MICROBIOLOGY CHAPTER 10 – CLASSIFICATION OF MICROORGANISMS

Taxonomy – science of the classification of organisms. THE THREE DOMAINS

Its goal; provides a means of identifying organisms. Living organisms are currently classified into three
domains. A domain can be divided into kingdoms.
THE STUDY OF PHYLOGENETIC RELATIONSHIPS
Ribosomes (rRNA) differ in all three cell types.
Charles Darwin 1. Eukarya (plants, animals, fungi)
- English naturalist; proposed natural selection was 2. Bacteria (with peptidoglycan)
responsible for the similarities and differences of 3. Archaea (with unusual cell walls)
organisms
- Organisms with traits best suited to an environment Carl R. Woese
have higher survival rate - proposed Domain above the Kingdom level
- Archaea and bacteria should have separate
Taxa (sing. taxon) domains on the evolutionary tree
- categories of organisms showing degrees of
similarities due to relatedness through evolution *Each domain shares genes with other domains through
horizontal gene transfer, which occurred within the
Systematics (Phylogeny) community of early cells.
- study of evolutionary history of organisms *DNA passed on from ancestors are described as
- The taxonomic hierarchy shows evolutionary, or conserved.
phylogenetic, relationships among organisms.
DOMAIN ARCHAEA
Carolus Linnaeus 1. Methanogens
- introduced a formal system of classification with two - strict anaerobes that produce methane (CH4)
(2) kingdoms: from carbon dioxide and hydrogen
1. Plantae 2. Extreme Halophiles
2. Animalia - require high concentrations of salt for survival
3. Hyperthermophiles
Carl von Nageli - normally grow in extremely hot environments
- proposed that bacteria and fungi belong to plant
kingdom (followed and believed for 100 years) *True nucleus is produced with the infolding of the
plasma membrane surrounding the nuclear region.
Ernst Haeckel Evidence: Gemmata Bacteria
- proposed Kingdom Protista to include bacteria, *Endosymbiotic Theory – nucleus was separated; allows
protozoa, algae, and fungi development of organelles

Robert G.E. Murray A PHYLOGENETIC TREE

- proposed Kingdom Prokaryotae/Monera - grouping organisms according to common
- Bacteria were separated into the Kingdom properties implies that a group of organisms
Prokaryotae in 1968. evolved from a common ancestor
- some information for eukaryotic phylogenetic
Robert H. Whittaker relationships is obtained from fossil records
- Living organisms were divided into five kingdoms in - some fossilized microorganisms include:
1969 (1 for Prokaryotes, 4 for Eukaryotes) o White Cliffs of Dover, England
o Stromatolites – filamentous bacteria
o Cyanobacteria-like microbes (oldest fossil)
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*Fossil evidence isn’t available for most prokaryotes, Prokaryotic Species

except for isolated living prokaryotes that existed for - population of cells with similar characteristics
(25-40 million years) - not directly tied to sexual conjugation
 Raul Cano – American microbiologist; grown
Bacillus sphaericus and other microbes Culture
embedded in fossilized plant resin called amber - bacteria grown in media
- often a clone (a population of identical cells
*If fossil evidence isn’t available, similarities in genomes derived from a single parent cell)
are used to group organisms into taxa. - sometimes a strain (A group of bacteria derived
 Fossil records agree with rRNA sequencing and from a single cell)
DNA hybridization. o Closely related strains constitute a bacterial
species.
Molecular clock
- describe the relationship between evolutionary rate CLASSIFICATION OF EUKARYOTES
and time, assuming that the rate of molecular
evolution is constant across species 1. Protists
- used to track path of Zika virus - unicellular eukaryotes
- diverse; where all organisms that didn’t fit to other
CLASSIFICATION OF ORGANISMS kingdoms can be found
- now divided into Clades (classified protists
Binomial Nomenclature according to phylogenetic evolution)
- genus name + species epithet - currently being assigned to kingdoms
- Latin words or latinized by adding:
- ales (order), aceae (family 2. Kingdom Fungi
- unicellular yeasts, multicellular molds,
Eukaryotes Species macroscopic mushrooms
- with nucleus; group of closely related organisms that - possesses hyphae (thin tubes composed of joined
interbreed only among themselves fungus cells)
- absorptive chemoheterotrophs that develop from
Genus – species that differ from each other but are spores or fragments of hyphae
related by descent
Family – related genera 3. Kingdom Plantae
Order – similar families - multicellular photoautotrophs
Class – similar orders - obtains energy through photosynthesis
Phylum – related classes - includes mosses, ferns, conifers, flowering plants
Kingdom – related phyla
Domain – related kingdoms 4. Kingdom Animalia
- multicellular ingestive heterotrophs
CLASSIFICATION OF PROKARYOTES - obtains nutrients and energy from ingested organic
- standard reference is Bergey’s Manual of matter through a mouth
Systematic Bacteriology; classification according to - includes sponges, worms, insects, vertebrates
phylogenetic relationships
- oldest known fossils from 3.5 billion years ago
- Classification does not include Kingdom (Domain,
Phylum, Class, Order, Family, Genus, Species)
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VIRUSES Morphological Characteristics

