Part
VII
17
THE DIVERSITY OF THE MICROBIAL
WORLD
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.
CHAPTER OBJECTIVES
After reading this chapter you should be able to:
•
•
•
•
•
•
•
•
discuss the rationale behind the science of taxonomy
discuss the meaning of the word species and the basis for grouping organisms into species
discuss the ways of classifying organisms
discuss the various characteristics used in taxonomy and explain why nucleic acid sequences are probably
the best indicators of microbial phylogeny and relatedness
discuss microbial evolution
discuss the three domains of living organisms (Bacteria, Archaea, and Eukarya)
discuss the classification scheme used in Bergey’s Manual of Systematic Bacteriology
discuss the dynamic nature of bacterial taxonomy and the new types of data that are contributing to the
changes being made
CHAPTER OUTLINE
I.
II.
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
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
Taxonomic Ranks
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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. Techniques for Determining 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
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
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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
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TERMS AND DEFINITIONS
Place the letter of each term in the space next to the definition or description that best matches it.
____ 1.
____ 2.
____ 3.
____ 4.
____ 5.
____ 6.
____ 7.
____ 8.
____ 9.
____ 10.
____ 11.
____ 12.
____ 13.
____ 14.
____ 15.
____ 16.
The science of biological classification
The scientific study of organisms to ultimately
characterize them and arrange them in an orderly
manner
A population of organisms that descends from a single
organism
A classification system based on evolutionary
relationships
A classification system based on mutually similar
attributes
A classification system based on the general similarity
of organisms, in which computers are used to calculate
association coefficients
The temperature at which the two strands of a doublestranded DNA molecule will separate from each other
The phenomenon in which two strands of nucleic acid
associate with each other because they share some
degree of sequence homology
A important technique in lipidomics used to classify
isolates
Organisms with great similarity that are grouped
together by numerical taxonomy methods
A general term for any group into which organisms are
placed
The evolutionary development of a species
A scheme that classifies organisms based on the
sequence of a group of housekeeping techniques
A taxonomy based on a wide range of phenotypic and
genotypic information
A DNA fingerprinting technique where genomic DNA
is cut at specific sites
A phylogenetic group defined only by an rRNA
sequence
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
k.
l.
m.
n.
o.
p.
fatty acid methyl ester
analysis
melting temperature (Tm)
multilocus sequence analysis
nucleic acid hybridization
numerical taxonomy
phenetic classification
phenon
phylogenetic (phyletic)
classification
phylogeny
polyphasic taxonomy
restriction fragment length
polymorphism analysis
ribotype
strain
systematics
taxon
taxonomy
FILL IN THE BLANK
1.
2.
3.
Prokaryotic strains that are characterized by biochemical or physiological differences are called
____________; those that differ morphologically are called ____________; and those that differ
antigenically are called ____________.
The most desirable classification system is one in which organisms are arranged into groups whose
members share many characteristics and in which the biological nature of organisms is reflected as much
as possible. These kinds of systems are called ____________ classification systems. The two most
common of these are ____________ systems, based on evolutionary relatedness, and ____________
systems, based on mutual similarity.
A variety of DNA fingerprinting methods are available for describing communities and isolates. REPPCR uses the amplification of
in genomic DNA. Another cuts the genome
into pieces to identify
. A third, which uses analysis of
point mutations is called
analysis.
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4.
Genetic drift or
introduces random mutations into the genome. If these provide a positive
benefit they are termed
.
5. The science of biological classification is called
. It is divided into three parts:
,
the arrangement of organisms into groups (
);
, the assignment of names to
organisms; and
, the process of determining that a particular organism belongs to a recognized
group. Microorganisms and other organisms are named according to the
.
6. The 16S rRNA of most major phylogenetic groups has one or more characteristic nucleotide sequences
called ____________ ____________ sequences, which distinguish each group from other groups, even
closely related ones.
7. The classification scheme favored by microbiologists divides all organisms into three ____________.
The prokaryotes are divided into
and
, and all eukaryotic organisms are placed
in ____________.
8. Phylogenetic relationships are illustrated in branched diagrams called
, which
can either be rooted or unrooted. These diagrams are based on calculations of the amount of difference
between gene sequences. The difference is often expressed as
,a
quantitative indication of the number of positions that differ between two aligned macromolecules.
9. For prokaryotes, one strain, the ____________ strain, is used to define the characteristics of a species.
Only those strains very similar to this strain are included in the species.
10. Many believe in the __________ theory that suggests that mitochondria and chloroplasts arose from
engulfed prokaryotes. These can no longer survive independently and are _____________ that have
retained at least some of their ____________. In the ______________ hypothesis the progenitor of
mitochondria was a ____________ that produced ____________ that was required by the host.
MULTIPLE CHOICE
For each of the questions below select the best answer or answers.
1.
2.
3.
