Classification of Microorganisms

Learning Outcomes: At the end of the lecture students should be able to
1. Define phylogeny.
2. Name the 3 Domains of the 3 Domain system of classification and recognize a
description of each.
3. Name the four kingdoms of the Domain Eukarya and recognize a description of
each.
4. Define horizontal gene transfer.
The Earth is 4.6 billion years old and microbial life is thought to have first appeared
between 3.8 and 3.9 billion years ago; in fact, 80% of Earth's history was exclusively
microbial life. Microbial life is still the dominant life form on Earth. It has been estimated
that the total number of microbial cells on Earth on the order of 2.5 X 10 30 cells, making
it the major fraction of biomass on the planet.
Phylogeny refers to the evolutionary relationships between organisms. The Three

Domain System, proposed by Woese and others, is an evolutionary model of phylogeny
based on differences in the sequences of nucleotides in the cell's ribosomal RNAs
(rRNA), as well as the cell's membrane lipid structure and its sensitivity to antibiotics.
Comparing rRNA structure is especially useful. Because rRNA molecules throughout
nature carry out the same function, their structure changes very little over time.
Therefore similarities and dissimilarities in rRNA nucleotide sequences are a good
indication of how related or unrelated different cells and organisms are.
There are various hypotheses as to the origin of prokaryotic and eukaryotic cells.
Because all cells are similar in nature, it is generally thought that all cells came from a
common ancestor cell termed the last universal common ancestor (LUCA). These
LUCAs eventually evolved into three different cell types, each representing a domain.
The three domains are the Archaea, the Bacteria, and the Eukarya.
Figure1: A phylogenetic tree based on rRNA data, showing the separation of bacteria,
archaea, and eukaryota domains.
More recently various fusion hypotheses have begun to dominate the literature. One
proposes that the diploid or 2N nature of the eukaryotic genome occurred after the
fusion of two haploid or 1N prokaryotic cells. Others propose that the
domains Archaea and Eukarya emerged from a common archaeal-eukaryotic ancestor
that itself emerged from a member of the domain Bacteria. Some of the evidence
behind this hypothesis is based on a "superphylum" of bacteria called PVC, members of
which share some characteristics with both archaea and eukaryotes. There is growing
evidence that eukaryotes may have originated within a subset of archaea. In any event,
it is accepted today that there are three distinct domains of organisms in
nature: Bacteria, Archaea, and Eukarya
The Archaea (archaebacteria)
The Archaea possess the following characteristics:
a. Archaea are prokaryotic cells.

b. Unlike the Bacteria and the Eukarya, the Archaea have membranes composed of
branched hydrocarbon chains (many also containing rings within the
hydrocarbon chains) attached to glycerol by ether linkages (Figure The cell walls
of Archaea contain no peptidoglycan.
c. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are
sensitive to some antibiotics that affect the Eukarya.
d. Archaea contain rRNA that is unique to the Archaea as indicated by the presence
molecular regions distinctly different from the rRNA of Bacteria and Eukarya.
Archaea often live in extreme environments and include methanogens, extreme
halophiles, and hyperthermophiles. One reason for this is that the ether-
containing linkages in the Archaea membranes is more stabile than the ester-
containing linkages in the Bacteria and Eukarya and are better able to withstand
higher temperatures and stronger acid concentrations.
The Bacteria (eubacteria)

Bacteria (also known as eubacteria or "true bacteria") are prokaryotic cells that are
common in human daily life, encounter many more times than the archaebacteria.
Eubacteria can be found almost everywhere and kill thousands upon thousands of
people each year, but also serve as antibiotics producers and food digesters in our
stomachs. The Bacteria possess the following characteristics:
a. Bacteria are prokaryotic cells.

