Phytophthora Species Associated with Roots of Native and Non-native Trees in Natural and Managed Forests


Roots act as a biological filter that exclusively allows only a portion of the soil-associated microbial diversity to infect the plant. This microbial diversity includes organisms both beneficial and detrimental to plants. Phytophthora species are among the most important groups of detrimental microbes that cause various soil-borne plant diseases. We used a metabarcoding approach with Phytophthora-specific primers to compare the diversity and richness of Phytophthora species associated with roots of native and non-native trees, using different types of soil inocula collected from native and managed forests. Specifically, we analysed (1) roots of two non-native tree species (Eucalyptus grandis and Acacia mearnsii) and native trees, (2) roots of two non-native tree species from an in vivo plant baiting trial, (3) roots collected from the field versus those from the baiting trial, and (4) roots and soil samples collected from the field. The origin of the soil and the interaction between root and soil significantly influenced Phytophthora species richness. Moreover, species richness and community composition were significantly different between the field root samples and field soil samples with a higher number of Phytophthora species in the soil than in the roots. The results also revealed a substantial and previously undetected diversity of Phytophthora species from South Africa.

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The University of Pretoria, the Tree Protection Co-operative Programme (TPCP) and the Department of Science and Technology–National Research Foundation (DST-NRF) Centre of Excellence in Tree Health Biotechnology (CTHB) provided financial support for the present study. M.V. was supported by ‘Juan de la Cierva Program’, Ministry of Economy, Industry and Competitiveness, Government of Spain. We thank Mrs. Diane White of Murdoch University and Mrs. Frances Brigg from Western Australian State Agricultural Biotechnology Centre for their assistance with 454 sequencings. Sappi Ltd. and the Institute for Commercial Forestry Research (ICFR), Pietermaritzburg, South Africa provided seeds of E. grandis and A. mearnsii, respectively. We thank Mr. Jan Nagel, Mr. Conrad Trollip, Mr. Joey Hulbert and Ms. Mandy Messal, as well as foresters from NCT Forestry Co-operative Limited and TWK Agri for assistance with the fieldwork. Dr. Almuth Hammerbacher (FABI) provided substantial assistance in revising the manuscript, for which we are most grateful.

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Correspondence to Tanay Bose.

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FIG. S1. Soil and root collection sites across Mpumalanga and KwaZulu-Natal provinces of South Africa. (A, B) Soil and root samples were collected from four sites spanning across KwaZulu-Natal and Mpumalanga Provinces of South Africa. Close-up maps of the sampling sites at (C) Howick, (D) Vryheid, (E) Melmoth and (F) Commondale. For each close-up map of the collection sites, pointers in blue = Eucalyptus grandis, red = Acacia mearnsii and purple = natural forest. Bar equals to 100 m. FIG. S2. Flowchart for soil and root sampling at each collection sites. At each site, a total of 12 soil and root samples (six each) were collected. For the field-collected root samples, amplicon library was directly prepared from the total genomic DNA. Each soil sample was divided into two parts and baited with sterile grown seedlings of Eucalyptus grandis and Acacia mearnsii. After 5 months of incubation, the roots were harvested from each seedling followed by preparation of amplicon library. In total, we sequenced 72 samples (18 samples per collection site × 4 sites) from four collection sites. FIG. S3. Maximum-likelihood phylogenies using complete ITS1 gene region for Phytophthora species recovered from metabarcoding of root samples. The consensus sequence of MOTUs for each taxon was used for these five analyses. Suffix HTRSA indicates MOTUs recovered from the present study. Taxa names in pink font indicate new reports from South Africa. Numerical on the branches show bootstrap value > 70%. (DOCX 42451 kb)


Table S1. A list of Phytophthora species detected through environmental sequencing of soil and root samples from South Africa (present and a previous study (Bose et al. 2018)). Data for all first reports for formally described taxa were sourced from IDphy ( (DOCX 37 kb)

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Bose, T., Wingfield, M.J., Roux, J. et al. Phytophthora Species Associated with Roots of Native and Non-native Trees in Natural and Managed Forests. Microb Ecol (2020).

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  • Community composition
  • Forestry
  • Metabarcoding
  • Species diversity
  • South Africa