Phytophthora diseases have become increasingly important in California almond production and often seriously impact orchard establishment. Phytophthora mediterranea and P. niederhauserii, isolated from crown and trunk cankers, and P. syringae, mostly obtained from aerial Phytophthora infections, were common species recovered. This represents a shift in species occurring on almond. Mycelial growth of a total of 195 isolates of these species was effectively inhibited by ethaboxam, fluopicolide, mandipropamid, and oxathiapiprolin, with effective concentration of fungicide required for a 50% effective concentration (EC50) values of 0.006 to 0.190 μg/ml, 0.006 to 0.317 μg/ml, 0.001 to 0.011 μg/ml, and 0.00011 to 0.00041 μg/ml, respectively, with similar ranges for each species. All isolates were sensitive to mefenoxam, with EC50 values ≤ 0.289 μg/ml. Phytophthora niederhauserii and P. syringae were also sensitive to potassium phosphite (KPO3; EC50 values 2.8 μg/ml to 60.8 μg/ml); however, all but 4 of the 63 isolates of P. mediterranea were resistant (EC50 values between 50.9 μg/ml and 464.3 μg/ml). Fungicidal versus fungistatic activity of the six fungicides at concentrations proportionally scaled based on field rates was determined by vital staining and germination of zoospore cysts of P. citrophthora that were fungicide-treated and then washed. Each fungicide significantly reduced cyst viability. Fluopicolide and oxathiapiprolin had the highest fungicidal activity, whereas KPO3 was mostly fungistatic. With high in vitro toxicity and high direct fungicidal activity at low concentrations, the new ethaboxam, fluopicolide, mandipropamid, and oxathiapiprolin have the potential to effectively manage Phytophthora diseases and also reduce pathogen populations. Oxathiapiprolin has been registered for almond, and registration for the other three fungicides is planned.

Four replant trials were conducted in California's San Joaquin Valley (SJV) to examine interactions of whole orchard recycling (WOR) and preplant soil fumigation. Soil fumigation has been used to manage Prunus replant disease and phytopathogenic nematodes, which are the most important replant problems of almond in the valley. WOR, the process of chipping or grinding an old orchard's biomass and incorporating it into the soil, is widely used in the SJV as an alternative to burning and offers environmental and agronomic benefits, but its impact on almond replant problems has not been explored in terms of crop yields. In all four trials, preplant fumigation benefited crop yields, providing evidence for site replant problems. WOR generally did not affect the benefits of fumigation, but on cultivar 'Monterey', yields in one trial were affected by significant WOR x fumigation interaction; WOR increased 'Monterey' yields in non-fumigated soil but not in fumigated soil. 'Nonpareil' yields were increased by a significant main effect of WOR, in both fumigated and non-fumigated soil. Collectively, the results indicate that WOR does not increase the risk of almond replant problems; instead, depending on cultivar, WOR may increase almond yields, either by lessening the impacts of replant problems or by improving crop performance regardless of replant problem presence.

Young almond ( Prunus amygdalus ) orchards replanted where old orchards of stone fruits ( Prunus sp.) have been removed are subject to physical, chemical, and biotic stressors. Among biotic challenges, for example, is almond/stone fruit replant disease (ARD; formally known as Prunus replant disease), which specifically suppresses the growth and yields of successive almond and other stone fruit plantings and is caused, in part, by a soil microbial complex. During four orchard trials representing different almond replant practices and scenarios in the San Joaquin Valley in California, we examined the impacts of phosphorus (P) fertilization on the growth of replanted almond. During all trials, P was applied to tree root zones just after replanting, and the impact was assessed according to trunk cross-sectional area (TCSA) growth for 2 years. Expt. 1 was performed where a previous almond orchard was cleared using whole orchard recycling (i.e., the old orchard was “chipped” and then turned into the soil). The land was replanted without preplant soil fumigation. We tested separate fertilizer treatments based on various P, nitrogen, micronutrient, and “complete” formulations. Expt. 2 was also performed where an old almond orchard was recycled, but the soil was preplant-fumigated before replanting. Here, we tested only P fertilization. Expts. 3 and 4 were conducted where an old peach ( Prunus persica ) orchard was removed. Here, P and nitrogen fertilizer treatments were tested among additional factors, including preplant soil fumigation (Expts. 3, 4) and whole orchard recycling chips (Expt. 4). During all four trials, P fertilization (P at 2.2 to 2.6 oz/tree within a few weeks after planting) significantly increased TCSA growth. The growth benefit was nuanced, however, by almond cultivar, date of replanting, rootstock, and other site-specific factors. Although P fertilization did not match the benefit of preplant soil fumigation for the management of ARD, our data indicated that P fertilization can improve the growth of young almond orchards in diverse replant settings with or without preplant soil fumigation and should be considered by California almond producers as a general best management practice.

