Fig 1.
Schematic overview of the sampling strategy of soil and tree samples in a ‘HoneyCrisp’ orchard block with rapid apple decline (RAD).
Sampling and pooling of shoots from three different positions in the tree canopy (top, middle, and base) (A), Sampling of root tissue and rhizosphere (B). Soil sampling for the analysis of soil physical and chemical properties (C).
Fig 2.
Composition of the bulk soil collected across the experimental apple orchard in a ‘HoneyCrisp’ block with rapid apple decline.
(A) Physical properties and (B) Chemical composition of soil samples ranging from the highest (blue) to the lowest (red) order.
Table 1.
Physicochemical properties and nutrient profiles from 0–20 cm topsoil in a commercial apple orchard in Wayne County, NY from RAD asymptomatic and symptomatic apple trees.
Fig 3.
Maximum, average, and minimum, temperatures (A), precipitation and relative humidity (B) obtained from the weather stations located at Phelps, Farmington, and Sodus, New York from 2013 to 2017.
Fig 4.
Scion and rootstock cross sections from ‘HoneyCrisp’ apple trees grafted onto M.9 (clone NIC 29) with rapid apple decline.
Three cuts of 5 cm were made above and below the graft union at the scion-rootstock junction. The following discoloration scale was used to estimate healthy and pigmented necrotic wood area in symptomatic apple trees: DS = 1, external wood discoloration, DS = 2, internal wood discoloration, DS = 3, co-occurrence of external and internal wood discoloration, DS = 4, edge-shaped discoloration (<50%), DS = 5, edge-shaped discoloration (>50%), and DS = 6, circular discoloration.
Fig 5.
Visual symptoms of wood decay in declined apple trees.
(A) Wood cross-sections showing rot-like decay around the graft union, (B) Cracks in the bark and internal wood from declined apple trees.
Table 2.
Detection of different viruses in root and shoot tissue of asymptomatic and symptomatic apple trees.
Fig 6.
Analysis of bacterial communities in root, shoot, soil, and rhizosphere samples from asymptomatic and symptomatic ‘HoneyCrisp’ apple trees as identified by sequencing 16S regions.
(A) Biplot from principal component analysis of the diversity indices obtained from 16S analysis of different samples, (B) Abundance of different bacterial classes in the rhizosphere, soil, root, and shoot samples, (C) Bacterial classes that show a significantly differential abundance between healthy and declined apple trees.
Fig 7.
Analysis of fungal communities in root, shoot, soil, and rhizosphere samples from asymptomatic and symptomatic ‘HoneyCrisp’ apple trees as identified by sequencing ITS regions.
(A) Biplot from principal component analysis of the diversity indices obtained from ITS sequence analysis of various samples, (B) Abundance of different fungal classes in the rhizosphere, soil, root, and shoot samples.