Taxonomy is one aspect of classification. Organisms are ordered into groups (taxa) and ranked in a
hierarchy according to established procedures and guidelines. In this manner, organisms are placed
into taxa of different organizational levels and the inter-relationships and boundaries between groups are
established.
Nomenclature
is another aspect of taxonomy. Names are assigned to organisms in a systematic
manner.
Identification of an organism is made possible by following the classification and nomenclature
guidelines and by various scientific approaches. This allows us to place an organism within its correct
position in the classification scheme.
I. Before scientists had a clear understanding of the nature of microbes the biological world was
classfied into: plants and
animals. Bacteria were placed with plants. Clearly, this scheme was
inadequate. The electron microscope demonstrated obvious differences between bacteria and
eukaryotes.
II. Based on nuclear and cellular properties a two kingdom was also produced: Prokaryotae and
Eukaryote. This was based primarily on presence of a true nucleus and having organelles sorrounded
or enclosed by a membrane.
III. In 1968 Whittaker proposed his famous 5 Kingdom system of living organisms. Bacteria were
classified under Kingdom Monera. Members of the Monera Kingdom were defined as "cells in
which nuclear material is not surrounded by a nuclear membrane."
IV. The 3 Kingdom of classification proposed by Woese in the 70's utilizes the sequence of the 16S
ribosomal RNA to classify organisms into: Eubacteria,
Archaebacteria and Eukaryota.
The Linnean system of Binomial Nomenclature
Carolus Linneaus developed a scientific system of naming organisms. The names used by Linneaus in
the Species Plantarum (1753) and the Systema Naturae (1758) are the basis of the system for plants and animals, respectively. He assigned two latinized names to each organism:
A genus consists of a group of similar species. Similar genera are grouped into a family. The species
name or "specific epithet" is unique to the new species. The genus name is indicated by a capital letter
whereas the species name starts with a lower case letter. By convention both names are italicized (or
underlined).
Example: Streptococcus pyogenes ---- Once a scientific name has been used in entirety it can subsequently be abbreviated as follows: S. pyogenes
Scientific names should be unique, unchanging and
descriptive. For example, the name may reflect
- the name of the person describing the organism
- the habitat of the organism
- the appearance of the organism
- some names may reflect a disease or infectious process caused by an organism (e.g., 'pyogenes'
describes the ability to produce pus)
The genetic variability of microbes is further subdivided into
subspecies or types:
a) A strain is equivalent to a clone and represents a population of genetically identical organisms that
have arisen from a single cell. Some strains of a bacterial species may be virulent, whereas others are
not.
b) Serovars are antigenically distinct organisms. For example, over 2,000 serovars of Salmonella
have been identified which are typed according to their flagellar
(H) and somatic (O) antigens.
Classification: The Three Domain System
The Three Domain System, proposed by Woese, is an evolutionary model of classification based on differences in the sequences of nucleotides in the cell's ribosomal and transfer RNAs, membrane lipid structure, and sensitivity to antibiotics. This system proposes that a common ancestor cell ("Cenancestor") gave rise to three different cell types, each representing a domain. The
three domains are the Archaea (archaebacteria), the Bacteria (eubacteria), and the Eukarya (eukaryotes). The Eukarya are then divided into 4 kingdoms: Protists, Fungi, Anamalia, and Plantae. A description of the three domains follows:
1. The Archaea (archaebacteria)
· The Archae are prokaryotic cells. Unlike the Bacteria and the Eukarya, they have membranes
composed of branched carbon chains
attached to glycerol by ether linkages and have cell walls
which contain no peptidoglycan. While they are not sensitive to some antibiotics which affect the
Bacteria, they are sensitive to some antibiotics that affect the Eukarya. The Archae have rRNA and
tRNA regions distinctly different from the Bacteria and Eukarya. They often live in extreme
environments and include
methanogens, extreme halophiles, and hyperthermophiles.
