Lecture 3: Characteristics and Classification of Microorganisms Flashcards
Involves the study, not of a single cell, but of a population of identical cells
Microbial Identification
Prerequisite of microbial identification
pure culture
_______ means that the isolate is free from other organisms and therefore containing only one species of the organisms
Pure culture
it involves the study of the organism’s size, shape of cells, their arrangement, differentiation and identification of structures and organization
Microscopic characteristics
__________ organisms have morphological features that are generally stable w/ environmental changes compare to ________
Eukaryotic, prokaryotic
Enumerate factors that can result to variation in the morphological features of the microorganism
Changes in the temperature, pH, medium composition
A valuable tool in studying morphological features
Microscope
Enumerate the morphological features observed under the microscope (10)
cell shape, cell size, colonial morphology, cellular inclusions, spore morphology (location & enlargement), color, staining behavior, arrangement, mode of reproduction, internal structures
Enumerate the usual shapes of bacteria (6)
Coccus, rod, spirillum, spirochete, budding and appendaged bacteria, filamentous bacteria
three basic shapes of bacteria
coccus, bacilli and spiral
inherent characteristics of an organism
shape and the cell arrangement
The genus that exhibits coccus (round or spherical) form
Staphylococcus
The genus that exhibits bacillus or rod form
Bacillus
The genus that exhibits elongated form
Fusobacterium
The genus that exhibits curved for
Vibrio sp
The genus that exhibits comma form
Bdelvibrio
The genus that exhibits club rod form
Cornybacterium
The genus that exhibits helical form
Helicobacterium
The genus that exhibits corkscrew form
Borrelia
The genus that exhibits filamentous form
Frankia
The genus that exhibits spiral form
Spirillum
The genus that exhibit stalk
Caulobacter
Enumerate unique or unusual shapes of microorganisms (2)
Star and square
An example of microorganism with star-shaped cells
Stella
An example of microorganism with square-shaped cells
Haloarcula and Haloquadratum
Two representatives of microorganism with star-shaped cells
S. humosa and S. vacuolata
Cells of genus Stella are gram _____, _______ and ______
negative, nonmotile and asporogenic
Where does genus Stella commonly found?
Freshwater, soil , sewage in widely separated geographical areas
The genus Stella has a group of ____, with ______ star-shaped ________
flat, six-pronged, prosthecobacteria
____________ is an extreme halophilic archaeon
Haloarcula
Haloarcula appears in sheets of ____ cells often in the shape of a square or triangle
65
Haloarcula are characterized by their _______ of _____ shaped, gram ____ cells that grow optimally at ____ °C
box, rectangular, negative,
____________ extremely halophilic obligately aerobic archaeon
Haloquadratum
Optimum salt concentration and pH level that Haloquadratum grows
18% salt and neutral pH
One validly published species of Haloquadratum
Haloquadratum walsbyi C23T
Cells of Haloquadratum are gram ____ and ___ and ____ and can form _____ sheets.
negative, square, flat, large
Division patterns among cocci w/ a single division plane and the cells generally occur in pairs
Diplococci
Division patterns among cocci with a single division plane, but the cells remain attached to form chains of variable length.
Streptococci
Division patterns among cocci formed from two perpendicular division planes
Tetrads
Division patterns among cocci that is divided in three perpendicular planes to produce a regular cuboidal arrangement of cells
Sarcinae
Division patterns among cocci that is divided in more than 3 planes to produce a characteristic grape-like cluster of cells
Staphylococci
Division patterns among cocci with single/individual cells distinctly separated from other cells
Solitary
Two other genus that Streptococci pattern is seen
Enterococcus and Lactococcus
microbes with tetrads pattern
Micrococcus luteus
microbes with sarcinae pattern
Sarcina maxima
microbes with staphylococcus pattern
Staphylococcus aureus
Which division pattern among cocci is shown (with attached image)
Diplococci
Which division pattern among cocci is shown (with attached image)
Sarcinae
Which division pattern among cocci is shown (with attached image)
Staphylococci
Which division pattern among cocci is shown (with attached image)
Streptococci
Which division pattern among cocci is shown (with attached image)
Tetrads
The smallest bacterium is approximately ____ μm in size and viruses are more or less ____ μm
1 , 0.1
The largest known bacterium with 400-750 μm in diameter
Thiomargarita namibiensis
the bacterium that reach up to 600 μm in size
Epulopiscium fishelsonii
Unit of measure of the size of microorganisms
micrometers (μm)
The Israeli scientist who first discovered the Epulopiscium
Lev Fishelson
Where does Lev Fishelson first discovered the Epulopiscium?
