Classification of Microorganisms Flashcards
Define Taxonomy
The science of the classification of organisms. Taxonomy’s goal is to show relationships among organisms, and allows us to identify them.
Define Phylogeny/ Systematics
The evolutionary history of a group of organisms; phylogenic relationships are evolutionary relationships.
Discuss the limitations of the 2-kingdom classification system.
As more information came into picture about various groups of plants and organisms, this system was found to be inadequate. The two kingdom system of classification was not suitable as due to a large diversity of among the organisms.
The main demerits of the system are:
Some protozoans like Euglena possess characters of both plants and animals, they are not classified in a particular group.
There is no proper distinction between prokaryotes and eukaryotes. Like in the case of bacteria without a nuclear envelope and cellular organelles are placed in the plant kingdom.
In the system both photosynthetic and non-photosynthetic organism are placed together in the kingdom plantae. For example the fungi lack chlorophyll and are saprophytic in nature, they are placed in the plant kingdom.
Organisms like the lichens do not fall either in the animal or plant kingdom.
Organisms like the diatoms are place under the plant kingdom while the protozoans are placed under the animal kingdom, these organisms are of the same level of organization and they reproduce by fission yet they are placed in different kingdoms.
Some organisms possess characters of both plants and animals like Euglena and Chlamydomonas, so they can belong to any kingdom.
Modes of nutrition considered in this system are assimilation and ingestion, absorption type of nutrition is not recognized.
How did Linnaeus contribute to the classification of microorganisms?
developed the 2 kingdom classification system and binomial nomenclature.
How did Whittaker contribute to the classification of microorganisms?
developed the 5 kingdom classification system and placed prokaryotes in their own kingdom, eukaryotes made up the other 4 kingdoms
How did Woese contribute to the classification of microorganisms?
He suggested to elevate the 3 cell types above kingdoms into domains.
Discuss the advantages of the 3-Domain system.
Developed by Carl Woese in 1978 the Three Domain system is based on modern molecular evidence, and uses the category Domain as a Superkingdom to emphasize the extremely ancient lineages that exist among prokaryotes and protista, and the relatively recent relationships of multicellular organisms.
What are the characteristics of the bacteria domain?
Prokaryotic
Contains peptidoglycan cell wall
Membrane lipids are composed of straight carbon chains attached to glycerol by ester linkage.
First amino acid in polypeptide chain: Formylmethionine
Sensitive to antibiotics
has rRNA loop
has common arm of tRNA
What are the characteristics of the archaea domain?
Prokaryotic
No peptidoglycan in cell wall
Membrane lipids are composed of branched carbon chains attached to glycerol by ether linkage.
First amino acid in polypeptide chain: methionine
Not sensitive to antibiotics
No rRNA loop
No common arm of tRNA
What are the characteristics of the Eukarya domain?
Eukaryotic
Contains no cell wall (animal); if cell wall is present it is made of carbohydrates (plant).
Membrane lipids are composed of straight carbon chains attached to glycerol by ester linkage.
First amino acid in polypeptide chain: methionine
Not sensitive to antibiotics
No rRNA loop
has common arm of tRNA
Taxa
Subdivisions used to classify organisms (singular, taxon)
ex. domain, kingdom, phylum
Systematics
The science of organizing groups of organisms into a hierarchy.
Molecular clock
An evolution timeline based on nucleotide sequences in organisms; The molecular clock is a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA or amino acid sequences for proteins.
All organisms evolved from _____________.
cells formed over 3 billion years ago.
Conserved DNA
DNA passed on from ancestors is described as conserved.
The domain Eukarya includes what 4 kingdoms?
Plantae
Fungi
Animalia
Protists
What do the domains Archaea and Bacteria have in common?
they are both prokaryotic
When were bacteria separated into the kingdom prokaryotae?
in 1978; 2 types of prokaryotes found, prokaryotic relationships were determined by rRNA sequencing
When were organisms divided into 5 kingdoms?
in 1969
How are living organisms currently classified?
into 3 domains ; a domain can be classified into kingdoms.
How are organisms classified?
