Transcript Lecture #4A ppt - College of Natural Resources, UC Berkeley

3rd Quiz, Name, date, email
• 1 Pick one of the following two:
– A)Explain how environmental changes can
increase severity of disease
– B)Why is it useful to be able to follow individual
genotypes (strains) of a microbe?
• 2 Pick one of the following two:
– A) What is the likleihood of a host shift for an
exotic pathogen?
– B)- What are R and avr genes?
“Emergent diseases”:
3: exotic pathogens
• 99% of times human responsible for their
introduction
Like the conquistadores brought
diseases that were lethal to
those who had never been
exposed to them, so do exotic
diseases cause true devastation
in plant communities because of
lack of coevolution between
hosts and microbes
California invaded: 1849 A.D.
Port Orford Cedar Root Disease
1950s
Sudden Oak Death
1990s
Canker-stain of
Sycamores 1980’s
Pitch canker disease
1980s
New hybrid root pathogen
1990s
Manzanita/madrone
die-back
White pine blister rust
1930s
Dutch Elm Disease
1960s
Oak root canker
2000
How can people transport
pathogens
• By transporting plants and plant parts
– Crops, and seeds
– Raw food
– Ornamental plants
Untreated lumber
Soil
Insects vectoring fungi
Military activity
The Irish Potato Famine
• From 1845 to 1850
• Phytophthora
infestans
• Resulted in the
death of 750,000
• Emigration of over 2
million, mainly to the
United States.
What favors invasion of exotic
fungi ?
– Density of host increases severity of disease
_ Presence of related hosts phylogenetic signal)
– Corridors linking natural habitats
– Synchronicity between host susceptibility and
pathogen life cycle
– Ecological and environmental conditions
– Disturbances
– Capacity of pathogen to survive in unfavorable
conditions
– Transmission rate
Girdling aerial ‘cankers’
removed from roots
Big Sur
2006
K. Frangioso
% Mortality of Tanoak by Stem Size Class
% Mortality
45
40
35
30
25
20
15
10
5
0
35.8
P. ramorum absent
Non-infec
ted plots
P. ramorum
present
Infec
ted plots
10.7 11.8
28.5
12.4
4.1
1-<5
34.1
5-<10
4.8
10-<20
>20
Tanoak st em diamet er size c lass (c m)
Wickland et al., unpublished
P. ramorum growing in a Petri dish
Organism new to science
•
•
•
•
Origin unknown
Biology unknown
Symptoms caused unknown
Immediately though highly regulated
Rhododendron:
In EU mostly a nursery
issue, but also present in
nurseries in US and Canada
Stem canker
Leaf necrosis
Phytophthora
ramorum
Sporangia
Chlamydospores
Is it exotic?
• Our studies have indicated that California
population is extremely simplified, basically
two strains reproducing clonally as expected
of an introduced organism
• Many hosts appear to have no resistance at
all
• Limited geographic distribution
Where does it come from?
• It is unknown where pathogen originally
comes from, but previous studies have shown
that California forest population is derived
from a relatively genetically diversified US
nursery population, indicating ornamental
nurseries were the most likely avenue for
pathogen introduction
Let’s look at its genetic
structure
• Need a number of independent and
neutral DNA markers
• Used AFLP, a technique that scans the
entire nuclear genome
• Are our isolates the same as the
European ones?
• Is the genetic structure suggestive of an
introduced or native species?
•US forest isolates
clearly distinct from EU
nursery isolates, also
have different mating
type
•Isolates from nurseries
in WA, OR, & BC both
of the US and EU types
•Potential for XXX sex
and recombination in
US nurseries
•US forest population
is genetically very
homogeneous,
trademark of an
introduced species
The entire genome was sequenced in
less than 3 years since discovery of organism
* 12 SSR loci (di- and tri- repeats identified)
* Loci selected to be polymorphic both between
and within continental populations
* 500+ representative isolates analyzed
CCGAAATCGGACCTTGAGTGCGGAGAGAGAGAGAGACTGTACGAGCCCGAGTCTCGCAT
Mating
Type
Growth
Rate
A1
Fast
A2
Slow
A2
Fast
Terminology
Genotype Lineage
Population
Results of 1st microsatellite
study
• There actually three distinct (genotypically
and phenotypically) lineages of P. ramorum
• Very low diversity in US forests (microsats
cannot discriminate among individuals,
clonality confirmed), only one lineage
• Several genotypes but only one lineage in EU
nurseries
• Three lineages in US nurseries
Was the pathogen first in US
forests or in US nurseries?
Slide 12
Was the pathogen first in US
forests or in US nurseries?
Slide 12
nurserie
forests
Where was it introduced?
• First reports mid 90’s
• Pathogen identified in
2000
• By then, the pathogen
was widespread
• CLUES: severity of
symptoms and
anedoctal stories
Positive isolation
P. ramorum
We found
same
genotypes in
nurseries and
forests proving
origin of wild
outbreak
Introduction phase
1- Escape of pathogen from
Infected nursery plants at two
locations: Mount Tamalpais
(Marin County), and Scott’s
Valley (Santa Cruz County)
2- Nurseries and two sites
have identical strain
composition, but distance
between sites is impossible
for natural spread of
organism
nurseries
What favors invasion of exotic
fungi ?
– Density of host increases severity of disease
– Corridors linking natural habitats
– Synchronicity between host susceptibility and
pathogen life cycle
– Ecological and environmental conditions
Bay/Oak association
Bay
Coast Live Oak (no sporulation)
Canker margin in phloem
Bleeding canker
Sporangia
Infectious diseases spread not randomly but around initial
infections
Site
Mantel test among all individuals.
