Unit 1: Introduction to microbiology and microbial evolution

Microbiology is the study of organisms too small to be seen clearly with the unaided eye — bacteria, archaea, fungi, protists, algae and viruses — and of their activities, evolution and relationships. As a formal discipline it dates from the 1670s (first observations) but matured only after 1860. Everything in this unit depends on a few founding ideas.

• Object of study: cells generally smaller than 1 mm, resolved only with microscopes; the working cut-off is roughly 200 µm (limit of the human eye).
• Two cell types: prokaryotic (no membrane-bound nucleus; Bacteria and Archaea) and eukaryotic (nucleus present; fungi, protists, algae).
• Non-cellular agents: viruses, viroids and prions, studied within microbiology though they are not cells.
• Guiding assumptions: microbes are the oldest, most abundant and most metabolically diverse life; and evolutionary relationships (phylogeny), not appearance alone, define natural groupings.

II. Historical Development of Microbiology

How a curiosity became an experimental science.

The field advanced in three overlapping stages: first observation, then the establishment of general principles, then a molecular and applied modern era.

A. Historical roots of microbiology

Microbiology began as microscopy and the slow overthrow of spontaneous generation.

• Robert Hooke (1665): described "cells" in cork in Micrographia, giving the discipline its central unit.
• Antonie van Leeuwenhoek (1676): using single-lens microscopes (~200–300× magnification), first observed "animalcules" — the first record of living microbes.
• Spontaneous generation debate: whether life arises from non-living matter.
  • Francesco Redi (1668): covered-meat experiments argued against it for maggots.
  • Louis Pasteur (1861): swan-necked flask experiment showed sterile broth stayed sterile until exposed to airborne microbes — decisive disproof.
• John Tyndall & tyndallization: demonstrated heat-resistant forms, explaining anomalous results and pointing toward endospores.

B. Microbial diversity and rise of general microbiology

General microbiology emerged when isolation, cultivation and causation became repeatable techniques.

• Germ theory of disease: specific microbes cause specific diseases.
  • Koch's postulates (1884): (1) organism present in every case, (2) isolated in pure culture, (3) reproduces disease when inoculated, (4) re-isolated from the new host.
• Pure-culture technique: solid media using agar (introduced via Fannie Hesse) and the Petri dish enabled single-species colonies.
• Founding applications: Pasteur's work on fermentation (yeasts), pasteurization, and the rabies and anthrax vaccines linked microbes to industry and medicine.
• Environmental microbiology: Sergei Winogradsky (chemolithotrophy, nitrogen and sulphur cycling) and Martinus Beijerinck (enrichment culture, nitrogen fixation) established that microbes drive geochemical cycles.

C. Modern era of microbiology

The modern era shifted from whole organisms to molecules, genes and communities.

• Molecular biology: the DNA double helix (Watson & Crick, 1953) and use of microbes as model systems (e.g., Escherichia coli, bacteriophage lambda).
• rRNA revolution: Carl Woese (1977) used small-subunit ribosomal RNA sequences to define a third domain, the Archaea.
• Recombinant DNA & biotechnology: restriction enzymes, plasmid cloning, and PCR (Kary Mullis, 1983) made microbes tools for genetic engineering.
• Genomics & metagenomics: the first free-living genome, Haemophilus influenzae (1995), and culture-independent sequencing of whole communities.

III. The Nature and Extent of Microbial Life

When microbes arose and how far they reach.

This section frames microbial life in time and space: it is ancient, ubiquitous and vastly varied.

A. Antiquity and extent of microbial life

Microbes are Earth's oldest and most widespread life form.

• Age: Earth formed ~4.6 billion years ago (Ga); microbial fossils (stromatolites) and isotopic carbon signatures indicate life by ~3.5–3.8 Ga.
• Great Oxidation Event (~2.4 Ga): cyanobacterial oxygenic photosynthesis raised atmospheric O₂, reshaping the biosphere.
• Endosymbiotic theory (Lynn Margulis): mitochondria and chloroplasts descend from engulfed bacteria — microbes gave rise to eukaryotic organelles.
• Extent: microbes inhabit soil, oceans, hot springs, deep subsurface rock and the human body; global bacterial + archaeal cells number ~10³⁰.
• Extremophiles: thermophiles (>80 °C), halophiles, acidophiles and psychrophiles define the physical limits of life.

B. Microbial diversity

Microbial diversity spans phylogeny, metabolism and habitat far beyond that of plants and animals.