Organisms are grouped into taxa according to phylogenic relationships (from a common ancestor)
How is information demonstrating the relationships between eukaryotes obtained?
information for eukaryotic relationships is obtained through the fossil record.
How is information demonstrating the relationships between prokaryotes obtained?
prokaryotic relationships are determined by rRNA sequencing. Because most prokaryotes do not leave behind fossil evidence.
Phylogenic Tree
A phylogenetic tree or evolutionary tree is a branching diagram or “tree” showing the inferred evolutionary relationships among various biological species or other entities—their phylogeny—based upon similarities and differences in their physical or genetic characteristics.
According to scientific nomenclature how are organisms named?
each organism is assigned 2 names, or a binomial; a genus and specific epithet or species.
Why are scientific names used?
because there are millions of organisms, common names can be used for 2 different species and can become confusing. Common names can also be in different languages. Because the organism has two names that are latinized it allows scientists worldwide to share information efficiently and accurately.
Differentiate culture, clone and strain.
a strain is a group of bacteria derived from a single cell, bacteria grown in media are called a culture and a pure culture is often a clone (a population of cells derived from a single cell). A clone can sometimes contain different strains which are indicated by numbers and letters following the species name.
List the major characteristics used to differentiate the 3 kingdoms of multicellular eukarya.
Fungi: absorptive chemoheterotrophs that develop from spores or fragments of hyphae
Plantae: Multicellular photoautotrophs
Animalia: Multicellular ingestive heterotrophs
Define protist
a unicellular or simple multicellular eukaryotes ; usually protozoa and algae. They are currently being assigned to kingdoms.
Genus
The first name of a scientific (binomial) name; The taxon between family and species.
Specific epithet
The second or species name in a scientific binomial
eukaryotic species
a group of closely related organisms that can interbreed with each other but do not breed with individuals of another species
How is the taxonomic hierarchy organized? What are the major taxa?
- Species
- Genus
- Family
- Order
- Class
- Phylum
- Kingdom
- Domain
What is the biological definition of family?
a group of related genera
Prokaryotic species
a population of cells with similar characteristics; prokaryotes reproduce asexually and utilize horizontal gene transfer
Closely related strains make up a ________________.
Bacterial species
Clades
a group of organisms believed to have evolved from a common ancestor
Why are viruses not classified in any of the 3 domains?
they are acellular and cannot grow outside of a host.
Viral species
A population of viruses with similar characteristics (morphology, genes, enzymes) that occupy a particular ecological niche (host).
Compare and contrast classification and identification.
Classification helps to identify a microorganism, once an organism is identified it can then be placed into a class. Microorganisms are identified for practical purposes, they are not necessarily identified by the same techniques by which they are classified.
Explain how staining and biochemical tests are used to identify bacteria.
Staining enhances morphological features which can be used to identify microorganisms. The presence of certain enzymes are detected by biochemical tests which also help to identify microbes.
Differentiate western blotting from Southern blotting.
Western blotting is a serological test which involves a technique that uses antibodies to detect the presence of specific proteins separated by electrophoresis. Southern blotting is a techniques that uses DNA Probes to detect the presence of a certain DNA in restriction fragments separated by electrophoresis; both use electrophoresis but one detects proteins and the other DNA.
Explain how serological tests and phage typing can be used to identify an unknown bacterium.
Serological tests involve reactions of microorganisms with specific antibodies; antibodies will only react to their specific antigen, if a reaction between the antibody and the antigen occurs then the identity, strain and species of the bacterium can be determined. Phage typing distinguishes certain types of bacterial species and strains by determining their susceptibility to various phages.
Southern blotting, DNA chips, and FISH are examples of _________________________.
nucleic acid hybridization techniques
Medical microbiology
The branch of microbiology dealing with human pathogens
Rapid identification methods
Bacterial identification tools that preform several biochemical tests simultaneously, to identify bacteria within 4-24 hrs.
Numerical Identification
Bacterial identification schemes in which test values are assigned a number. A tube with 15 biochemical tests is inoculated and then the tube is observed for results and positive results are assigned a number, the numbers are then added together to make a code number. The code numbers are put together to and compared to a computerized listing to identify the bacterium.
