General Introduction and Overview
Taxonomy is the science of biological classification
Classification is the arrangement of organisms into groups (taxa)
Nomenclature refers to the assignment of names to taxonomic groups
Identification refers to the determination of the particular taxon to which a particular isolate belongs
Importance of microbial taxonomy
Allows scientists to organize huge amounts of knowledge
Allows scientists to make predictions and frame hypotheses about organisms
Places organisms in meaningful, useful groups with precise names, thus facilitating scientific communication
Essential for accurate identification of microorganisms
Systematics is the scientific study of organisms with the ultimate object of characterizing and arranging them in an orderly manner
Microbial taxonomy is going through a period of great change due to the use of new molecular techniques
Microbial Evolution and Diversity
Earth is about 4.6 billion years old and fossilized remains of procaryotic cells that are 3.5 to 3.8 billion years old have been found in stromatolites and sedimentary rocks
Stromatolites are layered or stratified rocks that are formed by incorporation of mineral sediments into microbial mats
The earliest procaryotes were probably anaerobic
Aerobic cyanobacteria probably developed 2.5 to 3.0 billion years ago
The work of Carl Woese and his collaborators suggests that organisms fall into one of three domains
Eucarya-contains all eucaryotic organisms
Bacteria-contains procaryotic organisms with bacterial rRNA and membrane lipids that are primarily diacyl glycerol ethers
Archaea-contains procaryotic organisms with archaeal rRNA and membrane lipids that are primarily isoprenoid glycerol diether or diglycerol tetraether derivatives
Modern eucaryotic cells appear to have arisen from procaryotes about 1.4 billion years ago
One hypothesis for the development of chloroplasts and mitochondria involves invagination of the plasma membrane and subsequent compartmentalization of function
The alternative is the endosymbiotic hypothesis, which suggests the following:
The first event in the development of eucaryotes was the formation of the nucleus (possibly by fusion of ancient bacteria and archaea)
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)

Mitochondria may have arisen by a similar process (ancestors of Agrobacterium, Rhizobium, and the rickettsias have been suggested)
The endosymbiotic hypothesis has received support from the discovery of an endosymbiotic cyanobacterium that inhabits the biflagellate protist Cyanophora paradoxa and acts as its chloroplast; the endosymbiont is called a cyanelle
Taxonomic Ranks
The basic taxonomic group is the species
Procaryotic 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 procaryotic species is a collection of strains that share many stable properties and differ significantly from other groups of strains
A strain is a population of organisms that is distinguishable from at least some other population s in a taxonomic category; it is thought to have descended from a single organism or pure culture isolate
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
A genus is a well-defined group of one or more species that is clearly separate from other genera
In the binomial system of nomenclature devised by Carl von Linne (Carolus 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)
Classification Systems
Natural classification-arranges organisms into groups whose members share many characteristics and reflects as much as possible the biological nature of organisms
Phenetic systems group organisms together based on overall similarity
Frequently a natural system based on shared characteristics
Not dependent on phylogenetic analysis
Use unweighted traits
Best system compares as many attributes as possible
Numerical taxonomy
Information about the properties of an organism is converted to a form suitable for numerical analysis and is compared by means of a computer
The presence or absence of at least 50 (preferably several hundred) characters should be compared (morphological, biochemical and physiological characters)
An association coefficient is determined between characters possessed by two organisms
Simple matching coefficient-proportion that match whether present or absent
A treelike diagram called a dendrogram is used to display the results of numerical taxonomic analysis
The significance of the phenons is not always obvious but phenons with an 80% similarity often are equivalent to bacterial species
Phylogenetic (phyletic) systems-group organisms together based on probable evolutionary relationships
Has been difficult for procaryotes because of the lack of a good fossil record
Direct comparison of genetic material and gene products such as rRNA and proteins overcomes this problem