inside the intestines of a brown surgeonfis
The Epulopiscium was initially classifies as a _____ because of its ______ size
protist, gargantuan
_________ _________ was discovered by Linn Montgomery
Epulopiscium fishelsoni
____________ _________ is the largest heterotrophic bacterium
Epulopiscium fishelsoni
The one who performed an rRNA analysis in Epulopiscium fishelsoni which confirmed that it is actually bacteria but not validly published according to list of prokaryotic names with standing nomenclature
Norman Pace
The largest bacterium that could reach a diameter of 750 μm that can be seen by a naked eye
Thiomargarita namibiensis
Thiomargarita namibiensis was 1st isolated from the ocean sediments in the continental shelf of the ___________
Republic of Namibia
_________ ______ is a colorless, sulfur and nitrate storing gram negative coccus (_____________)
Thiomargarita namibiensis, gammaproteobacterium
Thiomargarita means “______ _____” in reference to the appearance of the cells containing microscopic sulfur granules that scatter incident light resulting to the cells pearly luster.
sulfur pearl
______ ______ are granules of organic or inorganic material in the cytoplasmic matrix that are stainable and visible in light compound microscope
inclusion bodies
Inclusion bodies are usually enclosed by a _______ membranes that separates from the cytoplasmic matrix.
single-layer
Functions (including special functions) of inclusion bodies,
energy and/or carbon reserves, reduces osmotic stress, (magnetosomes) navigation, (gas vacuole) buoyancy
How does inclusion bodies reduces osmotic stress in the cell?
When the production of insoluble form of the inclusion body matches the amount of substances dissolved in the cytoplasmic matrix
examples of organic type of inclusion bodies that act as stored carbon and energy sources
glycogen (amlylopectin-like) and starch
glycogen (amylopectin-like) and starch are easily detected after staining the cells with what soln? what colors are manifested after staining and observed under light microscope?
iodine, dark-blue and brown bodies
The most common inclusion body of prokaryotes
Poly-β-hydroxybutyric acid
When does Poly-β-hydroxybutyric acids (PHB) are produced?
When there is an excess carbon source in the cells
Monomers of Poly-β-hydroxybutyric acid and its polymers are easily stained by what dye?what colors are manifested after staining and observed under light microscope?
Lipophilic dye like sudan black, black
___________ the only known non-protein nitrogen polymer in cyanobacteria
Cyanophycin or cyanophycin granule polypeptide (CGP)
Cyanophycin or cyanophycin granule polypeptide are produced by most cyanobacteria and a few heterotrophic bacteria such as _________
Acinetobacter sp
cyanophycin or cyanophycin granule polypeptide are produced by cyanobacteria cells during _______.
stress (during phosphate or sulfate starvation)
cyanophycin granule polypeptide can be visualized using a staining method based on the ______ _____ _____, according to Watzer et al. (2015)
arginine-selective sakaguchi reaction
These are bacterial compartments consisting of polyhedral protein shells filled with what enzyme
Carboxysomes, ribulose-1 5-bisphosphate carboxylase-oxygenase (RuBisCO)
The predominant enzyme in carbon fixation and the rate limiting enzyme in the Calvin Cycle and a carbonic anhydrase
ribulose-1,5-biphosphate carboxylase-oxygenase (RuBisCo)
The carboxysomes functions to restrict access of RuBisCo to ___, an alternative substrate for this enzyme, and this ensures that RuBisCo ______ rather than ____ ribulose biphosphate.