• Structural diversity: cell shapes (cocci, bacilli, spirilla) and wall types (Gram-positive thick peptidoglycan vs Gram-negative thin wall with outer membrane).
• Metabolic diversity: classification by energy and carbon source.
  • Phototrophs vs chemotrophs: light-derived vs chemical-bond energy.
  • Autotrophs vs heterotrophs: CO₂ vs organic carbon.
  • Unique modes — chemolithotrophy (energy from inorganic molecules like H₂S, NH₃) and anaerobic respiration — occur only in prokaryotes.
• Physiological diversity: response to oxygen (aerobes, anaerobes, facultative, microaerophiles) and to temperature/pH ranges.
• Uncultured majority: over 99% of environmental microbes resist laboratory culture, known only through DNA — the "great plate-count anomaly".

IV. Ordering Microbial Life

Naming groups and mapping their descent.

Because microbes look alike, ordering them requires formal naming rules and molecular family trees.

A. Microbial classification and taxonomy

Taxonomy assigns organisms to ranked, named groups by shared characteristics.

• Definition: taxonomy = classification (grouping) + nomenclature (naming) + identification (assigning an unknown to a group).
• Hierarchy: Domain → Phylum → Class → Order → Family → Genus → Species.
• Binomial nomenclature (Linnaeus): two-part italicized Latin name, e.g. Escherichia coli — capitalized genus, lowercase species.
• Species concept for prokaryotes: a group with ≥70% DNA–DNA hybridization or ≥95–96% average nucleotide identity (ANI).
• Approaches contrasted:
  1. Phenotypic/classical: morphology, staining, biochemistry, growth conditions — practical but convergent traits mislead.
  2. Polyphasic: combines phenotype, chemotaxonomy (cell-wall, lipid, quinone profiles) and genotype for a robust consensus.
• Three-domain system (Woese): Bacteria, Archaea, Eukarya replaced the older five-kingdom scheme.

B. Accessing microbial phylogeny

Phylogeny reconstructs evolutionary relationships from conserved molecular sequences.

• Molecular chronometer: 16S rRNA (prokaryotes) / 18S rRNA (eukaryotes) — universal, functionally constant, ~1,500 bases, with conserved and variable regions.
• Workflow:

1. Extract DNA
2. PCR-amplify 16S rRNA gene (universal primers)
3. Sequence the amplicon
4. Align sequences (conserved regions as anchors)
5. Build tree from sequence differences

• Tree construction: distance methods (neighbour-joining), maximum parsimony, and maximum likelihood/Bayesian methods convert aligned differences into branching diagrams; branch length ∝ evolutionary change.
• Reading a tree: nodes = common ancestors; terminal tips = taxa; a monophyletic clade contains an ancestor and all its descendants.
• Complication — horizontal gene transfer (HGT): transformation, transduction and conjugation move genes between lineages, so single-gene trees can conflict; multi-gene and whole-genome phylogenies mitigate this.
• Culture-independent access: metagenomics and amplicon surveys reveal phylogeny of the uncultured majority directly from environmental DNA.

V. Microbial Interaction

How microbes relate to one another and to hosts.

Microbes rarely act alone; their interactions structure communities and ecosystems.

A. Microbial interaction

Interactions are classified by the net effect on each partner.

• Mutualism (+/+): both benefit.
  • Rhizobium–legume root nodules fixing N₂ in exchange for carbon; gut microbiota synthesising vitamin K and B-vitamins.
• Commensalism (+/0): one benefits, the other unaffected — skin flora using shed cells.
• Parasitism (+/−) and predation (+/−): one gains at another's expense — pathogens; Bdellovibrio preying on other bacteria.
• Competition (−/−): shared limiting resources suppress both, per Gause's competitive exclusion principle.
• Amensalism (−/0): one harmed, one unaffected — Penicillium secreting penicillin against neighbours.
• Syntrophy: metabolic cooperation where one organism's waste is another's substrate — H₂-producing fermenters feeding methanogens in anaerobic digestion.
• Communication and community structure:
  • Quorum sensing: cell-density signalling via autoinducers (e.g., acyl-homoserine lactones) triggers group behaviours such as bioluminescence and virulence.
  • Biofilms: surface-attached communities in an extracellular polymeric matrix, sharing nutrients and resisting antibiotics.
• Ecological significance: interaction networks drive biogeochemical cycling (carbon, nitrogen, sulphur), host health and disease, and the stability of every microbial ecosystem.