the fun-tastic world of fun-gi espm 107 matteo garbelotto€¦ · mycorrhizae: definition •...
TRANSCRIPT
The FUN-TASTICThe FUN-TASTIC
world ofworld of
FUN-GIFUN-GI
ESPM 107ESPM 107
Matteo Matteo GarbelottoGarbelotto
Photo: Amanita muscaria in Picea sp. root.
WHAT ARE FUNGI ?WHAT ARE FUNGI ?
• Individuals belonging to the kingdom fungi
• They are actually more closely related to animals than
plants (cell wall contains chitin, do not photosynthesize)
• The feed by extrogenous digestion (food base digested
outside their cells and then simple elements absorbed )
• Indefinite growth: size can range from unicellular
organisms such as yeasts to the largest beings in the
world
Largest living organisms in theLargest living organisms in the
world are fungiworld are fungi
Aerial view of a single fungalAerial view of a single fungal
individual growing in the soil andindividual growing in the soil and
killing treeskilling trees
Tens of acres occupied by a single individual, older thanTens of acres occupied by a single individual, older than
5000 years!!!! (Northern5000 years!!!! (Northern Michigan)Michigan)
Thanks to their web-like indefiniteThanks to their web-like indefinite
growth in soil and plant substratesgrowth in soil and plant substrates
and their way of digesting nutrientsand their way of digesting nutrients
fungi play a critical role in recyclingfungi play a critical role in recycling
nutrients which can then benutrients which can then be
reutilized by plantsreutilized 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 The weblike weblike structure of fungi, usuallystructure of fungi, usually
immersed in the soil or in plant matter isimmersed in the soil or in plant matter is
involved in an essential symbiosis thatinvolved in an essential symbiosis that
greatly enhances the ability of plants togreatly enhances the ability of plants to growgrow
•piant
•fungus
The visible part of root tips ofThe visible part of root tips of
most trees is actually a mantlemost trees is actually a mantle
of fungal of fungal hyphae hyphae fused with thefused with the
plant tissueplant 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 There are thousands of mycorrhzial mycorrhzial fungalfungal
species, and only at times do they produce thespecies, and only at times do they produce the
classical fruit body (e.g.mushrooms) aboveclassical fruit body (e.g.mushrooms) above
groundground
•In absence of fruit body: how can we identify them?
Diversity of fungi, but all have ideal structure for plantinfection:– hypha/cord/rhizomorph/infection peg/appressorium
– Sexual vs. asexual reproduction: can do both
– Do not photosinthesize
– Chitin in cell wall
– Exogenous digestion
– Indefinite growth
– Phenotypic plasticity and pleomorphisms
Septa
Pores
Pores
CELLS
Fungi… again!
•• ASCOASCOMYCETES
•• BASIDIOBASIDIOMYCETES
• OOMYCETES (fungus-like, water molds)
ASCOASCOMYCETES
•• Yeasts (fermentation,Yeasts (fermentation, human mycoses)human mycoses)
•• Truffles, morelsTruffles, morels
•• Penicillia Penicillia (penicillin), (penicillin), Fusaria Fusaria (potent(potent
toxins, damping off of seedlings), moldstoxins, 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
BASIDIOBASIDIOMYCETES
•• Mushrooms. Mushrooms. mycorrhizalmycorrhizal
•• Wood decay organismsWood decay organisms
• Rusts, Smuts
• Yeasts and damping off
Toadstools and huitacochle are
both basidiomycetes
Basidium means “club”, it
carries the basidiospores
(dispersion propagules) naked
Mycorrhizae are Fungi => absorptive(heterotrophic) => they need hosts =Plants.
Principal mycorrhizal groups:Ascomycetes, Basidiomycetes andZygomycetes.
Mycorrhizae: definition
• Mycorrhiza = in Greek “fungus-root” (Frank, 1885).
• Mycorrhizas are multifaceted associations comprising diverse
morphological, functional and evolutionary categories.
• Mycorrhizas are associations between fungal hyphae and organs of higher
plants concerned with absorption of substances from the soil.
“A symbiotic association essential for one or both partners,
between a fungus (specialized for life in soils and plants) and a
root (or other substrate-contacting organ) of a living plant, that
is primarily responsible for nutrient transfer. Mycorrhizas
occur in a specialized plant organ where intimate contact
results from synchronized plant-fungus development”.
• Most mycorrhizae mutualistic (= beneficial association relationship
between a plant root and a fungus), but not all. Full spectrum of variation
in plant-fungus association.
• There appears to be a continuum of plant responses to mycorrhizal
colonization ranging from positive to neutral or negative.
• In this way mycorrhizal fungi have a wide diversity of roles and can also
function as endophytes, necrotrophs and antagonists of non-host plants,
with roles that can vary during the life of associations. Possible phases:
» Free-living.
» Endophytic.
» Balanced mycorrhizas.