Major Characteristics Used in Taxonomy
Classical characteristics
Morphological characteristics-easy to analyze, genetically stable and do not vary greatly with environmental changes; often are good indications of phylogenetic relatedness
Physiological and metabolic characteristics-directly related to enzymes and transport proteins (gene products) and therefore provide an indirect comparison of microbial genomes
Ecological characteristics-include life-cycle patterns, symbiotic relationships, ability to cause disease, habitat preferences and growth requirements
Genetic analysis-includes the study of chromosomal gene exchange through transformation and conjugation; these processes only rarely cross genera; one must take care to avoid errors that result from plasmid-borne traits
Molecular characteristics
Comparison of proteins-useful because it reflects the genetic information of the organism; analysis is by:
Assessing Microbial Phylogeny
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
Phylogenetic trees
Made of branches that connect nodes, which represent taxonomic units such as species or genes; rooted trees provide a node that serves as the common ancestor for the organisms being analyzed
Developed by comparing molecular sequences and differences are expressed as evolutionary distance; organisms are then clustered to determine relatedness; alternatively, relatedness can be estimated by parsimony analysis assuming that evolutionary change occurs along the shortest pathway with the fewest changes to get from ancestor to the organism in question rRNA, DNA, and proteins as indicators of phylogeny
Association coefficients from rRNA studies are a measure of relatedness
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
DNA similarity studies are more effective at the species and genus level
Protein sequences are less affected by organism-specific differences in G+C content
Analyses of the three types of molecules do not always produce the same evolutionary trees
Polyphasic taxonomy
Uses a wide range of phenotypic and genotypic information to develop a taxonomic scheme
Techniques and information used depend on level of taxonomic resolution needed (e.g., serological techniques are good for identifying strains, but not genera or species
The Major Divisions of Life
Domains
Woese and collaborators used rRNA studies to group all living organism into three domains
Bacteria-comprise the vast majority of procaryotes; cell walls contain muramic acid; membrane lipids contain ester-linked straight-chain fatty acids
Archaea-procaryotes that: lack muramic acid, have lipids with ether-linked branched aliphatic chains, lack thymidine in the
T arm of tRNA molecules, have distinctive RNA polymerases, and have ribosomes with a different composition and shape than those observed in Bacteria
Eucarya-have a more complex membrane-delimited organelle structure
Several different phylogenetic trees have been proposed relating the major domains and some trees do not even support a three-domain pattern
One of the most important difficulties in constructing a tree is widespread, frequent horizontal gene transfer; a more correct tree may resemble a web or network with many lateral branches linking various trunks

Kingdoms
Whittakerís five-kingdom system was the first to gain wide acceptance
Animalia-multicellular, nonwalled eucaryotes with ingestive nutrition
Plantae-multicellular, walled eucaryotes with photoautotrophic nutrition
Fungi-multicellular and unicellular, walled eucaryotes with absorptive nutrition
Protista-unicellular eucaryotes with various nutritional mechanisms
Monera (Procaryotae)-all procaryotic organisms
VIII. Bergeyís Manual of Systematic Bacteriology
The First Edition of Bergeyís Manual of Systematic Bacteriology-primarily phenetic
Contains 33 sections in four volumes
Each section contains bacteria that share a few easily determined characteristics (e.g., morphology, gram reaction, oxygen relationships) and bears a title that describes these properties or provides the vernacular names of the bacteria included
The Second Edition of Bergeyís Manual of Systematic Bacteriology
Largely phylogenetic rather than phenetic
Consists of five volumes
A Survey of Procaryotic Phylogeny and Diversity

Volume 1 (of 2nd edition of Bergeyís Manual): The Archaea, and Deeply Branching and Phototrophic Genera
Archaea-divided into two phyla
Crenarchaeota-diverse phylum that contains thermophilic and hyperthermophilic organisms as well as some organisms that grow in oceans at low temperatures as picoplankton
Euryarchaeota-contains primarily methanogenic and halophilic procaryotes and also thermophilic, sulfur-reducing procaryotes
Bacteria
Aquificae-phylum containing autotrophic bacteria that use hydrogen as an energy source; most are thermophilic
Thermatogae-phylum containing anaerobic, thermophilic fermentative, gram-negative bacteria; have unusual fatty acids
ìDeinococcus-Thermusî-this phylum includes bacteria with extraordinary resistance to radiation and thermophilic organisms
Chloroflexi-this phylum consists of bacteria often called green nonsulfur bacteria; some carry out anoxygenic photosynthesis, while others are respiratory, gliding bacteria; have unusual peptidoglycans and lack lipopolysaccharides in their outer membranes
Cyanobacteria-a phylum consisting of oxygenic photosynthetic bacteria
Chlorobi-this phylum contains anoxygenic photosynthetic bacteria known as the green sulfur bacteria;
Volume 2: The Proteobacteria-devoted to a single phylum called Proteobacteria, which consists of a diverse array of gramnegative bacteria
Volume 3: The Low G+C Gram-Positive Bacteria-devoted to a single phylum called Firmicutes; all have a G+C content
50%; with the exception of the mycoplasmas, which lack a cell wall, they are gram positive; most are heterotrophs; includes genera that produce endospores
Volume 4: The High G+C Gram-Positive Bacteria-describes the phylum Actinobacteria; have G+C content 50-55%; includes filamentous bacteria (actinomycetes) and bacteria with unusual cell walls (mycobacteria)
Volume 5: The Planctomycetes, Spriocheates, Fibrobacteres, Bacteroidetes, and Fusobacteria-an assortment of deeply branching phylogenetic groups that are not necessarily related to one another although all are Gram negative
Planctomycetes-this phylum contains bacteria with unusual features, including cell walls that lack peptidoglycan and cells with a membrane-enclosed nucleoid; divide by budding and produce appendages called stalks
Chlamydiae-this phylum contains obligate-intracellular pathogens having a unique life cycle; they lack peptidoglycan
Spirochaetes-a phylum composed of helically shaped bacteria with unique morphology and motility
Bacteroides-this phylum contains a number of ecologically significant bacteria