Towards ecologically-based fertilizer recommendations that improve soil quality in high-density apple orchards

Final report for LS13-258

Project Type: Research and Education
Funds awarded in 2013: $140,000.00
Projected End Date: 09/30/2017
Region: Southern
State: Virginia
Principal Investigator:
Dr. Gregory Peck
Cornell University
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Project Information

Abstract:

Profitability of high-density orchards is dependent on obtaining sufficient vegetative growth and high fruit yields during the first three years after planting, a goal typically achieved through applying high rates of synthetically derived nitrogen fertilizer. The purpose of this project was to test sustainable soil fertility management practices for Mid-Atlantic and Southern apple growers by applying mulch and compost to apple orchards. Over three years, we sampled from study sites at Virginia Tech’s Alson H. Smith, Jr. Agricultural Research and Extension Center (AREC), and at the orchards of grower cooperators based in Virginia and Maryland. By the third year, the mulch treatments increased tree growth at all three sites. However, using compost either alone or in conjunction with calcium nitrate did not further increase tree growth at any of the sites. Additionally, the compost applications increased plant-available soil phosphorus at the AREC site and potassium at the Maryland site, but leaf tissue concentration did not increase correspondingly to the soil mineral content. Soil communities were analyzed using the Quantitative Insights Into Microbial Ecology software. Quality checking of the more than 1.5 million bacterial sequence reads and 0.25 million fungal reads showed that the greatest effect was due to location. The dominant bacterial Operational Taxonomic Units were most closely related to Proteobacteria, Acidobacteria, and Actinobacteria. Bacterial community changes that were consistent across locations were strongly associated with root-zone Proteobacteria, increasing by 26% due to the mulch application. Evidence for fertilizer-induced changes in the relative abundance of ammonia-oxidizing bacterial family were also apparent, and suggest that there are functional differences in nitrogen cycling resulting from both fertilizer and mulch. The mulch treatment increased the mycorrhizal fungal groups Glomeromycota by 16% and Agaricomycetes by 35%. However, Agaricomycetes also contain some species of decomposers and pathogens. Mycorrhizae would be of particular interest for further study because they’re the most likely candidate for playing a growth supportive role for apple trees. The ability to alter the microbial community has important ramifications for the bioavailability of plant nutrients, plant-root bacterial interactions, and therefore orchard sustainability.

Project Objectives:

Objective 1: Use an interdisciplinary approach to examine the benefits of utilizing carbon-based soil amendments in commercial apple orchard systems so that we can investigate the interaction between soil nutrient source and orchard productivity. Our project will investigate microbial community composition, biomass, and soil biological activity in the soil, particularly in the rhizosphere (the soil-root interface). The research will occur on replicated plots located in three separate regional apple orchards.

  • Our research utilizes a research farm trial comparing synthetic fertilizers (calcium nitrate), chicken litter compost, municipal yard waste compost, and treatments that integrate synthetic fertilizers with composts when applied to newly planted high-density apple trees.
  • We also developed two replicated on-farm trials with cooperating growers.
  • Among the three farm sites outlined in this objective, this research project spans 200 miles and puts growers throughout the Mid-Atlantic in close proximity to the test sites, which will encourage faster adoption of the most effective treatments.

Objective 2: Educate stakeholders in orchard nutrition management. Develop printed materials to support educational activities.

Cooperators

Click linked name(s) to expand
  • Bob Black
  • Bill Mackintosh
  • John Saunders
  • Dr. Mark Williams

Research

Materials and methods:

Experimental Design and Statistical Analysis

A split-plot, completely randomized design with four four-tree replications for each treatment was used at each location. The main plots are mulch versus no mulch. The four subplots are the fertilizer inputs: compost, calcium nitrate, both compost and calcium nitrate (CaNO3), and an unfertilized control. There is an untreated buffer tree between each subsplot and two untreated buffer trees between main plots. Mulch was applied at a 1-m width, 10-cm depth and mostly consisted of large-aggregate material that was sourced locally for each site.