Which of the following has NOT been used
in systematics?
a. physiology
b. epidemiology
c. ecology
d. morphology
e. All of the above have been used in
systematics.
What is a population of organisms that
descends from a single organism?
a. a species
b. a genus
c. a strain
d. a taxon
Which of the following are short conserved
nucleotide sequences useful for
phylogenetics?
a. restriction fragments
b. oligonucleotide signatures
c. single nucleotide polymorphisms
d. ribotypes
4.
5.
169
In the current phylogenetic scheme, protists
would be found in which of the following
domains?
a. Eukarya
b. Bacteria
c. Archaea
d. None of the above is correct.
Which of the following is NOT true about the
G + C content of organisms?
a. Organisms with similar G + C content
have similar base sequences.
b. Organisms with very different G + C
content have dissimilar base sequences.
c. Only if two organisms are alike
phenotypically does their similar G + C
content suggest relatedness.
d. All of the above are true about the G +
C content of organisms.
6.
7..
Which of the following is NOT considered a
classical characteristic for taxonomic
purpose?
a. ecological characteristics
b. G + C content
c. genetic analysis
d. morphological characteristics
e. All of the above are classical
characteristics for taxonomic
purposes.
What is the name of the genetic technique
that compares the sequences of several
housekeeping genes?
a. numerical taxonomy
b. multilocus sequence analysis
c. molecular chronometry
8.
9.
d. indirect electrophoresis
Which of the following is not a type of
genome fingerprinting?
a. REP
b. BOX
c. ERIC
d. All of the above are used for genome
fingerprinting.
Which of the following are the most
important genes for generating phylogenetic
trees?
a. SSU rRNA genes
b. aminoacyl tRNA synthetase genes
c. G + C-rich genes
d. ribozyme genes
TRUE/FALSE
____ 1.
____ 2.
____ 3.
____ 4.
____ 5.
____ 6.
____ 7.
____ 8.
____ 9.
____ 10.
____ 11.
____ 12.
____ 13.
____ 14.
____ 15.
____ 16.
The definition of a species as “a group of interbreeding or potentially interbreeding natural
populations that are reproductively isolated from other groups” is satisfactory for higher organisms
but not for microorganisms.
All gene sequences are equally useful for phylogenetic analysis.
Although prokaryotes do not reproduce sexually, the study of chromosomal gene exchange is
sometimes useful in their classification.
If DNA molecules are very different in sequence, they will not form stable hybrids.
DNA-DNA hybridization is useful for comparing closely related organisms; however, DNA-RNA
hybridization using tRNA or rRNA can be used to compare more distantly related organisms
because tRNA and rRNA genes have not evolved as rapidly as most other microbial genes.
Biochemical analysis of lipids is not useful in taxonomy.
The earliest prokaryotes were probably anaerobic.
The endosymbiotic hypothesis proposes that mitochondria and chloroplasts developed from freeliving prokaryotes that invaded a precursor to the eukaryotes and established a stable relationship.
In the three kingdom system, the two prokaryotic domains are most closely related.
Variation in G + C content among members of a particular genus usually is less than 10%.
Like the first edition, the second edition of Bergey’s Manual of Systematic Bacteriology
will use a phenetic classification scheme.
A prokaryotic species is most often defined as a collection of strains that have many stable
properties in common and differ significantly from other groups of strains.
Proteins are direct reflections of mRNA sequences and therefore are useful for comparing genomes
of different organisms.
The G + C content of DNA directly reflects base sequence.
The 16S and 5S rRNA molecules are the only macromolecules suitable for establishing
phylogenetic relationships.
Oligonucleotide signature sequences short variable sequences used for fine phylogenetic resolution.
CRITICAL THINKING
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?
170
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?
ANSWER KEY
Terms and Definitions
1. p, 2. n, 3. m, 4. h, 5. f, 6. e, 7. b, 8. d, 9. a, 10. g, 11. o, 12. i, 13. c, 14. j, 15. k, 16. l
Fill in the Blank
1. biovars; morphovars; serovars 2. natural; phylogenetic; phenetic 3. repetitive sequences, restriction fragment
length polymorphisms, single nucleotide polymorphisms 4. anagenesis, adaptive mutations 5. taxonomy;
classification; taxa; nomenclature; identification; binomial system; 6. oligonucleotide signature 7. domains;
Bacteria; Archaea, Eukarya 8. phylogenetic trees; evolutionary distance 9. type 10. endosymbiotic; organelles;
genome; hydrogen; -proteobacterium; hydrogen
Multiple Choice
1. e, 2. c, 3. b, 4. a, 5. a, 6. b, 7. b, 8. d, 9. a
True/False
1. T, 2. F, 3. T, 4. T, 5. T, 6. F, 7. T, 8. T, 9. F, 10. T, 11. F, 12. T, 13. T, 14. F, 15. F, 16. F
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