Characterization of soils conducive and non-conducive to Prunus replant disease

PLoS One. 2021 Dec 10;16(12):e0260394. doi: 10.1371/journal.pone.0260394. eCollection 2021.

Abstract

Successive orchard plantings of almond and other Prunus species exhibit reduced growth and yield in many California soils. This phenomenon, known as Prunus replant disease (PRD), can be prevented by preplant soil fumigation or anaerobic soil disinfestation, but its etiology is poorly understood and its incidence and severity are hard to predict. We report here on relationships among physicochemical variables, microbial community structure, and PRD induction in 25 diverse replant soils from California. In a greenhouse bioassay, soil was considered to be "PRD-inducing" when growth of peach seedlings in it was significantly increased by preplant fumigation and pasteurization, compared to an untreated control. PRD was induced in 18 of the 25 soils, and PRD severity correlated positively with soil exchangeable-K, pH, %clay, total %N, and electrical conductivity. The structure of bacterial, fungal, and oomycete communities differed significantly between the PRD-inducing and non-inducing soils, based on PERMANOVA of Bray Curtis dissimilarities. Bacterial class MB-A2-108 of phylum Actinobacteria had high relative abundances among PRD-inducing soils, while Bacteroidia were relatively abundant among non-inducing soils. Among fungi, many ASVs classified only to kingdom level were relatively abundant among PRD-inducing soils whereas ASVs of Trichoderma were relatively abundant among non-inducing soils. Random forest classification effectively discriminated between PRD-inducing and non-inducing soils, revealing many bacterial ASVs with high explanatory values. Random forest regression effectively accounted for PRD severity, with soil exchangeable-K and pH having high predictive value. Our work revealed several biotic and abiotic variables worthy of further examination in PRD etiology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Electric Conductivity
  • Fumigation
  • Hydrogen-Ion Concentration
  • Microbiota
  • Nitrogen / metabolism
  • Plant Diseases / microbiology*
  • Potassium / metabolism
  • Prunus / metabolism*
  • Seedlings
  • Soil
  • Soil Microbiology

Substances

  • Soil
  • Nitrogen
  • Potassium

Associated data

  • figshare/10.6084/m9.figshare.13661294

Grants and funding

G.T. Browne received partial funding for this research from the Almond Board of California (https://www.almonds.com/), (grant number PATH11) and the California Department of Pesticide Regulation (https://www.cdpr.ca.gov/) (grant number 12-PML-R003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.