6533b86ffe1ef96bd12cdfeb
RESEARCH PRODUCT
pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment
Najoi El AzhariDavid BruAnthony PerceptSylvaine ChabaudFabrice Martin-laurentsubject
Genetic Markers[SDV]Life Sciences [q-bio]Molecular Sequence DataBACTERIAL COMMUNITYSequence alignmentProtocatechuate-34-DioxygenaseActinobacteriaSOIL DNAchemistry.chemical_compoundBacterial ProteinsSequence Analysis ProteinMolecular markerProteobacteriaAmino Acid SequencePesticidesPhylogenySoil MicrobiologyPROTOCATECHUATE 34-DIOXYGENASEDNA PrimersGeneticsbiologyPhylogenetic treeRESTRICTION FRAGMENT LENGTH POLYMORPHISMPOLYMORPHISME DE RESTRICTIONBiodiversityGeneral Medicinebiology.organism_classificationCarbonActinobacteriaBiodegradation EnvironmentalchemistryGenetic markerInsect Science[SDE]Environmental SciencesRFLPProteobacteriaRestriction fragment length polymorphismSequence AlignmentAgronomy and Crop ScienceSoil microbiologyPolymorphism Restriction Fragment Lengthdescription
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 -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
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2007-04-12 | Pest Management Science |