title: Species-specific oligonucleotides for enumeration of Pseudomonas putida F1, Burkholderia sp. strain JS150, and Bacillus subtilis ATCC 7003 in biodegradation experiments.
abstract: Species-specific sequences were identified within the V4 variable region of 16S rRNA of two bacterial species capable of aromatic hydrocarbon metabolism, Pseudomonas putida F1 and Burkholderia sp. strain JS150, and a third, Bacillus subtilis ATCC 7003, that can function as a secondary degrader. Fluorescent in situ hybridization (FISH) with species-specific oligonucleotides was used for direct counting of these species throughout a phenol biodegradation experiment in batch culture. Traditional differential plate counting methods could not be used due to the similar metabolism and interactions of the primary degraders and difficulties in selecting secondary degraders in mixed culture. In contrast, the FISH method provided reliable quantitative results without interference from those factors.
authors.affiliation: Departments of Microbiology, Center for Environmental Toxicology and Technology, Colorado State University, Fort Collins, Colorado 80523, USA. nduteau@cvmbs.colostate.edu
authors.forename: N M
authors.initials: NM
authors.lastname: DuTeau
authors.forename: J D
authors.initials: JD
authors.lastname: Rogers
authors.forename: C T
authors.initials: CT
authors.lastname: Bartholomay
authors.forename: K F
authors.initials: KF
authors.lastname: Reardon
mesh_terms: D001412:Bacillus subtilis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D001483:Base Sequence; D001673:Biodegradation, Environmental; D019117:Burkholderia / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D017931:DNA Primers; D015342:DNA Probes; D006841:Hydrocarbons, Aromatic / Q000378:metabolism; D017404:In Situ Hybridization, Fluorescence; D016958:Pseudomonas putida / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
chemical_list: D017931:DNA Primers; D015342:DNA Probes; D006841:Hydrocarbons, Aromatic; D012336:RNA, Ribosomal, 16S