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

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Evolutionary Timeline

VirusesViroidsPrions

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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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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

1) Conjugation

Pilus

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