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Cassini Spacecraft found older terrainsand major fractures on moon Enceladus

Course crystalline ice which will degrade overtime.

Must be < 1000 years old!Organic compounds found in the fractures.Must be heated - required T > 100K (-173˚C)Erupting jets of water observed.Cause of eruptions not known….

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Mystery of Enceladus

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Lecture 17. Why Do You Need to Construct a Tree for Prokaryotes?  Trees as Frameworks

Drawing Trees

Trees can be drawn in different ways.Trees are assumed to branch dichotomously (branch in two).Trees show relationships.Branch lengths proportional to the amount of evolutionary change/rate. Relationships are inferred based on the sequence data

observed from extant organisms.Phylogenetic tree/Phylogeny shows evolutionary relationships.

root

rootroot

Sulfolobus

ThermofilumThermoproteus

pJP27pJP78

pSL22

pSL4

pSL50

pSL12Aquifex

ThermotogaThermomicrobium

Methanobacterium

ThermococcusMethanococcus

ARCHAEA

BACTERIA

EUCARYA

Thermus

EM17

Thermoplasma

OctSpA1-106

Methanothermus

OctSp92

Root

0.1 changes p er nucleotid e

Synechoccouschloroplasts

ClostridiumBacillus

CytophagaChlorobium

Agrobacterium

mitochondria

E. coliChromatium

Methanosarcina

Methanospirillum

Halobacterium

Marinemesophiles

Unrooted tree using 16S ribosomal RNA.

Most diversity is in the microbial world.

Is an evolutionary framework - can map traits onto the tree

Red lineages are thermophilic - all branch around the rootso early life lived at high temperatures

Independent lineages divergedinto low temperatures (blue).

Independent lineages ableto do photosynthesis (green).

Photosynthesis in Bacteria andEukarya/Eucarya.

Multicellular life arose late.

Tree of Life

1. Develop well resolved phylogenetic trees = evolutionary framework

2. Map traits (metabolic, morphological, habitat) onto the tree

3. Identify clades (groups that share an ancestor) with traits of interest

4. Compare appearance of traits with the geologic record

isotopic signatures, microfossils, etc.

5. Identify age constraints, determine which traits are ancient and derived

….Once you have one or two age constraints, a well-resolved tree will reveal

additional age constraints for sister and nested clades!

Mapping Traits Onto Trees

no aerobic growthaerobic growthequivocal

OctSpA1-106BH1BH60

QL3-43BH81BH92EM19

EM3BH3QL4-2

BSpN50

AquifexThermotoga

DeinococcusThermus

50 changes

-Proteobacteria

-Proteobacteria

-Proteobacteria

-Proteobacteria

Gram Positives(Low G+C)

Cyanobacteria

Green Sulfurs

Gram Positives (High G+C)

Green Non-Sulfurs

root toArchaea

******

***

Thermophilic Growth in Bacterial Domain

Euryarchaeota Crenarchaeota

mesophilicthermophilichyperthermophilic

≤2.35 Ga ≤2.35 Ga

First: hyperthermophilicThermophilic after 2.35 Ga(no cultured mesophiles)

First: hyperthermophilicThermophilic after 2.35 GaMesophilic growth after 2.52 Ga

Thermophilic Growth in Archaeal Domain

Just How Ancient is Thermophily?

100˚C

0˚C

Last

ste

riliz

ing

ast

eroi

d im

pact

time (billion years)

4.0 3.5

tem

pe

ratu

re

hot originof life

cold originof life

prebioticevolution

prebioticevolution

Miller & Lazcano, The Origin of Life-Did It Occur at High Temperatures?J. Mol. Evol., 1995

Origin of life could have occurred at any temperature.Something happened and last common ancestor was a thermophile.

-giant meteorite impact-random evolutionary accident-Panspermia-product of an early hot Earth

Reconstructing the Traits of Ancestors

SP

M

Gloeobacter violaceus

Cyanobium gracile

Synechococcus WH8102

Synechococcus WH7803

Prochlorococcus marinus

Synechococcus elongatus

Microcystis elabens

Microcystis holsatica

Synechococcus PCC6716

Leptolyngbya PCC7104

Leptolyngbya PCC7375

Synechococcus PCC7335

Halothece MPI96P605

Euhalothece MPI96N303

Cyanothece PCC7418

Halospirulina tapeticola

Spirulina subsalsa

Prochloron didemni

Pleurocapsa PCC7319

Dermocarpella incrassata

Myxosarcina PCC7312

Chlorogloeopsis PCC6912

Cylindrospermum PCC7417

Nodularia PCC73104

Nostoc PCC7120

Anabaena variabilis

Trichodesmium erythraeum

Planktothrix agardhii

Lyngbya PCC7419

Arthrospira platensis

1.2

1.3

1.6

1.9

0.9

1.0

3.0

2.1

1.6

4.9

5.7

6.1

8.7

6.8

4.4

6.1

6.6

10.2

6.1

5.1

2.5

6.7

8.4

8.3

7.8

8.1

SynP

ro

Syn.