» Exploitative mycorrhizas
» Antagonistic.
» Necrotrophic.
Description and Ecology (1)
Description and ecology (2)
• Most mycorrhizas can be described as balanced mutualistic
associations in which the fungus and plant exchange commodities
required for the growth and survival of both partners.
• The presence of mycorrhiza can increase the uptake of plant nutrients,
specially immobile ions such as P, Zn and Cu, but also mobile ions
such as S, Ca, K, Fe, Mg, Mn, Cl, Br, and N.
• They can increase plant resistance to drought, through improved
absorbance area.
• Increase tolerance to adverse conditions: heavy metals, salinity, pH,…
• The harsher the environment for plants, the more important the role of
mycorrhizae.
• The role of mycorrhizae can also change when the host plant is
stressed, e.g.: Tricholoma matsutake.
• E.g.: high levels of P in soil can inhibit spore germination in some VAM
species.
• Many other benefits: growth hormones, protection from pathogens,…
• Many species in the same plant species, some mycorrhizae shared by
several species, even between woody and herbaceous.
• There can be mycelial connections between neighbor plants (hyphal
networks).
• The majority of mycorrhizal associations provide substantial benefits to
both plants and fungi, and most plants (>90%) need them for their
development. Plants vs. mycorrhizae:
– Obligately mycorrhizal.
– Facultatively mycorrhizal.
– Nonmycorrhizal.
Description and ecology (3)
• ECM species belong to asco-, basidio-, and zygomycetes.
• ECM associations are characterized by the presence of the Hartig Net.
(=labyrinthine hyphae between root cells) and the mantle:
Hartig Net: hyphal envelope around active cortical cells. Primary zone
nutrient transfer fungus-plant.
Mantle: mat of fungal symbiont envoloping around ECM roots, either
smooth or with radiating hyphae (mycelial strands). Increase
absorption area.
• Most ECM are considered obligate simbionts incapable of independent life
without plants.
• ECM infections are initiated from spores, sclerotia (“mycelia =
underground spores”) , hyphae and/or roots of trees.
• Most common among forest and ornamental tree species, in families such
as: Pinaceae, Salicaceae , Betulaceae, Rosaceae, Leguminosae, Ericaceae,
and Juglandaceae.
ECM (Ectomycorrhizas) (1)
• ECM species can range from one host to many.
• Many ECM fruit bodies are edible mushrooms.
• Two basic morphological categories:
• Angiosperms (epidermal).
• Gimnosperms (cortical).
ECM (Ectomycorrhizas) (2)
Amanita caesarea
Different ECM in Angiosperms
and Gimnosperms
(epidermal and cortical).
Diagram of
typical ECM
A.muscaria in P. strobus
Mantle of ECM in P. tremuloidesAstraeus pteridis in E. maculata
A. muscaria in P. radiata
Hartig net in P. tremuloides root.
Suillus subluteus with P.
resinosa
• Vesicular arbuscular mycorrhizas (VAM) (= endomycorrhizas, endotrophic
mycorrhizas)
• Characterized by intracellular root penetration of root cortical cells:
Arbuscules: branch haustoria within root cortex cells; nutrient
exchange between the two symbionts.
Vesicules: hyphal swellings formed within the cells of plant roots (not
always present), to accumulate storage products .
• Produced by Glomalean fungi: Class Glomeromycota (=Zygomicota,
Glomales).
• Some plants can have both VAM and ECM.
• VAM are the most widespread and common root-fungus associations.
• All VAM are obligate simbionts.
• Structures in roots: hyphae, arbuscules, vesicules.
• Structure in soils: hyphae spores
VAM (Vesicular arbuscular mycorrhizas) (1)
VAM (2)
• About 80% plant species present VAM.
• However, apparently little diversity: few genera and few dozenspecies.
Arbuscule Glomus mosseae
VAM in Asarum canadense root
Importance of mycorrhizae in forestry and thefood industry (1)
Forestry and Range Management:
• Spatial distribution of mycorrhizae complex => relation with
establishment of ectomycorrhizal vegetation.
• Reforestations: inoculations. 2 billion tree seedlings grown annually in
USA => need of mycorrhizae (enhance survival).
• Mycorrhizae in herbaceous communities: increase importance in
restoration with herbaceous communities. Much research still needed.
• Relations herbaceous vs. woody species mycorrhizae.
• Consequences to forest and range management: environmental
conditions vs. mushrooms (ECM, basically).
• Particularly important in restoration of arid and semiarid ecosystems
• (=> Mediterranean areas, among others).
Food industry
• There are about 2500 sp of edible mushrooms. It includes about 200 edible
ECM, among them the most expensive and sought: T. melanosporum, T.
magnatum, Tricholoma matsutake, Boletus edulis, Cantharellus cibarius
and Amanita caesarea.
• Estimated annual value of mushrooms: 7.5x109 U$.
