Chapter 2 - Review of general microbiology
Objectives
1. Basic description of viruses, bacteria, fungi, algae, and protozoa
(size, cell components)
2. Basic functions of a bacterial cell
3. Importance of the cell wall and cell membrane to a bacterial cell
4. Major differences between eubacterial and eukaryotic DNA/RNA
5. Plasmid types and function
6. Information exchange between bacteria
7. Understand the four nutritional categories and give an example of a
microbe in each category
Evolutionary Timeline
4.5 4.0
3.0
2.0
1.0
Billions of years
0
Viruses
Viroids
Prions
http://www.astro.washington.edu/endsofworld/
MS2 bacteriophage
24nm
Polio virus 30nm
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Adenovirus
70nm
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Adenovirus DNA
PPPPP
PPP
PPPPPP
PP
PPPPPPP
PP
Human Immunodeficiency Virus
(HIV) 100nm
PPPPPPPP
PP
Tobacco Mosaic Virus
18 x 300 nm
T-4 bacteriophage 30 x 124nm
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IIIII
IIIIIIIIIIIIIIIIIII
IIIII
I
IIIIIIIIIIIIIIIIIIIII
IIII
Herpes virus 125nm
IIIIIIIIIIIIIIIIII
IIIII
Chlamydia elementary
body 450nm
Vaccinia virus
300 x 450 nm
T-4 bacteriophage DNA
E. coli bacterium 0.5-2um
Viruses
Bacteria
A dividing gram positive bacterium
Cell membrane
Cell wall
DNA
Size – ranges from 0.3 to 3 mm in length depending on
the environment
106 bacteria in a pinpoint colony
106 bacteria/gm soil required to observe significant
degradation activity
Bacterial Strategies for Survival
Nitrosomonas
Specialist
vs.
vs.
Pseudomonas
Jack-of-all-Trades
Nitrosomonas europaea
• Gram-negative, chemoautotroph
• Specializes in ammonia oxidation. These bacteria are important in
the treatment of industrial and sewage waste in the first step of
oxidizing ammonia to nitrate.
NH3
NO2
NO3
• Found in soil, freshwater, sewage, the walls of buildings and on the
surface of monuments especially in polluted areas where air contains
high levels of nitrogen compounds.
• Problematic because can reduce availability of nitrogen to plants and
hence limit CO2 fixation. Also may contribute significantly to the global
production of nitrous oxide.
• N. europaea strain Schmidt Stan Watson is now completely sequenced.
2715 predicted genes, 2.80 x 106 bp
overall G+C content = 50.8%
Pseudomonas aeruginosa
• Gram-negative, chemoheterotroph
• Versatile
• Found in soil, marshes, coastal marine habitats,
on plants and animals
• Problematic for cystic fibrosis, burn victims,
cancer, ICU patients
• P. aeruginosa PAO1 is now completely sequenced.
-
5570 predicted genes
6.3 x 106 bp (largest sequenced genome to date)
overall G+C content = 66.6%
isolated regions with lower G+C content may be result of recent
horizontal gene transfer
- > 500 genes are transcriptional regulators or environmental
sensors. Has more than twice the number of two-component
regulators than E. coli or B. subtilis.
The bacterial cell as the basic unit of life
What are the basic functions of a microbial cell?
• ability to reproduce
• ability to use food as an energy source
• ability to synthesize new cell components
• ability to excrete waste
• ability to respond to environmental changes
• ability to change through mutation
What are the basic components of a microbial cell?
• cell envelope
cell membrane
cell wall
glycocalyx
• appendages for motility and adhesion
• nucleic acids
• spores
Cell surface meets the outside world
Lipoteichoic acid
Teichoic acid
Porins
Lipopolysaccharide
Outer membrane
Peptidoglycan
Periplasmic
space
Proteins
Cell membrane
Membrane proteins
Gram negative
Lipids
Gram positive
Eubacteria have two main types of envelopes, Gram Positive and
Gram Negative.
Cell surface meets the outside world
Lipoteichoic acid
Teichoic acid
Porins
Lipopolysaccharide
Outer membrane
Peptidoglycan
Periplasmic
space
Proteins
Cell membrane
Membrane proteins
Gram negative
Lipids
Gram positive
Cell wall - The cell wall is a rigid structure composed of peptidoglycan that
maintains the characteristic shape of the cell.
• permeable to small molecules (<15,000)
Cell surface meets the outside world
Cell membrane – The cell membrane is a
highly selective barrier that enables cells
to take in nutrients and excrete waste
products
Proteins
= Phospholipid
• passive diffusion
• facilitated diffusion
• group translocation
• active transport
R1
O
CH2
R2
O
CH
H2C
O
O
P
O
CH2
CH2
NH2
O
Phosphatidylethanolamine
( where R1 and R2 are fatty acyl residues)
Cell surface meets the outside world
Lipoteichoic acid
Teichoic acid
Porins
Lipopolysaccharide
Outer membrane
Peptidoglycan
Periplasmic
space
Proteins
Cell membrane
Membrane proteins
Fig. 2.12
Gram negative
Lipids
Gram positive
How does the cell membrane fit into the cell envelope?
