Microbial Taxonomy and Diversity

Archaeal characteristics

Archaea are prokaryotes that differ from Bacteria in cell envelope chemistry, membrane lipids, and the translation machinery, so these features are reliable discriminating points in GATE-level questions.

Archaeal cell walls lack true peptidoglycan, which is a polymer of N-acetylglucosamine and N-acetylmuramic acid cross-linked by peptides containing D-amino acids. Archaeal walls instead consist of S-layer glycoproteins, pseudopeptidoglycan, or other polysaccharides and proteins. Therefore muramic acid and D-amino acids should not be treated as archaeal wall markers.

Membrane lipids are another key difference. Archaeal membranes use ether linkages between glycerol and isoprenoid chains such as phytanyl groups, whereas bacteria and eukaryotes use ester-linked fatty acids.

Extreme halophiles such as Halobacterium show how surface chemistry adapts to the environment. Their surface glycoproteins are rich in acidic residues such as aspartate and glutamate. The negatively charged carboxyl groups bind Na+ and K+ from the high-salt medium, which stabilizes the envelope and helps maintain osmotic balance. Basic or small neutral residues cannot supply this charge density.

Translation also separates archaea from bacteria. Archaeal protein synthesis starts with methionine on a non-formylated initiator tRNA, as in eukaryotes, so N-formylmethionine is a bacterial marker and not an archaeal one.

Bacterial identification methods

Identifying a bacterial species requires a method that discriminates at the species level, which usually means a specific genetic sequence or a highly specific molecular probe.

Fluorescent in situ hybridization (FISH) uses fluorescently labelled oligonucleotide probes complementary to rRNA sequences of a target taxon, so cells can be identified directly within a sample.

PCR amplification of a marker gene, usually 16S rRNA, followed by sequencing gives a sequence that is compared with reference databases for species assignment. The 16S rRNA gene is the standard molecular marker for identifying and classifying prokaryotes because it is highly conserved yet contains variable regions.

Nucleic acid hybridization depends on complementary base pairing between a labelled probe and the target sequence. Southern blotting is a hybridization technique in which DNA separated by electrophoresis is transferred to a membrane and probed with a labelled sequence.

Staining methods work at a different level. Gram staining separates bacteria into Gram-positive and Gram-negative groups according to cell wall composition, while acid-fast staining detects mycolic-acid-containing walls as in Mycobacterium and Nocardia. These are group-level tests and cannot by themselves name a species.

The G+C content of genomic DNA is a useful taxonomic property, but it is shared by many unrelated organisms and cannot identify a microorganism alone.

When a question asks for species identification, sequence-based or probe-based methods are the correct choices.

Spirochete morphology

Spirochetes form a phylum of helical, motile bacteria whose defining feature is a corkscrew-shaped cell with periplasmic flagella, also called axial filaments or endoflagella. The axial filaments lie in the periplasmic space between the outer sheath and the protoplasmic cylinder, and their rotation drives the characteristic twisting motility.

Members of this phylum include Borrelia, which causes Lyme disease, Leptospira, which has a hooked, tightly coiled cell and causes leptospirosis, and Treponema, which includes T. pallidum, the agent of syphilis.

Treponema pallidum is the typical example of a spirochete with axial filaments.

Helical shape alone does not define a spirochete. Spirulina is also helical, but it is a filamentous cyanobacterium, a photosynthetic organism of a different phylum, and it has no periplasmic flagella.

Non-motile pathogens such as Mycobacterium tuberculosis, Pasteurella multocida, and Shigella dysenteriae lack flagella and axial filaments, so the presence of axial filaments is a useful discriminating feature.

Viral genome types

Viral genomes are classified by the nucleic acid type (DNA or RNA), its strandedness, and its polarity or segmentation. Matching a virus to its genome therefore requires knowing these combinations.