Microbial Classification

How old is the Earth?

Approximately 4.6 billion years old.

How old are the earliest microbial fossils?

3.5–3.8 billion years old, mainly from prokaryotes.

What were the earliest microbial ancestors like?

Likely anaerobic organisms (did not require oxygen).

What was the Great Oxygenation Event (GOE)?

A rise in atmospheric oxygen caused by cyanobacterial photosynthesis.

Why was the GOE important for microbial diversity?

Increased oxygen drove diversification and new metabolic pathways.

When did viruses likely emerge?

Soon after the first life evolved.

Why don’t viruses have traditional fossils?

They do not fossilise, as they lack cellular structures.

What evidence do we have for ancient viruses?

Viral DNA can integrate into host genomes, leaving genetic traces.

What are Endogenous Viral Elements (EVEs)?

Viral DNA sequences permanently embedded in host genomes.

How much of the human genome is retroviral DNA?

Approximately 5–8%.

What do bioinformatics analyses show about virus evolution?

Viruses arose at least 100 million years ago, likely much earlier.

What is taxonomy?

The classification of organisms into groups; also called systematics.

What is the etymology of the word taxonomy?

From Greek “taxis” (arrangement/order) and “nomos” (law).

What is classification in taxonomy?

Arranging organisms into taxa based on similarity or evolutionary relationships.

What is nomenclature?

The assignment of names to taxonomic groups according to published rules.

What is identification in taxonomy?.

Determining that a specific isolate belongs to a particular taxon

What is phylogeny?

The evolutionary relatedness between species.

What is the etymology of phylogeny?

From Greek “phylon” (tribe/race) and “genesis” (origin/generation).

Why is classifying organisms important?

It helps scientists understand differences between organisms and organise biological diversity.

How does taxonomy help future science?

It catalogues organisms, building a knowledge base for future research.

How does taxonomy support research and discovery?

It allows scientists to make predictions and form hypotheses about organisms.

Why is grouping organisms useful?

It helps scientists work with related organisms more efficiently.

Why is taxonomy essential in microbiology?

It enables accurate identification of microbes, including pathogens.

What would happen without taxonomy?

Understanding the characteristics of isolates, especially pathogens, would be extremely difficult.

Is there a kingdom level in bacterial taxonomy?

No. In bacterial classification, there is no kingdom rank.

What is the taxonomic domain of bacteria?

Domain: Bacteria.

What is the phylum of Pseudomonas aeruginosa?

Proteobacteria.

What is the class of Pseudomonas aeruginosa?

γ-Proteobacteria (Gammaproteobacteria).

What is the order of Pseudomonas aeruginosa?

Pseudomonadales.

What is the family of Pseudomonas aeruginosa?

Pseudomonadaceae.

What is the genus and species of Pseudomonas aeruginosa?

Genus: Pseudomonas
Species: aeruginosa

What do the suffixes “-ales” and “-aceae” mean in taxonomy?

-ales = order, -aceae = family.

What is a scientific (binomial) name?

A Latinised, italicised two-part name made of genus + species.

How is a genus name written?

Capitalised and italicised (e.g., Escherichia).

How is a species name written?

Lowercase and italicised (e.g., coli).

How can a genus name be abbreviated?

To its first letter after first use (e.g., E. coli).

What does “Candidatus” mean in taxonomy?

Used when an organism cannot be grown in pure culture.

Give an example of a “Candidatus” organism.

Candidatus Chloracidobacterium thermophilum.

Can species names change over time?

The species name is stable, but it may be moved to a different genus based on new sequencing data.

What is a microbial species?

A collection of strains that share many stable properties and are clearly different from other groups.

What genetic criteria define a bacterial species?

Similar G+C content and >70% DNA–DNA hybridisation similarity.

What is G+C composition?

The proportion of guanine + cytosine compared to adenine + cytosine in the genome.

What is DNA–DNA hybridisation?

A classical method for determining bacterial species relatedness.

How does DNA–DNA hybridisation work?

DNA from strains A and B is heated to separate strands, mixed, and allowed to re-pair.

What does hybridisation temperature indicate?

Higher re-association temperature = greater genetic similarity.

Can variation exist within a microbial species?

Yes, species can contain distinct groups of strains with measurable differences.

What is a strain?

All descendants of a single, pure microbial culture.

What are biovars?

Strains differing in biochemical or physiological traits.

What are morphovars?

Strains that differ in morphology.

What are serovars?

Strains distinguished by antigenic properties.

What are pathovars?

Strains that differ in pathogenicity or host range.

What is the core genome?

Genes shared by all strains of a species.