elo

nga

tus

LP

P

PN

T

1.0

1.8

1.5

Th

ermosyn

echo

coccus

1.0

1.5

1.8

1.1

0.9

1.1

0.6

1.1

2.0

2.0

1.3

1.3

6.5

14.0

4.5

1.5

1.0

11.0

7.0

11.5

5.0

4.0

13.0

7.5

7.5

3.0

6.0

3.6

15.5

8.5

0.6-2.0

2.0-3.5

3.5-5.0

5.0-6.5

6.5-8.0

8.0-9.5

9.5-11.0

11.0-12.5

12.5-14.0

14.0-15.5

Cell Diameter (m)

Can reconstruct the size of the ancestors of major groups of organisms.

Modern cyanobacteria oftenhave large cells - identifyingfeature in the fossil record.Start seeing large diameterfossils with sheaths at ~ 2.0 m.

See fossil akinetes - resting stagestypical of the Nostocales at 1.7 Ga.

But early cyanobacteria allhad cell diameters < 2.0 m,around ~1.0 m.

Can Reconstruct Ecology

Early cyanobacteriaare unicellularcoccoids

Filaments arose later

Sheath has arisenmultiple times independently

Motility arose several times

Conclusion: traits tomake thick microbialmats not ancient.

Can Reconstruct Habitat

Earliest Cyanobacteria evolved in a freshwater environment. Several lineages have freshwaterancestors that then colonized marine environments.

Traits that are NOT Old/Ancient in the Archaeal Domain

≤ 2.32 Ga

d. NO3- reduction

can’t reduce NO3-

can reduce NO3-

≤ 2.32 Ga

≤ 2.32 Ga

a. SO42- reduction

can’t reduce SO42-

can reduce SO42-

≤ 2.32 Ga

Euryarchaeota Crenarchaeota

Traits that are NOT Old/Ancient in the Archaeal Domain, cont.

Euryarchaeota Crenarchaeota

≤ 2.32 Ga

can’t oxidize S˚

can oxidize S˚

f. S˚ oxidation

≤ 2.32 Ga

can’t oxidize sulfides

can oxidize sulfides

e. Sulfide oxidation

≤ 2.32 Ga≤ 2.32 Ga

Traits that ARE Old/Ancient in the Archaeal Domain

≤ 2.32 Ga

c. S˚ reduction

can’t reduce S˚

can reduce S˚

≤ 2.32 Ga

≤ 2.32 Ga

g. H2 oxidation

can’t oxidize H2

is a methanogen

can oxidize H2 ≤ 2.32 Ga

Euryarchaeota Crenarchaeota

Evolution of Habitat Traits in the Archaeal Domain

terrestrial/freshwater

marine

Habitat

≤ 2.32 Ga≤ 2.32 Ga

Acidophily

neutrophile (>pH 6)

acidophile (pH 4-6)

extreme (pH <4) acidophile ≤ 2.32 Ga≤ 2.32 Ga

Euryarchaeota Crenarchaeota

early: neutrophileslater: extreme acidophiles

early: acidophileslater: extreme acidophileslater: neutrophiles

early: marinelater: terrestrial (freshwater)

early: terrestriallater: marine

Summary of Reconstructed Ancient Habitats

Euryarchaeota:Temperatures > 80˚CNeutral pH, marine environmentMethanogen

Crenarchaeota:Temperatures > 80˚C

Slightly acidic, terrestrial environmentProbably a sulfur reducer

LCA

Crenarchaeota(terrestrial solfatara)

Euryarchaeota(marine hydrothermal vent)

Bacteria(terrestrial near-boiling

silica depositing spring)

We Have Three Major Microbial Lineages Because TheyAll Trace Back To Three Hydrothermal Ecosystems

Power of Frameworks

Not only reconstruct early traits of microorganisms.Can compare with the geologic record to identify when major

groups of microbes arose.How did origin of new microbial groups change the chemistry

of the early Earth, co-evolution of Earth and life.

1000 changes

Aquifex

Thermotoga

Deinococcus

Thermus

Green Non-sulfur Bacteria

High G + C Gram Positives

Cyanobacteria

Green Sulfur Bacteria

Low G + C Gram Positives

Proteobacteria

Clade One

Clade Two

with multiple genes from whole genome sequences

~2.7 Ga

~2.5 Ga

2.4 Ga

2.3 Ga

Lecture 18. Diversity of Microbial Life.  What Do Microbes Need to Survive?  Energy and

Metabolism.  Extremophiles, Photosynthesis, and Chemosynthesis.

reading: Chapter 6