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

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: 11/9/2021
Publication Date: 12/10/2021
Citation: Khan, A.R., Wicaksono, W., Ott, N.J., Poret-Peterson, A.T., Browne, G.T. 2021. Characterization of soils conducive and non-conducive to Prunus replant disease. PLoS ONE. 16(12). Article e0260394. https://doi.org/10.1371/journal.pone.0260394.
DOI: https://doi.org/10.1371/journal.pone.0260394

Interpretive Summary: In many California soils, successive orchard plantings of almond and other Prunus species exhibit stunted growth and reduced crop production for several years after replanting. The phenomenon, known as Prunus replant growth suppression or Prunus replant disease (PRD), can be prevented by preplant soil fumigation or anaerobic soil disinfestation, but its etiology is poorly understood. We related chemical, physical, and microbial variables among 25 diverse soils from California orchards and vineyards to the soils’ potential to induce PRD in a greenhouse bioassay. A soil was judged to have PRD induction potential when growth of Nemaguard peach seedlings in it was significantly increased by preplant fumigation or pasteurization, compared to growth in a non-treated control. We observed PRD induction in 18 out of 25 soils. Based on principal component analysis (a statistical approach that is used to relate biological responses to environmental variables), PRD induction potential was positively correlated with percentage of sand and negatively correlated with percentages of nitrogen and exchangeable potassium. The overall structures of soil microbial communities of bacteria, fungi and oomycetes based on Bray-Curtis dissimilarity distances differed significantly between PRD-inducing and non-inducing soils based on permutational analysis of variance (P = 0.002), but two-dimension non-metric multidimensional scaling of Bray-Curtis matrices failed to distinctly ordinate the inducing soils from non-inducing soils. Bacterial community structure among the soils was strongly correlated with soil pH and exchangeable K, but fungal and oomycete community structures were not significantly linked to soil variables. PRD-inducing soils were dominated by genera of sub-group-6 (phylum Acidobacteria), while non-inducing soils exhibited higher relative abundance of genus Pseudomonas. Among fungi, PRD-inducing soils were dominated by several poorly resolved ASVs classified only to the kingdom level, but non-inducing soils had a higher abundance of Trichoderma amplicon sequence variants. Our results suggested that examination of root microbial communities associated with PRD induction may be justified for additional insights into microbial associations with PRD induction in Prunus.

Technical Abstract: In many California soils, successive orchard plantings of almond and other Prunus species exhibit stunted growth and reduced crop production for several years after replanting. The phenomenon, known as Prunus replant growth suppression or Prunus replant disease (PRD), can be prevented by preplant soil fumigation or anaerobic soil disinfestation, but its etiology is poorly understood. We related physicochemical and microbial variables among 25 diverse soils from California orchards and vineyards to the soils’ potential to induce PRD in a greenhouse bioassay. A soil was judged to have PRD induction potential when growth of Nemaguard peach seedlings in it was significantly increased by preplant fumigation or pasteurization, compared to growth in a non-treated control. We observed PRD induction in 18 out of 25 soils. Based on principal component analysis, PRD induction potential was positively correlated with percentage of sand and negatively correlated with percentages of nitrogen and exchangeable potassium. The overall structures of microbial communities of bacteria, fungi and oomycetes based on Bray-Curtis dissimilarity distances differed significantly between PRD-inducing and non-inducing soils based on PERMANOVA (P = 0.002), but two-dimension non-metric multidimensional scaling of Bray-Curtis matrices failed to distinctly ordinate the inducing soils from non-inducing soils. Bacterial community structure among the soils was strongly correlated with soil pH and exchangeable K, but fungal and oomycete community structures were not significantly linked to soil variables. PRD-inducing soils were dominated by genera of sub-group-6 (phylum Acidobacteria), while non-inducing soils exhibited higher relative abundance of genus Pseudomonas. Among fungi, PRD-inducing soils were dominated by several poorly resolved ASVs classified only to the kingdom level, but non-inducing soils had a higher abundance of Trichoderma amplicon sequence variants. Our results suggested that examination of root microbial communities associated with PRD induction may be justified for additional insights into microbial associations with PRD induction in Prunus.