Date Available


Year of Publication


Degree Name

Doctor of Philosophy (PhD)

Document Type





Crop Science

First Advisor

Dr. Mark A. Williams


The objective of this research was to determine the effects of conventional inputs on soil chemical and biological properties compared to organic systems in a four year vegetable rotation. Tillage and cover crops were the same in all treatments to avoid confounding factors often present in similar research. Additional experiments investigated plant gene expression in organic and conventional management systems and in soils with decreased microbial diversity. Experimental plots were prepared in the spring of 2004; four replications of three management treatments, organic, low-input and conventional, were arranged in a randomized complete block design. The rotation consisted of edamame soybean, sweet corn, fallow (pastured poultry in organic plots), and potatoes. Soil samples were taken in the spring and fall of each year, along with data for pest damage, weed control, yield and quality. Soil samples were analyzed for enzyme activity (maximum activity under substrate saturation) and basic soil chemical properties. Treatments were compared over time using 2-Way ANOVA. Multiplex terminal-restriction fragment length polymorphism (M-TRFLP) profiles of the soil microbial community were compared using Multiple Response Permutation Procedures (MRPP). Multi-way ANOVA detected significant treatment effects over time in total carbon, nitrogen, Mehlich III K, Exchangeable K and exchangeable Na (p=0.05). Many significant changes in soil properties over time could not be attributed to treatment effects. All treatments produced similar yields, indicating that successful organic production of these vegetables is possible in Kentucky. Input costs for organic were 37% higher than conventional, due to the cost of organic fertilizer. The organic system required nearly 50% more labor hours than conventional or low-input. The low-input system was the most cost effective, with 58% less input expenses than the conventional system. Microarray analysis of approximately 37,500 Glycine max transcripts did not show significant differences in the gene expression between plants grown organically and conventionally, in plots with significant soil chemical and microbial differences. An experiment in progress is investigating changes in plant gene expression using real time RT-PCR in tomatoes grown in autoclaved soil and native field soil.



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