3: Microbial Diversity & the Tree of Life

why are bacteria the model system for heredity?

easy to use and manipulate

describe Griffiths experiment with Streptococcus pneumoniae (Strain S)

• something in Strain S kills mice

• mixing Strain S (heat killed) with Strain R still kills mice

• Avery-MacLeod-McCarthy showed that DNA from strain S was sufficient to cause Strain R to kill mice when DNA was transferred (transformed) from S to R

describe early versions of the tree of life (before Woese)

• monera (single celled organisms) were placed at the base of the tree

• based on comparing traits (visual) of organisms

• neglects microbial world

Woese’s modern tree of life

1. rRNA (genes that code for ribosomes) are remarkably conserved

2. present in all cells

3. functionally constant

4. long enough to make inferences on evolutionary relationships

LUCA

Last Common Universal Ancestor

• likely a form of extremophile that existed billions of years ago

why did they think LUCA was an extremophile?

Archaea and closest bacteria relatives are extremophiles

what technology lead to the breakthrough of Woese’s tree of life?

DNA sequencing technology

• isolated DNA from organisms

• made copies of rRNA gene by PCR

• sequence DNA

• anayze sequence

• generate phylogenic tree

list steps that led to formation of Woese’s Tree of Life

• isolated DNA from organisms

• made copies of rRNA gene by PCR

• sequence DNA

• anayze sequence

• generate phylogenic tree

all previous methods, including Woese tree, were built by isolating DNA from ____________

pure culture or species

use of rRNA genes allows researchers to isolate DNA from ________

environment

adding additional rRNA or other conserved genes allows for a tree with greater ____________

resolution

name for tree with greater resolution due to addition of rRNA or other conserved genes

concatenated tree

importance of resolution in concatenated tree

lots of processing power, helps find differences b/w closely related strains or species of bacteria

viruses break ________

the central dgma

was the finding of an Arsenic backbone in GFAJ-1 correct?

no

• glassware was contaminated with phosphorous

Woese’s Tree of Life explains everything except…

viruses

why would mitochondria be more closely related to bacteria than eukaryotes?

• have their own DNA (circular, like bacterial)

• aerobic respiration

• replicate independent of cell cycle

• double membrane indicates endosymbiotic theory (suggests ancestral relationship with bacteria)

why would the 1st experiment with S strains not be sufficient to say that DNA was the molecule of heredity/infection?

identified strain as being important, but did not isolate DNA within the strain

If I handed you a sample of water and said classify these microbes, how would you have done it in the 1500s, the 1700/1800s, and the 2000s, what would be the same and what would be different?

1500s -→ identify visually (classified as wee animacules)

1700-1800s → morphology

2000s → DNA sequencing, staining, electron microscopy

what do metagenomics allow for?

culture-independent study of microbes

seminal work was done in bacteria that led to understanding that …

DNA is the molecule of life

our phylogenetic understanding of how microbes and eukaryotes are related is fairly ________

recent