Download Lecture #6a ppt - College of Natural Resources, UC Berkeley

5th Quiz, Name, date, email
• Pick any two:
• Describe the difference between genotype and
phenotype. Which is the unit that natural selection
acts directly upon? Which is the unit of
inheritance?
• What is DNA barcoding
• Do we generally have to look at more or fewer
data when comparing closely related individuals
(as opposed to distantly related individuals)
• Imagine you are a plant pathologist and have been
asked to confirm whether a symptomatic tree in
Golden Gate Park has been infected with the
Sudden Oak Death pathogen. Descrube how you
might make this confirmation using genetic data
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, wallbound 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
DISEASES AND TREES
• What exactly is a disease? It is the outcome
of an interaction between a plant and the
environment, resulting in an altered
physiology of the host
• Sustained interaction=biotic
• Single event= abiotic
Human activities affecting
disease incidence in forests
• Introduction of exotic pathogens
• Planting trees in inappropriate sites
• Changing stand density, age structure,
composition, fire frequency
• Wound creation
• Pollution, etc.
Effects of fire exclusion
Effects of diseases on host
mortality, growth and reproduction
• Young plants killed before reaching
reproductive age
• Affect reproductive output
• Directly affect flowers and fruits
WGR
Complexity of forest diseases
• At the individual tree level: 3 dimensional
• At the landscape level” host diversity,
microclimates, etc.
• At the temporal level
Complexity of forest diseases
• Primary vs. secondary
• Introduced vs. native
• Air-dispersed vs. splash-dispersed, vs.
animal vectored
• Root disease vs. stem. vs. wilt, foliar
• Systemic or localized
Progression of cankers
Older canker with dry seep
Hypoxylon, a secondary
sapwood decayer will appear
Root disease center in true fir caused by H. annosum
Categories of wild plant diseases
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Seed decay
Seedling diseases
Foliage diseases
Systemic infections
Parasitic plants
Cankers, wilts , and diebacks
Root and butt rots
Floral diseases
Seed diseases
• Up to 88% mortality in tropical Uganda
• More significant when seed production is
episodic
Seedling diseases
• Specific diseases, but also diseases of adult trees
can affect seedlings
• Pythium, Phytophthora, Rhizoctonia, Fusarium
are the three most important ones
• Pre- vs. post-emergence
• Impact: up to 65% mortality in black cherry.
These diseases build up in litter
• Shady and moist environment is very conducive to
these diseases
Foliar diseases
• In general they reduce photosynthetic ability by reducing
leaf area. At times this reduction is actually beneficial
• Problem is accentuated in the case of small plants and in
the case other health issues are superimposed
• Often, e.g. with anthracnose,needle cast and rust diseases
leaves are point of entry for twig and branch infection with
permanent damage inflicted
Systemic infections
• Viral?
• Phytoplasmas
• Peronospora and smuts can lead to over
50% mortality
• Endophytism: usually considered beneficial
Grass endophytes
• Clavicipetaceae and grasses, e.g. tall fescue
• Mutualism: antiherbivory, protection from
drought, increased productivity
• Classic example of coevolutionary
development: Epichloe infects “flowers” of
sexually reproducing fescue, Neotyphodium
is vertically transmitted in species whose
sexual reproductive ability has been aborted
Parasitic plants
• True (Phoradendron) and dwarf mistletoe (Arceuthobium)
• Effects:
– Up to 65% reduction in growth (Douglas-fir)
– 3-4 fold mortality rate increase
– Reduced seed and cone production
Problem accentuated in multistoried uneven aged forests
Cankers, wilts, and die-backs
• Includes extremely aggressive, often easy to
import tree diseases: pine pitch canker,
Dutch elm disease, Chestnut blight, White
pine blister rust
• Lethal in most cases, generally narrow host
range with the exception of Sudden Oak
Death
Root diseases
• Extremely common, probably represent the
most economically damaging type of
diseases
• Effects: tree mortality (direct and indirect),
cull, effect on forest structure, effect on
composition, stand density, growth rate
• Heterobasidion, Armillaria, Phellinus
weirii, Phytophthora cinnamomi
Floral diseases
• Pollinator vectored smut on silene offers an example of
well known dynamic interaction in which pathogen drives
genetic variability of hosts and is affected by
environmental condition
• Puccinia monoica produces pseudoflowers that mimic real
flowers. Effects: reduction in seed production, reduction
in pollinators visits
POPULATION DYNAMICS
Species interactions and diversity
Density-dependence
• Most diseases show positive density dependence
• Negative dependence likely to be linked to limited
inoculum: e.g. vectors limited
• If pathogen is host-specific overall density may not be best
parameter, but density of susceptible host/race
• In some cases opposite may be true especially if alternate
hosts are taken into account
Counterweights to numerical
effects
• Compensatory response of survival can
exceed negative effect of pathogen
• “carry over” effects?
– NEGATIVE: progeny of infected individuals
less fit;
– POSITIVE; progeny more resistant (shown
with herbivory)
Disease and competition
• Competition normally is conducive to
increased rates of disease: limited resources
weaken hosts, contagion is easier
• Pathogens can actually cryptically drive
competition, by disproportionally affecting
one species and favoring another
Diseases and succession
• Soil feedbacks; normally it’s negative.
