections.

• Spirochetes: Motile, corkscrew-shaped bacteria, include Treponema (syphilis) and Borrelia (Lyme disease).

• Bacteroids: Inhabit digestive tracts, some species cause infections; Cytophaga degrades raw sewage.

Additional info: This guide covers the main features, diversity, and classification of prokaryotes, focusing on medically and ecologically significant groups. For further study, refer to the full textbook chapters and laboratory manuals.