• Most of the ECM mushrooms are now supplied from forest harvests.
Others
• Recreational collecting.
• Importance of commercial harvesting for many regional economies.
• VAM as biofertilizer:
• Increase crops with lower levels of nutrients.
• Reduction in agrochemical.
• Bioethical aspects.
• Mycorrhiza in control of soil borne pathogens: interactions mycorrhiza-
pathogen enhance breeding resistance.
Importance of mycorrhizae in forestry and thefood industry (2)
Genetic variation and evolution in fungi
Fungi possess many features that make them ideal for genetic research:
• Most fungi can be grown in pure culture: avoid environmental variability.
• High grow rates, very large number of progeny from each cross, short life
cycle, short genome size and low chromosome number. E.g. 23
chromosomes in humans against 7-20 in Eumycota => 3000 millions of bp
in nuclear DNA in humans vs. 19-47x106 bp in Eumycota.
• Fungi alternate difference n, 2n and/or n+n life patterns = more complex
life cycle, more variety of genetic approaches Haploid life cycles, many
genes expressed then => easy to detect mutant alleles compared with
diploid organisms.
Molecular techniques have been used to accurately identify EMs and their
isolates, detect infections, and monitor the development of infections in
soils.
• In EM among other markers PCR-RFLP (ITS, nuclear rRNA, mRNA) and
RAPD (in disuse). Isozymes to determine species.
• In VAM SSCP and RFLP, mainly (also RAPD).
However, microorganisms populations genetics have been delayed from
animals and plants pop gen, much information is now generation.
Three essential concepts:
1. Individual: careful with mycelial fungi (like mycorrhizae). Take into
account genetic identity and physical continuity, e.g., a colony from a
single spore = one individual.
2. Population (genetics): individuals which, as a result of proximity and
genetic similarity, readily interbreed and exchange genes.
3. Species: theoretical and practical difficulties in defining and
delimiting species => use of genospecies (limits of genetic
exchange).
Population genetics in fungi
Life cycles, mating systems and geneticexchange
Life cycles and the sexual process:
2 Cell (n) fusion (plasmogamy) 1 Dykarion (n+n)
Nuclear fusion (karyogamy) (2n) Meiosis (n)
Mating systems = breeding systems = sel-sterile = heterothallic: prevention of
mating between genetically identical cells. There are several kinds of
mating systems (bifactorial, two loci involved: AB) => increase variability.
Genetic exchange: if genetic differences between homologous chromosomes,
two ways of genetic recombination:
i. Chromosomes from both partners in the preceeding sexual fusion.
ii. Crossing-over = homologous chromosomes break and exchange genetic
material.
=> Increase variability.
(See Figure 5.4. page 214. Carlile and Watkinson, 1994).
Life cycle ofAscomycetes
Life cycle ofBasidiomycetes
Life cycle ofZygomycetes
• Traditional approach: morphology.
• Current approach: molecular biology. Importance of molecular
biology and population genetics on mycorrhizae and on fungi
markets.
• Future: classification trees based on genetics.
• “Mycorrhizas are three way-way interactions of plants, fungi,
and soils, so we must expect environmental and edaphic
factors to affect their structure and function”.
Mycorrhizas and molecular biology
Need of genetic characterization
• Soils that support vegetation are also inhabited by different communities
of fungi, with different and some unknown connections.
• In a forest, each single tree support sa complex community of
mycorrhizal species, that change with the development of the plant.
As an example I discuss Quercus garryana from Valentine et al. (2004):
• Virtually all root tips of Quercus garryana are ectomycorrhizal.
• Identification of species using morphological characteristics and RFLP.
Sample size: 20 trees, 160 samples in southern Oregon.
• Samples from the 10-20 cm of soil and from sporocarps above ground
(haploid).
• 39 ECM morphotypes: number reduced when RFLP.
• DNA analyses usually shows that morphotypes with slight variations in
morphology are genetically distinct. But not always.
• In other species and studies up to 80 morphotypes.
The mycorrhizal community (1)
• Usually many species occurring few times (79% in only one soil core).
• The most abundant Cenococcum geophilum (75% of soil cores): easily
recognizable from its characteristic radiate mantle morphology. Does this fact
partly affect its abundance in most studies?.
• Decrease in mycorrhizal diversity as a function of distance to the tree,
tending towards zero (consequences to management).
• ITS-RFLP patterns from ECM growing below ground did not match those
of sporocarps growing above ground: saprotrophes, fruiting
heterogeneity,… => Generally poor correlation between sporocarps and
ECM status or abundance.
Multiple species of mycorrhizas coexist within cm on a single fine root.
“Island effect”: isolated trees have limited access to ectomycorrhizal inocula
and therefore attain low ectomycorrhizal diversity.
The mycorrhizal community (2)
TheMycorrhizalcommunity
(3)
Morphotypes!!!
