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

Abstract

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.

Co-Infections by Fusarium circinatum and Phytophthora spp. on Pinus radiata: Complex Phenotypic and Molecular Interactions

“…Several Phytophthora species were reported to be associated with damping-off of seedlings, stem cankers, root rot, and decline of Pinus species, including P. austrocedri, P. cactorum, P. xcambivora, P. capsici, P. castaneae, P. cinnamomi sensu lato, P. citricola sensu lato, P. citrophthora, P. cryptogea, P. crassamura, P. drechsleri, P. fallax, P. humicola, P. kernoviae, P. nicotianae, P. obscura, P. pini, P. plurivora, P. syringae, and other unidentified Phytophthora spp. [29][30][31][32][33][34][35]. Pinus plants affected by Phytophthora crown and root rot show growth reduction, chlorosis, and decline [18].…”

“…During pathogen attack, different metabolic pathways are activated in the plant, including changes in primary energy-producing metabolism, plant defense mechanisms, and hormone signaling. Defense mechanisms are controlled by a series of genes, individually or synergistically involved in the resistance traits of plants [35][36][37][38]. As in the majority of plants, in conifers, the hypersensitive responses are the most commonly induced defense mechanisms against pathogens.…”

Epigenetic insight into regulatory role of chromatin covalent modifications in lifecycle and virulence of Phytophthora

“…Since then, many more Phytophthora species have been reported worldwide (Scott et al, 2019), with P. theobromicola being the most recently described species (Decloquement et al, 2021). Molecular phylogenetics and biogeographical data suggest the existence of around 326 Phytophthora species (Scott et al, 2019), and the reports of potential new species are still growing (Jeff-Ego et al, 2020;Legeay et al, 2020;Bose et al, 2021;Landa et al, 2021). Among the most studied species, P. infestans, P. ramorum, P. sojae, P. capsici, P. cinnamomi, and P. parasitica are considered in the Top 10 oomycete plant pathogens based on their scientific and economic importance (Kamoun et al, 2015).…”

“…theobromicola being the most recently described species (Decloquement et al ., 2021). Molecular phylogenetics and biogeographical data suggest the existence of around 326 Phytophthora species (Scott et al ., 2019), and the reports of potential new species are still growing (Jeff‐Ego et al ., 2020; Legeay et al ., 2020; Bose et al ., 2021; Landa et al ., 2021). Among the most studied species, P .…”

A new oomycete metabarcoding method using the rps10 gene

“…Riit et al (2016) developed primers targeting the ITS1 and ITS2 regions without the need for a semi-nested approach; those primers enabled assignment of 22% and 29% of OTUs to oomycetes (25% and 30% of reads, respectively). Other primers for ITS1 and other loci, including cytochrome c oxidase subunit I (cox1) and cytochrome c oxidase subunit II (cox2), have been used, but have either not been extensively tested or only target the genus Phytophthora (Esmaeili Taheri, Chatterton, Gossen, & McLaren, 2017;Fiore-Donno & Bonkowski, 2021;Landa et al, 2021;Riddell et al, 2019;Sapp et al, 2016). In summary, all the ITS1-based methods targeting oomycetes we are aware of have shortcomings regarding non-target amplification and/or taxonomic resolution.…”