BIOL 3702 Lecture Outline
Chapter 19 - Microbial Taxonomy and Phylogeny
Overview
The extraordinary diversity of the microbes is fascinating, yet very complex Due to the diverse nature of living organisms, it is desirable to categorize them into
groups based upon their similarities
Taxonomy - the science of biological classification
Classification - arrangement of organisms into groups or taxa (s., taxon) based
upon similarities or evolutionary relatedness
Nomenclature - assignment of names to taxonomic groups using special rules Identification - determining to which recognized taxon a particular organism
belongs
Why is taxonomy important?
Permits the organization of huge amounts of information Allows predictions and hypotheses to be made upon this information Places organisms in useful groups with precise names that permit effective
communication between investigators
Essential for the identification of organisms
The term systematics is often used in synonymy with taxonomy
This term is better defined as the scientific study of organisms with the ultimate
object of characterizing and arranging them in an organized manner
Actually encompasses other disciplines including morphology, ecology,
epidemiology, biochemistry, molecular biology, and physiology Microbial Evolution
Earth is estimated to be 4.6 billion years old First procaryotic cells, as evident from fossilized remains, appeared about 3.5-3.8
billion years ago and were likely anaerobic
Subsequent evolution of cyanobacteria and oxygenic photosynthesis occurred 2.53.0 billion years ago
Microbial diversity increased as an oxygen-rich environment developed Carl Woese and colleagues, studying rRNA sequences, suggest that procaryotes
divided into two distinct lineages early in the earths evolution
These workers also suggested that all living things can be placed into one of three
domains
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Copyright 2004 by Chester R. Cooper, Jr.
BIOL 3702 Lecture Outline
Chapter 19
Domains - placed above the phylum and kingdom levels of classification
Bacteria - procaryotic Archaea - procaryotic Eucarya - eucaryotic
Eucaryotes arose from procaryotes 1.4-2.7 billion years ago Two hypotheses for the evolution of eucaryotic cells
Organelles arose within procaryotes from the invagination of the plasma
membrane
Endosymbiotic hypothesis
Fusion
of ancient true bacteria and archaea to form a nucleus and a Golgi apparatus and chloroplasts develop later from a permanent symbiotic relationship with other bacteria, e.g., cyanelle (cyanobacterium) living inside the protist Cyanophora paradoxa
Mitochondria
Taxonomic Ranks
Classification of an organism requires that it be placed (ranked) in a group (taxon)
and given a specific name
Informal names - lactic acid bacterium Formal names - Lactobacillus acidophilus
Groups are hierarchical in nature Classification of an organism requires that it be placed (ranked) in a group (taxon)
and given a specific name
Informal names - lactic acid bacterium Formal names - Lactobacillus acidophilus
Groups are hierarchical in nature Categories used in any rank unites groups under it based upon common properties In procaryotes (in ascending order), some ranks have characteristic suffixes
Species (Note: do not capitalize first letter) Genus Family (suffix = -aceae) Order (suffix = -iales) Class Phylum Domain
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Copyright 2004 by Chester R. Cooper, Jr.
BIOL 3702 Lecture Outline
Chapter 19
Species - basic taxonomic group
In higher organisms, a species is defined based upon sexual reproduction Not a good criteria for bacteria - many procaryotes do not reproduce sexually
Procaryotic species - collection of strains that share many stable properties and differ
significantly from other groups of strains
Strain - population of organisms that is distinct from other populations within a
particular taxonomic category and is typically descended from a single organism or a pure culture
Biovars - biochemical or physiological Morphovars - shape Serovars - antigenic properties Type strain - standard, but not always the most representative member
Genus - a well-defined group of one or more species that is clearly distinct from other
genera
Naming of microbes uses a binomial system developed by Carolus Linnaeus
Genus - Escherichia Species - coli Abbreviated - E. coli, but only after the full name/epithet is used once; never start
a sentence with an abbreviation Classification Systems
Two basic types of classification systems are used:
Phenetic classification
Natural May
classification system that groups organisms together based upon mutual similarity of their phenotypic characteristics be used to infer possible evolutionary relationships solely on evolutionary relationships
Phylogenetic (phyletic) classification
Based Has
been difficult to use in the past for procaryotes due to a lack of a fossil record methods instead use gene sequences (e.g., RNA genes) or their products (proteins) to estimate phylogenetic relationships
Modern
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Copyright 2004 by Chester R. Cooper, Jr.
