Chapter 19: Microbial Taxonomy, Evolution & Classification

Modern microbiology utilizes a polyphasic taxonomy approach, integrating phenotypic characteristics (morphology, physiology, ecology) with genotypic and phylogenetic data. Unlike systems based on physical traits, phylogenetic classification arranges microbes according to inferred evolutionary relationships, largely relying on molecular characterization due to the lack of a microbial fossil record. The Small Subunit ribosomal RNA (SSU rRNA) sequence, specifically 16S in Bacteria and Archaea, serves as the primary molecular chronometer for inferring phylogenies and identifying organisms at the genus level, owing to its conserved function, slow mutation rate, and resistance to horizontal gene transfer (HGT). Advanced techniques like Whole-Genome Sequencing (WGS) have introduced metrics such as Average Nucleotide Identity (ANI) as the standard for defining microbial species, replacing older methods like DNA-DNA hybridization. Evolutionary relationships are graphically depicted in phylogenetic trees, which can be rooted or unrooted, built using distance-based or character-based methods. However, the pervasive occurrence of Horizontal Gene Transfer (HGT) complicates tree construction, leading microbiologists to differentiate between the universally shared core genome and the environmentally acquired pan-genome. The chapter also explores major evolutionary milestones, including the Endosymbiotic Theory, which explains the origin of mitochondria and chloroplasts from engulfed bacteria. Furthermore, it addresses the ongoing challenge of defining a microbial species due to a lack of sexual reproduction, proposing the ecotype model where adaptive mutations driven by natural selection lead to speciation. Accepted taxonomic assignments are cataloged in the authoritative, phylogenetically organized reference, Bergey’s Manual of Systematics of Archaea and Bacteria.