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Monitoring Microbial Populations Using Real-Time qPCR on the MJ Research Opticon 2 System

Hans-Peter Horz, Ph.D.1, Richard Kurtz, Ph.D.2, David Batey, Ph.D.2 and Brendan Bohannan, Ph.D.1
1Department of Biological Sciences, Stanford University, Stanford, CA
2MJ Research, Incorporated, South San Francisco, CA


Abstract
The levels of the amoA gene were used to measure the ammonia-oxidizing bacteria (AOB) population in soils maintained under 16 environmental regimes. DNA was extracted from soil samples and amoA levels analyzed by real-time quantitative PCR (qPCR) using SYBR Green I (SGI) detection chemistry on an MJ Research DNA Engine Opticon 2 continuous fluorescence detection system. Representative samples from the sixteen treatment groups showed amoA levels to vary over a 32-fold range.


Introduction
Microorganisms play a major role in the biogeochemical cycling of key elements. Numerous research groups have described bacterial diversity in natural environments and their changes over time and space.1, 2, 3 Little is known, however, about the impact of global environmental change on the microbial community in soil. To address this question, the Jasper Ridge Global Change Project (JRGC) simulates global change on a California grassland by the simultaneous manipulation of four major environmental factors: temperature, ambient CO2 concentration, precipitation, and nitrogen deposition, both individually and in combination.4 The JRGC study tests the hypothesis that specific environmental conditions affect the population size of ammoniaoxidizing bacteria (AOB).

AOB are responsible for the oxidation of ammonia to nitrite in the nitrification process. This process is essential for making nitrogen available to most
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