Tree Health and Disease

  • Does WOR affect the early tree growth of replanted almond orchards?
  • Does WOR pose long-term disease or root-lesion nematode risks to the replanted orchards?
  • What WOR management steps are recommended for minimizing almond disease risk? 

Orchard floorSoil constitutes a complex physical, chemical, and biological environment in which plant roots must reach and extract water and nutrients while supporting and anchoring the growing tree.

Many species of bacteria, fungi, oomycetes, and free-living nematode microbial community members decompose WOR plant matter, transforming nutrients into available forms that roots can extract. Our research found that several soil parameters that affect tree performance, including soil bulk density, nutrient content, water retention, water conductivity, and microbial activity, were affected favorably by WORBut the soil can harbor plant pathogens as well as beneficial microorganisms.

We conducted short-term trials to see how WOR may impact almond replant problems and other diseases. Almond planted after almond or other stone fruits without effective preplant soil fumigation may exhibit growth suppression in the first few years after replanting, resulting in delayed yield capacity. This growth suppression, called “Prunus replant disease (PRD)”, apparently results in part from negative effects from the previous orchard on soil microbial communities.

Prunus replant disease can occur with or without significant populations of phytopathogenic nematodes. Compared to PRD, phytopathogenic nematodes, another “replant problem”, tend to impact orchards later, after PRD effects have diminished. But root damage from nematode feeding can persist over the economic life of orchards.

WOR Effects on Early Tree Growth

In trials in orchards one and two years after replanting, WOR did not negatively affect:

  • the severity of Prunus replant disease
  • the effectiveness of pre-plant soil fumigation




WOR Effects on Long-Term Disease Risk

Results are inconclusive, but preliminary trials show no increase in root lesion nematodes with WOR.

Field trial results are not available for many known diseases of almonds. However, expert opinion suggests that the following diseases are unlikely to be aggravated by WOR:

  • phytophthora crown and root rots
  • band canker disease


Management Recommendations to Minimize Disease Risk

Chip wood with a screen size of 2” (not 4” or more)

Leave chips to dry thoroughly on the soil surface before incorporation

WOR is NOT advised when the previous orchard had:

  • Armillaria root rot
  • high and early incidence of butt rot
  • high incidence of crown gall

Results: whole-orchard recycling and almond orchard health

Observed impacts of WOR on Prunus replant disease

We have not found WOR to impact either the severity of PRD or benefits of preplant soil fumigation.

In two trials (see details in blue box), we tested four treatment combinations of WOR and preplant soil fumigation:

  • WOR without fumigation
  • WOR with fumigation
  • fumigation without WOR
  • no fumigation or WOR

In both trials, in the first year after planting, fumigation increased trunk cross-sectional area (TCSA), both with and without WOR residue present. These effects persisted through year 2 (Figure a). Increases in trunk cross-sectional area due to fumigation ranged from 19 to 34% with WOR chips and from 17 to 46% without chips.

Some stunting in trunk growth that was found with WOR, both with and without pre-plant fumigation, was later determined to be caused by temporary, manageable nitrogen immobilization that can be overcome by doubling the initial nitrogen application in the first year after replanting.

These experimental results indicate that growers may conduct WOR without fear of aggravating more severe Prunus replant disease or interfering with the benefit of preplant soil fumigation for prevention of PRD.

Effects of fumigation and WOR on tree growth in first two years
Figure A. Effect of preplant soil fumigation (1,3-dichloropropene plus chloropicrin) and whole orchard recycling (WOR) treatments on growth in trunk cross-sectional area of almond trees replanted at the Bakersfield location. Shown are: TOP LEFT: effect of preplant soil fumigation at year 1 (from time of planting) (P=0.01). TOP RIGHT: interaction of rootstock and WOR at year 1. LOWER LEFT: effect of preplant soil fumigation at year 2 (P=0.0001). LOWER RIGHT: interaction of rootstock and WOR at year 2 (P=0.10).

Observed impacts of WOR on soil microbial communities

Because the incidence of soil-borne diseases may be related to the overall balance of different microbial populations in the soil, we examined the effects of WOR on the composition of bacterial and fungal populations.