2. The Bacteria (eubacteria)
· The Bacteria are prokaryotic cells. Like the Eukarya, they have membranes composed of straight
carbon chains attached to glycerol by ester linkages. They have cell walls containing
peptidoglycan, are sensitive to traditional antibacterial antibiotics, and have rRNA and tRNA
regions distinctly different from the Archaea and Eukarya. They include: mycoplasmas,
cyanobacteria, Gram-positive bacteria, and Gram-negative bacteria.
3. The Eukarya (eukaryotes)
· The Eukarya (also spelled Eucaryota\a) have eukaryotic cells. Like the Bacteria, they have
membranes composed of straight carbon chains attached to glycerol by ester
linkages. If they
possess cell walls, those walls contain no peptidoglycan. They are not sensitive to traditional
antibacterial antibiotics and have rRNA and tRNA regions distinctly different from the Bacteria and
the Archaea. They include the following kingdoms:
a. Protista Kingdom: Protista are simple, predominately unicellular eukaryotic organisms.
Examples includes slime molds, euglenoids, algae, and protozoans.
b. Fungi Kingdom: Fungi are unicellular or multicellular organisms with eukaryotic cell
types. The cells have cell walls but are not organized into tissues. They do not
carry out
photosynthesis and obtain nutrients through absorption. Examples include sac fungi, club
fungi, yeasts, and molds.
c. Plantae Kingdom: Plants are multicellular organisms composed of eukaryotic cells.
The cells are organized into tissues and have cell walls. They obtain nutrients by
photosynthesis and absorption. Examples include mosses, ferns, conifers, and flowering
plants.
d. Animalia Kingdom: Animals are multicellular organisms composed
of eukaryotic cells.
The cells are organized into tissues and lack cell walls. They do not carry out photosynthesis
and obtain nutrients primarily by ingestion. Examples include sponges, worms, insects, and
vertebrates.
Two alternative approaches to microbial taxonomy:
I. Phenetic system: groups organisms based on similarity of shared phenotypic characteristics. For
example, we could place anaerobes in one group and aerobes in another. This may not always reflect
the correct evolutionary groupings of the organisms.
Bergey's manual is an example of a phenetic system. Microbes are organized into groups based on
both morphological (staining reactions, cell shape and arrangement, pigment production, appearance on
media) and physiological (growth requirements, biochemical tests, type of metabolism). This system can
be useful for identifying an unknown organism as you are doing in our laboratory.
This classical approach allows one to 'key'out an organism using a series of mutually exclusive
characteristics. For example: Is the organism gram positive or gram positive? Is the shape of
the
organism a coccus, bacillus or some other morphology? The key eventually narrows down the organism until an identification is possible.
Numerical Taxonomy
- Calculates the percentage of characteristics that two organisms or groups have in common
- A large range of traits (morphology, motility, biochemistry) are considered (at least 50!)
- The result of this classification is a similarity coefficient
(the percentage of the total number of
characters measured that are common to two organisms. Dendograms are produced to indicate
relatedness....do not worry about this computers programs can do all this for you!
II. Phylogenetic system: groups organisms based on their shared evolutionary heritage and descent.
Unlike, a phenetic system, organisms do not have to be
phenotypically similar in order to belong to the
same phylogenetic group. For example, based on genetic and molecular evidence, Pneumocystis
carinii is now considered to be more closely related to the fungi and is no longer believed to be a
protozoan (although it resembles a protozoan in many respects).
Molecular methods used to type and identify microbes
Two main approaches:
a)
comparing DNA or RNA sequences in one or more ways comparing amino acid sequences of a
protein or proteins
Molecular taxonomy
Uses some key assumptions in order to establish a time-line of evolutionary relatedness
- genetic mutations are random
- once a mutation occurs, all descendants of that cell will carry the mutation
- organisms that differ only slightly at the
genetic level have diverged more recently over the course
of evolution than organisms that differ significantly
a) DNA base composition
- Indicates relatedness of organisms
- Base composition is usually expressed as GC content
- If the GC content differs by a small percentage the organisms are not closely related
- The GC content itself
does not always mean that organisms are related. For example,
Mycoplasma and Bacillus have similar GC contents but are very different organisms
b) DNA fingerprinting
Comparison of the cleavage pattern (fingerprint) of the DNA from two organisms (one known, the
other unknown) can determine if they are related. Each organism has a unique restriction digest
profile
c) Hybridization of DNA probes
- The most widely used molecular method used to determine relatedness or organisms
- ssDNA is separated from ds DNA on a filter
- The DNA of one organism is radiolabelled and mixed at low concentrations with the
nonradioactive denatured DNA of the other organism
- The more related the organisms, the higher the degree of
complementary base pairing which can
be detected by a higher reading of radioactivity.
