title: Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon-degrading Alcanivorax strains.
abstract: The genus Alcanivorax comprises diverse hydrocarbon-degrading marine bacteria. Novel 16S rRNA-targeted oligonucleotide DNA probes (ALV735 and ALV735-b) were developed to quantify two subgroups of the Alcanivorax/Fundibacter group by fluorescence in situ hybridization (FISH), and the conditions for the single-mismatch discrimination of the probes were optimized. The specificity of the probes was improved further using a singly mismatched oligonucleotide as a competitor. The growth of Alcanivorax cells in crude oil-contaminated sea water under the biostimulation condition was investigated by FISH with the probe ALV735, which targeted the main cluster of the Alcanivorax/Fundibacter group. The size of the Alcanivorax population increased with increasing incubation time and accounted for 91% of the 4',6-diamidino-2-phenylindole (DAPI) count after incubation for 2 weeks. The probes developed in this study are useful for detecting Alcanivorax populations in petroleum hydrocarbon-degrading microbial consortia.
authors.affiliation: Marine Biotechnology Institute, Kamaishi Laboratories, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan. stubo@kamaishi.mbio.co.jp
authors.forename: K
authors.initials: K
authors.lastname: Syutsubo
authors.forename: H
authors.initials: H
authors.lastname: Kishira
authors.forename: S
authors.initials: S
authors.lastname: Harayama
mesh_terms: D001483:Base Sequence; D004275:DNA, Ribosomal / Q000032:analysis; D020563:Gammaproteobacteria / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D006838:Hydrocarbons / Q000378:metabolism*; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D015345:Oligonucleotide Probes; D010578:Petroleum / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000382:microbiology; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014877:Water Pollution, Chemical
chemical_list: D004275:DNA, Ribosomal; D006838:Hydrocarbons; D015345:Oligonucleotide Probes; D010578:Petroleum; D012336:RNA, Ribosomal, 16S