Association of Phytophthora with Declining Vegetation in an Urban Forest Environment

Abstract

<jats:p>Urban forests consist of various environments from intensely managed spaces to conservation areas and are often reservoirs of a diverse range of invasive pathogens due to their introduction through the nursery trade. Pathogens are likely to persist because the urban forest contains a mixture of native and exotic plant species, and the environmental conditions are often less than ideal for the trees. To test the impact of different land management approaches on the Phytophthora community, 236 discrete soil and root samples were collected from declining trees in 91 parks and nature reserves in Joondalup, Western Australia (WA). Sampling targeted an extensive variety of declining native trees and shrubs, from families known to be susceptible to Phytophthora. A sub-sample was set aside and DNA extracted for metabarcoding using Phytophthora-specific primers; the remaining soil and root sample was baited for the isolation of Phytophthora. We considered the effect on the Phytophthora community of park class and area, soil family, and the change in canopy cover or health as determined through sequential measurements using remote sensing. Of the 236 samples, baiting techniques detected Phytophthora species from 24 samples (18 parks), while metabarcoding detected Phytophthora from 168 samples (64 parks). Overall, forty-four Phytophthora phylotypes were detected. Considering only sampling sites where Phytophthora was detected, species richness averaged 5.82 (range 1–21) for samples and 9.23 (range 2–24) for parks. Phytophthora multivora was the most frequently found species followed by P. arenaria, P. amnicola and P. cinnamomi. While park area and canopy cover had a significant effect on Phytophthora community the R2 values were very low, indicating they have had little effect in shaping the community. Phytophthora cinnamomi and P. multivora, the two most invasive species, often co-occurring (61% of samples); however, the communities with P. multivora were more common than those with P. cinnamomi, reflecting observations over the past decade of the increasing importance of P. multivora as a pathogen in the urban environment.</jats:p>

Comparison of Primers for the Detection of Phytophthora (and Other Oomycetes) from Environmental Samples

“…Additionally, environmental DNA (eDNA) samples previously determined to contain various Phytophthora species were also amplified alone (runs 1-4) and together with the mock communities (runs 2-4). Individual eDNA samples from the study of Khdair et al [25] collected from parks in Perth, Western Australia were combined to generate four eDNA mixes (E1-4) expected to contain 16, 16, 26, and 32 species, respectively. #F = forward Illumina adaptor TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG; #R = reverse Illumina adaptor GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACAG; 1 forward only analysed; 2 amplification failed for P8, amplification was only successful for the mock community for P9; 3 P12 was tested for run4, but after repeated attempts we could not produce an PCR product; 4 P16 not used in current study as amplicon is too long for Illumina.…”

Globisporangium coniferarum sp. nov ., associated with conifers and Quercus spp.

“…Numerous oomycetes have been reported to be associated with the roots and rhizosphere of landscape trees. Phytophthora species have been reported to cause root rot and decline of trees, including conifers, in gardens, parks and nature reserve areas worldwide ( Erwin & Ribeiro 1996 , Barber et al 2013 , Jung et al 2019 , Giordana et al 2020 , Khdiar et al 2020 , Riolo et al 2020 , La Spada et al 2022 ). Several oomycetes have been reported from conifers in Iran, including P. nicotianae (from Cupressus arizonica and Pinus pinaster ), P. citrophthora (from Pinus sylvestris and Pinus elderica ), P. cactorum (from Pinus nigra ), P. citricola (from Pinus taeda ), and Pythium sp.…”

Survival of Phytophthora cryptogea and Phytophthora cactorum in Commercial Potting Substrates for Eucalyptus globulus Plants

“…Studies on the prevalence of Phytophthora species in an urban forest environment highlighted the need to understand which Phytophthora species become invasive and the pathways by which they move into the natural ecosystem [44]. There is a substantial capacity for several Phytophthora species such as Phytophthora × cambivora [12]; Phytophthora ramorum [10,11]; and Phytophthora cinnamomi to survive in potting mix components or soil [5,8,13,14].…”

“…Reducing the pathogen load in the plants for planting pathways is essential for attempts at improving the overall biosecurity in all parts of the world [4,22,47] Other approaches for reducing the impacts of invasive pathogens, such as testing and deploying host provenances showing greater resistance to a dominant pathogen [48], may prove successful but must also take into account the influence(s) of climate change on both the pathogens and hosts [49][50][51][52]. The often-reported diversity of Phytophthora species in regions with pathogen damage is a further factor complicating any approach using host resistance [30,44,53,54].…”