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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

2012 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 pattern 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.


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. Orchard soils yielded diverse responses in terms of nitrogen-cycling gene abundance an outcome which appears to have a greater relationship with long-term management practices/soil type rather than the consequence of short-term fertility amendments. Of particular note were observations concerning the size of the denitrifying bacterial communities based upon abundance of the nirK gene; which encodes an important step in the denitrification process leading to loss of nitrogen from orchard soils through volatilization. Abundance of the bacterial nirK gene was 1 to 2 orders of magnitude lower in high organic matter (OM) content orchard soils than in low OM content orchard soils. In addition, fertility amendments had no significant impact on bacterial nirK gene abundance detected in a high organic matter containing soil but urea amendment resulted in a significant (two orders of magnitude) increase in nirK abundance in a soil of low organic matter. Co-application of either urea or Brassica napus seed meal (nitrogen sources) with compost significantly reduced nirK abundance but only in the low OM orchard soil. In terms of orchard soil and inputs, fungal nirK gene abundance exhibited the same pattern. Thus, adding carbon as a strategy to retain nitrogen through decreased volatilization may be of significant benefit in low but not high OM containing orchard soils. Soil amendments had significant effects on the abundance of ammonia monooxygenase gene (amo) detected in apple rhizosphere soil. This gene encodes the enzyme involved in the first step of the nitrification process which results in transformation of ammonia nitrogen to nitrate nitrogen. Interestingly, the relative contribution of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) to the process of nitrification differed dramatically between the high and low organic matter soils. While ammonia oxidizing archaea (AOA) and bacteria (AOB) were nearly equivalent in the low OM soils, AOA abundance was over 10 times greater than AOB in the high organic matter soil system. Overall, the relative abundance of the NifH, AOB, and AOA genes compared to the NirK genes indicates a potentially greater capacity for nitrogen retention and plant availability, in high organic matter than low organic matter orchard soils. The relative differential abundance of AOB and AOA in soil systems is of significance because AOA are reported as being responsive to organic nitrogen and do not respond to inorganic N fertilizer. Soil pasteurization as a proxy for soil fumigation exhibited negligible rates of ammonia-oxidation indicating the removal of that portion of the microbial community involved in this process. These findings demonstrate that soil fumigation may adversely affect the process of nitrification in soil systems and could lead to significant N losses.


Last Modified: 10/30/2014
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