bis2c: lecture 35: symbioses across the tree of life

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

Lecture 35:

Interactions Across The Tree of Life

BIS 002C Biodiversity & the Tree of Life

Spring 2016

Prof. Jonathan Eisen

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Where we are going and where we have been…

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•Previous lecture: •34: Fungi

•Current Lecture: •35: The End

•Next Lecture: •36: The Future


The Tree of Life (used in LIFE Version 10)

3

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 4

BIS2C is ORGANIZED BY THE TREE OF LIFE

and

PHYLOGENY

The Tree of Life (used in LIFE Version 10)


Week 1

Phylogeny

Week 1: Phylogenetic Trees


Life on Mars

6

Week 2

Trees of Life?


Week 2

The Tree of Life

Week 2: The Tree of Life


Protists

BACTERIA

ARCHAEA

EUKARYA

Mitochondria

Chloroplasts

LifePlants

Protists

Protists

Protists

Protists

Protists

Fungi

Animals

8

Week 3

MicrobialDiversity

Week 3: Microbial Diversity


Weeks 4-5: Plants

9

Protists

BACTERIA

ARCHAEA

EUKARYA

Mitochondria

Chloroplasts

LifePlants

Protists

Protists

Protists

Protists

Protists

Fungi

Animals

Weeks 4-5

Plants


Weeks 4-5: Plants

10

Weeks 4-5

Plants


Protists

BACTERIA

ARCHAEA

EUKARYA

Mitochondria

Chloroplasts

LifePlants

Protists

Protists

Protists

Protists

Protists

Fungi

Animals

Weeks 7-9: Animals

11

Weeks 6-8

Animals


Weeks 7-9: Animals

12

Weeks 6-8

Animals


Protists

BACTERIA

ARCHAEA

EUKARYA

Mitochondria

Chloroplasts

LifePlants

Protists

Protists

Protists

Protists

Protists

Fungi

Animals

Week 6: Fungi

13

Week 9

Fungi


Week 6: Fungi

14

Week 9 Fungi


Napa Vineyard

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Pierce’s Disease


Pierce’s Disease• Caused by overgrowth of

Xylella fastidiosa, a bacterium

19




19

Xylem




• Blocks xylem circulation

• Eventually whole plant dies

• Vines, even whole vineyards, if infected may be destroyed

• Same bacterial species causes problems in many other plants

• Potential for billions of $$ of economic damage

• Many of world’s experts at UC Davis and other UCs

19

Xylem


Clicker Question

• What kind of symbiosis is the one between Xylella and Grapes?

• A: Mutualism

• B: Pathogenism

• C: Commensalism

• D: Parasitism

• E: Primary

20


Clicker Question

• What kind of symbiosis is the one between Xylella and Grapes?

• A: Mutualism

• B: Pathogenism

• C: Commensalism

• D: Parasitism

• E: Primary

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Pierce’s Disease

Should be easy to contain

Prevent plant to plant contact

Like w/ human infectious diseases


Vectors for Blood Borne Diseases

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• Obligate xylem feeder

• Transmits Xylella between plants

• Much like mosquitoes transmit malarial pathogen

• Only animal listed as possible “bioterror” agent by US DHS

!24

Glassy winged sharpshooter

GLASSY-WINGEDSHARPSHOOTERA Serious Threat to California Agriculture

FROM THE

UNIVERSITY OF CALIFORNIA’S PIERCE’S DISEASE RESEARCH AND

EMERGENCY RESPONSE TASK FORCE

Glassy-winged sharpshooter eggs are laid together on theunderside of leaves, usually in groups of 10 to 12. The eggmasses appear as small, greenish blisters. These blisters areeasier to observe after the eggs hatch, when they appearas tan to brown scars on the leaves.

Parasitized egg masses are tan to brown in color withsmall, circular holes at one end of the eggs.

This informational brochure was produced by ANRCommunication Services for the University of Califor-nia Pierce’s Disease Research and EmergencyResponse Task Force. You may download a copy of thebrochure from the Division of Agriculture and NaturalResources web site at http://danr.ucop.edu or from theCommunication Services web site athttp://danrcs.ucdavis.edu.

Download a copy of this brochure from http://danr.ucop.edu or http://danrcs.ucdavis.edu

For local information, contact your UC CooperativeExtension farm advisor:

Adults

Egg masses

Glassy-winged SharpshooterGeneralized Lifecycle

100

80

60

40

20

0

Jan.

Mar

.

May

July

Sept

.

Nov.

Glassy-winged sharpshooters overwinter as adultsand begin laying egg masses in late Februarythrough May. This first generation matures asadults in late May through late August. Second-generation egg masses are laid starting in mid-June through late September, which develop intoover-wintering adults.

