phytophthora species associated with urban and natural ... · p. parsiana - like p. taxon oaksoil...
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Phytophthora species associated with urban and natural
environments in Vancouver and Victoria, BC
Angela Dale, Nicolas Feau, Julien Ponchart, Guillaume Bilodeau, Jean
Berube, and Richard Hamelin
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Phytophthora – Plant Destroyer!!!
– Billion dollar losses in
agricultural industry
– Large scale mortality in forests
– Many have multiple hosts
– Have been known to jump to new hosts
– Affect trade through restrictions and quarantines
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Plant Destroyer … Really?
• Many notorious pathogens are associated with human activities – Agriculture – Trade – Forestry
• In many cases, large scale diseases result from the
movement of pathogens into new or un-natural habitats
• What is the impact of urban activities on the natural Phytophthora community structure in southwest BC?
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Natural Phytophthora community
• Most of our knowledge of the genus is limited to species associated with large-scale disease in agricultural and forest systems
• Recent studies suggest a diverse Phytophthora community in natural systems
• Many newly described species not associated with disease 201
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Field Sampling
Vancouver & Victoria
Urban
CDF
CWH
Urban natural interface
CDF
CWH
natural
CDF
CWH
202
Leaf baiting (2011)
Water samples (2012, 2013)
Soil samples (2012, 2013)
Water samples (2012, 2013)
Water samples (2012, 2013)
Soil samples (2012, 2013)
Soil samples (2012, 2013)
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Urban, interface and natural sites
203
Natural site: forested area with as little urban surroundings as possible
Interface site: natural park inside urban setting
Urban site: agricultural or residential region
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Soil and Water collections
204
• 10 sampling locations in each region
• 2012 fall and 2013 spring/summer
Baiting & culturing
Barcoding with ITS1 and 2
Meta DNA barcoding
ITS1 (metagenomics)
Soil samples
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Phytophthora are a small proportion of the Oomycete community in soil
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0%
20%
40%
60%
80%
100%
Natural Interface Urban
Fall 2012
Other Oomycetes
Pythium
Apodachlya
Saprolegnia
Aphanomyces
Phytophthora
Lagena
LagenidiumNatural Interface Urban
Summer 2013
% Phytophthora
1.5% 0.6% 2.0% 0.4% 0.9% 0.4%
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More Phytophthora positive samples in urban sites
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0%
10%
20%
30%
40%
50%
60%
CR SA GT BW GL CV PS HM PR HV BP MD SV
Natural
Interface Urban
Per
cen
t o
f sa
mp
les
wit
h
Ph
yto
ph
tho
ra
19%
37%
43%
Chi-square = 29.6573. The p-value is < 0.00001
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More Phytophthora positive samples in urban sites for all methods
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3% 19% 25%
Natural Interface Urban
Soil - baiting and culturing 25%
40% 45%
Natural Interface Urban
Soil - Meta DNA barcoding
29%
52% 58%
Natural Interface Urban
Water - baiting and culturing
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Urban sites have greater diversity
208
0.90
0.90
0.91
0.91
0.92
0.92
0.93
2.3
2.4
2.5
2.6
2.7
2.8
2.9
3
Urban Interface Natural
Sim
pso
n e
ven
ess
ind
ex
Shan
no
n r
ich
nes
s In
dex
Shannon richness Simpson eveness
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0% 20% 40% 60% 80%
Urban
Interface
Natural
0% 20% 40% 60% 80%
P. drechsleriP. erythroseptica
P. fragariae/P rubiP. hibernalis
P. quercina - likeP. siskiyouensis
unknown sp 4P. ilicis
P. lateralisP. medicaginis x cryptogea
P. megaspermaP. nemorosa
P. gallicaP. pseudosyringae
Unknown sp 1Unknown sp 3
P. inundataP. multivora
P. pseudotsugaeUnknown sp 2
P. quercinaP. europaea/P. uliginosa
P. cactorumP. syringae
P. cryptogeaP. gregata
P. hydropathicaP. riparia
P. amnicolaP. irrigata
P. polonicaP. cambivora
P. intercalarisP. plurivora/P. citricola
P. parsiana - likeP. taxon Oaksoil
P. chlamydosporaP. lacustris
P. gonapodyides
Frequency of species found
Water baiting and culturing Soil baiting and culturing
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0% 20% 40% 60% 80%
P. drechsleriP. erythroseptica
P. fragariae/P rubiP. hibernalis
P. quercina - likeP. siskiyouensis
unknown sp 4P. ilicis
P. lateralisP. medicaginis x cryptogea
P. megaspermaP. nemorosa
P. gallicaP. pseudosyringae
Unknown sp 1Unknown sp 3
P. inundataP. multivora
P. pseudotsugaeUnknown sp 2
P. quercinaP. europaea/P. uliginosa
P. cactorumP. syringae
P. cryptogeaP. gregata
P. hydropathicaP. riparia
P. amnicolaP. irrigata
P. polonicaP. cambivora
P. intercalarisP. plurivora/P. citricola
P. parsiana - likeP. taxon Oaksoil
P. chlamydosporaP. lacustris
P. gonapodyides
0% 20% 40% 60% 80%
Urban
Interface
Natural
Frequency of species found
Water baiting and culturing Soil baiting, culturing & DNA meta- barcoding
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Baiting vs DNA metabarcoding
• Largest differences between years (fall 2012 vs spring/summer 2013)
• Baiting and culturing soil did not yield a lot of Phytophthora
• Meta DNA-barcoding better for soil
• Higher diversity in meta-DNA barcoding
211
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
Soil Water Soil
% s
amp
les
wit
h P
hyto
ph
tho
ra
2012
2013
Baiting and culturing
Meta DNA-barcoding
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Conclusions
• Phytophthora make up a relatively small part of the soil community
• Urban environments have a higher Phytophthora diversity than natural environments
• Some species found in urban environments are common crop pathogens
• Some invasive species may be moving into natural environments
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Implications
• Increase our understanding of Phytophthora species and the native Phytophthora community
• This may help in detection, tracking, monitoring and managing outbreaks
• Possible early detection of invasive species
• Evaluate effectiveness of current quarantine measures
213
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Thanks!!!
• Special thanks to – the BC Ministry of Forests, an the
cities of Vancouver and Victoria – the members of the Hamelin lab for
assistance and field work – all the TAIGA project collaborators
214