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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 8 Lecture 8 Introduction to Microbial Diversity Part 2 BIS 002C Biodiversity & the Tree of Life Spring 2014 Prof. Jonathan Eisen 1
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BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Jan 19, 2017

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Page 1: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Lecture 8

!

Lecture 8 !

Introduction to Microbial Diversity Part 2

!!

BIS 002C Biodiversity & the Tree of Life

Spring 2014 !

Prof. Jonathan Eisen

1

Page 2: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Where we are going and where we have been

• Previous Lecture: !7: Microbial Diversity

• Current Lecture: !8: Microbial Diversity part 2

• Next Lecture: !9: Symbioses

2

Page 3: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Microbial Diversity

• Seven major lineages of eukaryotes

• Alveolates

• Stramenopiles

• Rhizaria

• Excavates

• Amoebozoans

• Plantae

• Opisthokonts

• Complications 1: Endosymbioses

• Complications 2: Lateral gene transfer3

Page 4: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Microbial Diversity

• Seven major lineages of eukaryotes

• Alveolates

• Stramenopiles

• Rhizaria

• Excavates

• Amoebozoans

• Plantae

• Opisthokonts

• Complications 1: Endosymbioses

• Complications 2: Lateral gene transfer4

Page 5: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Oversimplification of eukaryotic phylogeny

5

Page 6: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Phylogenetic diversity of eukaryotes

• As with bacteria and archaea, phylogeny of major groups based largely on molecular data.

• However, non-molecular data more useful for studies of eukaryotic phylogeny

• Major groupings, and the relationships among groups, still being resolved

• All organisms other than plants, animals and fungi are sometimes referred to as protists or microbial eukaryotes (note - paraphyletic)

6

Page 7: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 7

Alveolates

Alveolates Have alveoli or

sacs beneath surface of plasma membrane.

All are unicellular; many are photosynthetic.

Page 8: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

•Most are marine and are important photoautotrophic primary producers

•Mixture of pigments give them a golden brown color.

•Have two flagella, one in an equatorial groove, the other in a longitudinal groove.

Alveolates: Dinoflagellates

8

Certium tenue

Coral symbiont

Page 9: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Clicker Question

9

Page 10: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Clicker Question

What is the different between photoautotrophy and photoheterotrophy?

!

• A: The source of electrons

• B: The source of carbon

• C: The source of energy

• D: All of the above

10

Page 11: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Clicker Question

What is the different between photoautotrophy and photoheterotrophy?

!

• A: The source of electrons

• B: The source of carbon

• C: The source of energy

• D: All of the above

11

Page 12: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Alveolates: Apicomplexans• All parasitic

• Have a mass of organelles at one tip—the apical complex that help the parasite enter the host’s cells.

12

Apical complex • Plasmodium falciparum- Malaria kills 700,000-2,000,000 people per year—75% of them are African children

Page 13: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Alveolates: Ciliates

13 Movement in a ciliate from the gut of a termite

• All have numerous cilia, the structure is identical to flagella.

• Most are heterotrophic; very diverse group.

• Have complex body forms and two types of nuclei.

Page 14: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 14

Stramenopiles

Stramenopiles Two flagella, with rows of tubular

hairs on the longer one.

Page 15: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

•All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine.

Stramenopiles: Brown Algae

15

A community of brown algae: The marine kelp forest

Page 16: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Stramenopiles: Diatoms

16

A colony of the diatom, Bacillaria paradoxa

•Unicellular, but many associate in filaments. •Have carotenoids and appear yellow or brown. •Excellent fossil record •Most are photoautotrophic •Responsible for 20% of all carbon fixation. •Oil, gas source

Page 17: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Stramenopiles: Oomcyetes

Phytophthora

Potato Late Blight

• Non-photosynthetic. • Are absorptive heterotrophs • Once were classed as fungi, but

are unrelated.

17Sudden Oak Death

Page 18: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Clicker Question

18

Page 19: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Clicker Question

The similarity in appearance of ooymcetes to fungi is an example of _______

!

• A. Homology

• B. Homoplasy

• C. Divergent evolution

• D. Monophyly

19

Page 20: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Clicker Question

The similarity in appearance of ooymcetes to fungi is an example of _______

!

