Lecture 5: Microbial Taxonomy

Question 1

Define taxonomy

Answer 1

The science of biological classification

Question 2

List and define the 3 parts of taxonomy

Answer 2

1) Classification: based upon a selected scheme
2) Nomenclature: Assignment into taxa using rules
3) Identification: Determining where each organism fits

Question 3

What are the 4 main reasons for classifying organisms?

Answer 3

1) Establish relationships, and to differentiate
2) We have only scratched the surface
3) Serves as valuable reference
4) Opens line of communication

Question 4

How did Carl von Linne classify organisms?

Answer 4

-Used mainly anatomical characteristics
-Used 2 kingdoms and latinized names

Question 5

How did Carl von Nageli classify organisms?

Answer 5

Bacteria and fungi into plant kingdom

Question 6

What did Ernst Haeckel do for taxonomy?

Answer 6

He proposed Kingdom Protista

Question 7

Edouard Chatton proposed the term ‘________’

Answer 7

prokaryote

Question 8

Who founded the 5 kingdom system of taxonomy?

Answer 8

Robert H. Witaker

Question 9

Who proposed the idea of 3 domains? What were they based on, and in what other three ways did they differ?

Answer 9

1) Carl Woese
2) Based on rRNA sequences
3) Also differ in membrane lipid structure, tRNA, and antibiotic sensitivity

Question 10

Define phylogeny

Answer 10

The evolutionary development of a species

Question 11

Name the 3 phylogenetic groups and define them

Answer 11

1) Monophyletic: organisms that arose from a single common ancestor
2) Paraphyletic: A common ancestor, but doesn’t include all descendents
3) Polyphyletic: Multiple origins and do not share a common ancestor

Question 12

The binomial system consists of what 2 things?

Answer 12

Genus + species

Question 13

True or false: the binomial system always italicizes genus and species

Answer 13

True

Question 14

Define a strain. What does a strain descend from?

Answer 14

-Defined as a population of organisms that are distinguishable from others of the same species
-Descended from a single organism or pure culture

Question 15

List the 3 ways strains can vary, and define them

Answer 15

1) Biovars: biochemical and physiological properties
2) Morphovars: morphological properties
3) Serovars: antigenic properties

Question 16

Describe a type strain

Answer 16

-One of the first strains studied, it is the most characterized strain
-Most species have multiple type strains, depends on how much the species has been studied
-The strain that is the most typical for the species as a whole

Question 17

What are the 3 broad ways to classify bacteria? Which is the most accurate?

Answer 17

1) Phenotypic classification
2) Analytic classification
3) Genotypic classification
-Genomic is most accurate

Question 18

Define morphology

Answer 18

The form and structure of an organism or group of identical organisms

Question 19

Differentiate between microscopic and macroscopic classification

Answer 19

1) Microscopic classification: shape, pattern of groups, staining
2) Macroscopic classification: colony morphology, pigment production

Question 20

Differentiate between biotyping and serotyping

Answer 20

1) Biotyping: Biochemical markers
2) Serotyping: Detection of specific antigens

Question 21

Define antibiogram patterns and phage typing

Answer 21

1) Antibiogram patterns: Susceptibility to various antibiotics
2) Phage typing: Susceptibility to viruses that infect bacteria; bacteriophages

Question 22

Name 7 types of phenotypic classification

Answer 22

1) Morphology
2) Microscopic classification
3) Macroscopic classification
4) Biotyping
5) Serotyping
6) Antibiogram patterns
7) Phage typing

Question 23

What type of classification requires expensive instrumentation (e.g. mass spectrometry) and is labor intensive?

Answer 23

Analytic classification

Question 24

Give 4 examples of analytic classification

Answer 24

1) Cell envelope fatty-acid analysis
2) Whole cell lipid analysis
3) Whole cell protein analysis
4) Multilocus enzyme electrophoresis

Question 25

Give 6 examples of genotypic classification

Answer 25

1) Guanine plus cytosine ratio
2) DNA hybridization
3) Nucleic acid sequence analysis
4) Plasmid analysis
5) Ribotyping
6) Chromosomal DNA fragment analysis

Question 26

Name 4 groups of classical characteristics used to identify organisms

Answer 26

Morphological, physiological/metabolic, biochemical, and ecological

Question 27

What are the 2 main types of classical characteristics that can be used to classify organisms?

Answer 27

1) Physiological/ metabolic
2) Ecological

Question 28

Name 4 physiological/ metabolic characteristics that can be used to classify organisms

Answer 28

1) Motility
2) Luminescence
3) Photosynthetic pigments
4) Energy sources

Question 29

Name 5 ecological characteristics that can be used to classify organisms

Answer 29

1) Life cycle patterns
2) Symbiotic relationships
3) Ability to cause disease
4) Habitat preference
5) Growth requirements

Question 30

What are the two main categories of characteristics that can be used to identify organisms?

Answer 30

1) Classical characteristics
2) Molecular characteristics

Question 31

Name 5 molecular characteristics

Answer 31

1) Nucleic acid base composition
2) Nucleic acid hybridization
3) Nucleic acid sequencing
4) Genomic fingerprinting
5) Amino acid sequencing

Question 32

Describe nucleic acid base composition

Answer 32

•Usually measures G&C content, which usually only varies by ~10% in a genus
•A molecular characteristic

Question 33

Describe nucleic acid hybridization

Answer 33

-Complete hybridization can occur if the organisms are identical
-Partial hybridization can occur if they’re related
-No hybridization if they’re not related
-A molecular characteristic

Question 34

Describe nucleic acid sequencing and when it is best used

Answer 34

-Utilizes small subunit rRNAs (SSU rRNAs)
-Best measure for relatedness
-A molecular characteristic

Question 35

Describe small subunit rRNAs (SSU rRNAs)

Answer 35

-The molecules of choice for phylogenetics
-Have the same role in all organisms
-Part of complex ribosome structure (intolerant of mutations)
-Very well conserved (change very slowly over time)

Question 36

What are the molecules of choice for phylogenetics? Why?

Answer 36

SSU rRNAs, because they have the same role in all organisms and they’re very well conserved

Question 37

1) What does genomic fingerprinting consist of?
2) What type of characteristic is genomic fingerprinting?

Answer 37

1) PCR: polymerase chain reaction
-Amplifies a region of the DNA, can be used to identify causative agents
2) A molecular characteristic

Question 38

Describe amino acid sequencing; what does it reflect and what can it be differentiated based on?

Answer 38

-Directly reflects mRNA sequences
-Can be differentiated based on charge, immunogenicity, and fragmentation
-It’s a molecular characteristic

Question 39

Define the root

Answer 39

The last universal common ancestor (LUCA) of the 3 domains

Question 40

How do we know the eukarya and archaea have common ancestry at some point?

Answer 40

They share key proteins

Question 41

What 3 considerations should be made for microbial genetic diversity?

Answer 41

1) The world environment(s)
2) The extraterrestrial
3) Microbial mechanisms
-Mutations and gene transfer