Core Concepts in Microbiology: Genetics, Ecology, and Immunity

Posted on Oct 13, 2025 in Biology

Bacterial Genetics and Molecular Processes

Genome Replication and Gene Expression

Foundational Genetic Experiments

Griffith’s transformation experiment demonstrated that non-virulent bacteria could become virulent by absorbing DNA from dead virulent cells, proving that DNA is the genetic material. The Hershey and Chase experiment used radioactive labeling (phosphorus for DNA and sulfur for protein) to confirm that only DNA enters bacterial cells during phage infection, further establishing DNA as the genetic material.

DNA Structure and Replication

DNA has a double-helix structure with two antiparallel strands made up of nucleotides (A-T and G-C) and a sugar-phosphate backbone. In contrast, RNA is single-stranded with ribose sugar and uses uracil instead of thymine. DNA replication is semi-conservative, meaning each new molecule has one original and one newly synthesized strand.

Key proteins in replication include:

  • Helicase: Unwinds DNA.
  • Primase: Synthesizes RNA primers.
  • DNA Polymerase III: Main replication enzyme; performs proofreading.
  • DNA Polymerase I: Replaces RNA primers.
  • Ligase: Joins Okazaki fragments.
  • Single-strand binding proteins (SSBs): Stabilize the strands.

Replication starts at the origin of replication (OriC) and involves DnaA, helicase, and primase, forming the replisome at the replication fork.

Gene Expression: Transcription and Translation

An operon is a gene cluster transcribed under a single promoter. Polycistronic mRNA, common in prokaryotes, encodes multiple proteins. Transcription starts with sigma factors guiding RNA polymerase to the promoter, proceeds with elongation, and ends through rho-dependent or independent termination.

Codons are nucleotide triplets that code for amino acids:

  • Start codon: AUG.
  • Stop codons: UAA, UAG, and UGA.

Sense codons encode amino acids, and code degeneracy allows multiple codons for the same amino acid. Translation involves the ribosome assembling on mRNA, tRNA bringing amino acids, peptide bond formation, elongation of the protein, and release at the stop codon.

Regulation of Cellular Processes

Constitutive genes are always expressed. Bacterial gene regulation involves repressors, activators, operons, and riboswitches. Negative control uses repressors to block transcription, while positive control uses activators to enhance it.

The lac operon (including lacZ, lacY, and lacA) is induced by lactose and repressed by glucose (catabolite repression), controlled by the lac repressor and the CAP-cAMP complex. Riboswitches are regulatory RNA segments that bind metabolites to alter gene expression. Sigma factors help RNA polymerase recognize specific promoters and coordinate global transcription responses. Chemotaxis is guided by methyl-accepting chemotaxis proteins (MCPs) and enables movement toward or away from stimuli. CRISPR-Cas systems provide bacterial immunity by targeting and cutting foreign DNA.

Eukaryotic and Archaeal Genomics

Eukaryotic Replication and Expression

Eukaryotic DNA replication starts at multiple origins using ORC, helicase, and various DNA polymerases. DNA polymerase α adds RNA primers, while δ and ε handle lagging and leading strand synthesis, respectively. The end replication problem arises on the lagging strand and is resolved by telomerase adding telomeres.

Eukaryotic transcription is initiated by RNA polymerase II with transcription factors and includes post-transcriptional modifications:

  • The 5′ cap.
  • The poly-A tail.
  • Splicing (where introns are removed and exons code for proteins).

Eukaryotic genes are typically monocistronic, encoding one protein per mRNA. Compared to bacterial transcription, eukaryotic transcription uses more complex machinery and involves extensive processing.

Archaeal Processes

Archaeal replication has a single origin like bacteria, but the replication machinery resembles that of eukaryotes. Archaeal transcription is similar to eukaryotes but simpler. Regulation can occur during transcription, translation, and post-translation.

Mechanisms of Genetic Variation

A mutation is a permanent change in DNA and can be a point mutation, insertion, deletion, or frameshift, caused by replication errors, radiation, or chemicals. UV radiation can induce thymine dimers that distort the DNA helix.

Terminology includes:

  • Wild type: Normal sequence (WT).
  • Forward mutation: WT to mutant.
  • Reversion: Mutant to WT.

Mutations can be silent (no amino acid change), missense (amino acid change), nonsense (introduces stop codon), or frameshift (alters reading frame). Replica plating detects mutants by comparing colony growth under different conditions. DNA methylation helps regulate gene expression and mismatch repair. Excision repair involves removing and replacing damaged DNA.

Horizontal gene transfer (HGT) includes:

  • Homologous recombination: Exchange between similar sequences.
  • Site-specific recombination.
  • Conjugation: Plasmid transfer via a pilus.
  • Transformation: Uptake of free DNA.
  • Transduction: DNA transfer via bacteriophages.

Microbial Ecology and Environmental Interactions

Microbial Ecology and Community Structure

A habitat is a physical location, while a niche refers to the role or function of a microbe in an ecosystem. A microenvironment is the immediate, small-scale environment around a microbe and can change rapidly. Biofilms are microbial communities attached to surfaces in a self-produced matrix, offering benefits like protection, nutrient access, and gene exchange. Quorum sensing is a density-dependent communication method for coordinating behavior. A guild is a group of microbes with similar metabolism, and functional redundancy refers to different organisms performing the same function, which enhances ecosystem stability.

Microbial Interactions and Symbiosis

Types of symbiosis:

  • Mutualism: Both benefit (e.g., termites and gut protozoa).
  • Cooperation: Optional, both benefit.
  • Commensalism: One benefits, the other unaffected.
  • Predation: One kills the other (e.g., Bdellovibrio).
  • Parasitism: One benefits at the other’s expense.
  • Ammensalism: One is harmed, the other unaffected (e.g., antibiotic production).
  • Competition: Both harmed by limited resources.