- not composed of cells and do not have ribosomes - useful in identifying organisms, especially when
- use host’s anabolic machinery to multiply aided by differential staining techniques
- more closely related to its hosts than to other
viruses Differential Staining
- according to International Committee on - based on the chemical composition of cell walls
Taxonomy of Viruses - not useful in organisms that lack cell walls
o Viral Species - 2 types of differential staining
 it is a population of viruses with similar 1. Gram Stain (Gram-positive; Gram-negative)
characteristics that occupies a particular 2. Acid Fast Stain
ecological niche - for a more limited group of microbes
 obligatory intracellular parasites
- 3 hypothesis of its origin Biochemical Tests
1. They arose from independently replicating - use of enzymes to differentiate bacteria and yeasts
strands of nucleic acids (i.e. plasmids) - can differentiate among the genera
2. They developed from degenerative cells - use of selective and differential media can reduce
3. They coevolved with host cells time for organism identification
- Limitations of biochemical testing:
METHODS OF CLASSIFYING o mutations and plasmid acquisition can result
AND IDENTIFYING MICROORGANISMS in strains with different characteristics
o large number of biochemical tests needed for
Classification Scheme a correct identification
- provides a list of characteristics and a means for
comparison to aid in the identification of an Rapid Identification Methods
organism - designed to perform several biochemical tests
- Bergey’s Manual of Determinative Bacteriology – simultaneously
standard reference for laboratory identification of - can identify bacteria within 4-24 hours
bacteria - manufactured for enterics
*Only 1% of bacteria and archaea have been - sometimes called Numerical Identification
discovered.  results of each test are assigned a number
(1 for positive, 0 for negative)
Medical Microbiology - Automated Rapid Identification
- branch of microbiology that deals with human  lysis of cells
pathogens (only 5% or less of 11,500 total species  extraction of proteins through acetonitrile
listed in the Approved Lists of Bacterial names)  measurement of molecular mass through
mass spectrophotometer
Transport Media
- not nutritive; used to prolong viability of fastidious Serology
pathogens - science that studies serum and immune responses
- tube of transport medium; where the swab of a in serum
patient’s pus or tissue surface is inserted - Microorganims (carries or serves as antigens) that
enter the human body stimulate it to produce
antibodies (binds with antigen)
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Antiserum Phages/Bacteriophages
- solution of antibodies used in the identification of - bacterial viruses that usually cause lysis of the
microorganisms bacterial cells they infect
- known antisera can be used to identify unknown  when infected, there is an appearance of
bacteria clearings in bacterial growth called plaques
- highly specialized; infect only members of a
1. Slide Agglutination Test particular species or strains within a species
 unknown bacterium is placed in a drop of saline
on each of several slides Phage Typing
 different known antiserum is added - identification of bacterial species and strains by
to each sample determining their susceptibility to various phages
 bacteria agglutinate (clump) when mixed with - trace food-associated infections
antibodies produced in response to antigens
Fatty Acid Profiles
2. Serological Testing - can be used to identify some organisms
- useful in determining the identity of strains and  Fatty acids
species, as well as relationships among organisms - synthesized by bacteria
- includes ELISA and Western Blotting - constant for a particular species
 Serotypes/Serovars/Biovars  Fatty Acid Methyl Ester (FAME)
- strains with different antigens - used in clinical and public health laboratories
- same species, different strains - separation of cellular fatty acids to compare
 Rebecca Lancefield them to fatty acid profiles of known organisms
- classified streptococcal serotypes by studying
serological reactions Flow Cytometry
- identifies bacteria in a sample by measuring
 Enzyme-linked Immunosorbent Assay (ELISA) physical and chemical characteristics of cells
- widely used; fast and can be read by a computer without culturing it
scanner  Flow Cytometer
- used to detect AIDS through the presence of HIV - detects the presence of bacteria by detecting
 known antibodies are placed and adhered to the difference in electrical conductivity
the wells of a microplate between cells and surrounding medium
 unknown bacterium is added to each well  a moving fluid is forced through a small
 its reaction identifies the bacteria opening
 the fluid can be dyed by fluorescent
 Western Blotting  the fluid is illuminated by a laser
- used to identify antibodies in a patient’s serum  scattering of light provides info regarding cell
- confirms infection of HIV and Lyme Disease size, shape, density, surface through analysis
- proteins (antigens) are separated by of a computer
electrophoresis and can be detected by their
reactions with antibodies DNA Sequencing
DNA base composition
- can draw conclusions about organisms’ relatedness
- expressed as the % of Guanine-Cytosine base pairs;
can be used in the classification of organisms
- requires great amount of time
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DNA Fingerprinting 2. Southern Blotting

