….the branch of science concerned with
classification, especially of organisms; systematics. A
classification scheme.

Taxonomy:

…. the evolutionary development and
diversification of a species or group of organisms

Phylogeny:

Microorganisms can generally be grouped into three morphological
categories: wic are?

rods, cocci, and spirals

…….. are small and have simple shapes, so it is difficult to classify them on the basis of morphology. Exceptions are the.......

Bacteria and Archaea

cyanobacteria and actinomycetes

•
Phylogeny
–

Evolutionary history of a group of organisms
–
Inferred indirectly from nucleotide sequence data
•

Molecular clocks (chronometers)
–

-Certain genes are measures of evolutionary change
Major assumptions: nucleotide changes occur at a
constant rate, are generally neutral, and are random
-Needs to be calibrated with fossils record

..... have many easily distinguished features eg body plans and developmental processes, that can be used to describe hierarchies of relatedness

large organisms

gram positive have no wall while gram -ve have a ........

funny wall

unlike ....., microbes are morphologically simple and shape may have little to do with phylogeny

plants and animals wit complex morphology

bergey' manual for classification provided a useful way to classify ana unknown microbe based on structural,biochemical and phusiological characteristics. wat is the con for this system?

it is not based on evolutionary framework eg the gram negative bacteria are not a phylogenetically coherent group

The universal phylogenetic tree is based on..........

SSU rRNA genes

the 16s/18s rRna is the .................

functionally conserved.

regions in wic nucleotide sequence is conserved in all cells.

central component in protein synthesis

why use the 16s/18s rRna as a molecular chronometer?

universally distributed and conserved structure

coded for in organeller, nuclear, and prokaryotic genomes

slow-and fast evolving portions: hr and minute hands

statistically sufficient number of nucleotides

ancient and essential function

no lateral gene transfer lgt

Taxonomy

•

The science of identification, classification,
and nomenclature

–
The study of the diversity of organisms and
their relationships
–
Links phylogeny with taxonomy

Systematics

The polyphasic approach to taxonomy uses
three methods:

1. Phenotypic analysis
2. Genotypic analysis
3. Phylogenetic analysis

Phenotypic Analysis
•

Phenotypic analysis examines the
morphological, metabolic, physiological,
and chemical characters of the cell
•
E.g. fatty acid analysis

Genotypic analysis

No universally accepted concept of species for
prokaryotes

Current definition of prokaryotic species
–

Collection of strains sharing a high degree of
similarity in several independent traits
–
Most important traits include 70% or greater
DNA DNA hybridization and 97% or greater
16S rRNA gene sequence identity

Phylogenetic analysis
–

16S rRNA gene sequences are useful in
taxonomy; serve as “gold standard” for the
identification and description of new species
•
Proposed that a bacterium should be considered a
new species if its 16S rRNA gene sequence differs
by more than 3% from any named strain, and a new
genus if it differs by more than 5%

the universal phylogenetic tree is based on.....

ssu rRna genes

Endosymbiosis
theory

Bacterium (alphaproteobacteria)
incorporated into the ancestor to the
eukaryotic cell: aerobic respiration:
mitochondria
Bacterium (Cyanobacteria)
incorporated into the eukaryotic cell:
photosynthesis: chloroplast
Increased the metabolic diversity

species are of the same species if they share > 97% 16s rRna seq homology and > 70% genomic hybridization