Tanoak mycorrhizal communities
Douglas-fir: large mycorrhizal tips,
Tanoak: extremely small
Materials and methods: DNA is
electrically charged and if you put into an electric
field and in a gel matrix it will move through the
gel, following the current
Electrophoresis
The smaller the DNAfragment, the faster (thefurther) it will move
Gel placed in EthidiumBromide, fluorescesunder UV light
Conclusions
• EM taxa shared between two species, but notshown the same individual network is shared
• Lithocarpus may benefit, either if carbon isobtained from Douglas-fir, or at least cost ofmycorrhization is decreased for tanoaks
• More diversity in Douglas-fir probably explainedby older age
• A whole group of EM taxa more abundant ontanoaks: PREFERENTIAL ON TANOAKS?
• Shared EM are common, but great spatialheterogeneity
Study Area
Whitethorn
18S 5.8S 28S
ITS1 ITS2
Lactarius sp.
ITS Alignments
Hydnellumcaeruleum
Cenococcum
Ascom
ycete 37
Phialophora 1
Phialophora 2
Ascom
ycete 6
Lactarius 1
Basidiom
ycete 26
Basidiom
ycete 10
Ram
aria fennica var. violaceibrunnea
Ram
aria formosa
Cortinariod sp. 2
Piloderm
a 3
Basidiom
ycete 12
Cortinariod sp. 5
Melanogaster tuberiform
is
Russula 6
Russula 8
Tricholom
a 3
Ascom
ycete 11
Ascom
ycete 12
Ascom
ycete 2
Phialocephala fortinii
Ascom
ycete 29
Basidiom
ycete 14
Basidiom
ycete 23
Basidiom
ycete 32
Basidiom
ycete 4
Cortinariod sp. 1
Fungal 3
Piloderm
a 1
Russula 1
Russula em
etica
Russula 4
Russula 7
Sebacina 1
Tricholom
a 1
Tricholom
a 5
Alpolva trappei
Am
anita 1
Am
anita gemm
ata
Ascom
ycete 1
Ascom
ycete 10
Ascom
ycete 13
Ascom
ycete 14
Ascom
ycete 15
Ascom
ycete 16
Ascom
ycete 17
Ascom
ycete 18
Ascom
ycete 19
Ascom
ycete 20
Ascom
ycete 21
Ascom
ycete 22
Mortierella verticillata
Ascom
ycete 24
Ascom
ycete 25
Ascom
ycete 26
Ascom
ycete 28
Ascom
ycete 3
Ascom
ycete 30
Ascom
ycete 31
Neonectria radicola var. radicola
Ascom
ycete 33
Ascom
ycete 34
Ascom
ycete 35
Ascom
ycete 36
Ascom
ycete 4
Ascom
ycete 5
Ascom
ycete 7
Ascom
ycete 8
Ascom
ycete 9
Basidiom
ycete 1
Hydnellum
caeruleum
Basidiom
ycete 13
Basidiom
ycete 17
Basidiom
ycete 18
Basidiom
ycete 19
Basidiom
ycete 2
Entolom
a alpicola
Basidiom
ycete 21
Inocybe flocculosa
Basidiom
ycete 24
Basidiom
ycete 25
Basidiom
ycete 27
Basidiom
ycete 28
Basidiom
ycete 29
Basidiom
ycete 3
Basidiom
ycete 30
Basidiom
ycete 31
Basidiom
ycete 5
Basidiom
ycete 6
Basidiom
ycete 7
Basidiom
ycete 8
Basidiom
ycete 9
Boletus cf. edulis
Cortinariod sp. 3
Cortinariod sp. 4
Fungal 1
Fungal 2
Hygrophoroid sp. 1
Hym
enoscyphus 1
Lactarius 2
Lactarius 3
Lactarius 4
Lyophyllum 1
Phialophora 3
Piloderm
a 2
Piloderm
a 4
Russula 2
Russula 9
Sebacina 2
Thelephoroid 1
Thelephoroid 2
Thelephoroid 3
Thelephoroid 4
Thelephoroid 5
Tom
entella 1
Tom
entella 2
Tom
entella 3
Tom
entella 4
Tom
entella 5
Tom
entella 6
Tom
entella 7
Tom
entella 8
Tricholom
a 2
Tricholom
a 4
Tricholom
a
Tricholo
Trich
T
taxon sampled
Basidiomycete treeTricholomatoid
Cortinarioid
Amanitoid
Boletoid
RussuloidAtheliod
Thelephoroid
Gomphoid
Sebacina
Ramaria formosa
Tricholoma matsutake
Cenococcum geophilum
Sebacina
Tricholoma
Russuloid
6 SPECIES
3 SPECIES
6 SPECIES
11 SPECIES
In Moorea…
• Unknown number of VAM
• One species of EM (in Guyana 75)
– On exotic Pinus caribaea
– DNA places it as close relative of nurserygenotype from Europe
? Two characteristics are associated with EMin tropical and subtropical regions:monodominance and invasiveness (ability tofare well independent of soil) ?
