Microbio exam 3

Chapter 9

Taxonomy

(greek word for orderly arrangement) is the science of classifying organisms. (the picture shows the taxonomic hierarchy)

What does taxonomy provide?

• shows degree of similarity and differences between organisms

• provides structure to biological diversity

• Allows communication, comparison, and prediction.

Systematics (phylogeny)

the study of the evolutionary relationships among organisms 

• organisms are grouped based on shared characteristics and evolutionary history

Evolution of classification systems: 1735

Linnaeus: Two kingdoms- plantae and animalia

1800’s

Bacteria and fungi included plantae; kingdom protista proposed.

1969

Whittaker: five kingdom system- Monera, Protista, Fungi, Plantae, Animalia

1978

Woese: Three domain system based on rRNA sequences- bacteria, archaea, eukarya

Remember: The shifts reflect increasing understanding of genetic relationships

Three domains of life

Where did Eukaryotes originate from?

• infoldings of prokaryotic plasma membranes 

• endosymbiotic bacteria developed into organelles

Prokaryotes

• Unicellular, lack a nucleus and membrane-bound organelles

• Smaller and simpler cell structure than eukaryotes

• Reproduce asexually (mainly by binary fission)

• DNA is circular and found in the nucleoid region

• Bacteria: found in many environments, some pathogenic

• Archaea: often live in extreme environments (e.g., hot springs, salt lakes)

Eukaryotes:

• Protists: mostly unicellular, diverse nutrition, grouped by genetics

• fungi: unicellular or multicellular, absorb nutrients, reproduce by spores

• plantae: multicellular, photosynthetic, cellulose walls

• animalia: multicellular, ingest food, no cell walls

Viruses:

• not a part of any domain- not living by classical definition

• DNA or RNA, protein coat, replicate inside host

• Viral species: population of viruses with similar characteristics (morphology, genes, and enzymes) that occupies a particular ecological niche (host cell)

Traditional Identification Methods

Morphology, Staining, Biochemical tests, and culture characteristics

morphology

(shape and motility)

• observation of size and shape, arrangement (ex. cocci, bacilli, spirilla) 

• motility assessed via wet mount or motility agar

staining

gram, acid fast

biochemical tests

• detects enzymatic activity (ex. catalase, oxidase, urease)

• identifies metabolic pathways (ex. fermentation of sugars, use of specific characteristics)

culture characteristics

• colony morphology on agar (shape, color, margin, elevation)

• growth conditions (aerobic/anaerobic, temperature, pH range)

Identification tools

Bergey’s manual

Bergey’s Manual

• standard reference for identifying and classifying bacteria and archaea using features like cell wall composition, morphology, differential staining, O2 requirements, and biochemical traits

• most bacteria/archaea remain uncultured; identification relies on indirect methods

• Approved list of bacterial names: includes -11,500 species with accepted taxonomy; and less than 5% are human pathogens. 

Serology

study of serum and their immune responses

• Antigens: microorganisms are antigenic- they stimulate the body to form Antibodies in the serum/blood.

• Strains with different antigens are called serotypes, serovars, or biovars

Enzyme-linked immunosorbent assay (ELISA)

• most popular and widely used method

• known antibodies and an unknown type of bacterium are added to a well; a reaction identifies the bacteria 

Phage typing