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Chapter 2 - Review of general microbiology. Objectives Basic description of viruses, bacteria, fungi, algae, and protozoa (size, cell components) Basic functions of a bacterial cell Importance of the cell wall and cell membrane to a bacterial cell - PowerPoint PPT Presentation
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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 cell3. Importance of the cell wall and cell membrane to a bacterial cell4. Major differences between eubacterial and eukaryotic DNA/RNA5. Plasmid types and function6. Information exchange between bacteria7. Understand the four nutritional categories and give an example of a
microbe in each category
4.5 4.0 3.0 2.0 1.0 0
Billions of years
Eart
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Mic
robes
appea
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Hum
ans
Evolutionary Timeline
VirusesViroidsPrions
http://www.astro.washington.edu/endsofworld/
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIII
IIIII III
III IIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII IIIIIIIII
I
MS2 bacteriophage 24nm
T-4 bacteriophage 30 x 124nm
Tobacco Mosaic Virus18 x 300 nm
Chlamydia e lementarybody 450nm
Vaccinia virus300 x 450 nm
T-4 bacteriophage DNA
Polio virus 30nm
Adenovirus DNA
Adenovirus 70nm
Human Immunodeficiency Virus (HIV) 100nm
Herpes virus 125nm
E. coli bacterium 0.5-2um
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PPP P P PP P P P P P PP PPPPPPPPPPP
Viruses
DNACell wallCell membrane
A dividing gram positive bacterium
Bacteria
Size – ranges from 0.3 to 3 m 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 vs. Pseudomonas
Specialist vs. 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
• 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 envelopecell membranecell wall
glycocalyx• appendages for motility and adhesion• nucleic acids• spores
What are the basic functions of a microbial cell?
Cell surface meets the outside world
Eubacteria have two main types of envelopes, Gram Positive and Gram Negative.
Peptidoglycan
Periplasmicspace
Cell membrane
Membrane proteins
Lipids
Outer membrane
Lipopolysaccharide
Teichoic acid
Lipoteichoic acid
Porins
Proteins
Gram negative Gram positive
Cell surface meets the outside world
Peptidoglycan
Periplasmicspace
Cell membrane
Membrane proteins
Lipids
Outer membrane
Lipopolysaccharide
Teichoic acid
Lipoteichoic acid
Porins
Proteins
Gram negative 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 = Phospholip id
R1 O CH
R2 O CH O
H C O P O CH CH NH O
2
2 2 2 2
Phosphatidylethanolam ine( where R1 and R2 are fatty acyl residues)
Proteins
• passive diffusion
• facilitated diffusion
• group translocation
• active transport
Cell surface meets the outside world
How does the cell membrane fit into the cell envelope?
Peptidoglycan
Periplasmicspace
Cell membrane
Membrane proteins
Lipids
Outer membrane
Lipopolysaccharide
Teichoic acid
Lipoteichoic acid
Porins
Proteins
Gram negative Gram positive
Fig. 2.12
Appendages
Flagella
Fimbriae
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.
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
Transformation
Donor cell
Cell lysisand free DNA
Recipient cell
2) Transformation
Transductionbacterial cell
phagelytic cycle
transducingphage
transduced cell
3) Transduction
Alcaligenes eutrophus JM P134
80 kb plasm id pJP4 encodes genes for degradation of 2,4-D
Soil + 2,4-D Soil + 2,4-D + JMP134
Slow, incomplete degradationof 2,4-D over a 4 week period.
Complete degradation of 2,4-D in 4 weeks JMP134 was not recoveredafter 1 week. Three indigenous strains that degraded 2,4-D increased in numbersthe next 4 weeks. All three stra ins carriedthe pJP4 plasmid.
These results ind icate that there was gene transfer between the JMP134 and indigenous m icroorganisms. There are two possible mechanisms of gene transfer which may explain these results.
How was information transfer achieved?
DiGiovanni et al. 1996. Appl. Environ. Microbiol. 62:2521-2526.
Case Study 3.1
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. vegetative cell
sporulating cell
spore (endospore)
vegetative cell
germinating spore
outgrowth
Eukaryotes Fungi Algae Protozoa
Ribosomes
Mitochondrion
Endoplasmic reticulum
Nucleus
Nucleolus
Cell wall
Golgi apparatus
Storage vessicles
Microbial Nutrition
Carbon source
Energy source
Autotrophs (CO2)
Heterotrophs (organic carbon)
Phototroph (light)
Chemotroph (chemical)
CO2
C(H2O)• Light energy is harnessed through photosynthesis • Chemical energy is harnessed through oxidation of organic/inorganic substances
Photosynthesis
Oxidation of inorganics
Respiration
Nutritional classification
Viruses – living or nonliving?
Eubacteria –
Archaebacteria –
Cyanobacteria –
Algae –
Fungi –
Protozoa –
photoautotrophicphotoheterotrophicchemoautotrophicchemoheterotrophic
photoautotrophicchemoautotrophicchemoheterotrophic
photoautotrophic
photoautotrophic
chemoheterotrophic
chemoheterotrophicphotoautotrophicphotoheterotrophic
VirusesEubacteriaArchaebacteria Cyanobacteria Algae Fungi Protozoa
Based on size which microbial groups might you find at the soil surface? At 100 ft below the surface?
Based on nutritional requirements which microbial groups might you find at the soil surface? At 100 ft below the surface?
Discussion Questions