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

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.

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

“…Interestingly, pasteurization and fumigation treatments had similar effects on peach growth and root communities: both treatments revealed PRD induction in the same six of eight Prunus replant soils, a lack of PRD in two Prunus replant soils, and lack of PRD in the two grape replant soils. Such plant responses were not surprising in the bioassay, because under field conditions PRD is not induced in grape soils, and not all Prunus soils induce PRD (Browne, [unpublished]; [ 49 ]). Both fumigation and pasteurization resulted in clear shifts in root abundance of: Actinobacteria (reduced by both treatments, compared to control) and Gammaproteobacteria (increased by both treatments); Sordariomycetes (increased by both treatments) and the Pezizomycetes (decreased by both treatments); and oomycetes (decreased by both treatments).…”

“…We do not have root microbiome data that excludes nematode species from consideration in PRD induction. Nevertheless, in our previous report that related soil factors to PRD induction [ 19 ], we characterized the populations of nematodes in all 10 of the soils used in root microbiome examinations reported here and in 15 additional soils that were only part of the soil study; there was no relation between soil populations of nematode species and induction of PRD. Though our soil data suggest it unlikely, it is possible that adding root and soil nematode assays over the full course of the bioassay procedure that we used could reveal PRD contributions of nematode populations not apparent in this report.…”

“…The soils were collected in spring 2015 from 10 differently managed areas of land distributed across northern, central, and southern portions of California’s Central Valley. Physicochemical and microbial community features of these soils, as well 15 additional soils, were reported previously, including rRNA gene-amplicon-based characterizations of bacterial, fungal and oomycete communities and physical-extraction-based characterizations of resident nematode populations [ 19 ]. At the time of soil collection, capacity of the soils to induce PRD generally was not known.…”

Xylella fastidiosa Infection Reshapes Microbial Composition and Network Associations in the Xylem of Almond Trees

“…For almond trees, microbiota studies have mainly focused on the epiphytic communities on the phyllosphere (flowers and leaves) using culture-dependent and culture-independent approaches (Fridman et al, 2012;Izhaki et al, 2013;Aleklett et al, 2014), on fungal pathogens associated with almond wood decay based on conventional culture-dependent techniques 1 https://agroambient.gva.es/es/web/agricultura/xylella-fastidiosa (Gramaje et al, 2012;Olmo et al, 2016) or Prunus replant disease (Khan et al, 2021). However, to our knowledge, no study has addressed the characterization of xylem sap microbial communities in almond trees despite the fact that the microbial profile serves as a basis to identify bacterial and fungal taxa with a potential antagonistic activity that could be used to fight vascular pathogens or as potential biocontrol agents to suppress ALSD.…”