1. ¹Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen K, Denmark
2. ²Department of Ecology, Faculty of Life Sciences, University of Copenhagen, Frederiksberg C, Denmark
3. ³Microbial Ecology Program, Division of Biological Sciences, University of Montana, Missoula, MT, USA
4. ⁴Department of Natural Sciences, Faculty of Life Sciences, University of Copenhagen, Frederiksberg C, Denmark

Correspondence: CS Jacobsen, Department of Geochemistry, Geological Survey of Denmark and Greenland, Øster Voldgade 10, Copenhagen DK-1350, Denmark. E-mail: csj@geus.dk

Received 26 October 2007; Revised 29 January 2008; Accepted 31 January 2008; Published online 20 March 2008.

Abstract

Expression of the functional gene tfdA involved in degradation of phenoxyacetic acids such as 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-chloro-2-methylphenoxyacetic acid (MCPA) was investigated during degradation scenarios in natural unseeded soil samples. The results illustrate how messenger RNA (mRNA)-based analysis is well suited to quantitatively study the activity of specific microbial populations in soil using phenoxyacetic acid biodegradation as a model system. Via quantitative real-time PCR, a clear response to the presence of phenoxy acids was shown during degradation in soil amended with 20 mg 2,4-D or MCPA per kg soil. Further, we found a relatively high degree of correlation between expression of the functional gene and the rates of mineralization. Melting curve analyses of real-time PCR products, supported by tfdA-denaturing gradient gel electrophoresis analysis showed that, although only class I tfdA genes were apparent in the indigenous microbial population, class III tfdA genes became predominant during incubation, and were the only genes expressed during degradation of MCPA in soil. In contrast, both classes were expressed during degradation of the structurally similar compound 2,4-D. The ability to quantify microbial transcripts directly in environmental samples will have a profound impact on our understanding of microbial processes in the environment in future studies.