Ectomycorrhizal symbionts
Photo: Todd Osmundson
Rhizopogon sp.
Found only with the introduced Caribbean Pine (Pinus caribaea),and possibly with She-oak (a.k.a., Australian Ironwood; Casaurinaequisetifolia).
In Ecuador…
• Pinus radiata introduced at high elevation
• Trees dwarfed, but mushroom productionastonishingly high
• Only five mycorrhizal species introduced (hencelack of competition)
• Mycorrhizae may be able to use carbon sourcefrom rich volcanic carbon layer where grassesgrow---->long term impact on site productivity!
In Guyana…• Legumes, mostly Cesalpionidae
• No effect of EM on litter decomposition
• Clear effect of Ca
In South-East Asia
• Family Dipterocarpaceae is EM
• Tropical soils poor in minerals (especially if primarycover is taken out)
• EM increase survival and growth of seedlings in poorsoils (P, K, Mg, and CA)
• Significant host-specificity reported: possibly related topattern of distribution of trees (e.g. in Guyana, Costa-Rica, and Mexico EM associated with monodominance)
DISEASE!!
• Symptoms vs. signs; e.g. chlorosis vs.
fruit-body
• The disease triangle
host-pathogen-environment
• Susceptibility of individuals or of portionsof individuals
• Genetic variability
• Basic compatibility (susceptibility) betweenhost and pathogen
• Ability to withstand physiologicalalterations
Cankers byCankers by P. ramorum P. ramorum at 3 monthsat 3 monthsfrom time of inoculation on two coastfrom time of inoculation on two coastlive oakslive oaks
host-pathogen-environment
• Basic compatibility with host (virulence)
• Ability to maintain diversity: sex vs. no sex
• Size of genetic pool
• Agressiveness (pathogenicity) towardshosts
• Ability to survive without host
Chlamydospores of Chlamydospores of P. ramorumP. ramorum
Pr75Pr75 Qa Qa MontereyMonterey Pr87 Am Marin Pr87 Am Marin Pr86b Am Marin Pr86b Am Marin Pr86a Am Marin Pr86a Am Marin Pr84 Soil Marin Pr84 Soil Marin Pr82 Vo Marin Pr82 Vo Marin Pr80 Vo Marin Pr80 Vo Marin Pr72 Pr72 Rh Rh Alameda Alameda Pr65 Pr65 Qp Qp Santa Cruz Santa Cruz Pr58 Vo Marin Pr58 Vo Marin Pr50 Pr50 Qa Qa Sonoma Sonoma Pr201b Pr201b Rh Rh Santa Cruz Santa Cruz Pr201a Pr201a Rh Rh Santa Cruz Santa Cruz Pr47b Pr47b Qa Qa Sonoma Sonoma Pr47a Pr47a Qa Qa Sonoma Sonoma Pr35 Pr35 Qa Qa Sonoma Sonoma Pr28 Ld Sonoma Pr28 Ld Sonoma Pr24 Pr24 Qa Qa Sonoma Sonoma Pr22 Pr22 Qa Qa Sonoma Sonoma Pr20 Pr20 Qa Qa Sonoma Sonoma Pr19 Pr19 Qa Qa Napa Napa Pr16 Pr16 Qa Qa Santa Cruz Santa Cruz Pr13 Pr13 Qa Qa Santa Cruz Santa Cruz Pr11b Pr11b Qa Qa Monterey Monterey Pr11a Pr11a Qa Qa Monterey Monterey Pr10 Ld Monterey Pr10 Ld Monterey Pr08 Pr08 Qa Qa Napa Napa Pr06 Pr06 Qa Qa Marin Marin Pr05 Ld Marin Pr05 Ld Marin Pr04 Pr04 Qk Qk Marin Marin Pr03 Ld Marin Pr03 Ld Marin Pr88 Pr88 Uc Uc Sonoma Sonoma Pr89 Pr89 Uc Uc Sonoma Sonoma Pr90 Pr90 Qa Qa Marin Marin Pr91 Pr91 Uc Uc Sonoma Sonoma Pr97 Pr97 Qa Qa Napa Napa Pr102 Pr102 Qa Qa Marin Marin Pr103 Ld Marin Pr103 Ld Marin Pr104 Ld Marin Pr104 Ld Marin Pr107 Pr107 Uc Uc Sonoma Sonoma Pr110 Pr110 Uc Uc Marin Marin Pr112 Pr112 Uc Uc Marin Marin Pr113 Pr113 Uc Uc Marin Marin Pr114 Pr114 Uc Uc Marin Marin Pr115 Pr115 Uc Uc Marin Marin Pr116 Pr116 Uc Uc Marin Marin Pr136 Pr136 Uc Uc Marin Marin Pr156 Ld Oregon Pr156 Ld Oregon Pr157 Ld Oregon Pr157 Ld Oregon Pr158 Ld Oregon Pr158 Ld Oregon PrJL3.1 Ss Sonoma PrJL3.1 Ss Sonoma PrSDC21.6 Ss Sonoma PrSDC21.6 Ss Sonoma
Pr36 Pr36 Qa Qa Sonoma Sonoma Pr27 Pr27 Qa Qa Marin Marin
Pr57 Ld Santa Clara Pr57 Ld Santa Clara Pr70 Vo Marin Pr70 Vo Marin Pr159 Ld Oregon Pr159 Ld Oregon
Pr52a Pr52a Rh Rh Santa Cruz Santa Cruz Pr52b Pr52b Rh Rh Santa Cruz Santa Cruz PrCoen Rh PrCoen Rh Santa Cruz Santa Cruz
PrJL3.5.3 Ss Sonoma PrJL3.5.3 Ss Sonoma Pr106 Pr106 Uc Uc Sonoma Sonoma
Pr71 Pr71 Qa Qa Sonoma Sonoma Pr01 Pr01 Qa Qa Marin Marin
PrE9/95 PrE9/95 Rh Rh Germany Germany PrE16/99 PrE16/99 Vb Vb Germany Germany
PrE12/98 PrE12/98 Rh Rh Germany Germany PrE104 Water Germany PrE104 Water Germany
PrE69082 PrE69082 Rh Rh Germany Germany PrE9/3 Water Germany PrE9/3 Water Germany
