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pcaH , a molecular marker for estimating the diversity of the protocatechuate‐degrading bacterial community in the soil environment
Author(s) -
Azhari Najoi El,
Chabaud Sylvaine,
Percept Anthony,
Bru David,
MartinLaurent Fabrice
Publication year - 2007
Publication title -
pest management science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.296
H-Index - 125
eISSN - 1526-4998
pISSN - 1526-498X
DOI - 10.1002/ps.1357
Subject(s) - actinobacteria , biology , restriction fragment length polymorphism , genetics , phylogenetic tree , primer (cosmetics) , gene , molecular marker , proteobacteria , polymerase chain reaction , 16s ribosomal rna , chemistry , organic chemistry
Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring‐cleaving enzyme of the β‐ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices. Copyright © 2007 Society of Chemical Industry