We used DNA extraction and high-throughput sequencing of rRNA genes to monitor effects of WOR and preplant soil fumigation on soil and root communities of bacteria and fungi in replant trials. Results from the Bakersfield trial are shown below.

In the first year after soil treatments were applied, fumigation had large impacts on both bacterial and fungal soil communities, whereas WOR appeared to have large impacts only on fungal communities (Figure b). The most abundant genera comprising these communities are listed (Figure c).

It is not clear at this point whether the bacterial or fungal community responses to fumigation or WOR are relevant to tree health.

NMDS plot of soil microbes
Figure B. Effects of preplant soil fumigation (1,3-dichloropropene plus chloropicrin) and whole orchard recycling (WOR) treatments on bacterial and fungal domains of soil microbial communities in the Bakersfield trial during January and June in the year of planting. The communities were examined using high throughput sequencing of rRNA genes. Graphed symbols represent microbial communities in a sample, graphed using non-metric multidimensional scaling (NMDS). Samples are graphed according to the degree of dissimilarity among them; the more distance between two symbols, the more dissimilar their microbial communities.
Microbial genera
Figure C. Effects of preplant soil fumigation (1,3-dichloropropene plus chloropicrin) and whole orchard recycling (WOR) treatments on the most abundant genera of bacterial and fungal soil communities in soil of the Bakersfield trial. Samples were collected in January and June in the year of planting and used for high throughput sequencing of rRNA genes.

Observed impacts of WOR on nematode communities

Little is known about how or whether WOR affects nematode populations. Diverse nematode communities inhabit soil, with some species feeding on and damaging almond tree roots, other species surviving on roots of other plants (including weeds), and still others living freely and feeding on soil bacteria and fungi. Some fungi feed on nematodes. The web of interactions between plant-parasitic nematodes, free-living nematodes, and their respective predators is therefore complex, and it may take many years for effects of a process such as WOR to be manifested in the populations.

Preliminary data (Fig. d) shows that WOR did not increase plant-parasitic nematode populations at any of the seven field trial sites. However, none of the sites had problematic nematode infestations to begin with, so these data cannot be considered conclusive. Results varied widely between seven field sites. WOR seemed to sometimes increase free-living nematode populations, but seemed not to affect plant-parasitic nematode populations. 

At this time, we recommend treating nematode problems in a recycled orchard similarly as in a non-recycled orchard, with fumigation if necessary.

Nematode incidence
Figure D. Populations of free-living (top) and plant-parasitic (bottom) nematodes, compared between WOR and control plots.


Assessing potential impacts of WOR on other almond tree diseases

Incidences of almond tree diseases other than PRD at the replant trial sites have been very low and not impacted by WOR treatments. The two-year timeframe for these trials was too short to adequately assess WOR impacts on diseases that can affect orchards throughout their economic lifespans.

From our knowledge of pathogen biology, we have no reason to suspect that almond bloom or foliar pathogen populations would be directly impacted by WOR, although it is conceivable that some diseases that can be intensified by stress (e.g., non-infectious bud failure, bacterial canker) may even be suppressed by WOR, thanks to periodic reductions in water stress.

We offer the following WOR suggestions for almond disease situations in which WOR may or may not be advisable.


Almond disease situations in which WOR is not advised

Orchards with Armillaria root rot

Armillaria mellea (the oak root fungus) can survive for long periods in dead wood in or on soil – up to a year or more, according to Themis Michailides (UC ANR plant pathologist). Therefore, WOR may end up promoting this pathogen. Roger Duncan (UCCE Director for Stanislaus County) says that Armillaria-infected orchards should not be recycled, pointing out that “Management of oak root fungus includes removing as many infected roots as possible prior to replanting an orchard.”

However, Brent Holtz (UCCE Director for San Joaquin County) says there is uncertainty in how wood chips from WOR would affect this root disease. “This is an important pathogen to test for in our future work,” he says. “When a tree is excavated to be ground up [for WOR], only a very small amount of roots are actually pulled out with the tree.” So re-introducing infected roots is not the main issue, but does Armillaria take up residence in the buried wood chips instead? Dr. Holtz is currently designing research trials to help answer this question.

