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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

2013 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.


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. The use of organic residues in tree fruit production systems can have variable effects on fruit quality due to the often high content of nitrogen contained in these materials and the unpredictable rate of N mineralization, and thus plant availability. The use of Brassicaceae seed meal, a high nitrogen containing substrate, as a soil amendment for control of replant disease did not have adverse effects on quality of fruit obtained from the 2012 harvest of an orchard replanted in 2010. Seed meal amendment at planting did not alter fruit quality in terms of firmness. After 4 months storage under normal atmosphere at 40 F, no significant differences in Gala fruit firmness were observed among soil treatments (no treatment control, pre-plant soil fumigation, and Brassica juncea/Sinapis alba seed meal). Differences in fruit color were observed. Gala fruit from trees grown in the non-treated control replant soil exhibited enhanced color development relative to fruit from either the fumigated or seed meal amended soil. This finding indicated that the difference in fruit color may have resulted from a stress response rather than differences in fertility management as fumigated and non-treated plots received the same fertility input. Studies continued in multiple orchard soils to monitor the presence of specific microbial genes that function in the cycling of nitrogen. The goals are to gain an understanding of the active microbial populations responsible for nitrogen cycling in orchard soils and the effect of different fertility inputs on the abundance and diversity of these microbial groups. Interestingly, ammonia oxidizing microbial community was dominated by archaea, rather than bacteria in all three orchard soils examined. Within a confined climatic zone (north central Washington) the genetic composition of the ammonia-oxidizing community did not differ among orchard soils of varying fertility levels and texture suggesting that practices developed for management of this community should have application across diverse soil systems. Archaea rather than bacteria dominate the ammonia-oxidizing microbial community and must be considered when developing efficient fertility management programs.


Last Modified: 4/18/2014
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