[Moran’s I vs ln (geographic
distance)]
ID
Correlation P-value
coeff. (r)
(1000,000
perm)
ALL
-0.2153
<0.000001
0.5
0.4
Moran's I
0.3
0.2
0.1
0
-0.1
-0.2
10
100
1000
Mean Geographic Distance (m)
10000
100000
Synchrony pathogen-host
Susceptibility of oaks
(lesion size)
Average lesion (mm_)
80
60
40
Wetness > 12 h
20
0
0
6
12
18
24
30
36
42
48
54
Time (h)
2
Lesion area (mm)
50
40
30
Temp >19 C
20
10
0
15
17
19
21
23
25
Temperature (ЎC)
27
29
Bay Laurel / Tanoak SOD Spore Survey
35
Temp (C)
30
Rain (mm)
25
20
15
10
5
0
Date
How to control emergent
exotic diseases
• PREVENT THEIR INTRODUCTION
• LIMIT THE HUMAN-SPREAD OF
PATHOGENS (infected plants, plant
parts, dirty tools)
• EMPLOY HOST RESISTANCE
• CHEMICAL AND OTHER MITIGATION
STRATEGIES
Forest pathogens can never be
eradicated
PREVENT: Diagnose
Symptoms relatively generic, very
variable, and pathogen not always
culturable
DNA TESTS
LAB CULTURES
AgriFos and
PentraBark
Topical
Application
+
Agrifos vs. Azomite Treatments
(efficacy 1 - 24 months)
a
14
a
Canker Size (mm)
12
10
8
6
b
4
2
0
Azomite
Positive Control
Agrifos
Why emphasis on molecular
analyses?
• As a way to identify and quantify
microbes in the environment
• As a way to understand microbial
biology: how do microbes reproduce
and infect hosts
• As a way to determine epidemiology:
follow the movement of a strain
Why emphasis on molecular
analyses?
• As a way to determine potential for
spread: use genes as markers for
individuals
• As a way to determine whether
population of microbes is exotic or
native
• As a way to identify source of a
pathogen and migration patterns
Why emphasis on molecular
analyses?
• As a way to determine the size of the
gene pool of a pathogen, Important to
scale management options
• As a way to determine rapid
evolutionary changes linked to an
introduction
• As a way to determine epigenetic
effects
New host pathogen
combinations
• Pathogen stays/Plant moves: invasive
plant
• Pathogen moves/Plant stays: exotic
epidemic
• Pathogen moves/Plant moves:
biological control
Success. The “1:10” rule
• Can exotic withstand new environment
• Can it withstand attacks of predators
• Can it outcompete similar native
organisms by accessing resources
– Can a pathogen be pathogenic
– Can a pathogen be sufficiently virulent
• Invasion driven by ecological conditions
• Enemy release hypothesis
• Resource availability
(pathogenicity/virulence)
Pathogenicity
• Qualitative: ability to cause disease
• Often regulated by a single gene
• Avr genes in pathogen and resistance
genes in host
Gene for gene
• Resistance in host is dominant
• Virulence is recessive
ar aR
Ar AR
Gene for gene
• Resistance in host is dominant
• Virulence is recessive
ar aR
Ar AR
Resistance: no
disease
Functions of avr/R genes
• Avr genes may help detoxify plant
enzymes, secure necessary aminoacids
or proteins, plant toxins, promoting
pathogen growth. Normally they are
mobile, wall-bound products
• R genes normally recognize multiple avr
genes and start hypersensitive
response (programmed cell death)
Avr/R genes matches are
specific
• Race of the pathogen (avr1) matched
by variety of the crop (R1).
• At the base of crop breeding science
• If R genes target avr genes linked to
important housekeeping functions, they
are more durable
Can be R genes
accumulated?
• There is a cost associated with R genes
• Mostly R genes initiate costly defense
processed, often even when challenged
by innocuous microbes
• Some evidence that in absence of
specific avr, R are lost
Plants immune response
• Plants do not possess an immune system such as
that of animals
• They do recognize pathogens
• Recognition initiates secondary metabolic processes
that produce chemicals that will stop or slow
microbial infections: thickening of cell wall, premature
cell death (HR response), systemic resistance
Virulence: quantitative
response
• Multiple genes controlling:
– Phenotypic traits conferring virulence
– Production of plant detoxifying enzymes
– Production of plant toxins
CAN WE PREDICT:
• Success of an exotic microbe?
– Survival structures such as cysts, spores, etc
– Saprotrophic ability (ability to feed on dead matter)
– Degree of host specialization, the more specialized the
harder it may be to establish
– Phylogenetic distance of hosts (the closertive and new hosts
are, the easier the establishment)
– Similar ecology
CAN WE PREDICT:
• Levels of the epidemic?
– Density dependence: abundance of susceptible
hosts
– Genetic variation in host. In general it is assumed
that genetic variation in host populations slows
down epidemics, however backing data from
natural ecosystems is missing. It could be that low
genetic diversity associated with widespread
presence of resistance may be more beneficial
than genetic variability
CAN WE PREDICT:
• Selection of increased R in host?
– Host: R to exotic may be significantly present because it
identifies native pathogen.
– R may be absent.
– R may be present at low frequency. If host does not
exchange genes long distance, but only in areas already
infested there is a stronger selection process. Otherwise
locally selected R genes may be swamped by genes coming
from outside the area of infestation
– Shorter generation times favor pathogen