d) Nucleic acid hybridization
- Two organisms: grow one in [3H] thymine, the other one without it.
- Harvest and isolate DNA
- Denature DNA from one organism (heating) and bind it to a filter membrane
- Add denatured DNA from the other organism
- Wash and add S1 nuclease to remove any single stranded DNA
- Expose to X-ray film.
- If closely related they would anneal (bind) if conditions are right (60-70 C). You can get binding
using lower temperatures (35-55 C) but this is just background!!
Other methods for identifying bacteria
Serological tests
- Identify microbes by
reactivity with specific antibodies
- Serotyping developed by Rebecca Lancefield. Designed A through O system to identify variants
(serovars or serotypes) of Streptococci
- Enzyme-linked immunosorbent assay (ELISA)
- Immunofluorescent antibody testing (IFAT)
- Western blot
Evolutionary
chronometers
Choosing the right chronometer:
· the molecule should be universally distributed across the group chosen for study
· it must be functionally homologous in each organism (phylogenetic comparisons must start with
molecules of identical function)
· the sequence
should change at a rate commensurate with the evolutionary distance to be
measured; the broader the phylogenetic distance to be measured, the slower must be the rate at
which the sequence changes
Ribosomal RNAs as evolutionary chronometers:
- It is likely that the protein-synthesizing process is very old, and so rRNA molecules are very good
for discerning evolutionary relationships among living organisms
- This rRNA is also found the ribosomes of chloroplasts and mitochondria and is therefore present
in animals and plants.
- As the ribosome plays a critical role in protein synthesis most mutations in rRNA are harmful and
tend to occur very infrequently.
-
Therefore,16S rRNA is a very useful molecule for comparing relatedness of organisms over the
course of evolution.
- rRNAs are ancient molecules, functionally constant, universally distributed, and moderately
well conserved across broad phylogenetic distances
-the number of different possible sequences is large, so similarity in
two sequences always indicates
some phylogenetic relationship; the degree of similarity in rRNA sequences between two
organisms indicates relative evolutionary relatedness
Ribosomal RNA molecules:
-in prokaryotes they are 5S, 16S, and 23S
-16S and 23S each contain several regions of highly conserved sequence that allows for proper
sequence alignment, but contain sufficient sequence variability in other regions to serve as
phylogenetic chronometers
-5S has also been used but it is too small which limits its information usefulness
-16S is more experimentally manageable than 23S RNA and has been used extensively for
developing databases
-in eukaryotes, the 18S rRNA counterpart is the 16S rRNA
Signature sequences: short oligonucleotide sequences unique to a certain group or groups of
organisms.
-signatures defining each of the three primary domains have been identified
-other signatures defining the major taxa within each domain have also been detected
-signatures are generally found in defined regions of
the 16S rRNA molecule, but are only readily
apparent when the computer scans sequence alignments
-they allow for placing unknown organisms in the correct major phylogenetic group, and can be
useful for constructing genus and species-specific nucleic acid probes which are used exclusively
for identification purposes in microbial
ecology and diagnostics
- As the 16SrRNA is so highly conserved organisms are classified as separate species if their
sequences show less than 98% homology and are classified as different genera if their sequences
show less than 93% identity. Specific base sequences in the rRNA known as signature
sequences were
commonly found in particular groups of organisms
What level of classification does Staphylococcus represent?
Staphylococcus | |
Phylum: | Bacillota |
Class: | Bacilli |
Order: | Bacillales |
Family: | Staphylococcaceae |