BIOL 3702 Lecture Outline Taxonomic Characteristics
Chapter 19
Classical characteristics
Morphology Physiological/metabolic Ecological Genetic analysis
Transformation Conjugation Plasmid
content
Molecular characteristics
Proteins
Sequencing Physical,
of conserved proteins
kinetic, and regulatory properties
Nucleic acids
Base
composition
Hybridization Sequencing
of conserved genes, e.g., rRNA because it is generally stable yet changes over long periods of time
Microbial Phylogeny
There are a number of methods used to assess the phylogeny of microbes
Molecular chronometers - assumes that changes in conversed proteins or genes
occurs over time without destroying or altering the molecules function
Phylogenetic trees - compares molecular sequence differences of a conserved
gene or protein between organisms to generate a tree that expresses the differences as an evolutionary distance
Signature sequence - particular groups of microbes will possess unique
nucleotides at specific locations in 16S rRNA molecules
Signature sequence - particular groups of microbes will possess unique
nucleotides at specific locations in 16S rRNA molecules
Polyphasic taxonomy - taxonomic scheme which employs a wide range of stable
and accepted phenotypic and genotypic information
Modern microbial taxonomists generally employ phylogenetic trees derived from
rRNA comparisons
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Copyright 2004 by Chester R. Cooper, Jr.
BIOL 3702 Lecture Outline Divisions of Life
Chapter 19
Kingdom systems of classification
Five-kingdom system (Whittaker, 1960s) - based upon cell type, organization, and
the means of nutrient acquisition
Animals Plants Fungi
- multicellular eucaryotes, digestion
- multicellular eucaryotes, photosynthesis - unicellular eucaryotes, various methods of nutrition - procaryotes
- multicellular eucaryotes, absorption
Protista Monera
Six-kingdom system - differs from five-kingdom system by dividing procaryotes
into bacteria and archaea
Eight-kingdom system - further division of the protists using rRNA data and
grouping organisms into two empires (Eucaryota and Bacteria) containing a total of eight kingdoms
Universal/eucaryotic trees - provides for numerous lineages and great diversity
Domain system of classification - based on work of Woese and colleagues using
rRNA to group organisms into three domains
Archaea - procaryotic; differ from Bacteria in cell wall structure, membrane
composition, transfer RNAs, etc. [see details in Table 19.8]
Bacteria - procaryotic Eucarya - eucaryotic
Bergeys Manual
In 1923, David Bergey and colleagues set out to publish a definitive book on the
identification and classification of bacteria
Bergeys Manuals - the Bibles of bacterial identification/classification Three versions of these books:
Bergeys Manual of Determinative Bacteriology (currently in its 9th ed.) - species
identification
Bergeys Manual of Systematic Bacteriology, 1st ed. - phenetic system Bergeys Manual of Systematic Bacteriology, 2nd ed. - phylogenetic system of
classification
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Copyright 2004 by Chester R. Cooper, Jr.
BIOL 3702 Lecture Outline Survey of the Procaryotes
Chapter 19
Bergeys Manual of Systematic Bacteriology (2nd ed.) covers 25 phlya Bergeys Manual of Systematic Bacteriology (2nd ed.) covers 25 phlya Groups covered by each volume:
Volume 1
Domain
Archaea
Phylum
Crenarchaeota - thermophylic and hyperthermophylic sulfur metabolizers Euryarchaeota - methanogens, halophiles, and thermophilic sulfur reducers Bacteria Aquificiae - earliest branch of bacteria that contain autotrophs which utilize hydrogen for energy production Thermotogae - anaerobic, thermophilic, and fermentative Gramnegative bacteria Deinococcus Thermus - radiation resistant bacteria Phylum Chloroflexi - green non-sulfur bacteria that carries out anoxygenic photosynthesis Cyanobacteria - oxygenic photosynthetic bacteria Chlorobi - green sulfur bacteria that carry out anoxygenic photosynthesis - Gram negative
Phylum
Domain
Phylum
Phylum
Phylum
Phylum Phylum
Volume 2
Proteobacteria All
major nutritional types classes based upon rRNA data - oligotrophic forms including the purple nonsulfur
Five
Alphaproteobacteria
photosynthesizers
Betaproteobacteria
- metabolically similar to alphaproteobacteria - diverse methods of energy metabolism - contains pathogens - includes predators and the fruiting myxobacteria
Gammaproteobacteria Deltaproteobacteria
Epsilonproteobacteria
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Copyright 2004 by Chester R. Cooper, Jr.
BIOL 3702 Lecture Outline
Volume 3
Gram-positive Three
Chapter 19
low G+C DNA composition
classes of the phylum Firmicutes - tend to be anaerobic and endospore formers - mycoplasmas (no cell walls)
Clostridia Mollicutes Bacilli
- Gram-positive aerobes or facultative anaerobes, rods or cocci, some endospore formers high G+C DNA composition
Volume 4
Gram-positive All
belong to the phylum Actinobacteria are filamentous
Some
Volume 5
Gram-negative Various Nine
morphologies Planctomycetes - some have a membrane-bound nucleus Chlamydiae - obligate intracellular parasites important in disease
phyla of which four are presented below
Phylum Phylum Phylum
Spirochaetes - helical-shaped, Gram-negative motile bacteria (axial filaments) Bacteroidetes - ecologically significant species are found in this phylum
Phylum
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Copyright 2004 by Chester R. Cooper, Jr.
