Prokaryotic Diversity

Core Concepts

Prokaryotic cell structure

Prokaryotic cells are small (typically 1–5 micrometers) and simple by eukaryotic standards, but not poorly equipped:

• No nucleus: DNA is concentrated in a nucleoid, usually as a single circular chromosome. Plasmids — small extrachromosomal circles of DNA — carry additional genes, often for antibiotic resistance or special metabolic abilities.
• Cell wall: most prokaryotes have a rigid wall that gives shape and protects against osmotic pressure. In Bacteria, the wall is built from peptidoglycan (sugars cross-linked by peptides); Archaea lack peptidoglycan and use other chemistries.
• Additional structures: a capsule (sticky outer layer aiding attachment and evading immune defenses), flagella (motors for movement), pili and fimbriae (hairlike fibers for attachment and DNA transfer), and ribosomes smaller than eukaryotic ones — a difference antibiotics exploit.
• No membrane-bound organelles: many prokaryotes fold their plasma membrane inward to house the enzymes of respiration or photosynthesis.

The Bacteria–Archaea split

Both Bacteria and Archaea are prokaryotes, but molecular studies show they are deeply separate lineages — as different from each other as either is from eukaryotes. Key differences:

• Cell wall chemistry: Bacteria use peptidoglycan; archaeal walls do not.
• Membrane lipids: bacterial membranes use ester-linked lipids; archaeal membranes use ether-linked lipids, sometimes in a monolayer — an adaptation helping archaea survive extreme heat and acidity.
• Genetics: archaeal transcription and translation machinery more closely resembles eukaryotes' than bacteria's.
• Habitats: many archaea are extremophiles — thermophiles in hot springs, halophiles in salt lakes, methanogens in oxygen-free environments like swamps and animal digestive tracts — though archaea also live in ordinary soils and oceans.

Shapes and arrangements

Bacterial morphology is simple but characteristic: cocci (spheres), bacilli (rods), and spirilla (spirals; curved forms are vibrios). Cells arrange in diagnostic patterns: diplo- (pairs), strepto- (chains), staphylo- (clusters, like grapes), and palisades. Shape and arrangement help with preliminary identification in clinical labs, but reveal nothing about evolutionary relationships — a rod-shaped bacterium is not necessarily related to another rod.

Metabolic diversity

Prokaryotes exploit more metabolic strategies than all eukaryotes combined, classified by energy and carbon sources:

• Photoautotrophs: use light energy and carbon dioxide; cyanobacteria are the classic example and produced much of Earth's early oxygen.
• Chemoautotrophs: get energy from inorganic chemicals (hydrogen sulfide, iron, ammonia) and carbon from CO₂; found at deep-sea vents and in soils.
• Photoheterotrophs: use light for energy but need organic carbon from the environment.
• Chemoheterotrophs: get both energy and carbon from organic molecules — including decomposers, commensals, and pathogens (e.g., E. coli in the gut).

Oxygen tolerance also varies: obligate aerobes need O₂; obligate anaerobes are poisoned by it; facultative anaerobes prefer O₂ but can ferment without it; aerotolerant anaerobes ignore O₂ and ferment exclusively.

Reproduction and genetic exchange

Prokaryotes reproduce by binary fission — the cell copies its chromosome and splits in two — which is fast (many species can double in under an hour under ideal conditions). But they also shuffle genes in ways not tied to reproduction:

• Conjugation: direct transfer of DNA (often plasmids) between cells through a pilus — the main route by which antibiotic-resistance genes spread between species.
• Transformation: uptake of free DNA from the environment.
• Transduction: DNA moved between cells by a virus (bacteriophage).

These processes create genetic variation far faster than mutation alone and are major drivers of bacterial evolution — including the evolution of drug resistance.

Ecological roles

• Decomposers: break down dead organic matter, recycling carbon, nitrogen, and other nutrients.
• Nitrogen fixers: convert N₂ gas into ammonia usable by plants (e.g., Rhizobium in legume root nodules).
• Symbionts: live in and on larger organisms; the human gut microbiome aids digestion and produces vitamins.
• Bioremediators: some bacteria consume oil, heavy metals, or other pollutants — used to clean contaminated sites.
• Pathogens: a small minority cause disease, typically via toxins or tissue invasion (e.g., Streptococcus, Mycobacterium tuberculosis, Salmonella).

Biofilms

Prokaryotes often live in biofilms — surface-attached communities embedded in a slimy matrix of extracellular polymers. Biofilms form on teeth (plaque), medical implants, catheters, and pipes. Cells in biofilms are far more resistant to antibiotics and disinfectants than free-floating cells, which is why biofilm infections are hard to treat and industrial surfaces must be actively cleaned.

Common Confusions