Plants growing in their own soil repeatedly
have higher mortality rate. This is the main
reason for agricultural rotations and in
natural systems ensures a trajectory towards
maintaining diversity
• Phellinus weirii takes out Douglas fir and
hemlock leaving room for alder
Janzen-Connol
• Regeneration near parents more at riak of becoming
infected by disease because of proximity to mother
(Botryosphaeria, Phytophthora spp.). Maintains spatial
heterogeneity in tropical forests
• Effects are difficult to measure if there is little host
diversity, not enough host-specificity on the pathogen side,
and if periodic disturbances play an important role in the
life of the ecosystem
The red queen hypothesis
• Coevolutionary arm race
• Dependent on:
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Generation time has a direct effect on rates of evolutionary change
Genetic variability available
Rates of outcrossing (Hardy-weinberg equilibrium)
Metapopulation structure
• Rapid generation time of pathogens. Reticulated evolution
very likely. Pathogens will be selected for INCREASED
virulence. The more gene flow, the more “swamping” both
in hosts and pathogens
• In the short/medium term with long lived trees a pathogen
is likely to increase its virulence, unless there is a trade off
between virulence and transmission
• In long term, selection pressure should result in
widespread resistance among the host
Frequency-, or density
dependent, or balancing selection
• New alleles, if beneficial because linked to
a trait linked to fitness will be positively
selected for.
– Example: two races of pathogen are present, but
only one resistant host variety, suggests second
pathogen race has arrived recently
What is a pathogen?
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Strictly speaking a pathogen is the causal agent of disease
Bacteria
Viruses
Nematodes
Stramenopiles
Algae
Phytoplasmas
Higher plants
Signs vs. symptoms
• Sign is any manifestation of the causal
agent: fruit-body
• Symptom is the manifestation of the effects
of the disease in the host
Nematodes
And of course… fungi
• Fungi: saprophytic, symbionts, and pathogens
• Polyphyletic group in evolutionary terms
– Basidiomycetes
Ascomycetes
Zygomycets
Animals
Plants
Red algae
Brown algae
Myxomycetes
Diversity of fungi, but all have ideal structure for plant
infection:
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hypha/cord/rhizomorph/infection peg/appressorium
Sexual vs. asexual reproduction: can do both
Do not photosynthesize
Chitin in cell wall
Exogenous digestion
Indefinite growth
Phenotypic plasticity and pleomorphisms
Fungi do not photosynthesize
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Biotrophic: mycorrhyzae, rusts
Endophites: clavicipetaceae,
Necrotrophic; most pathogens
Saprobes: primary (involved in litter
decomposition)
Septa
Pores
Pores
CELLS
Thanks to their web-like indefinite
growth in soil and plant substrates and
their way of digesting nutrients fungi
play a critical role in recycling
nutrients which can then be reutilized
by plants
•Fungi like this one will actually decay
the woody matter and physically free
space for new generations of trees,
besides recycling the nutrients
The weblike structure of fungi, usually
immersed in the soil or in plant matter is
involved in an essential symbiosis that greatly
enhances the ability of plants to grow
•piant
•fungus
The visible part of root tips of most
trees is actually a mantle of fungal
hyphae fused with the plant tissue
What is the deal of this
mutualism?
• Fungus absorbs nutrients for plants
• Plant gives fungus carbohydrates it produces via
photosynthesis
There are thousands of mycorrhzial fungal species,
and only at times do they produce the classical fruit
body (e.g.mushrooms) above ground
•In absence of fruit body: how can we identify them?
DNA can be extracted from any part of an
organism, like the web-like hyphae emanating from
this root tip
•DNA sequence
identified these threads
as Tricholoma
matsutake
Fungi… again!
• ASCOMYCETES
• BASIDIOMYCETES
• OOMYCETES (fungus-like, water molds)
ASCOMYCETES
• Yeasts (fermentation, human mycoses)
• Truffles, morels
• Penicillia (penicillin), Fusaria (potent
toxins, damping off of seedlings), molds
Ascus is the sack in which the
spores are contained
Asci can be placed on a disk
(apothecium), many apothecia
can be together in a fruitbody
Morel fruitbody
Asci can be carried inside a flask
(perithecium)
Nectria
Ploidy is mostly
n
BASIDIOMYCETES
• Mushrooms. mycorrhizal
• Wood decay organisms
• Rusts, Smuts
• Yeasts and damping off
Toadstools and huitacochle are
both basidiomycetes
Basidium means “club”, it carries
the basidiospores (dispersion
propagules) naked
Most of their life, they are
n+n (dikaryons), some rare
ones are diploid
Oomycetes
• Belong to the kingdom Stramenopila, used
to be called Chromista
• Phytophthora, Pythium, Saprolegnia
H20
Oomycetes are not fungi
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Cellulose in cell wall
Ploidy is 2n
Result of sexual activity is oospore
(2n)
Meiosis, somatogamy, caryogamy
all occur at the same time
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Water adapted biology, flagellate
phase
No septa, holocoenocytic hyphae
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Chitin in cell wall
Ploidy is n, or n+n
Result of sexual activity is a spore
n
Meiosis, somatogamy,caryogamy
are usually interupted by vegetative
(somatic phase)
Better adapted for aerial
transmission
Septate hyphae
Phytophthora
• Some important plant pathogens, with very
well known history
– Phytophthora infestans and the Irish potato
famine
– Phytopthora cinnamomi and the Jarrah dieback
in Australia
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.
Phytophthora: “plant
destructor”
• Best known pathogen whose long-distance
transport linked to agriculture.
– Infected root-stocks
– Infested soil
– Infected plants
70 species of Phytophthora
• 60 until a few years ago, research accelerated, especially
by molecular analyses
• Differentiated on basis of:
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Type of sexual intercourse
Type of sexual activity
Number of hosts
Ideal temperature
Type of biology
Evolutionary history (Waterhouse-Cooke)
Hyphae, sporangia, and zoospores of P. ramorum
Zoospore
Most of their lifecycle
they are 2n
Have cellulose in cell
wall
Not fungi!!, but look
like them because of
convergent evolution