Diverse Phytophthora species, including many important plant pathogens, have been widely detected among surface water irrigation sources. In the past decade, metabarcoding has been used to characterize waterborne Phytophthora populations. Metabarcoding typically involves amplification of portions of the nuclear ribosomal internal transcribed spacers (ITSs) ITS1 or ITS2 from Phytophthora species, followed by indexed high-throughput sequencing. However, full-length sequences of the entire ITS region are required for resolution of many Phytophthora species. We used metabarcoding with Pacific Biosciences (PacBio) sequencing of full-length ITS amplicons to analyze populations of Phytophthora in waterways of the Stockton East Water District (SEWD) in the northern San Joaquin Valley of California. This approach yielded species-level resolution of many members of the Phytophthora community. Results were compared with those obtained by using ITS1 or ITS2 regions alone and were found to provide superior species resolution for P. pini, P. capsici, and P. gregata. Samples were collected throughout the 2021 irrigation season from five waterways across the SEWD. Thirty-eight Phytophthora species were detected in the waterways, including tree-crop pathogens P. acerina, P. cactorum, P. pini, P. x cambivora, P. niederhauserii, P. mediterranea, and P. taxon walnut. These pathogenic species were detected throughout the SEWD during most of the irrigation season. The results demonstrated the usefulness of full-length ITS amplicon sequencing for identifying Phytophthora species in environmental samples and suggested that some disease risk may be incurred by orchardists irrigating with SEWD water. Additional epidemiological studies will be required to critically evaluate this risk.

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.

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.

Many walnut orchards were inundated by flooding from the Feather and Stanislaus Rivers in winter and spring 2017 and developed bleeding cankers in trunk, root, and crown tissues exposed to the water. Orchard surveys and diagnostic isolations associated Phytophthora pini, P. chlamydospora, and P. gonapodyides with the cankers in 2017. Pathogenicity of P. pini was confirmed in seedlings and excised shoots of Juglans regia, but the other species caused negligible amounts of disease. Feather River and associated flood waters were assayed using culture-independent sequencing of rRNA gene amplicons and pear baiting methods; 14 species of Phytophthora were detected, including P. chlamydospora and P. gonapodyides, but not P. pini. Severe and prolonged walnut orchard flooding from rivers, such as occurred in 2017, places diverse mixtures of Phytophthora species from multiple sources into close, infective proximity with susceptible walnut tree scions. Systemic chemical or genetic protection strategies may be valuable for orchards subject to such flooding.

In regions in which surface water is used to irrigate deciduous fruit and nut tree nurseries or orchards and waterborne pathogens cause economic losses in the plantings, additional research is needed (a) to assess the epidemiological role of pathogen-infested irrigation water in the disease losses and (b) to develop strategic control practices for the diseases. In assessing the importance of waterborne pathogen populations and how to manage them, researchers should make realistic distinctions between cases in which detected waterborne pathogens will contribute significantly to the populations already resident in nursery and orchard soils and cases in which waterborne inocula have little practical significance. Beyond the concerns that surface sources of irrigation water may facilitate long-distance transport and co-mingling of pathogen populations, research is needed on the use of irrigation methods to minimize within-orchard and within-nursery spread and infection by waterborne pathogens.

Prunus replant disease (PRD) is an important soilborne complex that suppresses growth and productivity of replanted stone fruit and nut orchards. It is effectively managed with preplant soil fumigation but, due to regulatory challenges, nonfumigant-based control strategies for PRD and other soilborne disease problems may become increasingly important, especially in California. We examined the potential of preplant anaerobic soil disinfestation (ASD) for control of PRD in four repeated orchard replant trials on sandy loam soil near Parlier, CA. After removal of the old orchard trees, alternative ASD treatments, all using rice bran as the main carbon source, were implemented, starting in late September. The alternative treatments incorporated rice bran at (i) 20 t ha-1, alone, in 3.0-m-wide row strips; (ii) 20 t ha-1, preceded by incorporation of a sudangrass cover crop and followed by drip application of molasses (10 t ha-1), in 3.0-m-wide row strips; (iii) 20 t ha-1, alone, in 1.8-m-wide strips; or (iv) 12 t ha-1, alone, in 1.8-m-wide strips. All ASD-treated areas were covered with clear tarp and drip irrigated with 25 cm of water. Tarps remained for 6 weeks, during which the soil moisture level was kept at or above field capacity by drip irrigation. All trials included nontreated control and fumigated standard treatments. ASD raised temperature and reduced redox potential in soil at 15- and 46-cm depths for 6 weeks. Fumigation and ASD treatments both nearly eradicated bioassay inoculum of Pythium ultimum in the soil before almond trees were replanted and significantly affected almond tree root communities of fungi and oomycetes after planting. Fumigation treatments and ASD treatments with rice bran at 20 t ha-1 in 3.0-m strips increased tree growth significantly and by similar magnitudes. Among repeated experiments, mean increases in trunk cross-sectional area growth due to fumigation ranged from 137 to 264%, while the increases due to ASD at 20 t ha-1 in 3.0-m strips ranged from 148 to 214%, compared with controls. ASD offers effective control of PRD and is worthy of further optimization and testing for management of PRD and additional orchard replant problems.

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.

