BIOLOGY ECOLOGY GENETICS
of FOREST FUNGI
• Lesson 1 of BEG Spring 2011
• Taught by Dr. Matteo Garbelotto
– Matteog@berkeley.edu
– Office: 338 Hilgard Hall
– Office hours:
WEDNESDAYS at 3 pm, THURSDAYS at 1
pm
Course info
• One two hour lecture per week
• One quiz every week on previous lecture and
reading assignments
• NO syllabus, but….
• Some readings will be emailed to students
• Web site: www.matteolab.org
» Link to UCB course
» POWERPOINT LECTURES, assigned readings
» Posted on Fridays
Course info
• One final quiz (3 questions out of 9)
• One short Powerpoint presentation
• Possibility to improve grade by writing paper
(5 pages) on same topic as oral presentation
• One computer lab: use of software for genetic
analyses
• Participation in SOD blitz mandatory
GRADING
•
•
•
•
25% class participation
25% weekly quizzes
25% final quiz
25% oral presentation
COURSE PROGRAM-1
•
•
•
•
What is an emergent disease ?
What do plant diseases exactly do?
How do plant and pathogens interact?
What are the evolutionary
consequences of emergent diseases?
• What causes plant diseases
• How can we use genetic information to
identify a pathogen? DNA,
chromosomes and loci
COURSE PROGRAM-2
• DNA used to identify a species
• DNA used to identify an individual within
a species
• Following an individual pathogen to
understand infection process
• Using genes to tag individuals; how far
does an individual go?
• Identify populations and migration
among populations
COURSE PROGRAM-3
• Identify source of a pathogen and
phylogeography
• Determine whether a population is
introduced or native
• Rapid evolutionary changes linked to
introductions
• Epigenetics of disease
EMERGENT FOREST
DISEASES: ARE THEY A
THREAT TO NATIVE
ECOSYSTEMS?
Matteo Garbelotto
U.C.Berkeley
“Native diseases”:
• Indigenous microbes
• Plant ecosystems have co-evolved to resistance
• Native diseases are an important component of
forest ecosystems
“Roles of native diseases”:
• Thin natural populations of trees
• Optimal allocation of resources
• Selection for a genetically diverse host population
• Maintain tree ranges
• Succession: nutrient cycling
“Emergent diseases”:
diseases on the rise
• New introduced, exotic, organisms
• Good gone bad: e.g. climate change or
human activities trigger excessive
pathogenicity of native organism
DISEASE TRIANGLE
Pathogen
Host
Environment
DISEASE TRIANGLE
HIGH DISEASE
Pathogen
Host
Environment
Pathogen
Does it need a wound to infect a host?
Can it survive in the environment without a host?
soil, water
on alternate host
How does it move around?
airborne/waterborne
animal vectors
humans
Host
Must be physically present with pathogen
Must be physically compatible with pathogen
Must provide window of opportunity for infection
Genetic resistance?
often lack of resistance
if disease is introduced
What type of resistance?
simple= one gene
complex=several genes
100
90
80
70
60
50
40
30
20
10
0
Simple
Complex
Environment
Climatic
As modified per human management
Species composition
Plant density
“Emergent diseases”:
1: host
• New host-pathogen combinations:
exotic hosts
hosts planted off site
Cypress canker by Seiridium
cardinale
• Pathogen was first described in California in the 20s.
Later it was described in Italy where it started a
serous epidemic of Italian cypress
• Belief that pathogen is native to California: is that true
and why is it then causing a significant disease in our
state?
Conidia of Seiridium
cardinale observed by
optical microscope
and SEM
Use of molecular genetics to
resolve issue of origin of
pathogen
• Used a technique similar to the one
used in human forensics
• Native populations should comprise
many different individuals genetically
• Introduced populations should be
genetically simpler because of
bottleneck related to introduction events
RESULTS: CA vs. Europe
o California population diverse
genetically= native to the state
o European population show no
diversity=introduced
Fig. 3
Symptoms caused by Seiridium cardinale on
Cupressus macrocarpa (above) and
xCupressocyparis leylandii (right)
Why a disease in CA?
