Table of Contents
Overview of Domain Bacteria
Domain Bacteria includes all “true” bacteria: prokaryotic organisms that lack a membrane-bound nucleus and organelles, and that differ in several fundamental ways from Archaea and eukaryotes. They are extraordinarily diverse in form, metabolism, and habitat, and they play key roles in ecosystems, biotechnology, and human health.
In systematics, bacteria are not grouped by a single visible feature, but by a combination of morphological, physiological, ecological, and especially molecular characteristics (for example, comparisons of ribosomal RNA sequences).
This chapter concentrates on what distinguishes Bacteria as a domain, and how their diversity is classified and understood.
Fundamental Characteristics of Bacteria
Although “bacteria” are highly diverse, most members of this domain share some characteristic features.
Prokaryotic Cell Organization
Bacteria are prokaryotes. Typical bacterial cells:
- Lack a membrane-bound nucleus; their DNA is located in a nucleoid region.
- Usually have a single, circular chromosome (plasids may also be present).
- Do not possess membrane-bound organelles like mitochondria or chloroplasts.
- Often have additional structures such as:
- Cell wall (almost always present, but see exceptions like Mycoplasma).
- Flagella for motility.
- Pili (fimbriae) for attachment or DNA exchange.
- Capsules or slime layers for protection and adhesion.
The basic cell structure of prokaryotes is covered elsewhere; here the focus is on features particularly relevant to bacterial classification.
Peptidoglycan Cell Wall
A key distinguishing feature of Bacteria (versus Archaea and Eukarya) is the presence of peptidoglycan (murein) in their cell walls.
- Peptidoglycan is a mesh-like polymer composed of:
- Sugar chains (N-acetylglucosamine and N-acetylmuramic acid).
- Short peptide chains linking sugar strands.
Functions:
- Provides mechanical strength and protects against osmotic lysis.
- Determines cell shape (cocci, bacilli, spirilla, etc.).
- Is targeted by several important antibiotics (e.g., β-lactams) and by lysozyme.
Archaea do not have peptidoglycan; they may have pseudopeptidoglycan or other wall types, and eukaryotic cells either lack cell walls or use other polymers (cellulose, chitin).
Gram-Positive and Gram-Negative Bacteria
Based on the Gram staining method, bacteria are often categorized as:
- Gram-positive bacteria:
- Thick, multilayered peptidoglycan cell wall.
- No outer membrane.
- Teichoic acids often present.
- Retain crystal violet–iodine complex during staining → appear violet/purple.
- Gram-negative bacteria:
- Thin peptidoglycan layer.
- Outer membrane present, containing:
- Lipopolysaccharide (LPS; “endotoxin”).
- Porins (channels for small molecules).
- Do not retain crystal violet–iodine complex; counterstain → appear pink/red.
Systematically, Gram staining is not a perfect reflection of evolutionary relationships, but it remains useful as a practical and partially informative classification tool in microbiology and medicine.
Genetic and Molecular Features
Bacterial Chromosome and Plasmids
Bacteria typically have:
- A single circular chromosome:
- Located in the nucleoid.
- Contains essential genes for growth and reproduction.
- Plasmids:
- Small, usually circular DNA molecules.
- Replicate independently of the chromosome.
- Often carry accessory genes (e.g., antibiotic resistance, virulence factors, metabolic pathways).
- Can be transferred between bacteria, contributing to rapid adaptation and spread of traits.
Horizontal Gene Transfer
Bacterial evolution and classification are strongly influenced by horizontal gene transfer (HGT), the movement of genetic material between organisms other than by parent-to-offspring inheritance.
Main mechanisms:
- Transformation: uptake of free DNA from the environment.
- Transduction: DNA transfer by bacteriophages (bacterial viruses).
- Conjugation: direct cell-to-cell DNA transfer via conjugative pili and plasmids.
Consequences for systematics:
- Gene histories may differ from organismal histories.
