Prescott’s Microbiology, 9th Edition

19Microbial 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.

LEARNINGOUTCOMES

After reading this chapter you should be able to:

•explain the utility of taxonomy and systematics

•Draw a concept map illustrating the differences betweenphenetic, 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 ofmicrobial 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 inthe 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 tospecies 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

  1. 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

  1. 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
  2. Currently, a prokaryotic species is defined as a collection of strains that share many stable properties and differ significantly from other groups of strains
  3. This definition is not completely satisfactory and other definitions have been proposed
  4. 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
  5. Biovars—strains that differ biochemically or physiologically
  6. Morphovars—strains that differ morphologically
  7. Serovars—strains that differ in antigenic properties
  8. 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
  9. 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

  1. 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
  2. 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
  3. G + C content is taxonomically useful because variation within a genus is small but variation between genera is quite large
  4. Nucleic acid hybridization (DNA-DNA hybridization)
  5. 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
  6. This technique is useful for studying the relatedness of closely related organisms
  7. Nucleic acid sequencing
  8. 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
  9. Oligonucleotide signature sequences are short, conserved nucleotide sequences that are specific for a phylogenetically defined group of organisms
  10. Genomic fingerprinting
  11. 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
  12. 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
  13. 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
  14. Single nucleotide polymorphisms (SNP) detects diversity in noncoding regions of the genome
  15. Amino acid sequencing is useful because it directly reflects the genetic information of the organism
  16. Determination of the amino acid sequence of the protein is the most direct approach
  17. Indirect approaches include comparison of electrophoretic mobility, determination of immunological cross-reactivity, and comparison of enzymatic properties
  1. 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

  1. 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
  1. 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

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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