5. Taxonomy - Bacteria (final content starts here) Flashcards
what are the 3 components of taxonomy?
- nomenclature
- classification
- identification
- what is the system used for nomenclature?
- developed by who? when?
- each organism is given which 2 names
- most names are _________ and derived from (which 2 languages) OR derived from WHAT
- animalcules were originally classified in which class?
- taxonomy is an ________ __________ science
- binomial system –> used to name all cellular organisms including microorgs (to make sure we’re talking about the same thing)
- Carl Linnaeus (1707-1778) 1750s
- generic name (genus) + specific name (species)
- descriptive, Latin or Greek, from name of disvoerer
ie Salmonella typhi from Daniel Salmon + typhoid fever - Saccharomyces cerevisiae (sugar - fungus - beed)
- staphylococcus aureus (cluster - grain/berry - golden)
- Chaos! along with agents of fermentation, spermatozoa, cause of syphillis
- ever changing science! actinomyces pyogenes renamed twice recently bc no agreement on what genus it comes from
- plants, animals and organisms are capable of ___________ reproduction
- a species is a group of organism that can ______________
- do microorgs do sexual or asexual reproduction?
- so how to define species in microorgs? (2) + sub
- sexual! can mate, make babies and babies are fertile
- interbreed!
- some are capable of sexual (combination of genetic material from 2 individuals) BUT most reproduce asexually
- no clear definition –> so 2 methods for classification
1) overall similarity (phenetic) - morphology (but a lot look the same)
- physiology
- biochemistry (what they do)
2) evolutionary relationship (phylogenetic) –> who comes from who (DNA) - fossil record, ribosomal RNA sequences, multi-locus sequences typing, whole genome sequencing
*evolutionary history of microorgs is very incomplete
- how old is Earth?
- first evidence of microbial life can be found in _______, how many years ago?
- what are stromatolites?
- compare ancient and modern stromatolites
- 4.5 billion years old
- rocks! 3.5 billion years old
- microbial mats consisting of layers of filamentous prokaryotes, sediments and extracellular matrix –> living + growing!
*similar structure found in rocks 3.5 billion years old or younger - Anoxygenic phototrophic filamentous bacteria formed ANCIENT stromatolites.
- Oxygenic phototrophic cyanobacteria dominate MODERN stromatolites.
ORIGIN OF CELLULAR LIFE:
- Early Earch was _______ and much hotter/colder than present day
- first biochemical compounds were made of _______ systems that set the stage for origin of life
what are the 2 origin hypothesis? which one is most likely wrong?
- ANOXIC + much hotter
- first biochemical compounds (ie aa, lipids, nucleotides) –> made by abiotic systems (ie no life)
*all life originated from the same pool of cells (prot, DNA, RNA)
SURFACE ORIGIN HYPOTHESIS:
The first membrane-enclosed, self-replicating cells arose out of primordial soup rich in organic and inorganic compounds in ponds on Earth’s surface
- Dramatic temperature fluctuations (day/night) and mixing from meteor impacts, dust clouds, and storms argue against this hypothesis –> ie probably wrong
SUBSURFACE ORIGIN HYPOTHESIS
- Life originated in hydrothermal springs on the ocean floor
- Conditions would have been more stable (much more than surface origin)
- Steady and abundant supply of energy (e.g., H2 and H2S) was likely available at these sites
*creates deposition of minerals + chimney of hot water going up and meeting cold water
ORIGIN OF CELLULAR LIFE
- describe the order of events from origins of cellular life (when) to humans (7 steps ish)
KNOW THIS!
- 4.0 BYA: origins of cellular life
- divergence of bacteria and archaea (chemolitotrophs bc probs not enough organic material)
- 3.5 BYA: origins of anoxygenic photosynthesis (leave bottom of ocean to top = light!)
- 3.0 BYA: origins of cyanobacteria and oxygenic photosynthesis (chemoheterotrophs came later bc need enough organic material) –> started producing massive waste = O2
- 1.5-2.0 BYA: evidence of multicellular eukaryotes (from symbiotic relationship btw archaea and bacteria –> forms mitochondria in eukaryotes)
- 0.5 BYA: start of cambrian explosion (spread of plants) (end of proterozoic eon)
- phanerozoic eon: origins of first animals + extinction of dinosaurs + humans yay
ORIGIN OF CELLULAR LIFE
early forms of _____________ and ___________ metabolism would have supported production of large amounts of __________ compounds
- ________ material provided abundant, diverse and continually renewed source of __________ __________ ________, stimulating evolution of various ____________ metabolisms
- chemoautotrophic and photoautotrophic metabolism –> organic compounds!
- organic material –> source of reduced organic carbon –> various chemoheterotrophic metabolisms
what is the traditional method for classification of prokaryotes introduced 200 years ago? by who?
- describe its 3 characteristics
- give examples of phenotypic characteristics of taxonomic value
Phenetic: numerical taxonomy! by Micheal Adanson
- All characteristics should be considered of equal importance (unbiased).
- Classification should be based on as many features as possible.
- Organisms should be grouped based on overall similarity.
ex: colony morphology, gram reaction, ether or ester linkage, flagellation, spores, lactose metabolism, DA, antibiotic sensitivity…
PHENETIC:
what is calculated when you use numerical taxonomy? (2)
- how to illustrate?
- what is a phenon?
- method used today&
- A large number of characteristics are determined for each organism and the similarities between pairs of microorganisms are then calculated and expressed as the similarity coefficient (S) or the Jaccard coefficient (SJ).
S = number shared/total number tested
SJ = number shared / (total tested - number negative for both) - Construction of dendrogram to illustrate the relationship between the species. (if A and B have a S of 0.95, draw lines ish) –> if score is >0.85 –> same species VS if score > 0.75 = same genus)
- Phenon: group of organisms that have characters in common.
- not used today! bc microorgs exchange plasmids! so their characteristics don’t necessarily come from their ancestry
what is a mutation? give examples
- may be ________, _________ or __________ BUT most changes are ___________
- evolutionary pressure (stress) selects or discards mutation –> give 4 examples
- mutation = change in the genome of an organism –> ie nucleotide change, insertion, deletion, Gene duplication, gene loss and horizontal gene transfer (acquisition of a whole new gene from another organism)
- Genetic change may be silent, deleterious or beneficial (new function or change in activity) BUT most changes are neutral.
a) Adaptive mutations improve fitness of an organism, increasing survival in its environment (ie antibiotic resistance)
b) Silent mutations may be beneficial in other environments allowing the microorganism to colonize new niches (ie no effect in condition A but useful in condition B)
c) Deleterious mutation are usually lost (bc leads to death)
d) Accumulation of mutations may lead to speciation (rise of a new species).
PHYLOGENETIC:
- what did Carl Woese (1970s) say we should do? –> function?
- established what?
- provided what for bacteria?
*says we should look at DNA sequences + mutations! to help classify species
- sequencing of small subunit rRNA (SSU rRNA): 16S rRNA in prokaryotes and 18S rRNA eukaryotes
FUNCTION: rRNA sequencing is used to infer phylogeny of prokaryotes and other microorgs
- established presence of 3 domains of life: bacteria, archaea and eukarya
- provided unified phylogenetic framework for bacteria!
SSU rRNA
- mutations usually occur in conserved regions or variable regions of 16S rRNA?
- evolutionary relationship btw 2 organisms directly correlated to WHAT?
- few vs many differences –> mean they are closely related or not?
- conserved regions don’t change much bc interacts with other parts of ribosomes + if there are changes there, they would be deleterious = won’t be kept
SO accumulation of NEUTRAL mutations through time in variable regions (what connects conserved regions) –> genetic drift! - correlated to the number of mutation that have accumulated in each one
- FEW differences = closely related (ie E.coli and salmonella)
- MANY differences = diverge a long time ago (bacteria and archaea)
- universal phylogenetic tree:
are there 2 or 3 domains of life?
2 domains of life! bacteria and archaea!
- eukarya = descendants of archaea (well actually partnership btw bacteria and archaea)
- what is a well supported hypothesis for origin of eukaryotic cells?
- implies that mitochondria and chloroplasts arose from WHAT
- eukaryotic cell is _________ –> explain (2)
- eukaryotic cell is phylogenetically closer to bacteria/archaea?
- ENDOSYMBIOSIS!
- implies that mit and chloroplasts arose from SYMBIOTIC association of prokaryotes within another type of cell (primitive eukaryote/aka archaea)
*ie proto-eukaryote/archaea –> give rise to nucleus and organelles - first endosymbiotic event: consumed aerobic bacteria that evolved into mit –> modern heterotrophic eukaryote
- 2nd event: consumed photosynthetic bacteria that evolved into chloroplasts –> modern photosynthetic eukaryote
CHIMERIC!
- Eukaryotes have similar lipids and energy metabolisms to Bacteria
- Eukaryotes have transcription and translational machinery most similar to Archaea.
- Phylogenetically closer to Archaea.
do all bacteria have the same type of metabolism?
NO! all scattered in the tree (schéma with colored dots!) –> types of metabolism NOT restricted to each bacteria/species
EXAMPLES OF BACTERIA
a) streptomyces is a what?