Consortia are stable microbial communities, often found in aquatic environments. Microbiota encompasses all microbes living on or in a host, while normal flora refers to those commonly found in healthy individuals.

Biogeochemical Cycling

Biogeochemical cycling involves microbial recycling of elements such as carbon, nitrogen, sulfur, phosphorus, and iron.

  • Carbon Cycle: Photosynthesis fixes CO₂, while respiration and fermentation release it. Methanogenesis reduces CO₂ to CH₄ anaerobically.
  • Nitrogen Cycle: Includes nitrogen fixation (N₂ to NH₃, e.g., by Rhizobium), nitrification (NH₃ to NO₂⁻ to NO₃⁻), denitrification (NO₃⁻ to N₂), and ammonification (organic nitrogen to NH₃).
  • Sulfur Cycle: Features assimilatory reduction (S to organic compounds) and dissimilatory reduction (S as an electron acceptor).
  • Phosphorus Cycle: Lacks a gaseous phase, and microbes help solubilize phosphate.
  • Iron Cycle: Involves microbial redox reactions affecting iron availability.

Microorganisms in Terrestrial Environments

Soil is divided into horizons:

  • O: Organic material.
  • A: Topsoil with high microbial activity.
  • B: Subsoil.
  • C: Bedrock.

The rhizosphere is the soil region near plant roots with high microbial activity. Mycorrhizae are fungi-plant symbioses that exchange nutrients, and endophytes are microbes within plant tissues. Actinobacteria are abundant in soil and produce antibiotics. Soil microbes play vital roles in decomposition, nutrient cycling, and promoting plant growth.

Aquatic Ecosystems

Marine Environments

Marine environments are often oligotrophic (low nutrients), requiring microbes to adapt. Pelagibacter is the most abundant ocean bacterium, and Prochlorococcus is a common photosynthetic cyanobacterium. Ocean zones include the epipelagic (sunlit, high microbial activity) and deep zones (bathypelagic, abyssal, hadal), which host pressure-adapted microbes.

Freshwater Systems

Freshwater ecosystems include lentic (still water like lakes) and lotic (flowing water like rivers) systems. Stratification affects oxygen and microbial distribution. Eutrophication, caused by nutrient enrichment, leads to algal blooms and oxygen depletion. The microbial loop describes carbon and nutrient recycling via microbial interactions.

Water Pollution and Purification

Water pollution stems from domestic sewage, industrial waste, and agricultural runoff. Biochemical Oxygen Demand (BOD) measures the oxygen used by microbes to decompose organic matter. Coliforms, like E. coli, serve as indicators of fecal contamination. Water purification involves sedimentation, coagulation, filtration, and disinfection (chlorine or UV).

Wastewater treatment has three stages:

  • Primary: Physical removal.
  • Secondary: Biological treatment (activated sludge or trickling filters).
  • Tertiary: Chemical or advanced filtration.

Sludge digestion uses anaerobic microbes to break down organic matter and produce methane.

Pathogenesis and Host Defense Mechanisms

Microbial Diseases and Epidemiology

Pathogens are microbes that cause disease and use virulence factors like adherence mechanisms, toxins, and immune evasion. Infectious dose (ID50) refers to the number of microbes needed to infect 50% of hosts. Signs are observable (e.g., fever, rash), while symptoms are experienced (e.g., pain, fatigue). Diseases can be acute (rapid onset), chronic (long-term), or latent (dormant, then reactive). Transmission routes include direct contact, airborne, vehicle, and vector-borne.

Epidemiological terms:

  • Endemic: Constant presence.
  • Epidemic: Sudden increase.
  • Pandemic: Global spread.

Principles of Immunology

Innate Immunity: First Line of Defense

Innate immunity is the first defense line, including physical (skin, mucous membranes), chemical (pH, enzymes), and biological barriers (normal flora). Key innate immune cells include:

  • Neutrophils: Phagocytic first responders.
  • Macrophages: Phagocytosis and antigen presentation.
  • Dendritic cells: Link innate and adaptive immunity.
  • Natural killer (NK) cells: Destroy infected or cancerous cells.

Pattern recognition receptors (PRRs), such as Toll-like receptors (TLRs), detect pathogen-associated molecular patterns (PAMPs). The inflammatory response includes redness, heat, swelling, and pain, mediated by cytokines and histamines. The complement system is a protein cascade promoting opsonization, inflammation, and microbe lysis.

Adaptive Immunity: Specificity and Memory

Adaptive immunity is specific and memory-based, involving B and T lymphocytes. B cells mediate humoral immunity, producing antibodies (IgG, IgA, IgM, IgE, IgD), with plasma cells secreting them and memory B cells ensuring long-term protection. T cells provide cell-mediated immunity:

  • Helper T cells (CD4⁺): Activate other immune cells.
  • Cytotoxic T cells (CD8⁺): Kill infected cells.
  • Regulatory T cells: Prevent autoimmunity.

Antigen presentation involves MHC I (on all nucleated cells, presented to CD8⁺ T cells) and MHC II (on antigen-presenting cells, presented to CD4⁺ T cells). The primary immune response is slower with IgM dominance, while the secondary response is faster and stronger with IgG due to memory cells.

Vaccination and Immune Disorders

Immunological memory underpins vaccination, which can be live attenuated (e.g., MMR), inactivated (e.g., polio), subunit (e.g., HPV), toxoid (e.g., tetanus), or mRNA-based (e.g., COVID-19). Immune disorders include hypersensitivities, immunodeficiencies (e.g., SCID, HIV/AIDS), and autoimmune diseases (e.g., lupus, rheumatoid arthritis).