Cells can have flagella that allow them to move over short distances (um)
either toward nutrients or away from inhibitory substances.
Cells can have fimbriae that aid in attachment of cells to surfaces.
Flagella
Appendages
Fimbriae
Nucleic acids – A,T (U), C, G
DNA (gene)
transcription
RNA
translation
enzyme
Bacteria – DNA
• 1 closed circular chromosome
• plasmid(s)
RNA
• 16s-rRNA
• 16s-rDNA gene now used for classification
Eukaryotes – DNA
• DNA is found within a membrane-bound nucleus
• DNA synthesis and RNA transcription occur in the nucleus
RNA
• 18s-rRNA
• RNA translation (protein synthesis) occurs in the cytoplasm
The chromosome of a bacterial cell contains approximately
3 x 106 base pairs. If stretched out, the chromosome is 1
mm in length. In actively growing cells there are 2 to 4
copies of the chromosome since several replicating forks can
occur at the same time. Bacterial cells also contain small
circular pieces of DNA called plasmids.
Types of plasmids
Low-copy –number plasmids
1-2 copies/cell, usually > 10 kb
High-copy-number plasmids
10 – 100 copies/cell, usually < 10kb
Relaxed plasmids
not dependent on initiation of cell replication
Stringent plasmids
synchronized with replication of chromosome
Conjugative plasmids
self-transmissible between same/different
species, tra genes
Non-conjugative plasmids
not self-transmissible
Incompatible plasmids
cannot exist in together in the same cell
Inc P plasmids
exist in a wide variety of bacteria
Plasmid function
Cryptic plasmids
no known function (most)
Resistance plasmids
protect against antibiotics, metals, bacteriophage
Degradative plasmids
encode biodegradation of unusual metabolites
Plant interactive plasmids
mediate interaction between bacteria and plants
(Sym, Ti plasmids)
Miscellaneous plasmids
involved in a variety of functions, RNA
metabolism, conjugation, bacterial cell
envelope alteration
Information exchange between bacteria can occur in three
ways:
1) Conjugation
2) Transformation
3) Transduction
1) Conjugation
Pilus
2)
Transformation
Transformation
Donor cell
Cell lysis
and free DNA
Recipient cell
bacterial
cell
3) Transduction
Transduction
lytic cycle
phage
transducing
phage
transduced
cell
Case Study 3.1
Soil + 2,4-D
Soil + 2,4-D + JMP134
AlcaligeneseutrophusJM
P134
80kbplasm
idpJP4encodes
genesfordegradationof 2,4-D
Slow, incomplete degradation
of 2,4-D over a 4 week period.
Complete degradation of 2,4-D in
4 weeks JMP134 was not recovered
after 1 week. Three indigenous strains
that degraded 2,4-D increased in numbers
the next 4 weeks. All three strains carried
the pJP4 plasmid.
How was information transfer achieved?
These results indicate that there was gene transfer between the JMP134
and indigenous microorganisms. There are two possible mechanisms
of gene transfer which may explain these results.
DiGiovanni et al. 1996.
Appl. Environ. Microbiol.
62:2521-2526.
Bacterial spore formers: Gram positive bacteria can form spores
that are very resistant to heat, UV, and nutrient stress.
Spores can even withstand autoclaving. As a result, soil must
be autoclaved three times on consecutive days to achieve
complete sterilization. This allows spores to germinate in
between autoclaving events.
Eukaryotes
Fungi
Algae
Protozoa
Ribosomes
Mitochondrion
Endoplasmic
reticulum
Nucleus
Nucleolus
Cell wall
Golgi apparatus
Storage vessicles
Microbial Nutrition
Autotrophs (CO2)
Carbon source
Heterotrophs (organic carbon)
Phototroph (light)
Energy source
Chemotroph (chemical)
CO2
Photosynthesis
Respiration
Oxidation of inorganics
C(H2O)
• Light energy is harnessed through photosynthesis
• Chemical energy is harnessed through oxidation of organic/inorganic
substances
Nutritional classification
Viruses – living or nonliving?
Eubacteria – photoautotrophic
photoheterotrophic
chemoautotrophic
chemoheterotrophic
Archaebacteria – photoautotrophic
chemoautotrophic
chemoheterotrophic
Cyanobacteria – photoautotrophic
Algae – photoautotrophic
Fungi – chemoheterotrophic
Protozoa – chemoheterotrophic
photoautotrophic
photoheterotrophic
Viruses
Eubacteria
Archaebacteria
Cyanobacteria
Algae
Fungi
Protozoa
Discussion Questions
Basedononsize
nutritional
Based
which
requirements
which
microbial
groups
mightmicrobial
you
groups
you find at
find
at themight
soil surface?
Atthe
soilftsurface?
100 ft below
100
below theAtsurface?
the surface?