Prescott’s Microbiology, 9th Edition
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Microbial Taxonomy and the Evolution of Diversity
CHAPTER OVERVIEW
Microorganisms are tremendously diverse in size, shape, physiology, and lifestyle. This chapter introduces the
general principles of microbial taxonomy and presents an overview of the current classification scheme accepted by
most microbiologists. Subsequent chapters will examine the various groups of microorganisms in greater detail.
LEARNING OUTCOMES
After reading this chapter you should be able to:
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explain the utility of taxonomy and systematics
Draw a concept map illustrating the differences between phenetic, phylogenetic, and genotypic classification
outline the general scheme of taxonomic hierarchy
explain how the binomial system of Linnaeus is used in microbial taxonomy
review the approaches commonly used to determine taxonomic classification
assess the impact molecular methods have had on the field of microbial taxonomy and phylogeny
compare and contrast nucleotide sequencing and non-sequencing-based molecular approaches used in microbial
taxonomy and phylogeny
select an appropriate technique to identify a microbial genus, species, and strain
predict the basic biological as well as public health implications of microbial taxonomic identification
paraphrase the rationale underpinning the construction of phylogenetic trees
compare and contrast rooted and unrooted trees
outline the general considerations used in building a phylogenetic tree
characterize the challenges horizontal gene transfer introduces in the study of microbial evolution
diagram the endosymbiotic theory of the origin of mitochondria and chloroplasts
compare and contrast the two theories that address the origin of the nucleus
explain why the concept of a microbial species is difficult to define
list the “gold standard” taxonomic methods currently applied to species designation
explain the importance of adaptive mutations in giving rise to new ecotypes
employ Bergey’s Manual to investigate the defining taxonomic elements used for a bacterium or archaeon that
is unfamiliar to you
CHAPTER OUTLINE
I.
Introduction to Microbial Taxonomy
A. Taxonomy is the science of biological classification
1. Classification is the arrangement of organisms into groups (taxa)
2. Nomenclature refers to the assignment of names to taxonomic groups
3. Identification refers to the determination of the taxon to which a particular isolate belongs
4. Systematics is the scientific study of organisms with the ultimate object of characterizing and
arranging them in an orderly manner
B. Natural classification schemes arrange organisms into groups based on shared biological characteristics;
for higher organisms, morphology is the central defining characteristic; for prokaryotes, a polyphasic
approach using phenotype, genotype, and phylogenetics is needed
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Prescott’s Microbiology, 9th Edition
C.
Phenetic classification—groups of organisms based on mutual similarity of their phenotypic
characteristics
D. Phylogenetic classification—groups of organisms based on evolutionary history as determined by the
fossil record for higher organisms or SSU rRNA gene sequences for prokaryotes
E. Genotypic classification—groups of organisms based on the genetic similarity of whole genomes
II. Taxonomic Ranks
A. The taxonomic ranks (in ascending order) are: species, genus, family, order, class, phylum, and domain;
however, microbiologists often use informal names that are descriptive (e.g., methanogens, purple
bacteria, lactic acid bacteria)
B. The basic taxonomic group is the species
1. Prokaryotic species are not defined on the basis of sexual reproductive compatibility (as for higher
organisms) but rather are based on phenotypic and genotypic differences
a. Currently, a prokaryotic species is defined as a collection of strains that share many stable
properties and differ significantly from other groups of strains
b. This definition is not completely satisfactory and other definitions have been proposed
2. A strain is a population of organisms that is distinguishable from at least some other populations in a
taxonomic category; a strain is thought to have descended from a single organism or pure culture
isolate
a. Biovars—strains that differ biochemically or physiologically
b. Morphovars—strains that differ morphologically
c. Serovars—strains that differ in antigenic properties
d. The type strain is usually the first studied (or most fully characterized) strain of a species; it
does not have to be the most representative member
3. A genus is a well-defined group of one or more species that is clearly separate from other genera
C. In the binomial system of nomenclature devised by Linnaeus, the genus name is capitalized while the
specific epithet is not; both terms are italicized (e.g., Escherichia coli); after first usage in a manuscript
the first name will often be abbreviated to the first letter (e.g., E. coli); Bergey's Manual of Systematic
Bacteriology describes recognized prokaryotic species
III. Exploring Microbial Taxonomy and Phylogeny
A. Classical characteristics
1. Morphological characteristics—easy to analyze, genetically stable, and usually do not vary greatly
with environmental changes; often are good indications of phylogenetic relatedness
2. Physiological and metabolic characteristics—directly related to enzymes and transport proteins
(gene products) and therefore provide an indirect comparison of microbial genomes
3. Biochemical characteristics—analysis of lipids as fatty acid methyl esters (FAME) can be used for
phylogenetic assignment
4. Ecological characteristics—include life-cycle patterns, symbiotic relationships, ability to cause
disease, habitat preferences, and growth requirements
B. Molecular characteristics
1. Nucleic acid base composition
a. G + C content can be determined from the melting temperature (Tm); Tm, is the temperature at
which the two strands of a DNA molecule separate from one another as the temperature is
slowly increased
b. G + C content is taxonomically useful because variation within a genus is small but variation
between genera is quite large
2. Nucleic acid hybridization (DNA-DNA hybridization)
a. The temperature of incubation controls the degree of sequence homology needed to form a
stable hybrid; the percentage of stable hybrids formed in a mixture of DNA from two
organisms reflects the degree of sequence homology
b. This technique is useful for studying the relatedness of closely related organisms
3. Nucleic acid sequencing
a. rRNA gene sequences are most ideal for comparisons because they contain both evolutionarily
stable and evolutionarily variable sequences; PCR is used to amplify rRNA genes for
sequencing and comparison to large sequence databases
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manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
Prescott’s Microbiology, 9th Edition
b.