• A. Homology

• B. Homoplasy

• C. Divergent evolution

• D. Monophyly

20

Page 21: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Rhizaria

Rhizaria Unicellular, aquatic, with long, thin

pseudopods.21

Page 22: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Rhizaria: Cercozoans

Some cercozoans are aquatic, others live in soil.

They have diverse forms and habitats.

One group has chloroplasts derived from a green alga by secondary endosymbiosis.

Euglyphid

22

Chlorarachnion reptans

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Rhizaria: Foraminiferans

Sand beaches in the tropics

• Secrete shells of calcium carbonate. • Discarded shells make up limestone. • Create some beach sands • Used to date & characterize sedimentary

rocks. • Some live as plankton, others at sea bottom. • Thread-like, branched pseudopods extend

through pores in the shell and form a sticky net that captures smaller plankton.

23

Page 24: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Rhizaria: Radiolarians

• Have thin, stiff pseudopods reinforced by microtubules.

• The pseudopods increase surface area for exchange of materials; and help the cell float.

• Exclusively marine, most secrete glassy endoskeletons, many with elaborate designs.

24

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Excavates

25

Page 26: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Excavates: Diplomonads and Parabisalids

• Unicellular

• Lack mitochondria and most are anaerobic. This is a derived condition

• Giardia lamblia - a diplomonad - is a human parasite

• Trichomonas vaginalis - parabasalid - STD

26

Page 27: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Excavates: Heteroloboseans

• Amoeboid body form.

• Naegleria can enter humans and cause a fatal nervous system disease - “brain eating”

• Some can transform between amoeboid and flagellated stages.

27

Page 28: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Excavates: Euglenids

• Have flagella. • Some are

photosynthetic, some always heterotrophic, and some can switch.

28

Movement in the euglenoid Eutreptia

Page 29: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Excavates: Kinetoplastids

• Unicellular parasites with two flagella and a single mitochondrion.

• Mitochondrion contains a kinetoplast - structure with multiple, circular DNA molecules

• Includes trypanosomes and agents of chagas, sleeping sickness, Leishmaniasis

Trypanosoma sp.!mixed with blood cells

29

Page 30: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Amoebozoans

Amoebozoans Lobe-shaped pseudopods are used for

locomotion.

30

Page 31: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

• Not colonial; live as single cells

• Some secrete shells or glue sand grains together to form a casing.

• Many pathogens

31

Amoebozoans: Loboseans

Page 32: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Entamoeba histolytica

32

http://www.npr.org/blogs/health/2014/04/09/300991364/gut-eating-amoeba-caught-on-film

Page 33: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Amoebozoans: Plasmodial Slime Molds

• Individual motile cells can form single, multinucleate cell (plasmodium)

• Ingest food by endocytosis • Form spores on stalks called fruiting

bodies. • Found in cool, moist habitats

33

Page 34: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Amoebozoans: Cellular Slime Molds• Life cycle consists of individual motile cells that

ingest food by endocytosis • This is followed by the formation of single,

multicellular fruiting structure • Each cell retains its own plasma membrane

and individuality

34

Karyo

Page 35: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Plantae

35

The Plantae consist of several clades; all chloroplasts trace back to a single incidence of endosymbiosis.

Page 36: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Plantae: Glaucophytes

• Unicellular, freshwater organisms

• The chloroplast retains a bit of peptidoglycan between the inner and outer membrane.

36

Page 37: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Clicker Question

37

Page 38: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Plantae: Glaucophytes

• Unicellular, freshwater organisms

• The chloroplast retains a bit of peptidoglycan between the inner and outer membrane.

38

Which of the following groups do not have peptidoglycan in their cell envelopes? •A: Gram positive bacteria •B: Gram negative bacteria •C: Cyanobacteria •D: Crenarchaeota

Page 39: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Plantae: Glaucophytes

• Unicellular, freshwater organisms

• The chloroplast retains a bit of peptidoglycan between the inner and outer membrane.

39

Which of the following groups do not have peptidoglycan in their cell envelopes? •A: Gram positive bacteria •B: Gram negative bacteria •C: Cyanobacteria •D: Crenarchaeota

Page 40: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Plantae: Red Algae

40

• Most red algae are marine and multicellular. • Red pigment is phycoerythrin. •Many reproduce with spores

Motile spores from Purpureofilum

Audouinella pacifica

Spyridia

Page 41: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Plantae: Chlorophytes• Sister group to charophytes and land

plants.

