Enhanced release nitrogen fertilizers or slow release fertilizers are used to augment nitrogen use efficiency; it needs to be degraded into soluble nitrogen compounds, by a specific microbial catalyzed reaction. The objectives of this study are to compare different techniques of total soil DNA isolation, in the DNA quality and purity produced, to isolate a bacterium capable of methylene urea degradation and to studythe soil community shift pattern using Shannon indexes and the Dice coefficient after applying urea and methylene urea. Urea and methylene-urea-triazone were incorporated into the soil. DNA was extracted. Denaturant gradient gel electrophoresis was performed with the PCR amplicons. Shannon Wiener Index was determined by bands. A significantly greater biological diversity was observed in the sample group with methylene-urea-triazone. There was a difference between urea and the enhanced efficiency fertilizer in plant response and bacterial diversity. Microorganisms in soil need time to respond to environmental changes.