O2, carboxylates, oxygenates
Name 6 organic inclusion bodies
gas vesicles, crystal proteins, carboxysomes, cyanophycin, Poly-β-hydroxybutyric acid, glycogen/starch
A microorganism that forms crystal protein
Bacillus thuringiensis (Bt)
________ are pore-forming toxins used to control insect pests that range from caterpillars and beetles that infest crops to black flies and mosquitoes that transmit human diseases
crystal proteins / crystal toxin proteins
_____ are conical-shaped structures made of protein. They are impermeable to water and solutes but permeable to gases. Provides buoyancy for aquatic bacteria.
gas vacuoles
Microorganisms with gas vacuoles
Microcystis and Anabaena
Gas vacuoles appear as ___ ___ ___ under light microscopy
irregular bright inclusions
Name 3 inorganic inclusion bodies
magnetosomes, volutin, sulfur granules
Other term for magnetosomes
magnetic storage inclusions
This aids some bacteria to orient themselves within a magnetic field
Magnetosomes
Magnetosomes are made of intracellular particles of ___ ___ ___ or ________ _____ _______
oxide mineral magnetite (Fe3O4), sulfur-containing mineral greigite
True or false: magnetosomes are energy storage
False: allows only orientation for favorable conditions (where the oxygen concentration is low)
Other term for volutin granules
polymetaphosphate or metachromatic granules or polyphosphate reservoirs
inclusion bodies that are stored phosphate in the form of linear chains of inorganic pyrophosphate
volutin granules or polymetaphosphate or metachromatic granules or polyphosphate reservoirs
The staining dye that gives darker shade of blue in volutin granule
methylene blue
Volutin is derived from the specific epithet ________ ______ to which granules are particularly common
Spirillum volutans
Volutin granules are common to _____, especially _____, and in the ______
corynebacteria, C. diphteria, mycobacteria
this inclusion bodies are common in bacteria that uses hydrogen sulfide as electron source
Sulfur granules
Provide an example species of bacteria with sulfur granules
Thiomargarita namibiensis
9 structural, biochemical and physiological features of microorganisms
cell wall structure, cell wall lipids, whole cell composition, antigenic characteristics, photosynthetic and carotenoid pigments, growth requirements, metabolic characteristics, luminescence, antibiotic sensitivity
True or false: The Gram-negative bacteria have thicker peptidoglycan layer compared to Gram-positive bacteria
False
The simplest method to determine the characteristics of the bacterial cell wa
Gram staining
True or false: Gram positive bacteria retain the crystal violet – iodine complex (CV-I, primary and mordant dyes, respectively) in their thick peptidoglycan layer upon the addition of the decolorizer (75% ethanol) and won’t take up significantly the counterstain, safranin and retains the blue-violet color.
False: 95% instead of 75%
True or false: Gram negative bacteria are decolorized by ethanol due to its thin peptidoglycan layer. Gram negative cells will take up the red color of the counterstain.
True
______ _______ is used to describe the antibody response triggered by the antigens on a particular bacterium.
antigenic properties
True or false: When B pertussis antiserum, B parapertusis antiserum or saline is added to the suspensions. A positive result is indicated by no agglutination with one specific antiserum and by agglutination with saline
False: A positive result is indicated B agglutination with one specific antiserum and by NO agglutination with saline
Examples under antigenic characteristic
- Combination of known antiserum and unknown bacterium 2. Slide agglutination 3. ELISA 4. Western bl
ELISA stands for
Enzyme link immunoSorbent Assay
____ are the observable characteristics or traits of an organism which can be used in species differentiation
phenotype
These methods are often used in phenotypic analyses
Rapid ID kits and FAME
FAME stands for
Fatty acid methyl ester
Rapid ID kits are designed to test the _____, _____ ______, and subsequently determine the identity of a bacterium to certain level of accuracy.
nutritional, metabolic properties
Provide the FAME workflow (5 steps)
Bacterial culture, saponification and methylation, extraction, GC analysis peak naming and profile comparison to database, identification of bacteria by pattern recognition
Commonly employed molecular methods (5)
- direct gene and gene products 2. Comparison of proteins 3. Nucleic acid (G+C content and sequencing) 4. DNA-DNA hybridization 5. Genome finger printing (ribotyping)
______ ____ is a rapid approach for evaluating polymorphisms (genetic variation) b/w strains since it does not require lengthy process of sequencing.
genome fingerprinting
_______ are generally fragments of DNA generated from individual genes or whole genome
fingerprints
_________ is a discontinuous genetic variation resulting in the occurrence of several different forms or types of individuals among the members of a single species.