• If pathogen is native to California, why is it
causing such a serious disease?
• We observed that disease incidence is
variable with:
– cypress species,
– location,
Range of susceptibility
• Leyland cypress, Italian, monterey are
listed as most susceptible
• Arizona and McKnob are regarded as
more resistant
Range of susceptibility
• 90% of Leyland are heavily infected
• 10% of monterey
• LEYLAND CYPRESS IS AN ORNAMENTAL
CROSS, NOT NATIVE
Range of susceptibility
• Monterey is more susceptible in inland areas
where it is NOT NATIVE: we believe that
colder temperatures cause more wounds
that lead to infection
CONCLUSIONS
• Cypress canker is a serious disease in
Europe because pathogen was introduced
• Cypress canker is a serious disease in
California because hosts were introduced
either through planting off range (Monterey
cypress) or because host is artificial creation
(Leyland cypress); extinction of LEYLAND is
most likely
“Emergent diseases”:
2: environmental changes
• Forestry and intensive forest use:
timber production
tree felling and creation of stumps
fire exclusion and increase in density
oversimplified forest composition
changes in forest composition
changes in forest structure
Heterobasidion root disease
• Heterobasidion (a bracket or shelf
mushroom) infects trees through
wounds and stumps, then it spreads
through the roots to neighboring trees
• With tree felling,stumps and wounds are
created, suddenly exponentially
increasing infection levels
Heterobasidion shelf fruit-body
Use of molecular genetics:
• Differentiate Heterobasidion on fir/sequoias
(H. occidentalis) from that on pine/junipers
(H.irregularis)
• Show that airborne meiospores are
responsible for most infection of
Heterobasidion
• Show that in pines most infections start on
stumps and that in true firs most infections on
wounds
True firs
Pines
Each spore is a genetically different individual:
In pines we found the same genetic individual in stumps and
adjacent trees indicating direct contagion between the two
In true firs and true firs/sequoias we find same individual
in adjacent standing trees indicating infection not linked
to stumps but to wounds on standing trees
CONCLUSIONS:
• Logging activities increase Heterobasidion
infection because of stump creation in pines
and because of wounding in true firs
sequoias
• We have shown that in pine stumps H.
irregularis and H. occidentalis can both be
present and create a new hybrid entity
• We have shown that in the past these
hybridization events have lead to sharing of
genes among these two species (Horizontal
gene transfers)
Armillaria root diseases
• Armillaria, the honey mushroom, normally infects the
roots of trees. It can be a saprobe and a pathogen
and is common amongst oaks
• If woodland composition shifts to pine/oak, pines
become the target of attacks and gaps in canopy
enlarge over time. Stress (e.g. flooding) exacerbates
susceptibility
Clusters of Armillaria
How Does it Infect?
OAK
or
PINE
Two means of dispersal
to other trees:
DEAD
OAK
1.Mycelium can grow
through direct root contacts
and grafts with uninfected
trees.
2.Rhizomorphs can grow
through soil to contact
uninfected trees.
SOURCE: http://www.forestpathology.org/dis_arm.htm
l
What are Rhizomorphs?
• …“conglomerations of
differentiated parallel
hyphae with a protective
melanized black rind
on the outside.”
SOURCE: http://www.nifg.org.uk/armillaria.htm
• Rhizomorphs are able to transport food and
nutrients long distances which allows the fungus to
grow through nutrient poor areas located between
large food sources such as stumps.
SOURCE: http://botit.botany.wisc.edu/toms_fungi/apr2002.html
Humongous Fungus
It’s One of
U-HAUL’s
“Bizarre
Roadside
Attractions”
http://botit.botany.wisc.edu/toms_fungi/apr2002.html
CONCLUSIONS
Human activities shifting from oak
woodlands to mixed oak-pine lead
to large mortality gaps in pines
around oaks if honey mushroom is
present
CHANGING SPECIES
COMPOSITION LEADS TO
SEVERE DISEASE
Many gaps with very little regeneration and have not closed in
Change in gap area 19721999
Year
Area in gaps
(m2)
Percent in gaps
1972
6125
3.5
1999
53,981
31
“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.
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
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
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