phytophthora species associated with urban and natural ... · p. parsiana - like p. taxon oaksoil...

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

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

199

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?

200

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

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)





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

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

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%

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

More Phytophthora positive samples in urban sites for all methods

207

3% 19% 25%


Soil - baiting and culturing 25%

40% 45%


Soil - Meta DNA barcoding

29%

52% 58%


Water - baiting and culturing

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

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

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 metabarcoding

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

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

212

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

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

phytophthora species associated with urban and natural ... · p. parsiana - like p. taxon oaksoil...

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