- _______ growth
- produce what kind of spores? explain
- produce a lot of what?
b) Bdellovibrio is a what?
- how does it acquire nutrients?
- grows on agar plates?
- infects what type of bacteria?
- what is special morphologically?
a) STREPTOMYCES:
- filamentous actinobacteria
- hyphal growth (filament of cytoplasm usually not separated by cross-walls (ie not separated by cell wall ish)) –> becomes furry
- produce dessication (no more water) resistant spores at tip of an elevated structure called sprorophore
- a lot of antibiotics!!
b) BDELLOVIBRIO
- Predatory bacteria
- acquire nutrients from host cells! –> pathogen = infect other bacterial cells
- does NOT grow on agar plates –> adapted to parasitic lifestyle (ie lives in host)
- infects gram negative (attach to prey, go in periplasm and grow) –> VS doesn’t infect gram positive bacteria bc don’t have outer membrane
- very long flagella!!
EXAMPLES OF BACTERIA
c) Caulobacter
- is a what?
- found in what environment?
- unique cell cycle that includes what? describe
- what is a cool fact?
d) CHLAMYDIA
- is a what?
- grows only where?
- 2 cell variants: explain
- 2 spdcies
c) CAULOBACTER
- stalked bacteria
- aquatic environment
- includes cell differentiation! sedentary stalked mother cell + motile flagellated daughter cell
- has a flagellum to swim + a pilli/stalk (?) –> tip of stalk produces the stickiest substance known! lots of studies to try to use the glue instead of stitches
d) CHLAMYDIA
- obligate intracellular bacteria
- grow only inside host cells
1) elementary bodies: infectious, release from host cells, small, not metabolically active –> goal = transmit infection btw cells
- differentiate into reticulate bodies
2) reticulate bodies: intracellular, active growth
- bigger + metabolically active
- chlamydia trachomatis –> gives STD
- chlamydia pneumoniae –> gives pneumonia
ARCHAEA
- where are they usually found? they are _________philes
- extremophiles!
- found in where they make salts (hyperhalophiles)
- in molten sulfur, in hot springs…
- found in polyextreme geothermal Dallol area –> very hot, salty and acid conditions –> super bright colors from the archaea living there
BACTERIAL AND ARCHAEAL TAXONOMY
- bacterial taxonomy incorporates multiple methods for classification of old and new __________
- there is also a need to classify different WHAT
- polyphasic approach to taxonomy uses 3 methods + sub!
- old and new species!
- different strains of same species
1) PHYLOGENETIC ANALYSIS
a) 16S rRNA –> to the genus level
b) multi-locus sequencing typing: several different “housekeeping genes” (shared by all orgs, ie DNA polymerase) from a species are sequenced and aligned to the respective sequences of other individuals of the same species –> Has sufficient resolving power to distinguish between very closely related strains
2) PHENOTYPIC ANALYSIS
- motility, capsule, virulence
3) GENOTYPIC ANALYSIS
- presence/absence of specific genes, etc.
3rd branch of taxonomy = WHAT
- first step/goal ish? –> how? (5)
- what are 2 methods for identification?
IDENTIFICATION!
- Identification of an unknown microorganism will depend on the comparison of its properties with those of organisms that have already been classified and named (Type strains).
- Morphology
- Biochemical properties
- 16S rRNA sequencing.
- MLST
- Whole genome sequencing
*method depends on what you’re looking for!
1) dichotomous key
2) serotyping
*also biochemical methods to help with dichotomous key
IDENTIFICATION:
1) dichotomous key
- describe!
*use of biochemical methods –> 3 examples
2) serotyping
- based on what? –> give examples
- define antibody
- positive reaction?
- fast?
1) DICHOTOMOUS KEY
- ie you know that 5-6 possible bacteria can cause pneumonia so prepare a tree/branches to identify
- ie gram reaction –> negative or positive –> each go to their own branch where you look at glucose fermentation or morphology… etc –> gives you possibility of 8 bacteria depending on results
*use of BIOCHEMICAL METHODS to test for phenotypes
- ie MacConkey agar (lactose fermentation)
- catalase test
- API strips: sets of differential methods and biochemical tests –> not used anymore bc as expansive as doing genome sequencing
2) SEROTYPING:
- based on binding of specific antibody to surface structure! very specific
- ie LPS (O serotypes), capsule (K serotypes), Flagella (H serotypes)
*ie E. coli O157:H7
- antibodies = molecules of the immune system that recognize and bind to molecule on the surface of a microorganism or to secreted proteins.
- positive reaction = agglutination! (precipitate, masses are formed!)
