# Lecture 6: Bacteria and Archaea
## General Biology II — Organismal, Evolution & Ecology
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## Learning Objectives
By the end of this lecture, students will be able to:
1. Describe the key structural features of prokaryotic cells
2. Compare and contrast Bacteria and Archaea in terms of cell structure, genetics, and ecology
3. Classify prokaryotes by their metabolic diversity (energy source, carbon source, electron donors)
4. Explain mechanisms of genetic diversity in prokaryotes (mutation, HGT)
5. Describe the ecological importance of prokaryotes
6. Discuss the relevance of prokaryotes to human health, including the microbiome and pathogenesis
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## Lecture Content
### I. Prokaryotic Cell Structure
Prokaryotes are defined by the absence of a membrane-bound nucleus and membrane-bound organelles. They are typically small, ranging from 0.5 to 5 micrometers, which gives them a high surface area-to-volume ratio that facilitates the rapid metabolic rates for which they are known.
The **cell wall** is a defining structural feature that differs fundamentally between the two prokaryotic domains. Most bacteria possess a cell wall containing peptidoglycan, a polymer of sugars cross-linked by short polypeptides. Gram-positive bacteria have a thick peptidoglycan layer and stain purple with the Gram stain, while Gram-negative bacteria have a thin peptidoglycan layer overlaid by an outer membrane containing lipopolysaccharide (LPS). This outer membrane is clinically significant because LPS is an endotoxin capable of triggering severe immune responses, including septic shock. Archaea, by contrast, have cell walls that lack peptidoglycan entirely; some contain pseudopeptidoglycan, while others have an S-layer composed of protein.
The **plasma membrane** also differs between domains. Bacterial membranes, like those of eukaryotes, consist of a phospholipid bilayer with ester-linked fatty acids. Archaeal membranes are distinctive, featuring ether-linked isoprenoid chains that may form a monolayer or bilayer, conferring greater heat stability -- an adaptation that helps explain why many archaea thrive in extreme thermal environments.
External to the cell wall, many prokaryotes produce a **capsule or slime layer** of polysaccharides that provides protection and aids adhesion to surfaces. **Pili** (or fimbriae) are short protein appendages used for attachment, with specialized sex pili mediating conjugation. **Flagella** are long protein appendages that provide motility; bacterial flagella are made of flagellin and rotate like propellers, while archaeal flagella (archaella) are structurally distinct and assembled by a different mechanism.
The prokaryotic **genome** typically consists of a single circular chromosome located in the nucleoid region, which is not bounded by a membrane. Many prokaryotes also carry plasmids -- small circular DNA molecules bearing accessory genes such as those for antibiotic resistance. Prokaryotes are haploid, and their **ribosomes** are 70S (composed of 30S and 50S subunits), a feature that makes them targets for many antibiotics. Some bacteria, notably species of Bacillus and Clostridium, can form **endospores** -- extraordinarily resistant dormant structures that withstand extreme heat, desiccation, radiation, and chemical exposure. Endospores are not reproductive structures; one cell produces one endospore, which can remain viable for centuries.
A detailed labeled diagram comparing a Gram-positive and Gram-negative bacterial cell. Panel A (Gram-positive): Cross-section showing thick peptidoglycan layer, plasma membrane, teichoic acids embedded in the wall, cytoplasm with ribosomes and nucleoid. Panel B (Gram-negative): Cross-section showing thin peptidoglycan layer, inner membrane, periplasmic space, outer membrane with lipopolysaccharide (LPS) molecules protruding outward, and porins in the outer membrane. Both panels show common structures: flagellum, pili, capsule, plasmid, and chromosome. An inset shows the Gram staining results — purple for Gram-positive, pink for Gram-negative.
