Bacteria and Archaea: Structure, Diversity, and Biological Impact

Bacteria and Archaea

Introduction

Bacteria and Archaea are two of the three largest branches (domains) on the tree of life, with the third being Eukarya. Both are unicellular and prokaryotic, lacking a membrane-bound nucleus. Despite their similarities, they differ in the molecular composition of their plasma membranes and cell walls, and in their response to antibiotics.

• Prokaryotic cells: Cells without a nucleus or other membrane-bound organelles.

• Antibiotics: Drugs that target bacterial ribosomes, but do not affect those of archaea or eukaryotes.

Distinguishing Features of Bacteria and Archaea

Bacteria and Archaea can be differentiated by several molecular features:

Molecular Feature	Bacteria	Archaea
RNA polymerase	One type (five subunits)	One type (13 subunits; similar to eukaryotes)
Peptidoglycan in cell wall	Present	Absent
First amino acid in translation	Formylmethionine	Methionine
Histones associated with DNA	No	Yes

Why Do Biologists Study Bacteria and Archaea?

Biological Impact

Bacteria and Archaea are studied for their abundance, habitat diversity, and medical importance. They include extremophiles, organisms that thrive in extreme environments, and play roles in disease and bioremediation.

• Extremophiles: Organisms that live in extreme conditions (e.g., high temperature, salinity).

• Koch's postulates: Criteria to establish a causative link between a microbe and a disease.

• Germ theory: Infectious diseases are caused by microorganisms.

• Bioremediation: Use of microbes to clean up environmental pollutants.

Pathogenic Bacteria

Some Bacteria That Cause Illness in Humans

Pathogens are bacteria that cause disease. The following tables summarize key lineages, species, affected tissues, and associated diseases:

Lineage	Species	Tissues Affected	Disease
Firmicutes	Clostridium tetani	Wounds, nervous system	Tetanus
Firmicutes	Staphylococcus aureus	Skin, urogenital canal	Acne, boils, impetigo, toxic shock syndrome
Firmicutes	Streptococcus pneumoniae	Respiratory tract	Pneumonia
Firmicutes	Streptococcus pyogenes	Respiratory tract	Strep throat, scarlet fever
Spirochaetes	Borrelia burgdorferi	Skin and nerves	Lyme disease
Spirochaetes	Treponema pallidum	Urogenital canal	Syphilis

Lineage	Species	Tissues Affected	Disease
Actinobacteria	Mycobacterium tuberculosis	Respiratory tract	Tuberculosis
Actinobacteria	Mycobacterium leprae	Skin and nerves	Leprosy
Actinobacteria	Propionibacterium acnes	Skin	Acne
Chlamydiales	Chlamydia trachomatis	Urogenital canal	Genital tract infection
ε-proteobacteria	Helicobacter pylori	Stomach	Ulcer
β-proteobacteria	Neisseria gonorrhoeae	Urogenital canal	Gonorrhea
γ-proteobacteria	Haemophilus influenzae	Ear canal, nerves	Ear infections, meningitis
γ-proteobacteria	Pseudomonas aeruginosa	Urogenital canal, eye, ear canal, lungs	Infections of eye, ear, urinary tract, lungs
γ-proteobacteria	Salmonella enterica	Gastrointestinal tract	Food poisoning
γ-proteobacteria	Yersinia pestis	Lymph and blood	Plague

Koch's Postulates

Koch's postulates are a set of criteria used to establish a causative relationship between a microbe and a disease:

1. Microbe must be present in individuals suffering from the disease and absent from healthy individuals.

2. Microbe must be isolated and grown in pure culture away from the host.

3. If organisms from pure culture are injected into a healthy experimental animal, disease symptoms appear.

4. Organism isolated from diseased experimental animal, grown in pure culture, and demonstrated to be the same as the original organism.

The Germ Theory

Infectious diseases spread in three main ways:

1. Passed from person to person

2. Transmitted by bites from insects or animals

3. Acquired by ingesting contaminated food or water, or exposure to microbes in the environment

What Makes Some Bacterial Cells Pathogenic?

Virulence is the ability to cause disease and is a heritable, variable trait. Some species, such as Escherichia coli, have both pathogenic and harmless strains. Pathogenic strains often have larger genomes due to the acquisition of virulence genes, such as those coding for toxins (e.g., E. coli O157:H7).

Resistant Endospores

Some pathogenic bacteria produce resistant endospores, which are tough, dormant structures formed during environmental stress. Endospores contain a copy of the cell's DNA, RNA, ribosomes, and enzymes, and are resistant to heat, UV radiation, and antibiotics. They resume growth in favorable conditions and are involved in disease transmission.

Antibiotics and Biofilms

The Past, Present, and Future of Antibiotics

• Antibiotics: Molecules that kill bacteria or inhibit their growth; produced naturally by some soil bacteria and fungi.

• Discovered in 1928; widespread use began in the 1940s.