What is the accessory genome?

Genes present in some but not all strains, often linked to adaptation or virulence.

What is the pan-genome?

The total set of genes found across all strains of a species.

Where are recognised prokaryotic species formally described?

Bergey’s Manual of Systematic Bacteriology.

Why do we divide bacterial genomes into core and accessory parts?

Because strains within the same species show a lot of genetic variation.

What is the core genome?

The set of genes found in all members of a species.

What is the function of the core genome?

It contains the minimal genes required for survival in any environment.

What types of genes are in the core genome?

Essential housekeeping genes (e.g. replication, transcription, metabolism).

What is the accessory genome?

Genes found in some but not all strains of a species.

Are accessory genes essential?

No — they are non-essential in all environments, but useful in specific ones.

What is the role of the accessory genome?

Helps bacteria adapt to new niches, environments, or hosts.

How are accessory genes often acquired?

Through horizontal gene transfer (HGT).

What is the pan genome?

The total collection of all genes found across all strains of a species.

How do core, accessory, and pan genomes relate to each other?

• Core genome → present in all strains

• Accessory genome → present in some strains

• Pan genome → core + all accessory genes

What is horizontal gene transfer (HGT)?

The exchange of genetic material between prokaryotic cells, not from parent to offspring.

Why is HGT important in microbial evolution?

It drives genetic diversity and rapid adaptation in microbes.

How does HGT affect phylogenetic analysis?

It complicates phylogenetic trees, as genes may not follow a single line of ancestry.

What is vertical gene transfer (VGT)?

Parent-to-offspring transmission of genes during reproduction.

How do phylogenetic trees reflect VGT?

Genetic changes arise through mutation or recombination, producing clear ancestral lineages.

Between which organisms does HGT occur?

Between cells of the same species (intraspecies) or different species (interspecies).

How does HGT alter evolutionary relationships?

A gene from one species can appear in another, making them seem closely related even when their core genomes are different.

What is bacterial transformation?

Uptake of free DNA from the environment by a bacterium.

Where does environmental DNA come from?

From dying or lysed bacterial cells that release DNA.

: What does it mean for a bacterium to be competent?

It is in a special physiological state that allows it to take up foreign DNA.

How does DNA enter a competent cell during transformation?

Via a specialised DNA transport system.

What happens to DNA after uptake in transformation?

It can be integrated into the chromosome and then vertically inherited by daughter cells.

What is bacterial transduction?

Transfer of bacterial DNA mediated by a bacteriophage.

What is a bacteriophage?

A virus that infects bacteria (and archaea)

How does a bacteriophage normally inject DNA?

Using a protein “syringe” structure.

How does transduction occur during phage infection?

Bacterial DNA is mistakenly packaged instead of phage DNA.

Why doesn’t the recipient cell get infected during transduction?

Because the injected DNA is bacterial, not viral.

What must happen for transduced DNA to be inherited?

It must be stably integrated into the recipient chromosome.

What is bacterial conjugation?

Direct DNA transfer between cells via cell-to-cell contact.

What allows a donor cell to conjugate?

A special plasmid (F plasmid) carrying conjugation genes.

What is an F pilus?

A tube-like structure formed by the donor to connect to the recipient cell.

How is DNA transferred during conjugation?

The plasmid replicates, and a copy is transferred through the pilus.

What happens to the recipient cell after conjugation?

It gains the F plasmid and can now conjugate with other cells.

How do bacteria and archaea generate genetic variation despite asexual reproduction?

Through mutation and horizontal gene transfer, which introduce new genetic differences.

Why doesn’t asexual reproduction prevent diversity in bacteria?

Because genetic changes can still occur, even without sexual reproduction.

How do mutations contribute to variation in bacterial populations?

Random mutations arise in bacterial clones, creating genetic diversity.

What is the overall result of mutation and gene transfer in bacteria?

Variation within populations, allowing adaptation and evolution.

What is polyphasic taxonomy?

An approach that uses multiple classification systems together to identify and classify microbes.

Why is polyphasic taxonomy used?

No single method is sufficient to accurately classify a novel microbe.

What are the two main components of polyphasic taxonomy?

Phenetic classification and genotypic classification.

What is phenetic classification?

Compares observable characteristics (phenotypes) between organisms.

What is genotypic classification?

Compares genetic similarity between organisms.

What morphological traits are used in phenetic classification?

Colony morphology, colour, cell shape, size, and ultrastructure.

What staining traits are used in phenetic classification?

Gram stain behaviour and endospore staining.

Why is spore morphology important?

Spore shape and location help distinguish bacterial groups.