Clicker

• The glassy winged sharpshooter is an insect. Which of the following groups are insects part of?

• A. Chordata

• B. Diploblasts

• C. Deuterostomes

• D. Protostomes

• E. None of the above

!25

Clicker

• The glassy winged sharpshooter is an insect. Which of the following groups are insects part of?

• A. Chordata

• B. Diploblasts

• C. Deuterostomes

• D. Protostomes

• E. None of the above

!26

Symbiosis between Xylella and sharpshooter?

Symbiosis between Xylella and sharpshooters

Organism

Class of symbiosis A B

Mutualism + +

Commensalism + 0

Parasitism + -

!30

Symbiosis between Xylella and sharpshooter?

Organism


Mutualism + +

Commensalism + 0

Parasitism + -

!31


Organism


Mutualism + +

Commensalism + 0

Parasitism + -

!32Symbiosis between Xylella and sharpshooter?


Figure 35.11 The Pressure Flow Model

!33Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

Source cell

Phloem sieve tubeXylem

Sink cell

Sucrose

Sucrose

H2O

H2O

H2O

H2O

Which Would You Choose to Eat?



Source cell


Sink cell

Sucrose

Sucrose

H2O

H2O

H2O

H2O

35.12 Aphids Live off Phloem Sap

!35


Mosquito Feeding

36

Aphids are very successful (> 4000 species, everywhere you look)

!37



Source cell


Sink cell

Sucrose

Sucrose

H2O

H2O

H2O

H2O

!40

Xylem feeding insects also very successful

Plant vs. Insect

• Thicken walls

!41

Plant Adaptations Insect Responses• Better piercing

Plant vs. Insect

• Thicken walls

• Fill up xylem with toxins

• Immune response

• Remove key nutrients

!41


• Detoxify

• Immune suppression

• ????



Source cell


Sink cell

Sucrose

Sucrose

H2O

H2O

H2O

H2O

• Very low in sugar

How Deal With Very Low Sugar?


Tree Rain in Tahiti

!46



Source cell


Sink cell

Sucrose

Sucrose

H2O

H2O

H2O

H2O

• Very low in sugar

• Remove essential amino acids

• Remove vitamins and cofactors


• Thicken walls


• Immune response

• Reduced sugar

• Removes key amino acids

• Removes vitamins

• Removes cofactors


• Detoxify


• Pump a lot

• ???

• ???

• ???


• Thicken walls


• Immune response

• Reduced sugar





• Detoxify


• Pump a lot

• Eat other things



!50

Severe Feeding Constraints


• Thicken walls


• Immune response

• Reduced sugar





• Detoxify


• Pump a lot

• ???

• ???

• ???


• Thicken walls


• Immune response

• Reduced sugar





• Detoxify


• Pump a lot

• Evolve synthetic pathway




• Thicken walls


• Immune response

• Reduced sugar





• Detoxify


• Pump a lot

• ???

• ???

• ???

How Do Eukaryotes Get Many New Biochemical Functions?

• Eukaryotic organelles (plastids and mitochondria)

• Secondary symbioses (eukaryote with another eukaryote)

• Lichens (fungi and photosynthetic microbe)

• Coral & dinoflagellates (zooxanthellae)

• Ant - fungus farming

• Pogonophoran worms and chemosynthetic bacteria

• Legumes and N2 fixing bacteria

• Herbivores and cellulolytic gut microbes

• Wood eating organisms and gut microbes

!54


• Thicken walls


• Immune response

• Reduced sugar





• Detoxify


• Pump a lot

• Symbiosis

• Symbiosis

• Symbiosis

Moran N. A. PNAS 2007;104:8627-8633

©2007 by National Academy of Sciences !57

5

Sharpshooter:Cuerna sayi

bacteriomes

Sharpshooters harbor two obligatesymbionts in their bacteriomes

Moran et al. 2003 Environ. Microbiol.Moran et al. 2005 Appl. Environ. Microbiol.

Candidatus “Baumannia cicadellinicola” (Gammaproteobacteria)

Candidatus “Sulcia muelleri” (Bacteroidetes)

D Takiya

0.1mm

Bacteriome dissected from anterior abdomen of H. vitripennis

Orange-red portion- Baumannia only

Yellow portion- Baumannia and Sulcia

(Moran et al. 2003 Environmental Microbiology)

7

10!m

“Candidatus Baumannia cicadellinicola” (Gammaproteobacteria)

in “red” portion of bacteriome of Homalodisca vitripennis

N=host nucleus B=Bacteriocyte membrane E=Endosymbionts

Irregularly spherical

~2 !m diameter

Phylogeny of Sulcia muelleri from Auchenorrhyncha

(Hemiptera): the oldest insect symbiont

Moran et al. Appl Env Micro 2005

Permian

age fossils

(>270 myr)

•= 100% Bootstrap

•support, all methods

Broad congruence with host

relationships

Dates to the origins of vascular

plant-feeding in insects

Symbionts derived

from sharpshooters

Studying the microbe-like entities in the aphid gut

!58

Field Observations

5


bacteriomes





D Takiya

0.1mm






!59

Field Observations

Appearance of limited value

5


bacteriomes





D Takiya

0.1mm





!60

Culturing Field Observations



5


bacteriomes





D Takiya

0.1mm





!61


Key bacteria in sharpshooter gut have

not been cultured



5


bacteriomes





D Takiya

0.1mm





!62




DNA

Key bacteria in sharpshooter gut have

not been cultured

5


bacteriomes





D Takiya

0.1mm





• What is this issue with the difficulty in culturing organisms been called?

• A. Great microscope anomaly

• B. Great count anomaly

• C. Great plate count anomaly

• D. Grate cheese anomaly

• E. Great plating anomaly

!63

• What is this issue with the difficulty in culturing organisms been called?

• A. Great microscope anomaly

• B. Great count anomaly

• C. Great plate count anomaly

• D. Grate cheese anomaly

• E. Great plating anomaly

!64

• Who Are These Microbes?

!65

DNA extraction

PCRSequence

rRNA genes

Sequence alignment = Data matrixPhylogenetic tree

PCR

rRNA1

Yeast

Makes lots of copies of the rRNA genes

in sample

E. coli

Humans

A

T

T

A

G

A

A

C

A

T

C

A

C

A

A

C

A

G

G

A

G

T

T

CrRNA1

E. coli Humans

Yeast

!66

rRNA1 5’ ...TACAGTATAGGTGGAGCTAGCGATCGAT

CGA... 3’

PCR and phylogenetic analysis of rRNA genes

5


bacteriomes





D Takiya

0.1mm





DNA extraction

PCRSequence

rRNA genes

Sequence alignment = Data matrixPhylogenetic tree

PCR

rRNA1

rRNA2

Makes lots of copies of the rRNA genes

in sample

rRNA1 5’ ...ACACACATAGGTGGAGCTAGCGATCGAT

CGA... 3’

E. coli

Humans

A

T

T

A

G

A

A

C

A

T

C

A

C

A

A

C

A

G

G

A

G

T

T

CrRNA1

E. coli Humans

rRNA2

!67

rRNA2 5’ ...TACAGTATAGGTGGAGCTAGCGATCGAT

CGA... 3’

PCR and phylogenetic analysis of rRNA genes

!

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+#,()$-'.)&

!"#$%&"''()$&/"#$+'$/(0'/'+1-2#()&3.+-'4(& -4/(")-$/+#,()$-'.)&

5'$#4/#*+&,6/7889/-%.)$/%0+1)2$/3)/,05'$#4/#*+&,0+788:/455,0+-%.)$/%0+1)2$/3)/,0+

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5


bacteriomes





D Takiya

0.1mm





Baumania is close relative of Buchnera symbionts of aphids

SharpshootersAphidsAphidsAphidsAntsFlies

!68

• What Are They Doing?

!71

DNA extraction

PCR

!73

Genome sequencing

Sequence the whole genome

Predict functions by comparison to other organisms

5


bacteriomes





D Takiya

0.1mm





Predict metabolic networks from Genome

Wu et al. 2006 PLoS Biology 4: e188.

!74

Baumannia is a Vitamin and Cofactor Producing Machine


!75

BAUMANNIA IS A VITAMIN AND

COFACTOR PRODUCING MACHINE

Sulcia

!76

Sulcia makes essential amino acids

!77

SULCIA IS AN ESSENTIAL AMINO ACID PRODUCING

MACHINE


Baumannia makes vitamins and cofactors

Sulcia makes essential amino acids


Clicker Question

• What kind of symbiosis is the one between Baumania and Sharpshooters?

• A: Endemism

• B. Commensalism

• C. Mutualism

• D: Parasitism

• E: Pathogenism

79


Clicker Question

• What kind of symbiosis is the one between Baumania and Sharpshooters?

• A: Endemism

• B. Commensalism

• C. Mutualism

• D: Parasitism

• E: Pathogenism

80

• Where else have we seen microbes that are used in control of pests or pathogens?

!82

Pierce’s Disease

!83

Don’t Neglect your Symbionts

Find the Right Partner(s) and Work With Them …