MICROBIAL DIVERSITY

Survey of the Microbial World

Taxonomy: Naming, Classifying,
and Identifying Microorganisms

Microbial nomenclature- naming

microorganisms
Taxonomy- classifying living things
◦ Originated over 250 years ago with the work of Carl von
Linné
Identification- discovering and recording the
traits of organisms so they can be named and
classified
Levels of Classification
Figure 1.12
Assigning Specific Names
A standardized nomenclature allows
scientists from all over the world to
exchange information
The binomial system of nomenclature
◦ The generic (genus) name followed by the
species name
◦ Generic part is capitalized, species is lowercase
◦ Both are italicized or underlined if italics aren’t
available
◦ Staphylococcus aureus
 The Origin and Evolution of
Microorganisms
Phylogeny- the degree of relatedness
between groups of living things
Based on the process of evolution-
hereditary information in living things
changes gradually through time; these
changes result in structural and functional
changes through many generations
◦ Two preconceptions:
● All new species originate from preexisting species
● Closely related organisms have similar features because
they evolved from a common ancestor
Phylogeny usually represented by a tree-
showing the divergent nature of evolution
Figure 1.13
Figure 1.14
The new tree of eukaryotes showing Archaeplastida, and Stramenopila – the lineage of marine
algae

This summary is based on a consensus of recent phylogenomic studies. The colored groupings
correspond to the current 'supergroups.' Unresolved branching orders among lineages are shown
as multifurcations. Broken lines reflect lesser uncertainties about the monophyly of certain
groups. Star symbols denote taxa that were considered supergroups in early versions of the
supergroup model; thus, all original supergroups except Archaeplastida have either disappeared
or been subsumed into new taxa. The circles showed major lineages with no molecular data
when the supergroup model emerged, most often because they had not yet been discovered
(Burki et al. 2020).
The clade ‘SAR’ (stramenopiles, alveolates, and rhizaria) has been estimated
to comprise up to half of all eukaryote species (Burki et al. 2020).
Cellular
1. Prokaryotes: Archaebacteria, Eubacteria
2. Eukaryotes: Fungi, Algae, Protozoans
Acellular
1. Viruses
2. Viroids
3. Prions
Classification Schemes
1. Two-Kingdom System
2. Three-Kingdom System
3. Four-Kingdom System
4. Five-Kingdom System
5. 3-domain System
Two-Kingdom System
Kingdom Plantae and Kingdom Animalia
Classification of organisms into plants and
animals, respectively
By Linnaeus
This system did not distinguish between the
eukaryotes and prokaryotes, unicellular and
multicellular organisms and photosynthetic
(green algae) and non-photosynthetic (fungi)
organisms.
Was easily done and was easy to understand,
but, a large number of organisms did not fall
into either category
Three-Kingdom System
Proposed the German investigator Ernst
Haeckel in the 1860s
Kingdom Animalia, Kingdom Plantae, and
Kingdom Protista
Members of the kingdom Protista included
the protozoa, fungi, bacteria, and other
microorganisms.
microorganisms continued to be classified as
plants (for example, bacteria and fungi) or
animals (for example, protozoa).
Four-Kingdom System
Kingdom Virus, Kingdom Monera, Kingdom
Plantae and Kingdom Animalia within the
superkingdoms Prokaryota and Eukaryota.
Separate kingdoms are not recognized for the
microorganisms (Protista) or for the fungi,
which are placed in the plant kingdom.
 Five-Kingdom System
By R.H. Whittaker in1969
Kingdoms Monera, Protista, Fungi, Plantae, and
Animalia.
Character Kingdoms
Monera Protista Fungi Plantae Animalia
Cell type Prokaryotic Eukaryotic Eukaryotic Eukaryotic Eukaryotic
Cell wall Noncellulosic Present in some Present Present Absent
(Polysaccharide + (without (cellulose)
amino acid) cellulose)
Nuclear Absent Present Present Present Present
membrane
Body Cellular Cellular Multiceullar/ Tissue/ Tissue/organ/
organization loose tissue organ organ system
Mode of Autotrophic Autotrophic Heterotrophic Autotrophic Heterotrophic
nutrition (chemosynthetic (Photosynthetic) (Saprophytic/ (Photosynthe (Holoz o ic/
and and Parasitic) tic) Saprophytic
photosynthetic) Heterotrophic etc.)
and Heterotrophic
(saprophytic/para
sitic)
 3 Domains
In the 1970s, genetic comparisons using
small-subunit ribosomal RNA highlighted a major
problem with grouping all prokaryotic cells
together under the single kingdom of Monera. 
Some prokaryotic cells once considered bacteria
were more closely related to eukaryotes.
This required a larger phylogenic category to be
created: the domain.
Two of the three domains contain prokaryotic
cells (domains Bacteria and Archaea), and all
eukaryotic organisms reside under domain
Eukarya.
3 Domains
The Domains:
– Archae
– Bacteria
– Eukaryotes
• Characteristics include
– Ribosomes
– Membrane lipids
– tRNA
– antibiotics
Comparison (Pro vs. Eu)
• No nuclear
membrane
• 0.2-2.0 um
• No membraned
organelles
• Simple flagella, 2
proteins
• Glycocalyx: capsule
or slime layer
• True nucleus
• 10-100 um
Comparison (cont...)
Complex cell wall
(incl. peptidoglycan)
• Plasma membrane:
few if any sterols, no
carbos
• No cytoskeleton or
cyto streaming

• Simple cell wall, if

present
ComAparison (cont...)
Small Ribosomes-
70S
• DNA: Single,
circular, no histones
• Binary fission
• Recombination: no
meiosis, fragment
transfer only

• Large ribosomes -
80S + 70S in
Le Somatoscope (Gaston
Naessens)
https://www.youtube.com/watch?v=KGJW94ci
q4c

https://www.youtube.com/watch?v=Py-hutc5Z
NM