Next Article in Journal
Variations in Soil Properties and CO2 Emissions of a Temperate Forest Gully Soil along a Topographical Gradient
Previous Article in Journal
Evaluation of Early Bark Beetle Infestation Localization by Drone-Based Monoterpene Detection
Previous Article in Special Issue
Phytophthora Introductions in Restoration Areas: Responding to Protect California Native Flora from Human-Assisted Pathogen Spread
Open AccessArticle

Diversity of Phytophthora Species Detected in Disturbed and Undisturbed British Soils Using High-Throughput Sequencing Targeting ITS rRNA and COI mtDNA Regions

1
Spanish National Research Council (CSIC), Institute for Sustainable Agriculture, Alameda del Obispo s/n, 14004 Córdoba, Spain
2
Forest Research, Northern Research Station, Roslin EH25 9SY, UK
3
NIAB EMR, East Malling, Kent ME19 6BJ, UK
4
Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Rimvydas Vasaitis
Forests 2021, 12(2), 229; https://doi.org/10.3390/f12020229
Received: 11 January 2021 / Revised: 10 February 2021 / Accepted: 12 February 2021 / Published: 17 February 2021
Disease outbreaks caused by introduced Phytophthora species have been increasing in British forests and woodlands in recent years. A better knowledge of the Phytophthora communities already present in the UK is of great importance when developing management and mitigation strategies for these diseases. To do this, soils were sampled in “disturbed” sites, meaning sites frequently visited by the public, with recent and new plantings or soil disturbances versus more “natural” forest and woodland sites with little disturbance or management. Phytophthora diversity was assessed using high-throughput Illumina sequencing targeting the widely accepted barcoding Internal Transcribed Spacer 1 (ITS1) region of rRNA and comparing it with the mitochondrial cytochrome c oxidase I (COI) gene. Isolation of Phytophthora was run in parallel. Nothophytophthora spp. and Phytophthora spp. were detected in 79 and 41 of the 132 locations of the 14 studied sites when using ITS or COI, respectively. A total of 20 Phytophthora amplicon sequence variants (ASVs) were assigned to known Phytophthora species from eight clades (1a, 2, 2b, 3a, 5, 6b, 7a, 8b, 8c, 8d, 10a, and 10b) and 12 ASVs from six clades (1a, 2c, 3a, 3b, 6b, 7a, 8b, 8c, and 8d) when using ITS or COI, respectively. Only at two locations were the results in agreement for ITS, COI, and isolation. Additionally, 21 and 17 unknown Phytophthora phylotypes were detected using the ITS and COI, respectively. Several Phytophthora spp. within clades 7 and 8, including very important forest pathogens such as P. austrocedri and P. ramorum, were identified and found more frequently at “disturbed” sites. Additionally, eight ASVs identified as Nothophytophthora spp. were detected representing the first report of species within this new genus in Britain. Only three species not known to be present in Britain (P. castaneae, P. capsici, and P. fallax) were detected with the ITS primers and not with COI. To confirm the presence of these or any potential new Phytophthora species, sites should be re-sampled for confirmation. Additionally, there is a need to confirm if these species are a threat to British trees and try to establish any eradication measures required to mitigate Phytophthora spread in Britain. View Full-Text
Keywords: metabarcoding; forest diseases; oomycetes; soilborne pathogens metabarcoding; forest diseases; oomycetes; soilborne pathogens
Show Figures

Figure 1

MDPI and ACS Style

Landa, B.B.; Arias-Giraldo, L.F.; Henricot, B.; Montes-Borrego, M.; Shuttleworth, L.A.; Pérez-Sierra, A. Diversity of Phytophthora Species Detected in Disturbed and Undisturbed British Soils Using High-Throughput Sequencing Targeting ITS rRNA and COI mtDNA Regions. Forests 2021, 12, 229. https://doi.org/10.3390/f12020229

AMA Style

Landa BB, Arias-Giraldo LF, Henricot B, Montes-Borrego M, Shuttleworth LA, Pérez-Sierra A. Diversity of Phytophthora Species Detected in Disturbed and Undisturbed British Soils Using High-Throughput Sequencing Targeting ITS rRNA and COI mtDNA Regions. Forests. 2021; 12(2):229. https://doi.org/10.3390/f12020229

Chicago/Turabian Style

Landa, Blanca B.; Arias-Giraldo, Luis F.; Henricot, Béatrice; Montes-Borrego, Miguel; Shuttleworth, Lucas A.; Pérez-Sierra, Ana. 2021. "Diversity of Phytophthora Species Detected in Disturbed and Undisturbed British Soils Using High-Throughput Sequencing Targeting ITS rRNA and COI mtDNA Regions" Forests 12, no. 2: 229. https://doi.org/10.3390/f12020229

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop