bis2c. biodiversity and the tree of life. 2014. l35. symbioses

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Lecture 35

!

Lecture 35 !

Symbioses in Symbioses in Symbioses

!!

BIS 002C Biodiversity & the Tree of Life

Spring 2014 !

Prof. Jonathan Eisen1

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Where we are going and where we have been

• Previous Lecture: !34: Really big creatures

• Current Lecture: !35: Symbioses in Symbioses …

• Next Lecture: !The Final …

2

Napa Vineyard

!3

Pierce’s Disease

!4

• Pierce’s Disease

• Due to blockage of xylem circulation

• Caused by overgrowth of Xylella fastidiosa, a bacterium

• Vines, even whole vineyards, infected must be destroyed

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

!5

Pierce’s Disease

Xylem and Phloem

! Xylem sap: water and minerals mostly from roots to rest of plant.

! Phloem sap: products of photosynthesis such as sugars to sites of storage or use.

!6

From Lodish et al. 2000

Organism

Class of symbiosis A B

Mutualism + +

Commensalism + 0

Parasitism + -

!9Symbiosis between Xylella and grapes?

Symbiosis between Xylella and grapes

• II: How Pierce’s Disease Gets Around

• How does Xylella get from one plant to another?

!10

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

Apicomplexans have complex life cycles, often with two different hosts. !11

Plasmodium

• Obligate xylem feeder

• Transmits Xylella between plants

• Much like mosquitoes transmit malarial pathogen

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

!12

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.

!14http://www.youtube.com/watch?v=xz6kI3SSLJo

http://www.youtube.com/watch?v=xz6kI3SSLJo

Symbiosis between Xylella and sharpshooter?

Organism


Mutualism + +

Commensalism + 0

Parasitism + -

!16

Symbiosis between Xylella and sharpshooters

Organism


Mutualism + +

Commensalism + 0

Parasitism + -

!17Symbiosis between Xylella and sharpshooter?


Xylem and Phloem

! Xylem sap: water and minerals mostly from roots to rest of plant.

! Phloem sap: products of photosynthesis such as sugars to sites of storage or use.

!18


Conundrum

• Phloem sap is filled with sugar(s) and a variety of other compounds

• But low in most of the “essential” amino acids that animals cannot synthesize

!19

35.12 Aphids Live off Phloem Sap

!20

!21https://www.youtube.com/watch?v=3rqSWymHc6g

https://www.youtube.com/watch?v=3rqSWymHc6g

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

!22

Plant response to sap feeders

• Possible solutions to low aa in phloem ! Eat other things ! Evolve metabolic pathways to synthesize missing

nutrients ! Find some poor sap to make the stuff for you

!23

How to study microbes

• Key questions about microbes in environment: ! Who are they? (i.e., what kinds of microbes are they) ! What are they doing? (i.e., what functions and

processes do they possess)

!25

!28

Culturing Field Observations

Key bacteria in aphid gut have

not been cultured

Studying the microbe-like entities in the aphid gut

Appearance of limited value

DNA

• Who Are They?

!29

DNA extraction

PCR Sequence 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

!30

rRNA1 5’ ...TACAGTATAGGTGGAGCTAGCGAT

CGATCGA... 3’

PCR and phylogenetic analysis of rRNA genes

• What Are They Doing?

!33

DNA extraction

PCR

!34


Sequence the whole genome

Predict functions by comparison to other organisms

Aphid symbiont genomes

ESSENTIAL AMINO ACID

SYNTHESIZING MACHINE

!35

Organism


Mutualism + +

Commensalism + 0

Parasitism + -

!37


Symbiosis between bacteria and aphids?

• Obligate xylem feeder

• Transmits Xylella between plants

• Much like mosquitoes transmit malarial pathogen

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

!38

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.

!39

Xylem feeding insects also very successful

Xylem and Phloem


!40

Animal nutrition

• Xylem is frequently missing essential amino acids, vitamins and Co-Factors, and has only small amounts of carbon skeletons

!41

Plant response to sap feeders

• Possible solutions to no aa, vitamins, etc in xylem ! Eat other things ! Evolve metabolic pathways to synthesize missing

nutrients ! Find some poor sap to make the stuff for you

!42

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

©2007 by National Academy of Sciences !43

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

How to study microbes

• Key questions about microbes in environment: ! Who are they? (i.e., what kinds of microbes are they) ! What are they doing? (i.e., what functions and

processes do they possess)

!45

!48

Culturing Field Observations

Studying the microbe-like entities in the aphid gut

Appearance of limited value

DNA

Key bacteria in sharpshooter gut have

not been cultured

5


bacteriomes





D Takiya

0.1mm





• Who Are They?

!49

DNA extraction



PCR

rRNA1

Yeast


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

!50


CGATCGA... 3’


5


bacteriomes





D Takiya

0.1mm





Baumania is close relative of Buchnera symbionts of aphids

SharpshootersAphidsAphidsAphidsAntsFlies

!52

• What Are They Doing?

!54

DNA extraction

PCR

!56

Genome sequencing



5


bacteriomes





D Takiya

0.1mm





Predict metabolic networks from Genome

Wu et al. 2006 PLoS Biology 4: e188. !57

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040188

Baumannia is a Vitamin and Cofactor Producing Machine


VITAMIN AND COFACTOR

PRODUCING MACHINE


Baumannia is a Vitamin and Cofactor Producing Machine


NO PATHWAYS FOR ESSENTIAL AMINO ACID SYNTHESIS


DNA extraction



PCR

rRNA1

rRNA2


rRNA1 5’ ...ACACACATAG

GTGGAGCTAGCGATCGATCGA... 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

!61


CGATCGA... 3’


!

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+#,()$-'.)&

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

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5


bacteriomes





D Takiya

0.1mm





Wu et al. 2006 PLoS Biology 4: e188.

DNA extraction

PCR

!64

Genome sequencing



5


bacteriomes





D Takiya

0.1mm





Sulcia makes essential amino acids

!65


!66

ESSENTIAL AMINO ACID PRODUCING

MACHINE

Wu et al. 2006 PLoS Biology 4: e188.

Baumannia makes vitamins and cofactors


Organism


Mutualism + +

Commensalism + 0

Parasitism + -

!69


Symbiosis between bacteria & sharpshooters?

Pierce’s Disease

!70

Bacteria and archaea are key commensals of many eukaryotes

71

Examples of mutualisms discussed in class

• 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

!73

Don’t Neglect your Symbionts