Serology
Involves reactions of microorganisms with specific antibodies that detect specific antigens: Combine known anti-serum with unknown bacterium
Useful in determining the identity of strains and species, as well as relationships among organisms.
Examples:
Slide agglutination
ELISA
Western blot
antiserum
a blood derived fluid containing antibodies. (plural antisera) If an unknown bacterium is isolated in a pateint it can be tested against known antisera and often is identified quickly.
Slide agglutination test
a method of identifying an antigen by combining it with a specific antibody on a slide. A positive result is indicated by agglutination caused by interactions between antibodies and specific antigens.
serological testing
Techniques for identifying a microorganism based on its reaction with antibodies. Can differentiate species and strain.
Serovars/ Serotypes
A variation within a species
Biovar
A subgroup of serovars based on biochemical or physiological properties; also called a biotype.
ELISA
(enzyme-linked immunosorbent assay) A group of serological tests that use enzyme reactions as indicators.. This test is widely used because it is fast and can be read by a computer scanner. It looks for particular antigens in patient’s sample.
Bacteriophages
phage- a type of virus that infects bacteria and usually causes lysis in its host bacterium. They are particular and usually infect only one species or strain of bacteria
FAME
Fatty acid methyl ester; identification of microbes by the presence of a specific fatty acid; Fatty acid profiles can be used to identify some organisms.
DNA Probe
A short, labeled, single strand of DNA or RNA used to locate its complementary strand in a quantity of DNA.
Flow Cytometry
Flow cytometry measures physical and chemical characteristics of cells; A method of counting cells using a flow cytometer, which detects cells by the presence of a fluorescent tag on the cell’s surface.
DNA Base composition
The moles-percentage of guanine plus cytosine in an organism’s DNA; the percentage of GC pairs in the nucleic acid of cells can be used the classification of organisms. Helps scientists to determine relatedness among organisms. (high G+C and low G+C)
DNA Finger Printing
The number and sizes of DNA fragments (finger prints), or DNA fingerprints, produced by restriction enzymes digests are used to determine genetic similarities.
Nucleic Acid Amplification Tests
(NAATs) can be used to amplify a small amount of microbial DNA in a sample. The presence or identification of an organism is indicated by amplified DNA. Used when infectious agent cannot be cultured. Uses PCR, reverse transcription PCR and real time PCR.
Nucleic acid hybridization
Single strands of DNA, or DNA and RNA, from related organisms will hydrogen bond to form a double stranded molecule. The greater amount of base pairing between the 2 strands the greater the relatedness between the 2 organisms.
Examples of Applications:
Southern blotting
DNA chips
FISH
DNA chip/ Microarray
DNA probes are attached to a glass surface, used to identify nucleotide sequences in a sample of DNA. Can quickly identify a pathogen by identifying a gene that is unique to that pathogen. A sample of DNA is labeled with fluorescent dye and is added to the chip, hybridization between DNA probe and DNA in the sample is detected by fluorescence.
Ribotyping
the sequence of bases in ribosomal RNA can be used in the classification of organisms. Used to determine the phylogenic relationships between organisms. rRNA changes little over time.
Florescent In Situ Hybridization
Fluorescence in situ hybridization (FISH) is a cytogenetic technique that uses fluorescent probes that bind to only those parts of the chromosome with a high degree of sequence complementarity. FISH is used to determine the identity, abundance and relative activity of microorganisms in an environment and can be used to detect bacteria that have not yet been cultured.
looks at particular sequence of DNA or RNA
used in diagnostics to test for diseases like lupus.
Dichotomous key
an identification scheme based on successive paired questions; answering one question leads to another pair of questions, until an organism is identified.
What is the difference between dichotomous keys and cladograms?
Dichotomous (means cut in 2) keys are used for the identification of organisms and cladograms are used to show phylogenic relationships among organisms.
Cladogram
(clado- means branch) a dichotomous phylogenetic tree that branches repeatedly, suggesting the classification of organisms based on the time sequence in which evolutionary branches arose.
