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

Successive plantings of 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 microbial taxa in roots of Nemaguard peach, a rootstock for almond and other stone fruits. In a greenhouse bioassay, portions of 10 replant soils were treated with fumigation or pasteurization or left untreated as a control before being planted with peach seedlings. Ten weeks after planting, seedlings were considered PRD-affected if their top fresh weights in the control were significantly reduced, compared to the weights in pasteurization and fumigation treatments; plants with equivalent top weights in all treatments were considered to be non-affected. 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 among controls. Random forest (RF) analysis discriminated effectively between PRD-affected and non-affected root communities. Among the 30 RF top-ranked amplicon sequence variant (ASV) predictors, 26 were bacteria, two were oomycetes, and two were fungi. Among them, only Streptomyces scabiei, Steroidobacter denitrificans, Streptomyces bobili, and Pythium mamillatum had root abundances ≥5% that were either associated positively (former two ASVs) or negatively (latter two) with PRD. Thus, our findings were consistent with microbial mediation of PRD in roots and suggested taxa that may be involved in the mediation.

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

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.

Dose Response of Weed Seeds, Plant-Parasitic Nematodes, and Pathogens to Twelve Rates of Metam Sodium in a California Soil.

Metam sodium (sodium N-methyl dithiocarbamate, metam-Na) is widely used in agricultural and floricultural production for controlling soilborne plant pathogens, parasitic nematodes, and weeds. It undergoes rapid decomposition to the biocide methyl isothiocyanate (MITC) in moist soils. In this study, the efficacy of 12 concentrations of metam-Na (10 to 2,650 µmol kg-1 soil) to control seeds or tubers of five major weed species, three soilborne pathogens, and one parasitic nematode was evaluated in a sandy loam soil under controlled conditions. Soils were exposed to the fumigant in microcosms for 24 h at 10 and 20°C. Generation and dissipation curves of MITC in soil under controlled conditions showed that MITC concentrations in soils were highest 2 h after metam-Na application and decreased steadily over the 24-h incubation period. After 24 h, remaining MITC concentrations in soil microcosms at 10 and 20°C were 53 and 38% of the original amount applied, respectively, indicating a 20% reduction in MITC dissipation at the lower soil temperature. Logistic dose-response models were used to estimate the effective concentration necessary to reduce soil pest viability by 50 (LC50) or 90 (LC90) percent under both temperatures. Seed of Portulaca oleracea, with LC90 values of ≤1,242 µmol kg-1 soil, was the most sensitive to soil fumigation with metam-Na, followed by Polygonum arenastrum with LC90 values of ≤1,922 µmol kg-1 soil. At 10°C fumigation temperature, metam-Na at the highest dose tested in this study, 2,650 µmol kg-1 soil, was not sufficient to achieve adequate control of Stellaria media and Malva parviflora seed and Cyperus esculentus tubers. Weed control efficacy (average reduction in LC90 values) of metam-Na was between 25 and 60% higher if soils were fumigated at 20°C compared with 10°C, with the exception of M. parviflora. Phytophthora cactorum and Pythium ultimum were more sensitive to soil fumigation with metam-Na (LC90 ≤ 165 µmol kg-1 soil) than Verticillium dahliae (LC90 ≤ 737 µmol kg-1 soil). The nematode Tylenchulus semipenetrans was highly sensitive to soil fumigation with metam-Na (LC90 ≤ 98 µmol kg-1 soil), and the efficacy of control increased by 30% if soil was fumigated at 20°C compared with 10°C. In this sandy loam soil, metam-Na at a concentration of 850 µmol kg-1 reduced the viability of Portulaca oleracea and Polygonum arenastrum seeds, C. esculentus tubers, and all soilborne pathogens and parasitic nematodes tested by 90% at 20°C after 24 h exposure. These results indicate that metam-Na can provide effective pest and disease control at maximum label rate for the commercial formulation, but there was a reduction in efficacy at low temperature.

Fumigation efficacy and emission reduction using low-permeability film in orchard soil fumigation.

BACKGROUND: Many orchards use fumigation to control soilborne pests prior to replanting. Controlling emissions is mandatory to reduce air pollution in California. This research evaluated the effects of plastic film type [polyethylene (PE) or totally impermeable film (TIF)], application rate of Telone C35 [full (610 kg ha(-1) ), 2/3 or 1/3 rates] and carbonation at 207 kPa on fumigant transport (emission and in soil) and efficacy. RESULTS: While increasing fumigant concentrations under the tarp, TIF reduced emissions >95% (∼2% and <1% of total applied 1,3-dichloropropene and chloropicrin respectively) relative to bare soil, compared with ∼30% reduction by PE. All fumigation treatments, regardless of film type, provided good nematode control above 100 cm soil depth; however, nematode survival was high at deeper depths. Weed emergence was mostly affected by tarping and fumigant rate, with no effects from the carbonation. CONCLUSION: TIF can effectively reduce fumigant emissions. Carbonation under the studied conditions did not improve fumigant dispersion and pest control. The 2/3 rate with TIF controlled nematodes as effectively as the full rate in bare soil or under the PE film to 100 cm soil depth. However, control of nematodes in deeper soil remains a challenge for perennial crops.