Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes.

Interest in unheated plastic film-covered high tunnels to extend the growing season of high-value fruits and vegetables is growing rapidly, but sustainable soil management in intensively managed high tunnels is challenging. Yields, fruit quality, and soil quality in transition organic and conventional tomato were measured over the course of three growing seasons. Nitrogen (N) was applied at the rate of 112, 168, and 224 kg total N/ha in the form of chicken manure compost to the organic treatments and a polymer-coated slow-release urea fertilizer in the conventional treatments. Marketable yield of organically grown tomatoes was lower in Year 1 but equaled conventional tomatoes in Years 2 and 3. Soil quality as measured by total carbon (C) and N and microbial activity was significantly greater in organic tomato production at the end of the study. Significant phosphorus (P) and potassium (K) applied with the composted manure resulted in high soil P and K levels in organically managed high tunnels after just 3 years of application. Although compost is the most economical organic fertilizer and results in significant benefits in soil quality during the transition phase to organic production, a maintenance fertility plan is needed once available soil P reaches adequate to high levels. Combinations of compost and high N, low P organic fertilizers are needed for optimum maintenance fertility strategy for organic tunnel house production.