Models for the Future Apple Plots: Planting of Trees following Bio-remediation

Penn State Extension partners with growers in a "Models for the Future" project to provide on-farm demonstrations for new, young, and minority farmers. Two years of bio-remediation with rotation crops suppressed nematodes and improved soil health.
Models for the Future Apple Plots: Planting of Trees following Bio-remediation - Articles


The plots are supported by a USDA NIFA Beginning Farmer and Rancher Development Program grant to showcase best management practices for vegetables, small fruit, and tree fruit on commercial farms. The project is now in its final year, and our team has compiled the data we collected from our four orchard sites.

Following two years of rotations with biofumigant cover crops, apple trees were planted into strips of killed sod between middles of well-established endophyte-enhanced fescue. Photo: Tara Baugher, Penn State

Four model apple plots were established this year at orchards across Eastern and Central Pennsylvania. From east to west, sites were established at Bedminster Orchard in Bucks County, Scholl Orchards in Berks County, Twin Springs Fruit Farm in Adams County, and the Rock Springs Orchard at the Russel E. Larson Ag Research Center near State College. The model orchards were planted with two apple scab resistant cultivars, GoldRush and CrimsonCrisp. All trees are on the dwarfing rootstock G.11, with the exception of the Rock Springs site that planted CrimsonCrisp on M.9 Nic 29.

Prior to planting the trees, all sites were planted in cover crops, including sorghum sudangrass and rapeseed. The cover crops selected have been shown to suppress plant parasitic nematodes and to maintain soil health during the rotation between orchard plantings. In 2015 sudangrass was seeded as a summer cover, and was followed by rapeseed as a winter cover in late August/early September. The rapeseed was incorporated in April 2016, and a second rapeseed crop was planted for the summer.

Between each planting, the sudangrass and rapeseed covers were mowed with a flail mower, incorporated, and cultipacked. The varieties used (“Pioneer 877F” sudangrass and “Dwarf Essex” rapeseed), have high concentrations of bio-fumigant compounds, and were chosen for this project to help decrease nematode pressure within the plantings. Following two years of bio-remediation, a slow growing endophyte-enhanced fescue mix was planted in fall 2016. The well-established sod out-competes broadleaf weeds that may serve as reservoirs for viruses associated with tree decline.

Nematode comparisons before and after two years of cover crops

Plant parasitic nematodes transmit viruses, such as tomato ringspot virus, which causes union necrosis and decline. Nematodes were sampled before and after the cover crops were incorporated. After two seasons of cover cropping the model plot sites, populations of parasitic nematodes across all sites were zero (Table 1). Several nematodes that feed on roots, resulting in stunted tree growth, were also reduced to zero. During the final sampling, two replant sites adjacent to the Scholl Orchard and Rock Springs model plot sites that remained fallow were also sampled for nematodes (data not shown). These adjacent fields each contained high numbers of dagger nematodes, the principle vector for fruit tree viruses.

Table 1. Nematode assay results for "Models of the Future" apple plots following removal of previous orchard/crop and at various stages following bio-remediation with the cover crops sorghum sudangrass and rapeseed. Note: The tolerance level for dagger nematodes is zero.

Nematodes per 100cc of soil.

Model plotDateDaggerLesionSpiralLanceRingPinStunt
Rock SpringsApr-201548440160
Twin SpringsApr-201512004000

Soil health comparisons before and after two years of cover crops

Soil health is the ability of a soil to provide an environment that sustains and nourishes plants, soil microbes, and beneficial insects (Natural Resources Conservation Service – USDA-NRCS, 2013). A healthy soil needs to have good soil tilth, soil depth, and water holding capacity, while still draining well. Healthy soils should have adequate nutrients, low amounts of pathogenic organisms, and many beneficial organisms. The Cornell Soil Health Test examines many soil health parameters, and educators submitted samples for the Cornell Soil Health Test before and after two years of rotations with cover crops (Moebius-Clune et al., 2016).

The orchard soils in the model plots started out with good to excellent soil health with a couple of exceptions (Table 2). Aggregate stability, organic matter, and active carbon started low and were improved by preplant cover crops at the Bedminster orchard site. Organic matter started very low at the Rock Springs site but was not improved during the short timeframe. Research shows that organic matter adjustments occur over a longer timeframe, and we will continue to monitor the model plot sites. The average biomass added to each model plot, based on weights of 5-subplot samples, was 15,600 lbs per acre.

We conducted a separate study in 2017 to compare soil health from the bio-remediated model plots to the following treatments in commercial orchard sites: 1) no rotation, 2) fallow for two years, 3) agronomic crops (corn, soybeans) for two years, or 4) compost prior to planting (4 sites each). In this broader study, organic matter in the model plots was higher than in the “no rotation” or fallow plots. Compost sub-surface hardness was lower than all but the agronomic treatment. Compost soil protein index was equal to model plot levels but higher than the index of the other treatments. The soil protein index is an indicator of chemical and biological health of the soil, and is well associated with overall soil health.

Table 2. Soil health results for "Models for the Future" apple plantings at the beginning of site preparation and following incorporation of various cover crops and recommended soil amendments.

