Characterizing and Classifying Prokaryotes: Morphology, Reproduction, and Taxonomy

General Characteristics of Prokaryotic Organisms

Morphology of Prokaryotic Cells

Prokaryotic cells are the most numerous and 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 their identification and classification.

• Coccus: Spherical-shaped cells.

• Bacillus: Rod-shaped cells.

• Spirals: Includes spirilla (stiff) and spirochetes (flexible).

• Vibrio: Slightly curved rods.

• Coccobacillus: Intermediate between cocci and bacilli.

• Pleomorphic: Cells that vary in shape and size.

• Other shapes: Star-shaped, triangular, and rectangular forms also exist.

Endospores

Endospores are highly resistant, dormant structures produced by certain Gram-positive bacteria, such as Bacillus and Clostridium. A vegetative cell transforms into a single endospore, which can later germinate back into a vegetative cell when conditions improve. Endospores are not a means of reproduction but a defensive strategy against unfavorable conditions. They are of significant concern in food processing and healthcare due to their resistance and association with deadly diseases like anthrax, tetanus, and gangrene.

Reproduction of Prokaryotic Cells

All prokaryotes reproduce asexually. The three main methods are:

• Binary fission (most common): The cell duplicates its DNA, elongates, forms a cross wall, and divides into two identical daughter cells.

• Snapping division: A variation of binary fission where only the inner cell wall is deposited, causing the outer wall to snap and partially separate the daughter cells.

• Budding: A new cell develops from a bud on the parent cell, eventually detaching as a separate organism.

Some prokaryotes, such as actinomycetes, produce reproductive cells called spores at the ends of filamentous cells. These spores contain complete genetic information and can develop into clones of the organism. Fragmentation is another method, where the parental cell breaks into small motile filaments.

Viviparity is a unique reproductive method observed in Epulopiscium, where live offspring emerge from the body of the dead mother cell. This is the first noted case of viviparous behavior in prokaryotes.

Arrangements of Prokaryotic Cells

The arrangement of prokaryotic cells results from the planes in which cells divide and whether daughter cells remain attached after division.

• Cocci: Can form diplococci (pairs), streptococci (chains), tetrads (clusters of four), sarcinae (cuboidal packets), or staphylococci (clusters).

• Bacilli: Typically form single cells, pairs (diplobacilli), chains (streptobacilli), or palisades (side-by-side arrangements due to snapping division).

Modern Prokaryotic Classification

Three Domains of Life

Modern classification of prokaryotes is based on genetic relatedness, dividing all life into three domains:

• Archaea

• Bacteria

• Eukarya

Survey of Archaea

General Features

• Lack true peptidoglycan in cell walls

• Cytoplasmic membrane lipids have branched hydrocarbon chains

• AUG codon codes for methionine (like eukaryotes)

• Classified into two major phyla: Crenarchaeota and Euryarchaeota

• Reproduce by binary fission, budding, or fragmentation

• Not known to cause disease

Extremophiles

Extremophiles are archaea that require extreme conditions to survive, such as high temperature, acidity, or salinity.

• Thermophiles: Thrive at temperatures above 45°C; hyperthermophiles require temperatures over 80°C. Examples include Thermococcus and Pyrodictium.

• Halophiles: Inhabit highly saline environments, requiring over 9% NaCl. Many produce red or orange pigments for sunlight protection. Example: Halobacterium salinarum.

Methanogens

Methanogens are obligate anaerobes that produce methane gas from carbon dioxide, hydrogen, and organic acids. They play a crucial role in converting organic wastes in sediments to methane and are a primary source of environmental methane.

Survey of Bacteria

Deeply Branching and Phototrophic Bacteria

• Deeply Branching Bacteria: Considered similar to the earliest bacteria, autotrophic, and often found in habitats resembling early Earth.

• Phototrophic Bacteria: Acquire energy for anabolism by absorbing light with photosynthetic pigments. Most are autotrophic and are divided into five groups based on pigments and electron sources. The most important group for study is the cyanobacteria.