PrE14/98-a PrE14/98-a Rh Rh Germany Germany Pl33 Cl Del Norte
Pl16 Soil Josephine Pl27 Tb Del Norte0.1
Clone groupClone group
European groupEuropean group
P. P. lateralislateralis
((outgroupoutgroup))
100100
9696
9393
8989
6767
host-pathogen-environment
• Temperatures
• Shading
• Relative humidity
• Free standing water
• pH and any potentially predisposingfactors
• Nutrient status
Co
lon
y d
iam
ete
r (m
m)
at
13 d
ay
sC
olo
ny
dia
me
ter
(mm
) a
t 13 d
ay
s
Presence of free water
Between 6 and 12 hours requiredBetween 6 and 12 hours requiredfor infection of bay leavesfor infection of bay leaves
++
Temperature at 19 CTemperature at 19 C
COMMON GARDEN EXPERIMENTS NECESSARY
DISEASE: plant microbe
interaction• Basic compatibility need to be present
• Chemotaxis, thighmotropy
• Avirulence in pathogen matched by resistancein host according to the gene for gene model(vertical resistance)
• Pathogenicity factors such as toxins andenzymes important in the infection process
• Multi-locus , additive, horizontal resistanceconferred by multiple loci: harder to harness inbreeding programs but more durable
Gene for gene
• Resistance in host is dominant
• Virulence is recessive
ar aR
Ar AR
Because there are costs involved in havingresistance and in being virulent, bothtypes of alleles are maintained. This leadsto maintenance of genetic diversity of host.
Host specificity in tropical
ecosystems• Obvious signs of ongoing co-evolution
(pathogen more aggressive on plants that arerelated) indicate host specialization important intropics
• Gradient from biotrophic (high hostspecialization) to necrotrophic (low hostspecialization)
• If low diversity in host: more host specialization
• In limiting conditions (ability to grow in anoxia)then generalism expected
Some pathogen roles in
natural plant communities
• Selection of individuals best suited for the site
• Maintenance of genetic diversity and stability in host
plant populations
• Establishment or maintenance of host geographic
ranges
• Natural succession
• Regulation of stand density, structure, and
composition
Human activities affecting
disease incidence in forests
• Introduction of exotic pathogens
• Planting trees in inappropriate sites
• Simplifying genetic make-up of host
• 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
Categories of wild plant
diseases• 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
Stress cone crop BS on DF
Seedling diseases
• Specific diseases, but also diseases of adulttrees can affect seedlings
• Pythium, Phytophthora, Rhizoctonia, Fusariumare 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 conduciveto 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
A foliar pathogen employed as a
biological control of Myconia• Myconia extremely invasive plant from South
and Central America (ERH/EA)
• Fungal pathogen Colletotrichumgleosporoidoedes can be a foliar pathogen
• Released in Tahiti in early 2000s
• Pros: it seems to spread naturally even betweenislands
• Cons: it does not seem very effective especiallyin lower areas and/or where host populations aresmaller
Photo:
Donald E. Gardner, University of Hawaii
Better understanding why
Colletotrichum is not
effective• Are plants responding differently to pathogen
because they are genetically different: test withcommon garden experiment and artificialinoculation
• Are environmental conditions driving infectionsuccess: test with field inoculations at differentelevation
• Survey and check for relationship betweendensity and infection levels
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 fromdrought, increased productivity
• Classic example of coevolutionary development:Epichloe infects “flowers” of sexuallyreproducing fescue, Neotyphodium is verticallytransmitted in species whose sexualreproductive ability has been aborted
Endophytes: from mutualism
to parasitism
• In wheat: pathogenic fungi and phylloplane fungi bothpresents endophytically
• In Europe and Puerto Rico: leaves of healthy woodyplants harbor wood decay fungi (asociation with veins?)
