Random forest analysis reveals taxa predictive of Prunus replant disease in peach root microbiomes

Authors: KHAN, ABDUR - University Of California, Davis; WICAKSONO, WISNU - Universitat Graz; Ott, Natalia; Poret-Peterson, Amisha; Browne, Greg

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/20/2022
Publication Date: 10/13/2022
Citation: Khan, A.R., Wicaksono, W., Ott, N.J., Poret-Peterson, A.T., Browne, G.T. 2022. Random forest analysis reveals taxa predictive of Prunus replant disease in peach root microbiomes. PLOS ONE. 17(10). Article e0275587. https://doi.org/10.1371/journal.pone.0275587.
DOI: https://doi.org/10.1371/journal.pone.0275587

Interpretive Summary: Successive plantings of almond and other stone fruit orchards produce suboptimal growth and yield in many California soils due to a poorly understood soilborne disease complex, Prunus replant disease (PRD). We explored the hypothesis that PRD is mediated by certain bacterial, fungal, and water mold organisms in peach root systems. In a greenhouse test for PRD induction, portions of 10 different replant soils were given treatments of fumigation, pasteurization, or a control before being planted to peach seedlings. Ten weeks after planting, PRD induction was assessed among the soils. Those in which peach seedlings developed less shoot fresh weights in the control treatment, compared to the other treatments, were considered to be PRD inducing; the other soils were considered to be non-inducing. The roots were washed from the soil, frozen, extracted for total DNA, and used for metabarcoding of rRNA gene amplicons (a DNA fingerprinting approach) from bacteria, fungi, and oomycetes. High-throughput amplicon sequencing revealed that root microbial community shifts resulted from preplant treatments, and specific taxa were associated with PRD-induction in the controls. Random Forests (RF) analysis discriminated effectively between PRD-inducing and non-inducing root communities. Several RF top ranked amplicon sequence variants (ASVs) of Streptomyces, Steroidobacter, and Niastella were enriched in roots of PRD-affected plants, and relative abundances of these bacterial taxa were negatively correlated with plant biomass. On other hand, abundances of bacterial ASVs of Rhizobium, Rhizobacter, and Emiticicia and oomycete ASVs of Pythium were positively correlated with plant biomass. Thus, our findings were consistent with a hypothesis that root associated microbial communities contribute to induction of PRD and suggested specific taxa that may mediate the disease.

Technical Abstract: Successive plantings of almond and other Prunus species produce suboptimal growth and yield in many California soils due to a poorly understood soilborne disease complex, Prunus replant disease (PRD). We explored the hypothesis that PRD is mediated by certain microbial taxa in peach root systems. In a greenhouse assay for PRD induction, portions of 10 different replant soils were given treatments of fumigation, pasteurization, or a control before being planted to peach seedlings. Ten weeks after planting, PRD induction was assessed among the soils. Those that had reduced plant fresh weights in the control, compared to the other treatments, were considered to be PRD inducing; the other soils were considered non-inducing. The roots were washed from the soil, frozen, extracted for total DNA, and used for metabarcoding of rRNA gene amplicons from bacteria, fungi, and oomycetes. High-throughput amplicon sequencing revealed that root microbial community shifts resulted from preplant treatments, and specific taxa were associated with PRD-induction in the controls. Random Forests (RF) analysis discriminated effectively between PRD-inducing and non-inducing root communities. Several RF top ranked amplicon sequence variants (ASVs) of Streptomyces, Steroidobacter, and Niastella were enriched in roots of PRD-affected plants, and relative abundances of these bacterial taxa were negatively correlated with plant biomass. On other hand, abundances of bacterial ASVs of Rhizobium, Rhizobacter, and Emiticicia and oomycete ASVs of Pythium were positively correlated with plant biomass. Thus, our findings were consistent with a hypothesis that root associated microbial communities contribute to induction of PRD and suggested specific taxa that may mediate the disease.