Classification of Microorganisms Flashcards
1
Q
what is classification, phylogeny and taxonomy
A
- Classification: Organisation of organisms into progressively more inclusive groups on basis of phenotypic similarity or evolutionary relationships
- Phylogeny: Study of evolutionary history of organisms
- Taxonomy: Branch of science concerned with classification of organisms, grouped according to degrees of relatedness, enable identification and comparisons
- Bacterial Taxonomy: Incorporated multiple methods for identifying and describing new species, the polyphasic approach to taxonomy used three methods, phenotypic, genotypic and phylogenetic
2
Q
Describe elements of phenotypic classification
A
- Observable characteristics provide differentiable traits
- Morphology: Colony, cell size, shape, pattern of flagellation, presence of spore, inclusion bodies, capsules, s-layers, stalks / appendages, fruiting body formation
- Motility: Non-motile, gliding motility, swimming (flagellar) motility, swarming, motile by gas vesicles
- Metabolism: Mechanism of energy conservation (phototroph, chemoorganotroph, chemolithotroph), utilisation of individual C, N or S compounds, fermentation of sugars, N fixation
- Physiology: Temperature, pH / salt ranges for growth, response to oxygen (aerobic, facultative, anaerobic), presence of catalase or oxidase, production of extracellular enzymes
- Cell Lipid Chemistry: Fatty acids, polar lipids, respiratory quinones
- Cell Wall Chemistry: Presence or absence of peptidoglycan, AA composition of cross-links, presence or absence of cross-link inter-bridge
- Other Traits: Pigments, luminescence, antibiotic sensitivity, serotype, production of unique compounds
3
Q
Describe elements of genotypic classification
A
- Genome: Genetic composition of an organism, speciation of microorganisms, 1970’s
- Species posses a variety of individuals with different traits
- Sequence changes can be used as a molecular clock to estimate time since two lineages diverged.
- Major assumptions are that nucleotide changes accumulate in proportion to time, generally neutral and do not interfere with function, random.
- Most reliable if calibrated with evidence from geological record
4
Q
Describe elements of phylogenetic classification
A
- Evolutionary variation and analysis
- Genetic profile of an organism (genetic relatedness) using molecular biology methods
- Based on rRNA sequences present in all cells (16S rRNA prokaryotic, 18S rRNA eukaryotic)
- Most rRNA mutations are deleterious – very few mutations are neutral
- Evolution of 16S RNA is very slow and is a true reflection of an organisms evolutionary history
5
Q
Describe the history of classification systems over time
A
- 1735: Linnaeus classified living organisms into just two kingdoms, plants (algae) and animals (protozoa)
- 1857: Carl von Naegli placed bacteria and fungi into the plant kingdom
- 1937: Woese described 11 phyla of bacteria from analysis of rRNA genes isolated from cultured species.
- 1969: Robert Whittaker founded 5 kingdom system and bacteria were separated into the procaryotae and eukaryotes comprised other 4 kingdoms
- 1978: Carl Woese, three domain system (eukaryotes, bacteria and archaea)
- 1998: Analyses of rRNA genes from environmental samples as described by Norman Pace had revealed evidence for 36 bacterial phyla.
6
Q
What is the 3 domain system
A
- Organisms can be separated into 3 evolutionary groups, further divided into kingdoms
- Bacteria: All pathogenic prokaryotes and many non-pathogenic prokaryotes
- Archaea: Prokaryotes that do not have peptidoglycan in their cell walls
- Eukarya: Animals, plants, fungi and protists
- Origin: Woese used the nucleotide sequence of rRNA (SSU) and other RNA and protein sequences as an evolutionary chronometer
- rRNA Chronometer: Universally distributed across all organisms, it’s functionally similar between organisms (protein synthesis), sequences change slowly and sequences can be aligned between organisms
7
Q
What is nature microbiology and the tree of life
A
- Bacteria and archaea
- Incorporates new genomic data from uncultivated organisms into an expanded ‘tree of life’ (domain system)
- Reveals a striking number new lineages and microbial discoveries
- Number of major lineages without isolated representatives (can’t be cultured)
- Eukaryotes: Believed to be evolutionary chimaeras that arose via endosymbiotic fusion, probably involving bacterial and Archaeal cells
8
Q
What is scientific nomenclature
A
- 1735: Carolus Linnaeus established the system of scientific nomenclature now used worldwide
- Taxonomy: Life, domain, kingdom, phylum, class, order, family, genus species
9
Q
What is the difference between a species and strain
A
- Species: Groups of similar organisms within a genus, groups strains on the basis of genetic similarity
- Strain: Group of bacteria derived from a single cell, closely related strains constitute a bacterial species
10
Q
What is a microbiome / the human microbiome
A
- Microbiome: A functional collection of different microbes in a particular environmental system
- Microbiota: Describes the microbes in a microhabitat (often have unique microbiota), different microhabitats support difference microbes (skin, saliva, urogenital tract and gastrointestinal tract)
- Heat map provides knowledge of abundance / niches of strains / bacterial populations in body
- Human Microbiome: ~1013 microbes in human microbiome living in complex communities / microhabitats (skin, airways, oral, gastrointestinal, urogenital)
- Benefits: Development of biomarkers for predicting predisposition to disease, designing targeted therapies, personalised drug therapies and probiotics, establish symbiosis with host
- Microbiome Projects: Most bacteria cannot be cultured, however advanced sequencing (16sRNA) techniques allow for identification of different microbiota at different body sites
11
Q
Describe characteristic elements of prokaryotes
A
- Pre-nucleus, one circular chromosome (no nuclear membrane)
- No histones or organelles
- Peptidoglycan cell walls (bacteria), pseudomurein cell walls (archaea)
- Reproduce via binary fission
12
Q
Describe characteristic elements of eukaryotes
A
- True Nucleus, paired chromosome (nuclear membrane)
- Histones and organelles
- Polysaccharide cell walls
- Reproduce via mitotic spindle
13
Q
Compare archaea, bacteria and eukarya
A
- Cell type, cell wall, membrane lipids, first AA in protein synthesis, antibiotic sensitivity, rRNA loop, common arm of tRNA
- A: Prokaryotic, variation in composition, no peptidoglycan, branched C chains attached to glycerol via ether linkages, methionine, no, lacking, lacking
- B: Prokaryotic, contain peptidoglycan, straight C chains attached to glycerol via ester linkages, formylmethionine, yes, present, present
- E: Eukaryotic, vary in composition, contain carbohydrates, straight C chains attached to glycerol via ester linkages, methionine, no, lacking, present
14
Q
Describe characteristics of a virus, viroid and prion
A
- Viruses: Microorganisms not cells (informational parasite), consist of DNA or RNA core surrounded by protein coat (may be enclosed by a lipid envelope), replication only when a living host cell is present
- Kingdoms: Each have their own associated viruses, viruses from other kingdoms cannot infect others
- Prions: Small pieces of protein (infectious proteins), example (BSE / CJD)
- Viroids: Short pieces of naked infectious nucleic acids, cause plant diseases
15
Q
What are the major shapes of bacteria
A
- Coccus (round)
- Bacillus (rod)
- Pairs (diplococci, diplobacilli)
- Clusters (staphylococci)
- Chains (streptococci, streptobacilli)
- Star shaped (steel)
- Square (haloarcula)
- Coccobacillus (short rods)
