Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain

Carolyn E. Riddell, Debbie Frederickson-Matika, April C. Armstrong, Matt Elliot, Jack Forster, Pete E. Hedley, Jenny Morris, Peter Thorpe, David E. L. Cooke, Leighton Pritchard, Paul M. Sharp, Sarah Green

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Abstract

Forests and woodlands worldwide are being severely impacted by invasive Phytophthora species, with initial outbreaks in some cases occurring on host trees located in public parks and gardens. These highly disturbed sites with diverse planting practices may indeed act as harbours for invasive Phytophthora pathogens which are particularly well adapted to surviving in soil. High throughput Illumina sequencing was used to analyse Phytophthora species diversity in soil samples collected from 14 public garden/amenity woodland sites in northern Britain. Bioinformatic analyses revealed some limitations to using internal transcribed spacer as the barcode region; namely reporting of false positives and ambiguous species matches. Taking this into account, 35 distinct sequences were amplified across the sites, corresponding to 23 known Phytophthora species as well as twelve oomycete sequences with no match to any known Phytophthora species. Phytophthora pseudosyringae and P. austrocedri, both of which cause serious damage to trees and are regarded as fairly recent introductions to Britain, were the two most abundant Phytophthora species detected. There was no evidence that any of the detected Phytophthora species were more associated with any one type of host, healthy or otherwise. This study has demonstrated the ubiquity and diversity of Phytophthora species endemic in highly managed, extensively planted soil environments in Britain. Suggested improvements to the methodology and the practical implications of the findings in terms of mitigating Phytophthora spread and impact are discussed.

Original languageEnglish
Article numbere6931
Pages (from-to)1-31
Number of pages31
JournalPeerJ
Volume7
DOIs
Publication statusPublished - 16 May 2019

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public gardens
Phytophthora
United Kingdom
woodlands
Soil
Soils
soil
Biodiversity
Pathogens
Bioinformatics
Ports and harbors
Throughput
Libocedrus
Gardens
Forests
Oomycetes
Introduced Species
barcoding
edaphic factors
Computational Biology

Keywords

  • Phytophthora
  • Metabarcoding
  • ITS1 barcode
  • Illumina sequencing
  • Soil
  • Species diversity

Cite this

Riddell, C. E., Frederickson-Matika, D., Armstrong, A. C., Elliot, M., Forster, J., Hedley, P. E., ... Green, S. (2019). Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain. PeerJ, 7, 1-31. [e6931]. https://doi.org/10.7717/peerj.6931
Riddell, Carolyn E. ; Frederickson-Matika, Debbie ; Armstrong, April C. ; Elliot, Matt ; Forster, Jack ; Hedley, Pete E. ; Morris, Jenny ; Thorpe, Peter ; Cooke, David E. L. ; Pritchard, Leighton ; Sharp, Paul M. ; Green, Sarah. / Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain. In: PeerJ. 2019 ; Vol. 7. pp. 1-31.
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Riddell, CE, Frederickson-Matika, D, Armstrong, AC, Elliot, M, Forster, J, Hedley, PE, Morris, J, Thorpe, P, Cooke, DEL, Pritchard, L, Sharp, PM & Green, S 2019, 'Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain', PeerJ, vol. 7, e6931, pp. 1-31. https://doi.org/10.7717/peerj.6931

Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain. / Riddell, Carolyn E.; Frederickson-Matika, Debbie; Armstrong, April C.; Elliot, Matt; Forster, Jack; Hedley, Pete E.; Morris, Jenny; Thorpe, Peter; Cooke, David E. L.; Pritchard, Leighton; Sharp, Paul M.; Green, Sarah.

In: PeerJ, Vol. 7, e6931, 16.05.2019, p. 1-31.

Research output: Contribution to journalArticle

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AU - Riddell, Carolyn E.

AU - Frederickson-Matika, Debbie

AU - Armstrong, April C.

AU - Elliot, Matt

AU - Forster, Jack

AU - Hedley, Pete E.

AU - Morris, Jenny

AU - Thorpe, Peter

AU - Cooke, David E. L.

AU - Pritchard, Leighton

AU - Sharp, Paul M.

AU - Green, Sarah

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N2 - Forests and woodlands worldwide are being severely impacted by invasive Phytophthora species, with initial outbreaks in some cases occurring on host trees located in public parks and gardens. These highly disturbed sites with diverse planting practices may indeed act as harbours for invasive Phytophthora pathogens which are particularly well adapted to surviving in soil. High throughput Illumina sequencing was used to analyse Phytophthora species diversity in soil samples collected from 14 public garden/amenity woodland sites in northern Britain. Bioinformatic analyses revealed some limitations to using internal transcribed spacer as the barcode region; namely reporting of false positives and ambiguous species matches. Taking this into account, 35 distinct sequences were amplified across the sites, corresponding to 23 known Phytophthora species as well as twelve oomycete sequences with no match to any known Phytophthora species. Phytophthora pseudosyringae and P. austrocedri, both of which cause serious damage to trees and are regarded as fairly recent introductions to Britain, were the two most abundant Phytophthora species detected. There was no evidence that any of the detected Phytophthora species were more associated with any one type of host, healthy or otherwise. This study has demonstrated the ubiquity and diversity of Phytophthora species endemic in highly managed, extensively planted soil environments in Britain. Suggested improvements to the methodology and the practical implications of the findings in terms of mitigating Phytophthora spread and impact are discussed.

AB - Forests and woodlands worldwide are being severely impacted by invasive Phytophthora species, with initial outbreaks in some cases occurring on host trees located in public parks and gardens. These highly disturbed sites with diverse planting practices may indeed act as harbours for invasive Phytophthora pathogens which are particularly well adapted to surviving in soil. High throughput Illumina sequencing was used to analyse Phytophthora species diversity in soil samples collected from 14 public garden/amenity woodland sites in northern Britain. Bioinformatic analyses revealed some limitations to using internal transcribed spacer as the barcode region; namely reporting of false positives and ambiguous species matches. Taking this into account, 35 distinct sequences were amplified across the sites, corresponding to 23 known Phytophthora species as well as twelve oomycete sequences with no match to any known Phytophthora species. Phytophthora pseudosyringae and P. austrocedri, both of which cause serious damage to trees and are regarded as fairly recent introductions to Britain, were the two most abundant Phytophthora species detected. There was no evidence that any of the detected Phytophthora species were more associated with any one type of host, healthy or otherwise. This study has demonstrated the ubiquity and diversity of Phytophthora species endemic in highly managed, extensively planted soil environments in Britain. Suggested improvements to the methodology and the practical implications of the findings in terms of mitigating Phytophthora spread and impact are discussed.

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KW - Metabarcoding

KW - ITS1 barcode

KW - Illumina sequencing

KW - Soil

KW - Species diversity

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