• Extensive use led to the evolution of drug-resistant strains.

• Biofilms: Bacterial colonies enmeshed in a polysaccharide-rich matrix that shields bacteria from antibiotics.

Role in Bioremediation

Bioremediation

Bioremediation is the use of bacteria and archaea to clean up sites polluted with organic solvents. Water pollutants are toxic to eukaryotes, do not dissolve in water, and accumulate in sediments. Naturally existing populations of bacteria and archaea can grow in spills and degrade toxins.

Bioremediation Strategies

1. Fertilizing contaminated sites to encourage growth of existing bacteria and archaea.

2. Seeding contaminated sites with specific species of bacteria and archaea.

Studying Bacteria and Archaea

Methods

• Enrichment cultures

• Metagenomics

• Investigating the human microbiome

• Molecular phylogenetics

Diversification of Bacteria and Archaea

Themes in Diversification

• Genetic variation through gene transfer

• Morphological diversity

• Metabolic diversity

• Ecological diversity and global impacts

Genetic Variation through Gene Transfer

• Lateral gene transfer: Acquisition of traits not available via binary fission.

• Transformation: Uptake of DNA from the environment.

• Transduction: Viruses transfer DNA between prokaryotic cells.

• Conjugation: Direct cell-to-cell transfer of genetic material, including plasmid transfer.

Morphological Diversity

Bacteria exhibit extensive diversity in size, shape, and motility. They can be spherical, rod-shaped, spiral, or filamentous, and may move using flagella or glide along surfaces.

Cell-Wall Composition

• Gram stain: A dyeing system to examine cell walls.

• Gram-positive: Cells look purple; cell wall has extensive peptidoglycan.

• Gram-negative: Cells look pink; cell wall has thin peptidoglycan and an outer phospholipid bilayer.

Metabolic Diversity

• Phototrophs: Use light to excite electrons; ATP made by photophosphorylation.

• Chemoorganotrophs: Oxidize organic molecules; ATP made by cellular respiration or fermentation.

• Chemolithotrophs: Oxidize inorganic molecules; ATP made by cellular respiration.

• Autotrophs: Synthesize building-block compounds from simple materials.

• Heterotrophs: Absorb building-block compounds from their environment.

Key Lineages of Bacteria and Archaea

Bacteria

There are 29 recognized lineages of bacteria, classified by morphology, metabolism, and phylogenetic analysis.

Morphology	Metabolism	Relevance
Rods or filaments; branching chains	Chemotrophs; nitrogen fixation	Cause tuberculosis, leprosy; produce antibiotics
Spherical cells; clusters	Chemoheterotrophs	Cause strep throat, scarlet fever
Filaments, spheres, spirals; colonies	Phototrophs; nitrogen fixation	Produce oxygen, feed aquatic organisms
Rods or spheres; chains or clusters	Chemotrophs; fermentation	Used in food production; cause disease
Corkscrew-shaped	Chemotrophs; fermentation	Cause Lyme disease, syphilis

Actinobacteria

• Filamentous, forming branching chains

• Streptomyces and Arthrobacter: abundant in soil, decomposers, nitrogen fixation, toxin breakdown

• Over 3000 antimicrobial compounds from Streptomyces

Chlamydiae

• Least diverse; only 13 species

• Spherical, very small

• Parasitic endosymbionts (live inside host cells)

Cyanobacteria

• Independent cells, filaments, or colonies

• Abundant; produce oxygen, nitrogen, organic compounds

• Feed aquatic organisms

Firmicutes

• Common in animal intestines

• Symbiotic mutualism; aid digestion

• Used in agriculture, food processing; cause diseases

Proteobacteria

• Diverse morphology: stalked cells, fruiting bodies

• Cause disease; key roles in nitrogen cycling

Spirochaetes (Spirochetes)

• Corkscrew shape; flagella within outer sheath

• Motility by lashing movement

• Parasitic species cause disease; others common in aquatic habitats

Key Lineages of Archaea

Crenarchaeota

• Also called eocytes

• Found in harsh environments (hot springs, acidic, high-pressure)

Euryarchaeota

• Root word "eury" means "broad"

• Live in diverse habitats: high salt, acidic, deep-sea vents

• Methanopyrus genus lives near black smokers

Thaumarchaeota

• Recently recognized, ancient lineage

• Abundant in oceans, estuaries, soils

• Mesophilic: grow best at moderate temperatures

Practice Questions

Gram-Positive Cell Identification

If a cell has a thick cell wall comprised of peptidoglycan, it is most likely Gram-positive.

Metabolic Classification

A bacterium that acquires both energy and carbon-carbon bonds from decaying organisms is classified as a chemoorganoheterotroph.

Additional info:

• Chemoorganoheterotrophs obtain energy and carbon from organic compounds.

• Gram-positive bacteria are important in medicine and industry due to their cell wall structure.