Cyanobacteria

Cyanobacteria are Gram-negative phototrophs that use chlorophyll a and generate oxygen during photosynthesis. They are believed to have transformed Earth's early anaerobic atmosphere into an oxygen-rich one. Some cyanobacteria can fix atmospheric nitrogen in specialized cells called heterocysts, separating this process from oxygenic photosynthesis due to enzyme sensitivity to oxygen.

G + C Content in Classification

The percentage of guanine-cytosine base pairs (G + C content) in a genome is used to classify Gram-positive bacteria. Those with less than 50% G + C are considered "low G + C bacteria," while those with higher content are "high G + C bacteria."

Low G + C Gram-Positive Bacteria

• Clostridia: Rod-shaped, obligate anaerobes, many form endospores, and are important in medicine and industry.

• Mycoplasmas: Lack cell walls, are pleomorphic, and are the smallest free-living cells. They colonize mucous membranes and are associated with pneumonia and urinary tract infections.

• Bacillus: Common in soil, form endospores, and include species important in agriculture and disease (e.g., Bacillus anthracis causes anthrax).

• Listeria: Can contaminate food, reproduce under refrigeration, and cause serious infections.

• Lactobacillus: Non-spore-forming rods, beneficial in the body and used in food production.

• Streptococcus and Enterococcus: Cause a variety of diseases, including pharyngitis, pneumonia, and wound infections.

• Staphylococcus: Commonly found in humans; some strains cause serious diseases and are resistant to antibiotics (e.g., MRSA).

High G + C Gram-Positive Bacteria (Phylum Actinobacteria)

• Corynebacterium: Pleomorphic aerobes/facultative anaerobes, known for causing diphtheria.

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

• Actinomycetes: Form branching filaments, important in soil ecology and antibiotic production (e.g., Streptomyces).

Survey of Bacteria: Gram-Negative Proteobacteria

Overview

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

Alphaproteobacteria

• Typically aerobes, capable of growing at low nutrient levels.

• Some have prosthecae (extensions for attachment and nutrient absorption).

• Important genera: Azospirillum, Rhizobium (nitrogen fixers), Rickettsia (causes typhus), Brucella (causes brucellosis).

Betaproteobacteria

• Thrive in low-nutrient habitats; metabolically overlap with alphaproteobacteria.

• Important genera: Nitrosomonas (nitrification), Neisseria (gonorrhea, meningitis), Bordetella (whooping cough), Burkholderia (lung infections in cystic fibrosis).

• Some genera form flocs in sewage treatment (e.g., Zoogloea, Sphaerotilus).

Gammaproteobacteria

• Largest and most diverse class; includes purple sulfur bacteria, intracellular pathogens, methane oxidizers, glycolytic facultative anaerobes, and pseudomonads.

• Important pathogens: Legionella (Legionnaires’ disease), Coxiella (Q fever), Pseudomonas (UTIs, swimmer’s ear, lung infections).

• Enterobacteriaceae family includes Escherichia coli, a model organism in research and a common gut inhabitant.

Deltaproteobacteria

• Includes Desulfovibrio (sulfur cycle), Bdellovibrio (bacterial predator), and myxobacteria (form fruiting bodies and myxospores).

Epsilonproteobacteria

• Includes Gram-negative rods, vibrios, or spirals.

• Important genera: Campylobacter (intestinal infections), Helicobacter (ulcers).

Zetaproteobacteria

• Identified by metagenomic sequencing; oxidize iron in marine environments.

Other Gram-Negative Bacteria

• Chlamydias: Gram-negative cocci, cause neonatal blindness, pneumonia, and the most common bacterial STD in the US.

• Spirochetes: Flexible, motile, helical bacteria; includes Treponema (syphilis) and Borrelia (Lyme disease).

• Bacteroids: Includes Bacteroides, an obligate anaerobe in the digestive tract, and Cytophaga, which degrades wood and sewage.