Why is classification and identification important?
it allows us to identify disease causing bacteria and provide proper treatment. Also it is Important for monitoring emerging infectious diseases determining new strains versus new species.
_____________ hierarchy shows ___________ relationships among organisms.
Taxonomic
phylogenetic
When was the all species inventory started and what is its purpose?
2001-2005
Kevin Kelly and Stewart Brand - the All-Species Inventory: The goal is to identify and name every living thing, all in a single human generation. This effort will be organized by the newly created All-Species Foundation, which has already raised $1 million for the project. What the moon shot did for technology, the All-Species Inventory hopes to do for ecology.
rRNA was used to divide all living things into 3 groups, why? what is unique about the rRNA of organisms in the same domain?
only three different types of rRNA, based on sequence differences) at the same time, rRNA within a group (called a Domain) is highly conserved (very similar among all organisms in that Domain).
Classification based on ________________.
grouping by similarities (inherited from a shared common ancestor) thus illustrates both the unity and diversity of life (diversity – descent with modification).
Archaea are more closely related to Eukaryotes than to other prokaryotes, based on rRNA sequence data, how can you tell?
Archaea and Eukaryotes are even on the same branch of the evolutionary tree
Eubacteria
true, “typical” bacteria
Archaea
atypical bacteria
Eukarya
nucleated organisms
Endosymbiotic theory
Symbiogenesis, or endosymbiotic theory, is an evolutionary theory that explains the origin of eukaryotic cells from prokaryotes. It states that several key organelles of eukaryotes originated as a symbiosis between separate single-celled organisms.
Culture
Grown in laboratory media
Clone
Population of cells derived from a single cell
Strain
Genetically different cells within a clone. Numbers and letters are used to identify strains (e.g. E. coli O157:H7 versus other strains)
Why are viruses not included in the classification scheme?
not placed in kingdom nor domain – not composed of cells – cannot grow without a host cell.
We still classify them based on nucleic acid sequence similarities, structural characteristics, enzymes, etc.
e.g. DNA versus RNA viruses; coronaviruses versus noroviruses
What are the kingdoms within the domain eukarya?
Animalia
Plantae
Fungi
Protista
- Grouped into clades based on rRNA
Protista
A catchall kingdom for eukaryotic organisms that do not fit other kingdoms
Fungi
Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments
Plantae
Multicellular; cellulose cell walls; usually photoautotrophic
Animalia
Multicellular; no cell walls; chemoheterotrophic
Classification
Placing organisms in groups of related species. Lists of characteristics of known organisms
Identification
Matching characteristics of an “unknown” to lists of known organisms.
Morphological characteristics are useful for __________.
Useful for identifying eukaryotes
Differential staining different types
Gram staining, acid-fast staining
What do Biochemical tests do?
Determines presence of bacterial enzymes
Antigen
In immunology, an antigen is a molecule capable of inducing an immune response on the part of the host organism, though sometimes antigens can be part of the host itself. In other words, an antigen is any substance that causes an immune system to produce antibodies against it.
usually some kind of a surface structure like a flagellum.
Phage typing
Identification of bacterial species and strains by determining their susceptibility to various phages.
How does a DNA chip work?
A DNA chip can be manufactured to contain many synthetic single strands of DNA sequences . Each DNA sequence is unique to a bacterial species
Unknown DNA from a patient sample is separated into single strands enzymatically cut and labeled with a fluorescent dye
The tagged DNA will bind only to the complimentary DNA on the chip. The bound DNA will be detected by its fluorescent dye and analyzed by a computer.
*used more for research than diagnostics
PCR
Polymerase Chain reactions can be used to amplify a small amount of microbial DNA in a sample. The presence or identification of an organism is indicated by amplified DNA detects specific genes in a patient’s sample, uses restriction enzymes on both the control and the patient’s sample. Because only DNA cut with the same restriction enzymes can anneal together.
Restriction enzyme digest
A restriction digest is a procedure used in molecular biology to prepare DNA for analysis or other processing. It is sometimes termed DNA fragmentation (this term is used for other procedures as well).