Response variables measured included:

  • Tree growth by trunk cross-sectional area on an annual basis
  • Leaf nutrient status (20 leaves were collected from each tree in the treated block from current season’s growth)
  • Soil nutrient status (taken to 10-cm depth from two locations on either side of each tree approximately 26 cm from the base of the tree)
  • Terminal shoot growth and branching
  • Fruit yields and quality (year three)
  • Soil microbial biomass and community structure
Research results and discussion:

Tree growth

At all three sites, the mulch treatments had a greater impact on tree growth than the sub-plot fertilizer treatments. However, increased tree growth was not always statistically different between trees with and without mulch. Other studies suggest that increased tree growth during the first few years of growth are maintained for the long-term but up to five years of data are usually required.

Plant-available Soil Nutrients and Leaf Nutrients

At the AREC site, the compost and compost + CaNO3 treatments increased soil phosphorus concentration, and those same treatments increased soil potassium concentration at the Maryland site. There were no differences in the soil mineral concentrations at the Tyro site. The increased soil phosphorus and potassium concentrations did not always cause an increase in leaf mineral levels, but relationships appeared to be emerging. Some treatment differences were found for soil calcium, magnesium, and zinc, but these were not of a large magnitude. None of the treatments resulted in increased leaf nitrogen content for any of the sites.

Soil Bacterial Communities

Soil communities were analyzed using the software Quantitative Insights Into Microbial Ecology (QIIME). Quality checking of the more than 1.5 million bacterial sequence reads and 0.25 million fungal reads showed that the greatest effect, not surprisingly was due to location. It is striking to note, the effect that mulch can have on the community over the relatively short time period of the experiment. The dominant Operational Taxonomic Units (OTUs) were most closely related to Proteobacteria, Acidobacteria, and Actinobacteria. Bacterial community changes, that were consistent across locations were strongly associated with root-zone Proteobacteria, increasing by 26% due to mulch. Evidence for fertilizer-induced changes in the relative abundance of ammonia-oxidizing bacterial family were also apparent, and suggest that there are ecologically significant and functional differences in nitrogen cycling resulting from both fertilizer and mulch. The changing bacterial community likely has important ramifications for the bioavailability of plant nutrients, plant-root bacterial interactions, and therefore orchard sustainability.

Soil Fungal Communities

Although overall patterns of change were similar to the bacterial community, extraction of high-quality soil fungal DNA was more difficult. There are multiple reasons for this, one of which is related to the number of copies of the target marker gene, and the chemical reactivity of the soil. The MD and Tyro orchards provided sound results and with the highest veracity for interpretation. Fungal communities between these two locations, which were expected, were different. The differences span across the major Phyla with the major ones comprising Glomeromycota (3%), Zygomycota (10%), Ascomycota (27%) and Basidiomycota (32%) the predominant sequence data. The effects of compost amendment we’re less clear, but a more elaborate set of methods may help to describe those differences. 

The addition of an organic amendment such as mulch can over several years have a large impact on soil dynamics. These were reflected in the current experiment by showing changes in the fungal communities. Mulch increased the growth promoting of close relatives of mycorrhizal fungal groups Glomeromycota by 16%, and Agaricomycetes by 35%. In the latter case, however, Agaricomycetes, also contain some species of decomposers and pathogens. This group in particular, would be of particular interest for further study because they’re the most likely candidate for playing a growth supportive role for apple trees.

In this regard, a group closely aligned with Tremelomycota declined by 27%. The significance of this latter result is difficult to determine because this group contains a broad range of decomposers, plant growth promoters, and disease-causing fungi. The literature is dominated by studies of disease related taxa, however, and so in the case of this group the pathogenic importance of the relative decline should be interpreted cautiously. The changes in the above groups, however, set the stage for testing of hypotheses using more focused molecular techniques to ascertain the role of fungal communities resulting from the effect of mulch, and other organic amendments. Pleosporales, a family of bacteria containing members of the Venturia genus (the causal organism for apple scab) were noticeably lower due to the mulch, declining by 80%, containing 2.8 to 1.8% in non-mulch compared to mulched treatments. These percentages of taxa may be seen as small to a non-specialist, but in a soil with 1,000 of taxa, any group with 0.1% or more of the total sequence reads are considered to be relatively dominant taxa. Although it is not known if the mulch treatment resulted in disease suppression, it has been reported previously that the addition of organic matter to soil tends to have greater growth promoting and lower relative abundance of pathogenic organisms. Our results are an important step forward for understanding the huge diversity of bacterial and fungal community types in apple orchards, and their potential for change due to orchard management.