• In coniferous forests: some wood decay fungi endophyticand their growth triggered by increased oxygen let in bywounds or self pruning, e.g. Echinodontium tinctorium
Tropical leaves: “hotspots of
diversity”• In a transect from the arctic to Panama:
– Increased incidence
– Increased diversity
– Broader host range
• Endophytes include many undescribed species. 20+ species perhost. Would increase at least 4 times the estimate of fungi in theworld from, 1.5 (based on 6 taxa per plant in the UK) to 6 M. Manyspecies not found anywhere else!!
• Horizontal transfer, favored by leaf wetness, but timing and hostpreference are still unclear
• Because of the large cryptic diversity of soil andplant-associated fungi, an important component of the2008 fungal sampling was the development ofprotocols for obtaining fungal DNA from substratesincluding soil, leaves, and wood, and the constructionof clone libraries from which DNA can be sequencedand analyzed to assess phyletic diversity. Culturing ofleaf and wood substrates was conducted in order toprovide collections for taxonomic identification.Sampling of airborne spores was conducted in order tocapture additional fungal species not associated withthe focal plant species.
Environmental sampling: overview
Leaf library 1 (3 host species):• High PCR/sequencing success rate from colony picks
• Tags obtained through search on 79 of 95 T3/T7-primed clones• 44 unique top BLAST hits
• (BLAST-based) “species” shared between 3 hosts =4; 2 hosts=9
Preliminary Results (III): clone libraries
Testing for timing of infection
and host preference
• Monitor leaves from flushing to maturity of two sympatricspecies (bag some leaves as control)
• Isolate endophytic fungi from both after surfacesterilization to avoid contaminants
• Subculture isolates on media amended with leaves fromeither host and see if there is an effect
Do endophytes of Miconia
protect it from Colletotrichum
• Theobroma cacao more resistant to infection byPhytophthora when leaves are endophytically colonized
• If it is possible to obtain Miconia without endophytes acomparative inoculation could be performed
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
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 representthe most economically damaging type ofdiseases
• Effects: tree mortality (direct and indirect),cull, effect on forest structure, effect oncomposition, stand density, growth rate
• Heterobasidion, Armillaria, Phellinus weirii,Phytophthora cinnamomi
Wood-decay fungi
• The most important group of macrofungi (both basidio-
and ascomycetes) on Moorea
• Considered essential element for nutrient cycling, soil
formation and carbon budget in ecosystem
• Important element for successful regeneration
• Important in creating physical space for new growth in
understory
DEADWOODOLOGY:the ecology of dead wood
• White rotters (attack
lignin)
• Large substrates
(trunk)
• Host specific
• Endophytic stage
• Early colonizers
• Pathogenic
• Persistent fruitbodies
• Brown rotters (only
attack cellulose)
• Small substrates
(twigs,small branch)
• Generalist
• Active decayers only
• Late colonizers
• Saprobic
• Ephemeral fruitbodies
Species richness of decay fungi
• Amount of coarse woody debris (CWD):estimated that 90% reduction in CWD, 50%species extinction
• Size of CWD positively correlated to absolutenumbers (not per unit of volume though): space& ecology (presence of heartwood, etc.)
• Size of habitat not as important as age of habitat
Wood decay in tropics
• Richness of spp. correlates with better decomposition:Cyrilla racemiflora in Puerto Rico
• CWD not larger in tropics: why? Faster decay rates,more effective and/or rich decay communities?
• Number of macrofungi correlates with number of trees
• How does this all fit with suggested– Less host specificity of fungi in tropics
– Less diversity of fungi in tropics (based on macrofungi)
Testing for host specificity
• Survey mushrooms: focus on common ones, and oneones growing on relatively intact substrates
• Based on observations, make prediction of host specificvs. generalist decayer
• Grow in media amended with host tissue andunameneded
• Show enhanced growth of host-specific fungus on host-amended medium
Sampling: transects + sporocarp
collecting
• Vast majority consists of wood decay species,particularly Polyporaceae s.l., Marasmiaceae s.l.,Mycenaceae
Preliminary Results (I): sporocarp
taxonomy
Wood saprotrophs and pathogens
Photos: Todd Osmundson
Most commonly observed in Inocarpus fagifer (Tahitian Chestnut) -Hibiscus tiliaceus forests; occasionally on coconut palm (Cocosnucifera) and in cloud forests.
