title: Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil.
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.
authors: Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen K, Denmark.
authors: Jacob
authors: J
authors: Baelum
authors: Mette H
authors: MH
authors: Nicolaisen
authors: William E
authors: WE
authors: Holben
authors: Bjarne W
authors: BW
authors: Strobel
authors: Jan
authors: J
authors: Sørensen
authors: Carsten S
authors: CS
authors: Jacobsen
mesh_terms: D015084:2,4-Dichlorophenoxyacetic Acid / Q000032:analysis / Q000378:metabolism*; D008456:2-Methyl-4-chlorophenoxyacetic Acid / Q000032:analysis / Q000378:metabolism*; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics; D001426:Bacterial Proteins / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D001673:Biodegradation, Environmental; D049308:Dioxygenases / Q000032:analysis / Q000235:genetics* / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D015870:Gene Expression; D008969:Molecular Sequence Data; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000032:analysis / Q000378:metabolism; D044366:Transition Temperature
chemical_list: D001426:Bacterial Proteins; D012987:Soil; D012989:Soil Pollutants; D015084:2,4-Dichlorophenoxyacetic Acid; D008456:2-Methyl-4-chlorophenoxyacetic Acid; D049308:Dioxygenases