Oligonucleotide signature sequences are short, conserved nucleotide sequences that are specific
for a phylogenetically defined group of organisms
4. Genomic fingerprinting
a. Multilocus sequence typing (MLSA) compares the sequences of several housekeeping genes,
giving finer phylogenetic resolution and avoiding confusion from lateral gene transfers; MLST
(multilocus sequence typing) was originally developed to distinguish between closely related
strains
b. PCR-amplified DNA fragments are digested with restriction enzymes giving mixtures of DNA
molecules of characteristic lengths called restriction fragment length polymorphisms (RFLP);
patterns generated from rRNA genes are called ribotypes
c. PCR primers directed at repetitive sequences (BOX, ERIC, REP) in prokaryotic genomes
generate a distinct series of DNA amplicons that enables identification to the species level
d. Single nucleotide polymorphisms (SNP) detects diversity in noncoding regions of the genome
5. Amino acid sequencing is useful because it directly reflects the genetic information of the organism
a. Determination of the amino acid sequence of the protein is the most direct approach
b. Indirect approaches include comparison of electrophoretic mobility, determination of
immunological cross-reactivity, and comparison of enzymatic properties
IV. Phylogenetic Trees
A. Inferred evolutionary relationships based on DNA sequence homologies are displayed as trees where the
branches and nodes represent operational taxonomic units (OTUs) that include species and genera
B. Sequences are first aligned, then compared to generate distance matrices; cluster analysis (neighbor
joining) or character-based analysis (maximum likelihood) are used to form groups and these can be
represented as a phylogenetic tree; the statistical power of the tree is determined by bootstrap analysis
C. Trees can be unrooted (compared within the group) or rooted, with a distantly related outgroup added to
provide a point of reference
V. Evolutionary Processes and the Concept of Microbial Species
A. The three domain tree (Archaea, Bacteria, and Eukarya) is based on comparisons of rRNA gene
sequences; the root is considered the last universal common ancestor (LUCA); it suggested that Archaea
are more closely related to Eukarya than Bacteria, even though Bacteria and Archaea are prokaryotes
B. Endosymbiotic theory suggests that the domain Eukarya arose by incorporating bacterial endosymbionts
and losing their cell walls; over time the endosymbionts genome was reduced with many genes moving to
the host cell nucleus; endosymbionts developed into organelles such as mitochondria, chloroplasts, and
hydrogenosomes
C. Traditional species concepts are difficult to apply to microorganisms; a variety of genetic, biochemical,
and physiological measurements have been used to define microbial species; similarities in rRNA
sequences and DNA-DNA hybridization is often used today
D. Microbial evolutionary processes are mainly driven by genetic drift (anagenesis) due to mutation and
recombination with adaptive mutations improving competitiveness; two models have emerged:
1. The metapopulation model suggests that separated patches of related organisms diversify to the point
that they are considered different taxons arising from common ancestors
2. The ecotype model suggests more abrupt diversification due to adaptive mutations that lead to
extinctions of other community members
VI. Bergey’s Manual of Systematic Bacteriology—contains a description of all prokaryotic species
A. The First Edition of Bergey’s Manual of Systematic Bacteriology—primarily phenetic
B. The Second Edition of Bergey’s Manual of Systematic Bacteriology—largely phylogenetic rather than
phenetic; consists of five volumes
CRITICAL THINKING
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any
manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
Prescott’s Microbiology, 9th Edition
1.
Phylogenetic and phenetic schemes for classifying bacteria do not always agree with each other. Why not?
Under what circumstances would it be more advantageous to use a phylogenetic scheme? In what situations
would a phenetic scheme be better? How can this disagreement be resolved?
2.
The gene sequences for SSU rRNAs are used for phylogentic analysis and treemaking. Of all the possible genes
that could have become the standard, why was this gene chosen? Why would these genes be useful in
determining phylogenies? How would lateral gene transfer affect the tracing of lineages through evolutionary
time?
3.
Given the haploid genome and short generation times of eubacteria, do you think the rate of evolutionary
change would be expected to be greater or lesser in comparison with eukaryotic organisms?
CONCEPT MAPPING CHALLENGE
Construct a concept map using these words to describe the process of microbial taxonomic identification. Provide
your own linking terms.
Taxonomy Phenetic Morphology MSLA Strain
Species
Genotypic Physiology
Ribotype
Parsimony Species Phylogenetic Ecology G+C content DNA-DNA hybridization (Cot
curve)
SSU rRNA sequence
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any
manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.