### II. Prokaryotic Diversity: Bacteria vs. Archaea
Domain Bacteria encompasses the enormous diversity of prokaryotes encountered in everyday life. Among its major phyla, the **Proteobacteria** are the largest and most diverse group, subdivided into alpha, beta, gamma, delta, and epsilon classes and including familiar genera such as E. coli, Salmonella, Rhizobium, and Helicobacter. **Cyanobacteria** are the oxygenic photosynthesizers that produced Earth's oxygen and gave rise to chloroplasts through endosymbiosis. The **Firmicutes** are Gram-positive bacteria that include Bacillus, Clostridium, Staphylococcus, and Lactobacillus. **Actinobacteria**, also Gram-positive but with high G+C DNA content, include Mycobacterium (the causative agent of tuberculosis) and Streptomyces (prolific producers of antibiotics). The **Spirochaetes** are spiral-shaped bacteria responsible for syphilis (Treponema) and Lyme disease (Borrelia). The **Chlamydiae** are obligate intracellular parasites.
Domain Archaea was originally thought to comprise organisms restricted to extreme environments, but molecular surveys have revealed that archaea are widespread in moderate habitats including ocean water, soil, and the human gut. The **Euryarchaeota** include methanogens (which produce methane), extreme halophiles (which thrive in high-salt environments), and some thermophiles. The **Crenarchaeota** include many thermophiles and hyperthermophiles found in hot springs and deep-sea vents. The **Thaumarchaeota** are abundant in the oceans and play an important role in the nitrogen cycle as ammonia oxidizers. The **Asgard archaea** -- including Lokiarchaeota and Thorarchaeota -- are of particular evolutionary interest because they are the prokaryotes most closely related to eukaryotes, lending support to models in which eukaryotic cells arose from within the archaeal domain. Notably, no archaeal pathogens of humans have been identified.
### III. Metabolic Diversity
Prokaryotes are the most metabolically diverse organisms on Earth, exploiting energy and carbon sources far beyond anything available to eukaryotes. Their metabolic strategies can be classified along three axes. By energy source, organisms are either **phototrophs** (using light) or **chemotrophs** (using chemical energy). By carbon source, they are **autotrophs** (fixing CO2 into organic carbon) or **heterotrophs** (obtaining carbon from organic molecules). By electron donor, they are **lithotrophs** (using inorganic molecules such as H2, H2S, NH3, or Fe2+) or **organotrophs** (using organic molecules).
Combining these categories produces four major metabolic strategies. **Photoautotrophs** use light energy to fix CO2, as exemplified by cyanobacteria and purple sulfur bacteria. **Chemoautotrophs** (chemolithoautotrophs) use inorganic chemicals for both energy and carbon fixation, including the nitrifying, sulfur-oxidizing, and iron-oxidizing bacteria that drive biogeochemical cycles. **Photoheterotrophs** use light energy but require organic carbon sources, as seen in purple non-sulfur bacteria. **Chemoheterotrophs** use organic chemicals for both energy and carbon -- this is the strategy shared by most bacteria and all animals.
The relationship between prokaryotes and oxygen is equally varied. Obligate anaerobes are killed by O2 (such as Clostridium). Facultative anaerobes can switch between aerobic and anaerobic metabolism depending on oxygen availability (such as E. coli). Obligate aerobes require O2 (such as Mycobacterium tuberculosis). In anaerobic respiration, some prokaryotes use electron acceptors other than O2, including nitrate, sulfate, ferric iron, or CO2.
Nitrogen fixation -- the conversion of atmospheric N2 to ammonia (NH3) -- is one of the most ecologically critical metabolic processes on Earth, and it is performed exclusively by certain prokaryotes. The nitrogenase enzyme that catalyzes this reaction is extremely sensitive to oxygen. Nitrogen-fixing bacteria include Rhizobium (symbiotic with legumes), Azotobacter (free-living), and many cyanobacteria. By making atmospheric nitrogen available in biologically usable forms, these organisms underpin the productivity of virtually all ecosystems.
