Fundamentals of Microbiology (Biology 240)
Course notes
Dr. Josh D. Neufeld
Topic 2: Bacteria
Learning Objectives
By the end of this module you should be able to:
• identify the five cell morphologies and describe what they can and can’t
tell you about a microorganism’s habitat;
• explain why decreasing cell size can be a strong selective advantage for
bacteria in some environments;
• list two bacteria with cells that are exceptions to the typical size and
explain why it is an advantage for some bacteria to be larger;
• list the components of a bacterial cell and the key features of each
component;
• describe the structure and role of each layer of the cell envelope;
• contrast the cell envelope of Gram-positive bacteria with that of Gram-
negative bacteria;
• describe three methods of transporting compounds across the bacterial
cell membrane;
• explain how some antibiotics target the bacterial cell wall;
• identify bacterial cell surface features and their purposes; and
• contrast different methods of bacterial cell motility.
As shown in Figure 2.1, different species of bacteria associate with different cell
shapes (“morphologies”): spherical (“coccus” – singular, “cocci” – plural,
“coccoid” – adjective), rod (also “bacillus” - singular, bacilli - plural), curved rod
(“vibrio” – singular, “vibrios” – plural, “vibroid” - adjective), spiral-shaped
(“spirillum – singular, “spirilla” – plural), or variable in shape (“pleiomorphic”).
Some bacteria grow as trichomes (unbranched filaments) or hyphae (branching
filaments). Note that clumps of hyphae are called mycelia.
Bacteria, depending on species and growth conditions, can also vary in size. See
Figure 2.4 and pay attention in class as we discuss the advantages of being
small or big.
For a discussion of large bacteria, see the review published by Schulz and
Jørgensen published in Annual Review of Microbiology (see pdf in lecture folder).
The cytoplasm of a bacterial cell contains many different molecules and internal
components (Table 2.1), the largest of which is the nucleoid. Bacterial cells may
also contain inclusion bodies, such as those for carbon and sulfur storage, or
microcompartments, such as gas vesicles, magnetosomes, and carboxysomes
(Figure 2.7).
Fundamentals of Microbiology (Biology 240)
Course notes
Dr. Josh D. Neufeld
The plasma membrane consists of a phospholipid bilayer embedded with
proteins (Figure 2.9). These proteins have various functions including nutrient
transport, energy capture, and sensory systems (Figures 2.11, 2.12).
In addition to a plasma membrane, most bacteria also have a semi-rigid cell wall.
Some even have a second outer membrane. Collectively, all of these layers
are referred to as the cell envelope.
The cell wall of bacteria is made of a thin sheet called peptidoglycan. It
prevents the cell from lysing due to turgor pressure and is only found in bacteria.
Peptidoglycan is composed of a glycan backbone (alternating molecules of N-
acetylglucosamine and N-acetylmuramic acid) connected by peptide cross-links.
Figures 2.14 and 2.15 will help you to understand the structure of peptidoglycan.
Gram-positive bacteria have teichoic acids, a type of acidic polysaccharide,
embedded in the peptidoglycan layer. The structure of a particular teichoic acid is
shown in Figure 2.21.
Gram-negative organisms have a more complex cell envelope (Figure 2.22) that
includes an outer membrane, exterior to the peptidoglycan cell wall. The space
between the inner and outer membranes, which includes the peptidoglycan, is
called the periplasm. The outer membrane consists of a phospholipid bilayer
and lipopolysaccharide (Figure 2.23). Porins are proteins that span the outer
membrane and allow small molecules to cross the membrane (Figure 2.24).
Many prokaryotes possess flagella, which they use to propel themselves. This
ability to propel themselves is called motility. Some bacteria have polar flagella,
which are attached at the end of the cell. Other bacteria have peritrichous
flagella, which are distributed around the cell. See Figure 2.26 for a depiction of
flagellar structure. As you can see, flagella are complex, elaborate structures.
The long filament is made up of subunits of flagellin protein. Another type of
protein forms the hook, which connects the filament to the basal body. The
basal body is a motor that is embedded in the cytoplasmic membrane and cell
wall and rotates.
Flagellar rotation, like a propeller, rather than pulling like an oar, is what propels
the cell. Counterclockwise rotation propels the cell forward in a run, while
clockwise rotation causes the cell to tumble or propels the cell backward (Figure
2.27).
Why are bacteria motile? Motility must confer a selective advantage; otherwise it
would not be worth the effort to expend the energy that motility requires. It turns
out that motile bacteria can respond to the presence of favourable or detrimental
Fundamentals of Microbiology (Biology 240)
Course notes
Dr. Josh D. Neufeld
chemicals by moving toward or away from them. When bacteria respond in this
way to chemicals, it is called chemotaxis. Bacteria sense a chemical gradient in
a temporal manner, rather than a spatial manner. Figure 2.28 shows how the
chemical gradient can influence the duration of runs, resulting in biased net
movement up or down the gradient. Besides chemotaxis, there are other types of
taxis:
• phototaxis - light
• aerotaxis - oxygen
• osmotaxis - osmotic strength
Many types of structures and cell inclusions are found only in certain types of
bacteria. Some of these are described in Section 2.5.
fimbriae - aid cells to adhere to surfaces (Figure 2.31 - 3rd edition or Figure
2.32 - 2nd edition)
pili - conjugation, attachment to host cell, motility (Figure 2.31 - 3rd edition or
Figure 2.32 - 2nd edition)
s-layer - protein layer outside cell, protection from bacteriophages and
predatory bacteria (Figure 2.35 - 3rd edition or Figure 2.36 - 2nd edition)
capsule - polysaccharide layer outside cell, attachment to host cells,
protection from host immune system, resistance to desiccation (Figure 2.32 -
3rd edition or Figure 2.33 - 2nd edition)
The International Code of Nomenclature of Bacteria is a classification system
that has been created to describe and keep track of bacterial species. The
system involves a taxonomic hierarchy with the levels Domain, Phylum, Class,
Order, Family, Genus, and Species. Bacteria are grouped based on genetic,
metabolic, and physical similarities.
A relatively new organization is starting to change/update taxonomy for bacteria
and archaea, using the originally described representative microorganism for
naming entire phyla, and using robust phylogenetic methods to delineate
taxonomic groups better than before. This has led to often confusing and
relatively frequent name changes for groups of bacteria and archaea that we
know well. Until the dust has settled during this time of transition, our course
uses “traditional” names for bacterial and archaeal taxonomic ranks, but please
know that many names are in flux. This organization is the Genome Taxonomy
Database (GTDB; based in Australia): [Link]