Microorganisms are tremendously diverse in size, shape, physiology and lifestyle. This chapter introduces general principles of microbial taxonomy and presents an overview of the current classification scheme. Subsequent chapters will examine the various groups of microorganisms in greater detail.

After reading this chapter you should be able to:

• discuss the rationale behind the science of taxonomy
• discuss the three domains of living organisms (Eubacteria, Archaea, and Eucarya)
• discuss the meaning of the word species and the basis for grouping organisms into species
• discuss the two ways (phylogenetic and phenetic) 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 the classification scheme(s) used in 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

1. General Introduction and Overview

1. Taxonomy is the science of biological classification
2. Classification is the arrangement of organisms into groups (taxa)
3. Nomenclature refers to the assignment of names to taxonomic groups
4. Identification refers to the determination of the particular taxon to which a particular isolate belongs
5. Systematics is the study of organisms with the ultimate object of characterizing and arranging them in an orderly manner
6. New molecular techniques are being used in classifying microorganisms but the traditional approaches still have value

1. Microbial Evolution and Diversity

1. Fossilized remains of bacterial cells around 3.5 to 3.8 billion years old have been found in stromatolites and sedimentary rocks
2. Stromatolites are layered or stratified rocks that are formed by incorporation of mineral sediments into microbial mats
3. The earliest bacteria were probably anaerobic
4. Aerobic cyanobacteria probably developed 2.5 to 3.0 billion years ago
5. The work of Carl Woese and his collaborators suggests that organisms fall into one of three domains (empires) into which the traditional kingdoms are distributed

1. 1. Eucarya - contains all eucaryotic organisms

1. Modern eucaryotic cells appear to have arisen from procaryotes about 1.4 billion years ago
2. One hypothesis for the development of chloroplasts and mitochondria involves invagination of the plasma membrane and subsequent compartmentalization of function
3. The alternative is the endosymbiotic hypothesis which suggests the following

1. The first event in the development of eucaryotes was the formation of the nucleus

(possibly by fusion of ancient eubacteria and archaea)

2. Chloroplasts were formed from free-living photosynthetic bacteria that entered into a

symbiotic relationship with the primitive eucaryote (cyanobacteria and Prochloron have been suggested as possible candidates)

3. Mitochondria may have arisen by a similar process (ancestors of Agrobacterium,

Rhizobium, and the rickettsias have been suggested)

4. The endosymbiotic hypothesis has received support from the discovery of an endosymbiotic

1. Taxonomic Ranks

1. The taxonomic ranks (in ascending order) are: species, genus, family, order, class and kingdom
2. Microbiologists often use less formal group (section) names that are descriptive (e.g., methanogens, purple bacteria, lactic acid bacteria, etc.)
3. The basic taxonomic group is the species
4. Bacterial species are defined on the basis of sexual reproductive compatibility (as for higher organisms) but rather are based on phenotypic and genotypic differences

1. A bacterial species is a collection of strains that share many stable properties and differ

1. Biovars - strains that differ biochemically or physiologically
2. Morphovars - strains that differ morphologically
3. Serovars - strains that differ in antigenic properties

1. The type strain is usually the first studied (or most fully characterized) strain of a species;

1. A genus is a well-defined group of one or more species that is clearly separate from other genera
2. The binomial system of nomenclature devised by Carl von Linne (Carolus Linnaeus) is used in which 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)
3. Bergey's Manual of Systematic Bacteriology focuses on the classification and biology of bacteria but often is more detailed than is necessary for identification
4. Bergey's Manual of Determinative Bacteriology is a single volume that is intended for use in identifying bacteria

1. Classification Systems

1. Natural classification - arranges organisms into groups whose members share many

characteristics and reflects as much as possible the biological nature of organisms

2. Phenetic systems group organisms together based on overall similarity

1. Frequently a natural system is based on shared characteristics
2. Not dependent on phylogenetic analysis
3. Use unweighted traits
4. Best system compares as many attributes as possible

1. Numerical Taxonomy

1. Information abouth the properties of an organism is converted to a form suitable for

numerical analysis

2. Compared by means of a computer
3. The presence or absence of at least 50 (preferably several hundred) characters should be compared

1. Morphological, biochemical and physiological characters should be included
2. Determine an association coefficient between characters possessed by two organisms

1. Simple matching coefficient-proportion that match whether present or absent
2. Jaccard coefficient - ignores characters that both organisms lack

1. Arrange to form a similarity matrix
2. Organisms with great similarity are grouped together into phenoms

1. A treelike diagram called a dendrogram is used to display the results of numerical

taxonomic analysis

2. The significance of the phenoms is not always obvious but phenoms with an 80%

1. Phylogenetic (phyletic) systems group organisms together based on probable evolutionary

1. Has been difficult for bacteria because of the lack of a good fossil record
2. Direct comparison of genetic material and gene products such as rRNA and proteins overcomes this problem