- Some traits (e.g., antibiotic resistance) may spread across distant lineages.
- Molecular phylogenies often use genes that are less affected by HGT (e.g., core ribosomal genes) to reconstruct deeper relationships.
Ribosomes and rRNA
Bacterial ribosomes are:
- 70S in size, composed of:
- 50S large subunit.
- 30S small subunit.
The small subunit contains 16S rRNA, which is widely used as a molecular marker in bacterial systematics:
- 16S rRNA sequences:
- Are present in all bacteria.
- Change relatively slowly, preserving information about evolutionary relationships.
- Allow construction of phylogenetic trees and identification of major bacterial lineages (phyla).
This approach revealed that “bacteria” are not a simple group but include many deeply divergent clades.
Diversity of Form and Lifestyle
Morphological Diversity
Common bacterial cell shapes include:
- Cocci: spherical (e.g., Staphylococcus, Streptococcus).
- Bacilli: rod-shaped (e.g., Escherichia coli).
- Vibrios: comma-shaped (e.g., Vibrio cholerae).
- Spirilla and spirochetes: spiral-shaped (e.g., Spirillum, Treponema).
Cells can arrange into:
- Chains, clusters, pairs.
- Filaments or multicellular-like aggregates.
- Complex structures like biofilms attached to surfaces.
Morphology alone is insufficient for classification but is diagnostic in combination with other traits.
Metabolic Versatility
Bacteria exhibit almost every metabolic strategy known, including:
- Energy sources:
- Phototrophy (light as energy source).
- Chemotrophy (inorganic or organic compounds as energy source).
- Carbon sources:
- Autotrophy (CO₂ as carbon source; e.g., cyanobacteria).
- Heterotrophy (organic compounds as carbon source).
- Electron donors/acceptors:
- Aerobic respiration (O₂ as final electron acceptor).
- Anaerobic respiration (e.g., nitrate, sulfate, CO₂).
- Fermentation (organic compounds as both donors and acceptors).
Metabolic traits are crucial in ecological classification (e.g., nitrogen-fixing bacteria, sulfur-oxidizing bacteria) and for identifying bacteria in clinical and environmental settings.
Ecological Roles
Bacteria occupy almost every environment on Earth, including:
- Soil, freshwater, and marine habitats.
- Extreme environments (high temperature, salinity, acidity, alkalinity, pressure).
- Surfaces and internal environments of plants, animals, fungi, and other microbes.
Major ecological functions:
- Decomposition of organic matter.
- Nutrient cycling:
- Nitrogen fixation, nitrification, denitrification.
- Sulfur and iron cycling.
- Primary production (e.g., cyanobacteria in oceans and freshwater).
- Symbioses:
- Mutualistic relationships (e.g., gut microbiota, plant root nodules).
- Commensal and pathogenic interactions with hosts.
These ecological functions form an important basis for grouping bacteria into functional categories in ecology and applied microbiology, complementing phylogenetic classification.
Systematics and Major Bacterial Lineages
From Phenotypic to Molecular Classification
Historically, bacterial classification was based on observable and testable features:
- Cell shape and arrangement.
- Gram reaction.
- Growth properties (temperature, oxygen tolerance).
- Biochemical tests (substrate utilization, enzyme activities).
- Pathogenicity, host range.
Modern systematics relies primarily on molecular data, especially:
- 16S rRNA gene sequences.
- Whole-genome sequences.
- Comparative genomics (shared gene content, synteny).
These data revealed:
- Many previously unrecognized deep lineages.
- That some phenotypically defined groups are not monophyletic.
- A need for a flexible and evolving taxonomic system.
Taxonomic Ranks within Bacteria
Within Domain Bacteria, higher-level taxa often used in systematics include:
- Phylum (plural: phyla).
- Class.
- Order.
- Family.
- Genus.
- Species.
