title: Development of a hierarchical oligonucleotide primer extension assay for the qualitative and quantitative analysis of Cylindrospermopsis raciborskii subspecies in freshwater.
abstract: A newly-developed molecular method, hierarchical oligonucleotide primer extension (HOPE), was used to analyze various groups within the species Cylindrospermopsis raciborskii. PCR-amplified internally transcribed spacer sequences of 16S-23S from C. raciborskii in reservoir samples of Taiwan and Kinmen were examined. One of eight sequevars in the clone libraries was closely related to strains obtained from the European continent, while the others, designated of Taiwan (TW) type, belonged to a novel group. Optimized HOPE analyses showed that C. raciborskii distributed in different reservoirs with a relative abundance of 0.5% to 76.4% in the cyanobacterial communities. They further detected the concurrence of three C. raciborskii subpopulations, in which European and TW groups were predominant. The TW sequevars accounted for greater than 87.5% of C. raciborskii in the reservoirs Taihu, Yangmin, Jinsha, and Mudan, while this decreased to 55.4-58.1%, accompanied by a proportional increase of the European group, in reservoirs Lantan and Renyi. These findings revealed the complex subspecies structure within C. raciborskii and the subspecies dynamics associated with geographic locations.
authors.affiliation: Department of Environmental Engineering, National Cheng Kung University, Taiwan. enewujh@mail.ncku.edu.tw
authors.forename: Jer-Horng
authors.initials: JH
authors.lastname: Wu
authors.forename: Mao-Hsuang
authors.initials: MH
authors.lastname: Hsu
authors.forename: Ching-Hui
authors.initials: CH
authors.lastname: Hung
authors.forename: I-Cheng
authors.initials: IC
authors.lastname: Tseng
authors.forename: Tsair-Fuh
authors.initials: TF
authors.lastname: Lin
mesh_terms: D001483:Base Sequence; D046891:Cylindrospermopsis / Q000145:classification* / Q000235:genetics; D017931:DNA Primers / Q000235:genetics*; D004269:DNA, Bacterial / Q000302:isolation & purification; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005618:Fresh Water / Q000382:microbiology*; D014644:Genetic Variation; D008969:Molecular Sequence Data; D058889:Molecular Typing / Q000379:methods*; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013624:Taiwan; D014871:Water Microbiology
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S