1. Major Characteristics Used in Taxonomy

1. Classical Characteristics

1. Morphological characteristics are easy to analyze, genetically stable and do not vary

greatly with environmental changes; often are good indications of phylogenetic

relatedness

2. Physiological and metabolic characteristics are directly related to enzymes and transport

proteins (gene products) and therefore provide an indirect comparison of microbial

genomes

3. Ecological characteristics include life-cycle patterns, symbiotic relationships, ability to

cause disease habitat preferences and growth requirements

4. Genetic analysis includes the study of chromosomal gene exchange through

1. Molecular Characteristics

1. Comparison of proteins is useful because it reflects the genetic information of the

1. Determination of the amino acid sequence of the protein
2. Comparison of electrophoretic mobility
3. Determination of immunological cross-reactivity
4. Comparison of enzymatic properties

1. Nucleic acid base comparison (G + C content)

1. Can be determined by determination of the melting temperature (T_m) which is related

to the temperature at which the two strands of a DNA molecule separate from one another as the temperature is slowly increased

2. Taxonomically useful because variation within a genus is usually less than 10% but

1. Nucleic acid hybridization

1. Determines the degree of sequence homology
2. The temperature of incubation controls the degree of sequence homology needed to form a stable hybrid

1. Nucleic acid sequencing

1. rRNA gene sequences are most ideal for comparisons because they contain both

evolutionarily stable and evolutionarily variable sequences

3. Recently, complete bacterial genomes have been sequenced; direct comparisons of

1. Assessing Microbial Phylogeny

1. Molecular Chronometers - based on the assumption of a constant rate of change, which is

not a correct assumption; however, the rate of change may be constant within certain genes

2. Phylogenetic Trees

1. Made of branches that connect nodes, which represent taxonomic units such as species or

genes

2. Rooted trees provide a node that serves as the common ancestor for the organisms being

analyzed

3. Developed by comparing molecular sequences and differences are expressed as

evolutionary distance

4. Organisms are then clustered to determine relatedness; alternatively, relatedness can be

1. rRna, DNA, and Proteins as Indicators of Phylogeny

1. Association coefficients from rRna studies are a measure of relatedness
2. Oligonucleotide signature sequences occur in most or all members of a particular phylogenetic group and are rarely or never present in other groups even closely related ones; useful at kingdom or domain levels
3. DNA similarity studies are most effective at the species and genus level
4. Protein sequences are less affected by organism-specific differences in G + C content
5. The three types of molecules do not always produce the same evolutionary trees

1. The Major Divisions of Life

1. Empires (Domains)

1. Eubacteria - comprise the vast majority of procaryotes; peptidoglycan contains

muramic acid; membrane lipids contain ester-linked straight-chain fatty acids

2. Archaea - procaryotes that lack muramic acid and have lipids with ether-linked

branched aliphatic chains, tRNAs lack thymine, RNA polymerase is distinctive,

ribosomes have a different composition and shape when compared to the Eubacteria

3. Eucarya - have a more complex membrane-delimited organelle structure
4. Several different phylogenetic trees have been proposed relating the major domains and some trees do not even support a three-domain pattern

1. Kingdoms

1. Five Kingdom system

1. Animalia - multicellular, nonwalled eucaryotes with ingestive nutrition
2. Plantae - multicellular, walled eucaryotes with photoautotrophic nutrition
3. Fungi - multicellular, and unicellular, walled eucaryotes with absorptive nutrition
4. Protista - unicellular eucaryotes with various nutritional mechanisms
5. Monera (Procaryotae) - all procaryotic organisms

1. Six Kingdom system - separate Monera into Eubacteria and Archaeobacteria
2. Eight Kingdom system (two empires)

1. Separates procaryotes into Eubacteria and Archaeobacteria
2. Redefines protists into several better-defined kingdoms

1. Bergey's Manual of Systematic Bacteriology - A detailed work that contains descriptions of all

procaryotic species currently identified

1. The First Edition of Bergey's Manual of Systematic Bacteriology - primarily phenetic

1. 33 sections in 4 volumes
2. Each section contains bacteria that share a few easily determined characteristics and bears a title that describes these properties or provides the vernacular names of the bacteria included
3. There is considerable disagreement between the phenetic system in Bergey's and

phylogenetic relationships as determined by a variety of means

4. Despite limitations it is the most widely accepted system for identifying bacteria

1. The Second Edition of Bergey's Manual of Systematic Bacteriology

1. Twice the number of species with 170 newly described genera
2. Largely phylogenetic rather than phenetic
3. Will not be available for some time yet
4. Pathogenic species are not grouped together but rather are scattered throughout the five volumes according to their phylogenetic relationships

IX. A Survey of Bacterial Phylogeny and Diversity - based on the 2^nd edition of Bergey's

1. Volume 1: The Archaea, Cyanobacteria, Phototrophs and Deeply Branching Genera

1. Archaea - divided into two kingdoms

1. organisms as well as some organisms that grow in oceans at low temperatures as
2. picoplankton
3. b. Euryarchaeota - contains primarily mathanogenic and halophilic bacteria and also
4. thermophilic, sulpher-reducing bacteria

1. Eubacteria - complex with several small groups of phototrophs, cyanobacteria, and

1. Volume 2 - Gram negative proteobacteria (purple bacteria) - complex group
2. Volume 3 - Gram positive bacteria with low G + C content (< 50%)
3. Volume 4 - Gram positive bacteria with high G + C content (> 50-55%)
4. Volume 5 - An assortment of deeply branching phylogenetic groups that are not necessarily related to one another although all are Gram negative