b. Like the Eukarya, they have membranes composed of unbranched fatty acid
chains attached to glycerol by ester linkages
c. The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain
peptidoglycan.
d. Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to
most antibiotics that affect Eukarya.
e. Bacteria contain rRNA that is unique to the Bacteria as indicated by the presence
molecular regions distinctly different from the rRNA of Archaea and Eukarya.
Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-

negative bacteria.
Mycoplasmas are the smallest and simplest self-replicating bacteria.
The mycoplasma cell contains the minimum set of organelles
essential for growth and replication: a plasma membrane, ribosomes,
and a genome consisting of a double-stranded circular DNA molecule
The Eukarya (eukaryotes)

The Eukarya (also spelled Eucarya) possess the following characteristics:
a. Eukarya have eukaryotic cells.

b. Like the Bacteria, they have membranes composed of unbranched fatty acid
chains attached to glycerol by ester linkages.
c. Not all Eukarya possess cells with a cell wall, but for those Eukarya having a cell
wall, that wall contains no peptidoglycan.
d. Eukarya are resistant to traditional antibacterial antibiotics but are sensitive to
most antibiotics that affect eukaryotic cells.
e. Eukarya contain rRNA that is unique to the Eukarya as indicated by the presence
molecular regions distinctly different from the rRNA of Archaea and Bacteria.
The Microbial Eukarya are subdivided into the following kingdoms:
1. Protista Kingdom: Protista are simple, predominately unicellular eukaryotic

organisms. Examples includes slime molds, euglenoids, algae, and protozoans.
2. Fungi Kingdom: Fungi are unicellular or multicellular organisms with eukaryotic
cell types. The cells have cell walls but are not organized into tissues. They do
not carry out photosynthesis and obtain nutrients through absorption. Examples
include sac fungi, club fungi, yeasts, and molds.
3. Kingdom Chromista: Contains algae
It used to be thought that the changes that allow microorganisms to adapt to new
environments or alter their virulence capabilities was a relatively slow process occurring
within an organism primarily through mutations, chromosomal rearrangements, gene
deletions and gene duplications. Those changes would then be passed on to that
microbe's progeny and natural selection would occur. This gene transfer from a parent
organism to its offspring is called vertical gene transmission.
It is now known that microbial genes are transferred not only vertically from a parent
organism to its progeny, but also horizontally to relatives that are only distantly related,
e.g., other species and other genera. This latter process is known as horizontal gene
transfer. Through mechanisms such as transformation, transduction, and conjugation,
genetic elements such as plasmids, transposons, integrons, and even chromosomal
DNA can readily be spread from one microorganism to another. As a result, the old
three-branched "tree of life" in regard to microorganisms now appears to be more of a
"net of life."
Microbes are known to live in remarkably diverse environments, many of which are
extremely harsh. This amazing and rapid adaptability is a result of their ability to quickly
modify their repertoire of protein functions by modifying, gaining, or losing their genes.
This gene expansion predominantly takes place by horizontal transfer.
Summary
1. Phylogeny refers to the evolutionary relationships between organisms.
2. Organisms can be classified into one of three domains based on differences in
the sequences of nucleotides in the cell's ribosomal RNAs (rRNA), the cell's
membrane lipid structure, and its sensitivity to antibiotics.
3. The three domains are the Archaea, the Bacteria, and the Eukarya.
4. Prokaryotic organisms belong either to the domain Archaea or the domain
Bacteria; organisms with eukaryotic cells belong to the domain Eukarya.
5. Microorganism transfer genes to other microorganisms through horizontal gene
transfer - the transfer of DNA to an organism that is not its offspring.

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Learning Outcomes: At the end of the lecture students should be able to

Phylogeny refers to the evolutionary relationships between organisms. The Three

a. Archaea are prokaryotic cells.

The Bacteria (eubacteria)

a. Bacteria are prokaryotic cells.

Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-

The Eukarya (eukaryotes)

a. Eukarya have eukaryotic cells.

The Microbial Eukarya are subdivided into the following kingdoms:

1. Protista Kingdom: Protista are simple, predominately unicellular eukaryotic

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