Orchards with high and early incidence of butt rot

Species of Ganoderma and other fungi that incite wood rot, resulting in lodging of almond trees, are well-adapted to decay of and survival in almond tree wood. Ganoderma adspersum, a new wood-rotting almond threat in California, is especially virulent and can even kill young almond trees. As of 2017, G. adspersum was found in Central Valley from Madera County south. Our current suggestion is not to conduct WOR in orchards infested with G. adspersum and/or expressing high and early incidence (more than 5% incidence in orchards <15 years old) of butt rot.

The above suggestion is based on risk avoidance; further research is needed to develop evidence-based management rules for Ganoderma and WOR. “I don’t think we have enough information to recommend this either way,” says David Doll (former UCCE Farm Advisor for Merced County). Brent Holtz says that he is “skeptical about the concern over Ganoderma... the spores are very common and it needs a wound in the bark for entry.” Themis Michailides believes that removing any Ganoderma-infected trees out of the orchard before WOR should be a sufficient precaution. The best answer may depend on the Ganoderma species, which may be difficult to ascertain without expert assessment.

Orchards with high incidence of crown gall

Although the crown gall agent Agrobacterium tumefaciens is not known for competitiveness in soil and wood environments, it is possible that virulent bacteria released from galls during WOR could transfer gall-inducing plasmids (DNA fragments) to Agrobacterium populations in the soil, thereby perpetuating the potential for crown gall disease in a new orchard. Experts disagree on the practical level of risk posed by crown gall when recycling almond orchards. “This requires some research to really make a hypothesis for management,” says Elizabeth Fichtner, UCCE Farm Advisor for Tulare County.

Roger Duncan advises against recycling almond orchards with heavy crown gall infestation, but adds that “this would likely apply to very few orchards.” Themis Michailides suggests “the grower could remove the crown-gall-infected trees and then proceed with recycling the rest of the orchard trees.” David Doll is “unsure if this matters for almonds,” though he would avoid WOR in crown-gall-infested walnuts. Until better data are available, almond growers with crown gall will have to make their own determination of risk avoidance.

  Additional management steps for cases in which WOR is not advisable: In orchards where WOR is not advised, growers should consider disposing of the wood by burning or off-site disposal. Although populations of the wood-inhabiting pathogens can be reduced by fumigation, inoculum may persist, especially in large pieces of wood.


Almond disease situations in which WOR is advisable

Orchards with typical low incidences of Phytophthora crown and root rots

It is unlikely that WOR would have large impacts on almond tree diseases incited by Phytophthora species. Although Phytophthora can survive indefinitely in soil, it is generally not competitive in dead tissues, so it is unlikely that WOR chips from Phytophthora-infected trees would introduce and support new inoculum into an orchard’s soil. However, spreading WOR chips from an orchard with a Phytophthora problem into a field not known to have Phytophthora is not advised.

There may be some good news about Phytophthora and WOR. Although it’s too soon to tell, “we have some evidence that the wood chips have decreased Phytophthora root rot,” says Brent Holtz. “Phytophthora has cellulose in its cell walls, and when wood-decomposing fungi break down the cellulose in the wood chips, they may also break down the cell walls of Phytophthora.” Furthermore, reproduction, spread, and infection by Phytophthora species are favored by extended periods of soil water saturation, and to the extent that WOR improves soil water infiltration, incidence of these diseases may even be reduced.

Orchards with typical, low incidence of band canker disease

Although Botryosphaeria and Neofusicoccum fungi that incite band canker disease have been shown to survive in stumps and dead wood, the more thoroughly the WOR chips are incorporated into soil, the less likely the fungal pathogen will be to infect the replanted trees.

Botryosphaeria expert Themis Michailides says that these fungal spores can survive in prunings for 18 months, even when buried under an inch of soil. “Burying the tissues in the soil will not allow them to spread spores in the open environment,” he says. “However, tissues exposed on the surface of the soil can release spores for several months,” and “they will be problematic.” A combination of small chip size, thorough drying, and thorough incorporation could help reduce risk, but further research is needed.


Additional management for cases in which WOR is advisable: Even in cases where WOR is apparently advisable, chipping wood with a screen size of 2” (not 4” or more) and letting the chips dry thoroughly on the soil surface before incorporation may reduce disease risk.