Hybridization Analysis of Microbial DNA from Fuel Oil–Contaminated and Noncontaminated Soil

Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil

“…Enrichment of PAH-degraders is a common phenomenon during the course of PAH biodegradation (Guo et al, 1997;Piskonen et al, 2005). Therefore, in this study, the large enrichment of three TRFLP fragments might also be linked to the enrichment of some PAH-degraders.…”

Detection and Enumeration of Aromatic Oxygenase Genes by Multiplex and Real-Time PCR

“…strain DNT; 3, P. putida F1; 4, P. putida HS1; 5, P. putida mt-2. (12,17). PCR with the RMO primers produced an amplicon of approximately 460 bp with P. mendocina KR1 despite two predicted mismatches with each primer.…”

Diversity of Alkane Hydroxylase Systems in the Environment

“…While in some studies alkB homologs were detected in 10-40% of the bacterial population [97,101,102], other groups did not detect alkB homologs at all [99,100]. AlkB homologs that are closely related to the P. putida GPo1 enzyme appear to be common in gram-negative strains only (probably pseudomonads) [76].…”

“…Alaskan sediments Colony hybridization with alkB 39% of viable heterotrophs from uncontaminated soil contain alkB gene probe 67% of viable heterotrophs from contaminated soil contain alkB [97] Contaminated soil PCR followed by Southern blot Detection and quantification of alkB (and other genes) in soil: 1-10 with alkB gene probe gene copies per gram of soil can be detected [98 Variety of cold ecosystems PCR, and Southern blots None of the psychrophilic alkane degraders possess genes with alkB gene probe with high homology to P. putida alkB [99] Fuel oil-contaminated site Dot-blots DNA extracted from soil shows no significant hybridization with an alkB-gene probe [100] Shallow aquifer Southern blots 10-20% of the total bacterial community hybridizes with alkB gene probe with an alkB gene probe [101] Various sources PCR with highly degenerate Most alkane-degrading strains contain distantly related alkB homologs (54 bacterial strains) primers for alkB homologs (homology not sufficient for Southern or dot-blots) [50] Shallow aquifer Dot-blots with DNA extracted alkB genotypes start at 11% of total community, and peak at (natural attenuation site) from aquifer samples 52% after injection of synthetic jet fuel in the aquifer [102] Various sources Southern, colony and dot-blots, alkB genes (close homologs) are widespread only in short-chain n-alkane (54 bacterial strains) PCR followed by Southern degrading pseudomonads [76] Rhizosphere vs. bulk soil Multiplex PCR At a contaminated site alkB was 10 times more prevalent in the endophytic community compared to the bulk soil community [103] Propane and butaneDot-blots 8 of 15 strains (including pseudomonads and rhodococci) utilizing bacteria gave a strong signal, and 7 a weak signal with the IMT37 gene [37] Land treatment unit (LTU) PCR, terminal restriction alkB increased in abundance during the first 3 weeks of LTU operation, fragment length polymorphism and comprised > 80% of the total PCR products [104] Arctic and Antarctic soil PCR-hybridization Rhodococcal alkB genes occur in contaminated and pristine soils, and colony hybridization P. putida alkB occurs more frequently in contaminated soils [105] similar genes in other butane degraders (pseudomonads, rhodococci and unidentified bacteria). In a dot-blot experiment, 8 out of 15 propane or butane-degrading bacteria gave a strong signal with the gene-probe, while the remaining 7 gave a weak but detectable signal [37].…”