• Synapomorphies include chlorophyll a and b, and starch as a storage product.

• >17,000 species; marine, freshwater, and terrestrial. Unicellular to large multicellular forms.

Chlamydomonas

41

Movement in the green alga Volvox

Micrasterias

Page 42: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Plantae: Charophytes and Land Plants

STAY TUNED

42

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Opisthokonts

Page 44: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

•Choanoflagellates are sister to the animals.

•Some are colonial and resemble a type of cell found in sponges.

44

The choanoflagellate Salpingoeca sp. feeding

Opisthokonts: Choanoflagellates

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Opisthokonts: Fungi and Animals

STAY TUNED

Page 46: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Eukaryotic Diversity

• Seven major lineages of eukaryotes

• Alveolates

• Stramenopiles

• Rhizaria

• Excavates

• Amoebozoans

• Plantae

• Opisthokonts

• Complications 1: Endosymbioses

• Complications 2: Lateral gene transfer46

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 47

The Bacteria

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Oversimplification of eukaryotic phylogeny

48

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Diverse Organelles

49

Mitochondrion Chloroplast

Nucleus

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Endosymbioses in eukaryotic evolution

50

Prokaryotic cell

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Endosymbioses in eukaryotic evolution

50

Cell wall

Prokaryotic cell

Page 52: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Endosymbioses in eukaryotic evolution

50

DNA

Cell wall

Prokaryotic cell

Page 53: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Endosymbioses in eukaryotic evolution

50

DNA

Cell wall

Prokaryotic cell

Page 54: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Endosymbioses in eukaryotic evolution

50

DNA

Cell wall

Prokaryotic cell

The protective cell wall was lost.

Page 55: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Endosymbioses in eukaryotic evolution

50

DNA

Cell wall

Prokaryotic cell

Infolding of the plasma membrane added surface area without increasing the cell’s volume.

The protective cell wall was lost.

Page 56: BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Endosymbioses in eukaryotic evolution

50

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51

Endosymbioses

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Endosymbioses

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Cytoskeleton (micro-filament and micro-tubules) formed.

Endosymbioses

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Cytoskeleton (micro-filament and micro-tubules) formed.

Internal membranes studded with ribosomes formed.

Endosymbioses

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51

Endosymbioses

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Endosymbioses

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Endosymbioses

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As regions of the infolded plasma membrane enclosed the cell’s DNA, a precursor of a nucleus formed.

Endosymbioses

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Early digestive vacuoles evolved into lysosomes using enzymes from the early endoplasmic reticulum.

As regions of the infolded plasma membrane enclosed the cell’s DNA, a precursor of a nucleus formed.

Endosymbioses

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Microtubules from the cytoskeleton formed eukaryotic flagellum, enabling propulsion.

Early digestive vacuoles evolved into lysosomes using enzymes from the early endoplasmic reticulum.

As regions of the infolded plasma membrane enclosed the cell’s DNA, a precursor of a nucleus formed.

Endosymbioses

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Endosymbioses

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Endosymbioses

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Proteobacteria

Endosymbioses

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Proteobacteria

Endosymbioses

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Mitochondria formed through endosymbiosis with a proteo-bacterium.

Proteobacteria

Endosymbioses

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Endosymbioses

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Endosymbioses

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Cyanobacteria

Endosymbioses

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Endosymbiosis with cyanobacteria led to the development of chloroplasts.

Endosymbioses

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Flagellum

Eukaryotic cell

Chloroplast

Mitochondria

Nucleus

Endosymbiosis with cyanobacteria led to the development of chloroplasts.

Endosymbioses

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Mitochondrial Symbiosis

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Mitochondrial Symbiosis

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Mitochondrial Symbiosis

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Mitochondrial Symbiosis

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Bacteria

Mitochondrial Symbiosis

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Bacteria

Mitochondrial Symbiosis

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Bacteria

Mitochondrial Symbiosis

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Bacteria Archaea

Mitochondrial Symbiosis

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Bacteria Archaea Eukaryotes

Mitochondrial Symbiosis

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Bacteria Archaea Eukaryotes

Mitochondrial Symbiosis

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Bacteria Archaea Eukaryotes

Mitochondrial Symbiosis

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Bacteria Archaea Eukaryotes

Mitochondrial Symbiosis

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Bacteria Archaea Eukaryotes

Mitochondrial Symbiosis