- detects genetic similarities and differences through - identify unknown microorganisms
comparing patterns of two DNA fingerprints - use of DNA probes in rapid identification
- used to determine the source of hospital-acquired methods
infections - detection of specific DNA
- aims to produce DNA bar code
3. DNA Chips/Microarray
DNA fingerprint - detects a pathogen in a host/environment by
- produced when restriction fragments are identifying a unique gene to the pathogen
separated by electrophoresis - composed of DNA probes
- patterns (numbers and sizes of DNA fragments or - use of fluorescent dye as DNA label of the
DNA fingerprints produced by restriction enzymes) organism
are compared to detect genetic similarities and - hybridization of DNA probe and DNA sample is
differences detected by fluorescence

Restriction fragments  Ribotyping and Ribosomal RNA Sequencing

- produced when restriction fragments cut a - used to classify organisms and determine
molecule of DNA wherever a specific base phylogenetic relationships
sequence occurs - detects bacteria without culturing it
- used to classify newly discovered organisms
Nucleic Acid Hybridization
- determines the extent of similarity between base  Fluorescent In Situ Hybridization (FISH)
sequences of two organisms - uses fluorescent dye-labeled DNA or RNA
- Single strands of DNA, or of DNA and RNA, from probes to stain microorganisms in situ
related organisms will hydrogen-bond to form a - determines identity, abundance, relative
double-stranded molecule activity of microorganisms
- measures the ability of DNA strands from one - detects bacteria without culturing it
organism to hybridize (bind through
complementary base pairing) with DNA strands of PUTTING CLASSIFICATION METHODS TOGETHER
another organism
- hybridization level of 70% or above indicates that 2 Dichotomous Keys
organisms belong to the same species - identification of organisms is based on successive
- PCR, Southern blotting, DNA chips, and FISH are questions with 2 possible answers until organism is
examples of nucleic acid hybridization technique identified

1. Nucleic Acid Amplification Tests (NAATs) Cladograms

- used to amplify a small amount of microbial - maps that show phylogenetic relationships among
DNA to levels that can be tested by gel organisms
electrophoresis  2 rRNA sequences are aligned
- presence or identification of organism is  % of similarity between sequences is identified
indicated by amplified DNA  horizontal branches are drawn with length
- use of PCR, reverse-transcription PCR, real- proportional to % of similarity
time PCR  species under one node (branch point) arose
- George Whipple used PCR to determine from the same ancestor
causative agent of Whipple’s disease