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United States Department of Agriculture

Agricultural Research Service

Related Topics

Research Project: Greater System Efficiency and Fruit Quality Via Soil Microbiology

Location: Physiology and Pathology of Tree Fruits Research

2011 Annual Report


1a.Objectives (from AD-416)
1. Assess the rooting behavior of apple as affected by different resource inputs (e.g. mineral fertilizer, compost, seed meal) and determine the relative contribution of soil biology and input to root development. 2. Examine the effect of fertility management programs on the dynamics of nematode and protozoan communities in the apple rhizosphere through application of T-RFLP and real-time quantitative PCR analysis. 3. Key genes steering microbial nitrogen cycling in the apple rhizosphere will be quantified under different resource input programs and linked to efficiency of use in the orchard ecosystem. 4. Determine the effect of altered soil biology on fruit quality characteristics including ripening; coloring; and long term storage quality.


1b.Approach (from AD-416)
Rooting behavior of apple in response to soil amendments and the contribution of native biology to these amendments will be assessed initially in greenhouse experiments. Short-term studies will employ apple seedlings and longer-term studies will utilize M9 rootstock as the plant material in these experiments. Initial trials will examine the effect of soil treatments on growth and architecture of apple seedling root systems when established in native and pasteurized soil systems. Seedlings will be grown in native and pasteurized soils with or without application of soil amendments. Overall seedling biomass will be determined after eight weeks growth in the respective soils. Root architecture will be assessed using winrhizo software analysis. It is generally assumed that organic matter based fertilizers will enhance soil fauna populations, but only a marginal number of materials (typically manure-based) have been examined). We possess preliminary data indicating that certain organic fertilizers will negatively impact soil fauna communities, including free living nematodes. Developing strategies to augment rather than suppress these populations will contribute positively to tree productivity both directly and indirectly. We will utilize real-time quantitative PCR and T-RFLP analysis to assess the effect of fertility management programs on quantitative and qualitative aspects of nematode and protozoan communities resident to apple orchard soils. Sustainable management of fertility inputs should seek to obtain a highly efficient turnover of minerals, with particular emphasis on minimizing nitrogen losses due to leaching of nitrogen and losses of gaseous N products. Previous studies have commonly ignored the fact that nitrogen turnover is the result of a network of closely interlinked processes. Therefore, we will investigate the effects of different fertility amendments on multiple transformation events within the nitrogen cycle in orchard soils and the specific microbial populations associated with these processes. Specifically, we will utilize real-time PCR to monitor expression of key genes steering microbial nitrogen cycling in the apple rhizosphere under different resource input programs and link expression patters to efficiency of nitrogen use in the orchard ecosystem. Fertility inputs significantly influence fruit quality through its effect on fruit ripening and capacity to retain desired eating characteristics under long-term storage. We will assess the impact of different fertility management practices on quality of fruit under long-term controlled atmosphere storage conditions. Documents Trust with Washington tree Fruit Research Commission.


3.Progress Report

This project relates to objective 1 of the associated in-house project, which seeks to determine the relative contribution of chemistry and soil biology to the control of soil borne diseases that is realized through soil incorporation of mustard (Brassica juncea) plant residues. Studies were conducted to determine the effect of fertility inputs on apple rootstock root development and the abundance/function of microbial genes involved in the cycling of nitrogen in apple orchard soils. In addition, the effect of bacterial strains belonging to the genus Streptomyces on M9 apple rootstock root development was examined. In a sandy texture orchard soil, root development of M9 rootstock was enhanced or depressed in a nitrogen amendment-dependent manner. Urea application significantly reduced lateral root formation relative to all other soil treatments including the no treatment control soil. Application of compost in concert with urea eliminated the negative effect on root development observed in soils treated with urea alone, but lateral root formation was not improved relative to the control. These trends were only observed in a natural orchard soil, and were abolished in the pasteurized orchard soil, indicating that these responses were biologically-mediated. Isolates of Streptomyces recovered from the rhizosphere of M9 apple rootstock enhanced root and overall plant development. The type of nitrogen amendment significantly altered abundance of microbial genes involved in N cycling, and thus could result in altered retention or loss of N from orchard soils. Abundance of the gene nirK , which encodes for an important step in the process leading to loss of nitrogen by volatilization, was highest in soils treated with urea, and significantly lower in soils for which nitrogen was supplied in the form of canola seed meal. Addition of compost in concert with either nitrogen source resulted in a significant decrease in nirK abundance. Suppression of nirK abundance by compost treatment may be an effective means to reduce the loss of nitrogen from orchard soils through volatilization. These data suggest that orchard management practices, such as those that increase in soil organic matter content, could demonstrably reduce the loss of nitrogen from this orchard soil system. Activity and progress were monitored through contacts with the Washington Tree Fruit Research Commission and reports submitted to the funding entity.


Last Modified: 4/18/2014
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