Polymorphism
______ a method of gene fingerprinting that exploits the unique DNA sequences of different organisms/strains.
ribotyping
provide the ribotyping workflow (6 steps)
- different strains of bacteria 2. extract DNA 3. cut DNA with restriction enzyme 4. do gel electrophoresis 5. transfer DNA to nylon filter 6. hybridize with DNA probes
what enzymes are used in restriction digest of DNA, wherein these genomic DNA is cut at specific sites and generates different lengths
restriction endonuclease enzymes
Provide the PCR amplification of the 16S rRNA gene (8 steps)
- Isolate DNA 2. Amplify 16S rRNA gene 3. Run on agarose gel to check for correct size 4. fluorescent dye labelling 5. sequencing 6 alignment of sequences 7. blast 8. generate phylogenetic tree
Provide phylogenetic tree generating programs
MEGA, ClustalW
MEGA stands for
Molecular Evolutionary genetic analysis
_______ ____ is a method of DNA sequencing based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication
sanger sequencing
______ ________ acts like a copying machine that produces lots of copies of DNA
PCR machines
________- is a visual chart generated during DNA analysis by electrophoresis
electropherogram
True or False: in electropherogram, a good peak will be recording 1 amino acids and two peaks rising together or very low peak signal will be recording a N or unknown amino acid
true
_________ finds regions of local similarity between sequences. This program compares nucleotide or protein sequence to sequence databases and calculates the statistical significance of matches. This also can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
BLAST
BLAST stands for
Basic local alignment search tool
_____ creates public databases, conducts research in computational biology, develops software tools for analyzing genome data and disseminates biomedical info etc
NCBI
______ simplest method in the determining the DNA base composition
mol % G+C
mol % G+C is determined by ____ _____ __ ___
Melting point of DNA
What type of chromatography is utilized in determining the melting point of DNA
High pressure liquid chromatography
True or False: the mol % G+C will be very far to the same in closely related organisms
False, mol % G+C will be very close to the same in closely related organisms
What does G+C content by more than about 10% mean in two organisms?
The genome of the two organisms have quite different base sequences, indicating that they are not closely related
Is it safe to assume that organisms with the same G+C content also have similar DNA base sequences?
No, because, two very different base sequences can be constructed from the same proportions of A+T and G+C base pairs
Other name for DNA-DNA hybridization
nucleic acid hybridization
_____ ______ directly compares the similarity of the genomes of the microorganisms to determine the relatedness or similarity b/w closely related strains
DNA-DNA hybridization
at what percent of the shared 16S rRNA gene sequence similarity it is suggested at which the DNA-DNA reassociation experiments should be done? why at this point it is being done?
98.7-99%, for testing the genomic uniqueness of a novel isolates
Determination of degree of hybridization: organisms identical
complete hybridization
Determination of degree of hybridization: organisms related
partial hybridization
Determination of degree of hybridization: organisms unrelated
no hybridization
The DNA segments whose identity is already known and used in hybridization are called ___ ___ ____ or ____?
nucleic acid probes, probes
DNA-DNA hybridization values ranging from 70-100% means
two strains belong to the same species
DNA-DNA hybridization values ranging from <70-25%
two strains belong to the same genus
DNA-DNA hybridization values ranging from <25-7%
two strains belong to the different genera
enumerate ecological properties with taxonomic significance (4)
1.life cycle patterns
2. nature of symbiotic relationship
3. ability to cause disease in the host
4. preferred habitat