LEFT: Ganoderma sp. (lucidumgroup), a white rot fungus
ABOVE RIGHT: Auricularia cf. polytricha, the “wood ear” or “tree ear” fungus. Aclose relative of this rubbery-gelatinous mushroom is commonly found, thinlysliced, in Chinese soups.
RIGHT: Schizophyllum commune, the“split-gill fungus,” is reported nearlyworldwide.
LEFT: Pleurotus sp., a relative of the oyster mushroom.
Wood saprotrophs and pathogens
(continued)
Photos: Todd Osmundson
ABOVE: Polypores (Polyporus and relatives); diverse and difficult to identify. A varietyof morphological forms (shelflike, crustlike, stalked, etc.) are found on Moorea.
LEFT: Lentinus sajor-caju, reported from tropicalhabitats in many parts of the world.
ABOVE RIGHT: A variety of small, white mushroomscan be found on decaying wood; Campanella sp. is justone example.
Litter saprotrophs
Photos: Todd Osmundson
Decomposers of dead plant leaves and herbaceousstems
Phallus sp., a netted stinkhorn.
Agaricus sp., a relative of the portobellomushroom (though the species pictured here isprobably mildly toxic).
Seed saprotrophsAt present, only reported from seeds of Tahitian Chestnut(Inocarpus fagifer)
LEFT: Melanotus? sp., a fungus that appears to be restrictedto I. fagifer seeds.
RIGHT: Psathyrella sp. Similar-looking fungi are found on theground in Moorea; DNA sequence data are therefore beingexamined to determine whether the taxon found on decaying I.fagifer seeds is distinct.
Photos: Todd Osmundson
Dung saprotrophs
Photos: Todd Osmundson
Coprinus sp. onhorse dung
Anellaria sp.on horse dung
Additionally, Psilocybesp. is reported by localsto be found on cattledung, but has not beencollected to-date byBiocode mycologists
Found on dung of introduced mammalian herbivores.
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:
– 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
• In the short/medium term with long lived trees a
pathogen is likely to increase its virulence
• In long term, selection pressure should result in
widespread resistance among the host
Island Biogeography: a fungal
perspective• In the 1920’s widespread was the belief
that viable fungal spores were everywhereand that they would germinate whereverconditions were favorable
• This is still a strong belief for microbialecologists
• Fungi are microbes, but in many respectstheir ecology and evolution is explained byecology and evolution of their hosts
Genetic structure
• Seems to be highest for host specific fungi
and lowest for generalist species.
Wood saprobes (large metapopulations)
Generalist pathogens (need habitat)
Mycorrhizal fungi (need habitat)
Host specific pathogens (genetic structure mimicsclosely host or is more restricted than hostdepending on biology)
Effects shaping current structure
• Age of isolation
• Distance from neighbor
• Size of population
• Dispersal ability
• Specificity of substrate
• Lack of habitat
• Presence of geographicalbarrier
• Number and size offounding events
•Sp
ore
loa
d
•distance
Results• Simplified genetic structure of populations
– Low genotypic diversity
– Loss of polymorphisms
– Higher number of fixed and rare alleles
• Simplified communities– Lower number of species
• Highly structured populations– Lack of migration where habitat not present
– Inability to overcome barriers (mountains)
• Speciation
Fungal examples 1: broad
metapopulations• Generalist late phase wood decayer
Schyzophyllum communis & Lentinus eodesspp. complex
• Migration over large areas, not planetary, butthousands of km
• Dispersal hypothesized: airborne in strong windsfor first and infected wood for second
Fungal examples 2: barriers to gene flow• Tricholoma matsutake is genetically structured between
valleys in Hunnan, but not within valleys
Fungal examples 3: lack of habitat• Coriolopsis caperata grows exclusively on white
mangroves. When mangroves are missing for more than50 km we see strong structure as a result of lack ofmigration. If population is small, loss of polymorphismswas detected. Mangrove stands are like islands
Distances =PhiST between pairs of
populations. Above diagonal is the Probability
Random distance > Observed distance (1000
iterations).
Coco Solo Bocas David
Coco Solo 0.000 0.000 0.000
Bocas 0.2083 0.000 0.000
David 0.1109 0.2533 0.000
•Fungus from mangrove
not the same as from other
hosts: mangrove stands
can be regarded as islands
Coalescent analyses identified split
between Caribbean and Pacific
populations. Unidirectional migration from
Caribbean followed by lack of gene flow:
protosecies?
Fungal examples 4: effect of lack of
habitat (lack of host) on mycorrhizal
community:Islands of trees which survived Mount Vision Fire
log(S) = 0.53 + 0.20 Log(Area)
Log(m2)
0 1 2 3 4 5 6
0.2
0.4
0.6
0.8
1.0
1.2
1.4
1.6
1.8
R? = 0.74
Power Law Species Area Relationship for EM Fungi
p = 0.0003
Log S
pecie
s
•Trend for distance of patch from forest but not as strong as size