TY - JOUR
T1 - Degradation of 4-chloro-2-methylphenoxyacetic acid in top- and subsoil is quantitatively linked to the class III tfdA gene
AU - Bælum, Jacob
AU - Henriksen, Trine
AU - Hansen, Hans Christian Bruun
AU - Jacobsen, Carsten Suhr
PY - 2006/2
Y1 - 2006/2
N2 - The tfdA gene is known to be involved in the first step of the degradation of the phenoxy acid herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) in several soil bacteria, but bacteria containing other tfdA-like genes have been isolated as well. A quantitative real-time PCR method was used to monitor the increase in the concentration of tfdA genes during degradation of MCPA in sandy topsoil and subsoil over a period of 115 days. Quantitative PCR revealed growth in the tdfA-containing bacterial community, from 500 genes g-1 soil to approximately 3 × 104 genes g-1 soil and to 7 × 10 5 genes g-1 soil for topsoil initially added to 2.3 mg MCPA kg-1 (dry weight) soil and 20 mg MCPA kg-1 (dry weight) soil, respectively. We analyzed the diversity of the tfdA gene during the degradation experiment. Analyses of melting curves of real-time PCR amplification products showed that a shift in the dominant tfdA population structure occurred during the degradation period. Further denaturing gradient gel electrophoresis and sequence analysis revealed that the tfdA genes responsible for the degradation of MCPA belonged to the class III tfdA genes, while the tfdA genes present in the soil before the occurrence of degradation belonged to the class I tfdA genes. The implications of these results is that the initial assessment of functional genes in soils does not necessarily reflect the organisms or genes that would carry out the degradation of the compounds in question.
AB - The tfdA gene is known to be involved in the first step of the degradation of the phenoxy acid herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) in several soil bacteria, but bacteria containing other tfdA-like genes have been isolated as well. A quantitative real-time PCR method was used to monitor the increase in the concentration of tfdA genes during degradation of MCPA in sandy topsoil and subsoil over a period of 115 days. Quantitative PCR revealed growth in the tdfA-containing bacterial community, from 500 genes g-1 soil to approximately 3 × 104 genes g-1 soil and to 7 × 10 5 genes g-1 soil for topsoil initially added to 2.3 mg MCPA kg-1 (dry weight) soil and 20 mg MCPA kg-1 (dry weight) soil, respectively. We analyzed the diversity of the tfdA gene during the degradation experiment. Analyses of melting curves of real-time PCR amplification products showed that a shift in the dominant tfdA population structure occurred during the degradation period. Further denaturing gradient gel electrophoresis and sequence analysis revealed that the tfdA genes responsible for the degradation of MCPA belonged to the class III tfdA genes, while the tfdA genes present in the soil before the occurrence of degradation belonged to the class I tfdA genes. The implications of these results is that the initial assessment of functional genes in soils does not necessarily reflect the organisms or genes that would carry out the degradation of the compounds in question.
UR - http://www.scopus.com/inward/record.url?scp=33144468213&partnerID=8YFLogxK
U2 - 10.1128/AEM.72.2.1476-1486.2006
DO - 10.1128/AEM.72.2.1476-1486.2006
M3 - Article
SN - 0099-2240
VL - 72
SP - 1476
EP - 1486
JO - Applied and Environmental Microbiology
JF - Applied and Environmental Microbiology
IS - 2
ER -