Taxonomy Prokaryotes

Question 1

Who invented the binomial system of taxonomy?

Answer 1

Carl Linnaeus in 1700s

Generic + Specific Name –> usually descriptive

Taxonomists refine classifications

Did King Philip Come Over For Good Sushi

Question 2

General classification system categories

Answer 2

Phenetic (numerical) - overall similarity

Phylogenetic - evolutionary relationships

Question 3

Why does taxonomy of plants/animals not work for microorganisms?

Answer 3

Because the definition is based on organisms which can interbreed but most microbes reproduce asexually

Evolutionary history of microorganisms is very incomplete and dates back 3.5 byo

Question 4

Stromatolites are

Ancient vs. modern stromatolites

Answer 4

Microbial mats of layers of filamentous prokaryotes, sediments and ECM

Ancient stromatolites are dominated by anoxygenic bacteria whereas modern are dominated by oxygenic bacteria

Question 5

Subsurface vs. surface origin hypotheses

Evolutionary development stages:

Answer 5

Surface: primordial soup arose membrane enclosed self replicating cell with inorganic and organic materials inside
- but conditions would have been too unstable - theory against argument

Subsurface: life originated in hydrothermal vents - stable conditions, with steady supply of energy as H2S and H2

Theoretically: building blocks –> catalytic + self-replicating RNA, protein synthesis, DNA, lipid bilayer development and horizontal gene transfer —> LUCA –> bacteria + archaea
- began as chemoautotrophs and then produced enough O2 in the atmosphere that other heterotrophs appeared in different niches

Question 6

Why is it theorized early self-replicating system was RNA?

Answer 6

RNA can bind small molecules

RNA has catalytic activity (ribozymes)

RNA can be copied like DNA

But DNA is more stable

Question 7

Michael Adanson invented

Answer 7

Phenetic taxonomy 200 years ago

1) All characteristics of equal importance
2) Classify based on as many features as possible
3) Organisms grouped by similarity which is calculated as a similarity or Jaccard coefficient

Doesn’t work considering how vastly different similar lineages can be in catabolic pathways

Question 8

What is a Phenon?

Similarity coefficient?

Jaccard coefficient?

Answer 8

From Phenetic taxonomy, a group of organisms that share characteristics in common

Similarity coefficient: shared/tested characteristics

Jaccard coefficient: shared/total characteristics not shared

Question 9

How mutations affect evolutionary change

Answer 9

Adaptive mutation improve fitness of organism and increase survival

Silent mutations may be beneficial in new niches

Deleterious mutations are usually lost

Accumulation of mutations —> speciation

Question 10

Carl Woese

Comparitive rRNA sequencing

Answer 10

1970’s sequence small subunit rRNA in prokaryotes (16S) and eukaryotes (18S) –> established 3 domains of life and created phylogenetic taxonomy

1) Amplification of gene encoding SSU rRNA
2) Sequencing of genome of rRNA
3) Analysis of sequence in reference to other sequences

What is used today to infer phylogeny of prokaryotes and other microorganisms !

Question 11

Conserved vs. variable regions in SSU rRNA

Answer 11

Conserved regions include DNA which remains between different organisms whereas variable regions can be the sites of accumulated differences and neutral mutations (genetic drift)

Evolutionary relationship between organisms is correlated with number of accumulated mutations
- alignment of similar sequences allows for this

More differences —> longer time since divergence

Question 12

Why are eukaryotic cells chimeric?

Answer 12

similar lipids and energy metabolism to bacteria

transcription and translation machinery similar to archaea

phylogenetically more similar to ARCHAEA

Question 13

Hypotheses for formation of eukaryotic cell

Answer 13

1) Eukaryotes began as lineage with nuclei and then acquired mitochondria/chloroplats

2) Eukaryotes arose from association between H2-producing bacterium symbiont (become mitochondria) and H2-consuming archaea host
- archaea host later developed nucleus to protect DNA from bacteria

Question 14

Filamentous Actinobacteria

Answer 14

Ex. Streptomyces

hyphal growth - cytoplasm filament not separated by cross walls (coenocytic)

produce dessication resistant spores at tip of sprorophore

Question 15

Predatory bacteria

Answer 15

Ex. Bdellovibrio

Infects other bacterial cells, acquires nutrients from host cell, does not grow on agar plates

Does not target gram positive (no periplasm)

Question 16

Stalked bacteria

Answer 16

Ex. Caulobacter

Aquatic bacteria

Unique cell differentiation cell cycle: sedentary mother stalk and motile flagellated daughter cell

Fun fact: tip of stalk secretes stickiest substance known

Question 17

Obligate intracellular bacteria

Answer 17

Ex. Chlamydia

Grows only inside a host and produces:

Elementary bodies: infectious particles released from host cells

Reticulate bodies: intracellular active growth stage

Question 18

Polyphasic approach to taxonomy of bacteria and archaea

Answer 18

To classify different strains of the same species

1) Phylogenetic analysis (16S rRNA MLST sequencing)
2) Phenotypic analysis (motility, capsule, virulence)
3) Genotypic analysis (presence/absence of specific genes)

Question 19

rRNA MLST

Answer 19

MultiLocus Sequence Typing

Housekeeping genes from different species are sequenced and aligned to each other to compare

Can distinguish between very closely related strains

Question 20

Identification methods that are phenetic

Identification methods that are phylogenetic

Answer 20

Phenetic: morphology, physiology, biochemistry, GC ratio, DNA-DNA hybridization

Phylogenetic: fossil records, ribosomal RNA sequences, MLST, whole genome sequencing

Question 21

Methods of identifying an unknown microorganism (5) and what they are

Answer 21

Mostly used in diagnostic lab:
1) Morphology
2) Biochemical properties - ex. selective and differential mediums

3) 16S rRNA sequencing and MLST

4) Dichotomous key - layers of yes no questions to narrow down a species

5) Serotyping - use of antibodies in a bacterium to identify it, positive reaction –> agglutination
- addition of antibodies will bind specific antigen such as LPS (O), capsule (K), flagella (H), hemaglutinin 1 and neuraminidase 1 (H1N1)