OrchardYearAWC g/gSurface Hardness psiSub-surface Hardness psiAS %OM %ACE Value

SR mg

Active C ppmpH
Rock Springs20150.1920030017.72.3--3825.7
Twin Springs20150.3426630062612.70.688785.8

Key to Index Values

Available Water Capacity (AWC)

A measure of porosity of the soil. It is measured by the amount of water held by the soil sample between field capacity and wilting point by applying different levels of air pressure. It is an indicator of how well crops will fair under droughty conditions.

Surface Hardness

A measure of compaction in the top 6 inches of soil as determined with a penetrometer. It is an indicator of physical and biological health of the soil. High surface hardness can severely restrict the ability of roots to penetrate the soil.

Subsurface Hardness

Similar to surface hardness, except at a depth of 6-18 inches. High subsurface hardness can prevent deep rooting in soil.

Aggregate Stability (AS)

A measure of how well soil holds together under rainfall or other rapid wetting stresses. It is measured as the percentage of soil aggregates (or crumbs) that hold together under a simulated rainfall. Good aggregate stability helps prevent crusting, runoff, and erosion, and facilitates aeration, infiltration, water storage, seed germination, and root and microbial health.

Organic Matter (OM)

A measure of carbonaceous material in the soil that is biomass or biomass-derived. OM provides a slow-release pool for nutrients, and promotes resistance to drought and extreme rainfall.

ACE soil protein index (ACE Value)

Measures autoclave citrate extractable proteins in the soil, which acts as a index for total proteins in the soil. It is an indicator of chemical and biological health of the soil, and is well associated with the overall soil health.

Soil Respiration (SR)

A measure of carbon dioxide released by the soil, which indicates the level of metabolic activity of the soil microbial community. This influences organic matter accumulation, as well as aggregate formation and stabilization.

Active Carbon (Active C)

Measures the portion of soil organic matter available as a food source for soil microbes. High active carbon is associated with a large population of soil microbes, which can help maintain disease resistance, nutrient cycling, aggregation, and many other essential soil functions.

Arturo Diaz, model plot cooperator, demonstrates proper training of the central leader in a tall spindle training system. Photo: Tara Baugher, Penn State

Orchard Establishment

Now that the sites are in their final year, the trees have been planted to a tall spindle training system . To continue ensuring trees are off to a good start, the central leaders of each tree are regularly tied to a trellis support system . Trees were scouted weekly beginning in early June to prevent damage from mites, aphids, leafhoppers, Japanese beetles, and diseases, along with weeds that could reduce tree growth during this important establishment phase. To streamline scouting, Penn State orchard scouts used and evaluated a Penn State orchard scouting mobile app developed for the project . The app allows the scouts to enter scouting data into a spreadsheet on their phone or tablet in a way that can easily be shared with others that need access to the data. The sheets also automatically calculate block averages of all the pests and populate the results to a summary page. These features reduce the need to perform tedious calculations and data transfer by hand. Model plot scouts found the app easy to use and said the app streamlined the scouting process, allowing them to monitor orchards in a shorter amount of time.

Trees were scouted weekly to prevent damage from mites, aphids, leafhoppers, Japanese beetles, and diseases, along with weeds that could reduce tree growth during this important establishment phase. Photo: Tom Jarvinen

Trees received two applications of calcium nitrate in the spring, and are under drip irrigation to promote excellent growth in the establishment years. Vigorous shoots directly beneath the leader were removed so the leader does not have any competition for growth. This will allow trees to develop an optimal tree structure for fruiting in subsequent years.

Living Classrooms

The “Models for the Future” plots are serving as “living classrooms” where Penn State educators and growers learn from each other. We extend special appreciation to our grower cooperators—Jake Scholl, Brett Saddington, Michael and Jesse King, David Deardorff, Arturo Diaz, Anton Shannon, Lisa Miskelly, Joe Buzzelli, David and Art King, Alfonso Manzo, and Corey and Vicky McCleaf.

Using grower records from this project, Lynn Kime developed interactive budgets for making decisions on orchard replant practices . For example, the reduction of dagger nematodes to the zero tolerance level resulted in an economic savings of $1000 to $2000 per acre based on the cost of nematicides, and the addition of organic matter represented a potential economic benefit of $1030 per acre based on the costs of compost and application.

Additional cover cropping and pre-plant practices are discussed in a Penn State Extension video. 

To learn more about the model plots and “living classroom” demonstrations in your region of the state, contact:

This project is supported by the Agriculture and Food Research Initiative of the National Institute of Food and Agriculture, Grant # 2015-70017-22852.


Moebius-Clune, B.N., D.J. Moebius-Clune, B.K. Gugino, O.J. Idowu, R.R. Schindelbeck, A.J. Ristow, H.M. van Es, J.E. Thies, H.A. Shayler, M.B. McBride, K.S.M Kurtz, D.W. Wolfe, and G.S. Abawi, 2016. Comprehensive Assessment of Soil Health – The Cornell Framework, Edition 3.2, Cornell University, Geneva, NY.

Natural Resources Conservation Services: Soil Health. 2013. Retrieved August 1, 2017