Applicability of the functional gene catechol 1,2-dioxygenase as a biomarker in the detection of BTEX-degradingRhodococcusspecies

Abstract

Aims: Catechol 1,2‐dioxygenase is a key enzyme in the degradation of monoaromatic pollutants. The detection of this gene is in focus today but recently designed degenerate primers are not always suitable. Rhodococcus species are important members of the bacterial community involved in the degradation of aromatic contaminants and their specific detection could help assess functions and activities in the contaminated environments. To reach this aim, specific PCR primer sets were designed for the detection of Rhodococcus related catechol 1,2‐dioxygenase genes. Methods and Results: Primers were tested with genetically well‐characterized strains isolated in this study and community DNA samples were used as template for Rhodococcus specific PCR as well. The sequences of the catabolic gene in question were subjected to multiple alignment and a phylogenetic tree was created and compared to a 16S rRNA gene based Rhodococcus tree. A strong coherence was observed between the phylogenetic trees. Conclusions: The results strongly support the opinion that there was no recent lateral gene transfer among Rhodococcus species in the case of catechol 1,2‐dioxygenase. Significance and Impact of the Study: In gasoline contaminated environments, aromatic hydrocarbon degrading Rhodococcus populations can be identified based upon the detection and sequence analysis of catechol 1,2‐dioxygenase gene.

Detection and Quantification of Functional Genes of Cellulose- Degrading, Fermentative, and Sulfate-Reducing Bacteria and Methanogenic Archaea

“…Of the more than 70 glycoside hydrolase families defined on the basis of amino acid sequence identity in their catalytic domains (18), cellulases are found in 15 families (families 5,6,7,8,9,10,11,12,26,44,45,48,51,60, and 61) (24,40). The cellulase type does not correlate closely with phylogeny: most cellulolytic microorganisms produce cellulases that belong to different families, and cellulases of the same family occur in widely different microorganisms (4).…”

“…Some examples include the use of the large alpha subunit of benzylsuccinate synthase to monitor anaerobic hydrocarbon-degrading bacteria (5), the monitoring of ars genes for the identification and quantification of arsenicmetabolizing bacteria (45), and the detection of catechol 1,2-dioxygenase in aromatic-hydrocarbon-degrading Rhodococcus spp. (48). In the field of mine drainage/metal remediation, functional genes have been used to target SRB (17,26), but the methods have suffered both from a lack of broad specificity for SRB and from the inability to distinguish SRB from sulfuroxidizing bacteria (SOB).…”

Degradation of monoaromatics by Bacillus pumilus MVSV3

“…The ortho pathway of catechol degradation is also called as the β-ketoadipate pathway, and it has been studied in both gram negative and positive bacteria 7 . Although the importance of gram positive BTEX degrading bacteria is well known, only limited information is available about their detection in contaminated environment 8 . The present study reports the degradation of BTEX by an isolated bacteria Bacillus pumilus MVSV3 with the characterization of C12D isolated from the bacteria.…”

De Novo Genome Project for the Aromatic Degrader Rhodococcus pyridinivorans Strain AK37

“…It was identified by molecular taxonomy as R. pyridinivorans and deposited into the National Collection of Agricultural and Industrial Microorganisms (NCAIM PB1376), Hungary. Regarding its metabolic properties, it has been described as a good BTEXdegrading strain (14).…”