Chapter 2  - Review of general microbiology
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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

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Chapter 2 - Review of general microbiology

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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

  • Major differences between eubacterial and eukaryotic DNA/RNA

  • Plasmid types and function

  • Information exchange between bacteria

  • Understand the four nutritional categories and give an example of a microbe in each category

Evolutionary Timeline

Oxygen atmosphere forms

Microbes appear

Earth forms



4.5 4.0 3.0 2.0 1.0 0

Billions of years






A dividing gram positive bacterium


Cell membrane

Cell wall

Size – ranges from 0.3 to 3mm 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

  • 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

  • Nitrosomonas europaea

  • Gram-negative, chemoautotroph

  • 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

Eubacteria have two main types of envelopes, Gram Positive and Gram Negative.

Cell surface meets the outside world

  • 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

  • passive diffusion

  • facilitated diffusion

  • group translocation

  • active transport

Fig. 2.12

Cell surface meets the outside world

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.








Nucleic acids –A,T (U), C, G

DNA (gene)

  • 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.

Plasmid function

Cryptic plasmidsno known function (most)

Resistance plasmidsprotect against antibiotics, metals, bacteriophage

Degradative plasmidsencode biodegradation of unusual metabolites

Plant interactive plasmidsmediate interaction between bacteria and plants

(Sym, Ti plasmids)

Miscellaneous plasmidsinvolved in a variety of functions, RNA

metabolism, conjugation, bacterial cell

envelope alteration

Types of plasmids

Low-copy –number plasmids1-2 copies/cell, usually > 10 kb

High-copy-number plasmids10 – 100 copies/cell, usually < 10kb

Relaxed plasmidsnot dependent on initiation of cell replication

Stringent plasmidssynchronized with replication of chromosome

Conjugative plasmidsself-transmissible between same/different

species, tra genes

Non-conjugative plasmidsnot self-transmissible

Incompatible plasmidscannot exist in together in the same cell

Inc P plasmidsexist in a wide variety of bacteria

  • Information exchange between bacteria can occur in three ways:

  • Conjugation

  • Transformation

  • Transduction

1) Conjugation


2) Transformation

3) Transduction

Case Study 3.1

How was information transfer achieved?

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.





Microbial Nutrition

Autotrophs (CO2)

Heterotrophs (organic carbon)

Carbon source

Energy source

Phototroph (light)

Chemotroph (chemical)




Oxidation of inorganics


  • Light energy is harnessed through photosynthesis

  • Chemical energy is harnessed through oxidation of organic/inorganic

  • substances

Nutritional classification

Viruses – living or nonliving?

Eubacteria –

Archaebacteria –

Cyanobacteria –

Algae –

Fungi –

Protozoa –














Based on nutritional requirements which microbial groups might you find at the soil surface? At 100 ft below the surface?

Based on size which microbial groups might you find at the soil surface? At 100 ft below the surface?

Discussion Questions








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