Assignment to phyla and classes is now largely sequence-based. The formal naming and acceptance of taxa follow international codes of nomenclature for prokaryotes.
Examples of Important Bacterial Phyla
Without going into exhaustive detail, several phyla illustrate bacterial diversity:
- Proteobacteria:
- Very large and diverse group.
- Includes many well-known genera, both free-living and pathogenic.
- Metabolically versatile: phototrophs, nitrogen-fixers, sulfur-oxidizers, and others.
- Firmicutes (often Gram-positive):
- Thick peptidoglycan cell walls.
- Includes spore-forming genera.
- Many are important in food production, medicine, and the gut microbiota.
- Actinobacteria:
- High G+C Gram-positive bacteria.
- Many soil-dwelling species that produce antibiotics.
- Some are important human pathogens.
- Cyanobacteria:
- Oxygenic photosynthesizers (perform photosynthesis similar to plants).
- Major primary producers in aquatic systems.
- Probably ancestral to chloroplasts via endosymbiosis.
- Bacteroidetes:
- Abundant in the gut microbiota of many animals.
- Important degraders of complex organic compounds.
Numerous additional phyla (including many known mainly from environmental DNA) reflect that much bacterial diversity remains poorly characterized or even uncultured.
Special Features Relevant to Classification
Endospores and Other Survival Structures
Certain bacterial groups (notably within Firmicutes) form endospores:
- Highly resistant dormant structures.
- Survive extreme heat, drying, radiation, and chemicals.
- Germinate back into vegetative cells under favorable conditions.
The presence of spore-forming ability is an important diagnostic and taxonomic feature within those lineages.
Oxygen Requirements and Tolerance
Oxygen relationships can be used in both ecological and taxonomic characterization:
- Obligate aerobes: require oxygen for growth.
- Obligate anaerobes: killed by oxygen.
- Facultative anaerobes: can grow with or without oxygen.
- Microaerophiles: require low oxygen concentrations.
- Aerotolerant anaerobes: do not use oxygen but tolerate its presence.
These traits correlate with certain clades but also evolve repeatedly, so they are supporting rather than defining characters at higher taxonomic ranks.
Motility and Surface Structures
Features such as:
- Flagella type and arrangement.
- Presence and type of pili.
- Capsule composition.
are used in species- and genus-level classification and in identifying pathogens. For example:
- Different flagellar antigens are used to distinguish strains within a species.
- Capsule composition can be linked to virulence and used in serotyping.
Importance of Bacteria in Systematics and Evolution
Bacteria and the Tree (or Network) of Life
Because bacteria are extremely ancient and diverse, and because of prevalent horizontal gene transfer, the evolution of Bacteria is not always well described by a simple branching tree.
Implications for systematics:
- Deep relationships between major bacterial phyla can be difficult to resolve.
- The early history of life appears more like a network with gene exchange among lineages.
- Nevertheless, bacterial 16S rRNA phylogenies support Domain Bacteria as distinct from Archaea and Eukarya.
Bacteria as Models and Tools
Several bacterial species are central to biological research and applied systematics:
- Model organisms in molecular biology and genetics.
- Hosts for recombinant DNA and genetic engineering.
- Indicators for water quality and contamination.
- Reference strains anchoring taxonomic descriptions.
These well-characterized strains help define species boundaries, calibrate diagnostic methods, and serve as standards for classifying newly discovered bacteria.
Summary
Domain Bacteria encompasses an immense diversity of prokaryotic life forms unified by shared cellular features, especially the presence of peptidoglycan cell walls and characteristic ribosomal structures, but divided into numerous lineages distinguished by molecular, morphological, and ecological traits.
Modern systematics of Bacteria relies heavily on comparative sequence analysis (particularly 16S rRNA and whole genomes), revealing a complex pattern of relationships influenced by horizontal gene transfer. Understanding the diversity and classification of bacteria is essential for ecology, medicine, biotechnology, and for reconstructing the evolutionary history of life.