Participation Summary
3 Farmers participating in research

Education

Educational approach:

The study sites have already been a source of discussion and demonstration for the public and commercial apple growers in the Mid-Atlantic region. During an open house at the AREC on 16 Aug 2014, our research team gave two presentations on this project to nearly 85 people. Many of these individuals were very interested to learn about the emphasis on sustainability that is included in this project. On 10 Sept 2014, a group of nearly 50 growers and associated industry personal toured the AREC research site to learn about the first year’s results. On 25 Aug 2015, the AREC plots were used to demonstrate possible organic fertilizer and weed control strategies to 50 growers at a Commercial Organic Apple Production Field Day. Our team also organized and moderated a scientific colloquium on the “Impact of Rootstocks on Mineral Nutrition” at the American Society for Horticultural Science’s 2016 Annual Conference in Atlanta, GA. We gave a talk entitled, “Soil Microbial Mediation of Mineral Uptake by Apple Rootstocks”, and included some of the results from this SSARE funded project.

Educational & Outreach Activities

15 Consultations
1 On-farm demonstrations
1 Published press articles, newsletters
3 Webinars / talks / presentations
3 Workshop field days

Participation Summary

50 Farmers
10 Ag professionals participated

Learning Outcomes

25 Farmers reported changes in knowledge, attitudes, skills and/or awareness as a result of their participation

Project Outcomes

5 Farmers changed or adopted a practice
2 Grants received that built upon this project
Project outcomes:

Objective 1: Use an interdisciplinary approach to examine the benefits of utilizing carbon-based soil amendments in commercial apple orchard systems so that we can investigate the interaction between soil nutrient source and orchard productivity.

Our research utilized a research farm trial comparing synthetic fertilizers (calcium nitrate), compost, municipal yard waste compost, and treatments that integrated synthetic fertilizers with composts applied to newly planted high-density apple trees. We also developed two replicated on-farm trials with cooperating growers. Among the three farm sites outlined in this objective, this research project spans 200 miles and puts growers throughout the Mid-Atlantic in close proximity to the test sites, which will encourage faster adoption of the most effective treatments.

 

Recommendations:

This three-year long project showed promising results for documenting the positive impacts of carbon-based amendments to apple orchard agro-ecosystems. Additional research should focus on wood and bark chip mulches. While the mulch treatments increased tree growth at all three sites, using compost either alone or in conjunction with calcium nitrate did not further increase tree growth at any of the sites. Additionally, the compost applications increased plant-available soil phosphorus at the AREC site and potassium at the Maryland site, but leaf tissue levels did not directly correspond to the soil mineral content. Growers should utilize compost applications based on the specific nutrient needs at their location, as well as on leaf mineral tests, and soil texture and organic matter content. Overall, our study showed that if increased tree growth is the primary purpose for applying a fertilizer, such applications may be unwarranted, whether from a compost or synthetic source. However, compost can increase soil properties that are associated with long-term soil fertility, such as organic matter, soil carbon, and microbial respiration. It is possible that these increases will positively impact orchard productivity in future years. Longer-term studies are needed to understand the effects of these fertilization practices as the orchard matures and reaches full productivity.

Additionally, it is well documented that mulches can retain and moderate soil moisture and temperature, but we did not measure these variables in our study. Future research should seek to understand whether the increased apple tree growth and changes in microbial communities that we observed were related to soil moisture, soil temperature, carbon addition, or a combination of these factors. Another benefit of mulches is to reduce weed growth. Future studies should investigate whether the use of mulches in orchards can result in a reduction of herbicide applications without sacrificing tree growth, thus increasing orchard sustainability.

Lastly, some of the organisms that we identified in the microbial community analysis have been reported to be disease suppressive. Other studies have shown that the addition of organic matter to a soil results in greater growth promoting and lower relative abundance of pathogenic organisms. Our results are thus an important step forward for understanding the huge diversity of bacterial and fungal community types in apple orchards, and their potential for change due to practical types of orchard management. These results support a main focus of our study, that is that organic amendments drive microbial communities to increase apple orchard productivity. Future research should apply treatments similar to those used in this study to orchard soils with high populations of pathogenic organisms as a means of naturally fostering microbial biocontrol.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.