The grinding and incorporating into soil of whole almond trees, during orchard removal, may provide a sustainable practice that could enhance air and soil quality. Removed orchards are typically either pushed out and burned or ground up and removed. Stored carbon is lost from the orchard site. Woody debris incorporated into soils could increase organic matter, enhance carbon sequestration, and improve soil quality and tree yield. The objective of this project was to compare the grinding up of whole trees with burning as a means of orchard removal. Twenty-two rows of an experimental orchard were used in a randomized blocked experiment with two main treatments, whole tree grinding and incorporation into the soil versus tree pushing and burning. The whole tree grinding did not stunt replanted tree growth. Sampling from plots showed elevated levels of fungal and bacterial feeding nematodes (Tylenchidae) along with associated woody soil aggregates in the grind treatment. Fungal mycelium was readily observed colonizing woody aggregates and significantly more basidiomycetes (mushrooms) were observed in the grind plots. No difference in yield was observed in 2011, however, in 2012 and 2013 (P=0.08) greater yields were observed in the grind treatment when compared to the burn. In 2010, more carbon, organic matter, and a greater cation exchange capacity were initially observed in the burned plots, but by 2012 and 2013 the grind plots had significantly more calcium, manganese, iron, magnesium, boron, nitrate, copper, as well as higher electrical conductivity, organic matter, total carbon, and organic carbon. Soil pH was significantly lower in the grind treatment plots. Leaf petiole analysis in 2013 showed significantly greater levels of nitrogen, potassium, phosphorus, manganese, and iron from trees growing in the grind treatment, while magnesium and sodium levels were significantly less.

The grinding and incorporating into soil of whole almond trees, during orchard removal, could provide a sustainable practice that could enhance air and soil quality. Removed orchards are typically either pushed out and burned or ground up and removed. Stored carbon is lost from the orchard site. Woody debris incorporated into soils could increase organic matter, enhance carbon sequestration, and improve soil quality and tree yield. The objective of this project was to compare the grinding up of whole trees with burning as a means of orchard removal. Twenty-two rows of an experimental orchard were used in a randomized blocked experiment with two main treatments, whole tree grinding and incorporation into the soil versus tree pushing and burning. The whole tree grinding did not stunt replanted tree growth. Sampling from plots showed elevated levels of fungal and bacterial feeding nematodes (Tylenchidae) associated woody soil aggregates in the grind treatment. Fungal mycelium was readily observed colonizing woody aggregates and more basidiomycetes (mushrooms) were observed in the grind plots. Yields were determined in 2011 and 2012 and there were no differences between the grind and burn treatments. In 2010, more carbon, organic matter, and a greater cation exchange capacity were initially observed in the burned plots, but by 2012 the grind plots had significantly more calcium, manganese, iron, magnesium, boron, nitrate, copper, electrical conductivity, organic matter, total carbon, and organic carbon. The soil pH was significantly less in the grind treatment plots.

Our research goal was to use recent advances in global positioning system (GPS) and computer technology to apply just the right amount of fumigant where it is most needed (i.e., in a small target treatment zone in and around each tree replanting site) to control Prunus replant disease (PRD). We developed and confirmed the function of (1) GPS-based software that can be used on cleared orchard land to flexibly plan and map all of an orchard's future tree sites and associated spot fumigation treatment zones and 2) a tractor-based GPS-controlled spot fumigation system to quickly and safely treat the targeted tree site treatment zones. In trials in two almond orchards and one peach orchard, our evaluations of the composite mapping and application system, which examined spatial accuracy of the spot treatments, delivery rate accuracy of the spot treatments, and tree growth responses to the spot treatments, all indicated that GPS spot fumigation has excellent potential to greatly reduce fumigant usage while adequately managing the PRD complex.

The most common rootstock for Juglans regia (Persian or “English” walnut) in California is Paradox, typically a hybrid of J. hindsii (Northern California black walnut) × J. regia. Unfortunately, Paradox is very susceptible to Armillaria root disease. The relative resistance to Armillaria mellea of six clonally propagated Paradox rootstocks (AX1, Px1, RR4 11A, RX1, Vlach, VX211) was evaluated and compared with that of clonally propagated J. hindsii rootstock selection W17, J. regia scion cultivar Chandler, and Pterocarya stenoptera (Chinese wingnut). In a growth-chamber assay, plants were micropropagated and rooted in vitro before inoculating the culture medium with A. mellea. At two months post-inoculation, the most resistant and susceptible Paradox rootstocks were AX1 and VX211, respectively, with 9% vs. 70% mortality, and this finding was consistent across three isolates of A. mellea and three replicate experiments. This broad range of resistance within Paradox is consistent with past field trials that tested other genotypes. Our finding of similarly high susceptibility of ‘Chandler’ and W17 (61% vs. 69% mortality) is in contrast to two field trials, in which other J. regia genotypes were more susceptible than those of J. hindsii. A third trial, however, identified some J. regia genotypes as more resistant than those of J. hindsii. Therefore, it is possible that W17, which was not previously tested, is an Armillaria-susceptible genotype of J. hindsii. Based on our findings of repeatable mortality levels across three isolates of A. mellea and three replicate experiments, the growth-chamber assay has promise, albeit with confirmed resistant and susceptible controls, for identifying putative resistant rootstocks (e.g., AX1) in preparation for a field trial with controlled inoculations.