### IV. Genetic Diversity and Reproduction
Prokaryotes reproduce asexually through binary fission, and their rapid generation times -- E. coli, for example, can double every 20 minutes under optimal conditions -- allow mutations to accumulate quickly in large populations, generating substantial genetic variation.
Beyond mutation, prokaryotes acquire genetic diversity through **horizontal gene transfer** (HGT), which occurs via three distinct mechanisms. **Transformation** involves the uptake of free DNA from the environment by naturally competent cells. **Transduction** is the transfer of DNA between bacteria via bacteriophages (bacterial viruses) that accidentally package host DNA into phage particles. **Conjugation** is the direct transfer of DNA -- usually a plasmid -- from a donor cell (F+) to a recipient cell (F-) through a sex pilus. When the F plasmid integrates into the bacterial chromosome, creating an Hfr (high-frequency recombination) cell, chromosomal genes can also be transferred. HGT is enormously important because it allows traits such as antibiotic resistance to spread rapidly across species boundaries.
Antibiotic resistance is now recognized as one of the most pressing public health challenges of our time. Resistance genes are frequently carried on plasmids, making them readily transferable by conjugation. The mechanisms of resistance include enzymatic degradation of the antibiotic, efflux pumps that expel the drug from the cell, modification of the antibiotic's target site, and reduced membrane permeability. The overuse of antibiotics in medicine and agriculture creates intense selective pressure favoring resistant strains -- natural selection in action at a scale visible within human lifetimes. MRSA, multi-drug resistant tuberculosis, and carbapenem-resistant Enterobacteriaceae (CRE) represent particularly alarming examples.
A diagram showing three mechanisms of horizontal gene transfer in bacteria. Panel A (Transformation): A bacterial cell lyses, releasing free DNA fragments into the environment; a nearby competent bacterium takes up a DNA fragment and incorporates it into its chromosome by recombination. Panel B (Transduction): A bacteriophage infects a donor bacterium, accidentally packages host DNA into a phage particle, then injects this DNA into a new recipient bacterium. Panel C (Conjugation): A donor cell (F+) with an F plasmid extends a sex pilus to a recipient cell (F-), creating a cytoplasmic bridge; the F plasmid is replicated and transferred, converting the recipient to F+. Each panel shows the before, during, and after stages clearly.
### V. Ecological Roles of Prokaryotes
Prokaryotes are indispensable to the functioning of Earth's ecosystems. As **decomposers**, they break down dead organic matter, recycling carbon, nitrogen, phosphorus, and sulfur back into forms that other organisms can use. Their roles in **biogeochemical cycles** are unmatched: they drive nitrogen fixation, nitrification, and denitrification in the nitrogen cycle; decomposition, methanogenesis, and CO2 fixation in the carbon cycle; and sulfur oxidation and reduction in the sulfur cycle.
Prokaryotes engage in the full spectrum of **symbiotic relationships**. Mutualistic partnerships include the nitrogen-fixing association between Rhizobium and legumes and the cellulose-digesting bacteria in ruminant guts. Commensal relationships characterize many of the bacteria living on human skin and in the gut. Parasitic bacteria cause disease.
The **human microbiome** has emerged as one of the most exciting frontiers in biology. Approximately 38 trillion bacterial cells inhabit the human body -- roughly equal to the number of human cells. The gut microbiome alone aids digestion, synthesizes essential vitamins (including K and B12), trains the developing immune system, and protects against pathogenic colonization. Disruption of the microbiome, a condition known as dysbiosis, has been linked to obesity, inflammatory bowel disease, allergies, and even mental health disorders.
Beyond their ecological roles, prokaryotes serve numerous practical applications. **Bioremediation** harnesses their metabolic capabilities to clean up environmental pollutants such as oil spills and heavy metal contamination. In industry, prokaryotes are essential for food production (yogurt, cheese, sauerkraut), antibiotic manufacturing (Streptomyces), genetic engineering (E. coli as a workhorse of biotechnology), and biofuel production.
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