Development of a Hierarchical Oligonucleotide Primer Extension Assay for the Qualitative and Quantitative Analysis of Cylindrospermopsis raciborskii Subspecies in Freshwater
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 Kinm...
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| Veröffentlicht in: | Microbes and Environments 2010, Vol.25(2), pp.103-110 |
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| creator | Wu, Jer-Horng Hsu, Mao-Hsuang Hung, Ching-Hui Tseng, I-Cheng Lin, Tsair-Fuh |
| description | 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. |
| doi_str_mv | 10.1264/jsme2.ME09186 |
| format | Article |
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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.</description><identifier>ISSN: 1342-6311</identifier><identifier>EISSN: 1347-4405</identifier><identifier>DOI: 10.1264/jsme2.ME09186</identifier><identifier>PMID: 21576860</identifier><language>eng</language><publisher>Japan: Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles</publisher><subject>Base Sequence ; Cylindrospermopsis - classification ; Cylindrospermopsis - genetics ; Cylindrospermopsis raciborskii ; DNA Primers - genetics ; DNA, Bacterial - isolation & purification ; DNA, Ribosomal - chemistry ; DNA, Ribosomal - genetics ; DNA, Ribosomal Spacer - genetics ; Fresh Water - microbiology ; Genetic Variation ; HOPE ; Molecular Sequence Data ; Molecular Typing - methods ; Phylogeny ; Polymerase Chain Reaction - methods ; relative abundance ; RNA, Ribosomal, 16S - genetics ; RNA, Ribosomal, 23S - genetics ; Sequence Analysis, DNA ; Taiwan ; Water Microbiology</subject><ispartof>Microbes and Environments, 2010, Vol.25(2), pp.103-110</ispartof><rights>Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology</rights><rights>Copyright Japan Science and Technology Agency 2010</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c536t-3b02f4549dd2e4ace6d2b2607373ca35d0089e2a5f958de92ed6a53599e9fbc53</citedby><cites>FETCH-LOGICAL-c536t-3b02f4549dd2e4ace6d2b2607373ca35d0089e2a5f958de92ed6a53599e9fbc53</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,1883,4024,27923,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21576860$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wu, Jer-Horng</creatorcontrib><creatorcontrib>Hsu, Mao-Hsuang</creatorcontrib><creatorcontrib>Hung, Ching-Hui</creatorcontrib><creatorcontrib>Tseng, I-Cheng</creatorcontrib><creatorcontrib>Lin, Tsair-Fuh</creatorcontrib><title>Development of a Hierarchical Oligonucleotide Primer Extension Assay for the Qualitative and Quantitative Analysis of Cylindrospermopsis raciborskii Subspecies in Freshwater</title><title>Microbes and Environments</title><addtitle>Microbes Environ.</addtitle><description>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.</description><subject>Base Sequence</subject><subject>Cylindrospermopsis - classification</subject><subject>Cylindrospermopsis - genetics</subject><subject>Cylindrospermopsis raciborskii</subject><subject>DNA Primers - genetics</subject><subject>DNA, Bacterial - isolation & purification</subject><subject>DNA, Ribosomal - chemistry</subject><subject>DNA, Ribosomal - genetics</subject><subject>DNA, Ribosomal Spacer - genetics</subject><subject>Fresh Water - microbiology</subject><subject>Genetic Variation</subject><subject>HOPE</subject><subject>Molecular Sequence Data</subject><subject>Molecular Typing - methods</subject><subject>Phylogeny</subject><subject>Polymerase Chain Reaction - methods</subject><subject>relative abundance</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>RNA, Ribosomal, 23S - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Taiwan</subject><subject>Water Microbiology</subject><issn>1342-6311</issn><issn>1347-4405</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNo9kcFu1DAQhiMEoqXlyBVZ4pzi2LGzOa6WbYtUVBD0HE3sSddLYgfbKexD9R3x7qZ78dgzn_7xzJ9lHwp6VTBZft6GAdnVtzWti4V8lZ0XvKzysqTi9eHOcsmL4ix7F8KWUs5Fxd5mZ6wQlVxIep49f8En7N04oI3EdQTIrUEPXm2Mgp7c9-bR2Un16KLRSL57M6An638RbTDOkmUIsCOd8yRukPyYoDcRonlCAlbv3za-JJYW-l0wYd9mteuN1d6FEf3gxn3WgzKt8-G3MeTn1KaKMhiIseTaY9j8hYj-MnvTQR_w_Rwvsofr9a_VbX53f_N1tbzLleAy5rylrCtFWWvNsASFUrOWSVrxiivgQlO6qJGB6Gqx0Fgz1BIEF3WNddcmjYvs01F39O7PhCE2Wzf59P_QFKWsqrRfViYqP1IqDRI8ds2Y1gN-1xS02ZvTHMxpZnMS_3FWndoB9Yl-cSMBqyOwDREe8QSAjyZZMMsx0RyOWfZUVRvwDVr-HzmiqD4</recordid><startdate>2010</startdate><enddate>2010</enddate><creator>Wu, Jer-Horng</creator><creator>Hsu, Mao-Hsuang</creator><creator>Hung, Ching-Hui</creator><creator>Tseng, I-Cheng</creator><creator>Lin, Tsair-Fuh</creator><general>Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles</general><general>Japan Science and Technology Agency</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>C1K</scope><scope>F1W</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope></search><sort><creationdate>2010</creationdate><title>Development of a Hierarchical Oligonucleotide Primer Extension Assay for the Qualitative and Quantitative Analysis of Cylindrospermopsis raciborskii Subspecies in Freshwater</title><author>Wu, Jer-Horng ; Hsu, Mao-Hsuang ; Hung, Ching-Hui ; Tseng, I-Cheng ; Lin, Tsair-Fuh</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c536t-3b02f4549dd2e4ace6d2b2607373ca35d0089e2a5f958de92ed6a53599e9fbc53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Base Sequence</topic><topic>Cylindrospermopsis - classification</topic><topic>Cylindrospermopsis - genetics</topic><topic>Cylindrospermopsis raciborskii</topic><topic>DNA Primers - genetics</topic><topic>DNA, Bacterial - isolation & purification</topic><topic>DNA, Ribosomal - chemistry</topic><topic>DNA, Ribosomal - genetics</topic><topic>DNA, Ribosomal Spacer - genetics</topic><topic>Fresh Water - microbiology</topic><topic>Genetic Variation</topic><topic>HOPE</topic><topic>Molecular Sequence Data</topic><topic>Molecular Typing - methods</topic><topic>Phylogeny</topic><topic>Polymerase Chain Reaction - methods</topic><topic>relative abundance</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>RNA, Ribosomal, 23S - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>Taiwan</topic><topic>Water Microbiology</topic><toplevel>online_resources</toplevel><creatorcontrib>Wu, Jer-Horng</creatorcontrib><creatorcontrib>Hsu, Mao-Hsuang</creatorcontrib><creatorcontrib>Hung, Ching-Hui</creatorcontrib><creatorcontrib>Tseng, I-Cheng</creatorcontrib><creatorcontrib>Lin, Tsair-Fuh</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><jtitle>Microbes and Environments</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wu, Jer-Horng</au><au>Hsu, Mao-Hsuang</au><au>Hung, Ching-Hui</au><au>Tseng, I-Cheng</au><au>Lin, Tsair-Fuh</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development of a Hierarchical Oligonucleotide Primer Extension Assay for the Qualitative and Quantitative Analysis of Cylindrospermopsis raciborskii Subspecies in Freshwater</atitle><jtitle>Microbes and Environments</jtitle><addtitle>Microbes Environ.</addtitle><date>2010</date><risdate>2010</risdate><volume>25</volume><issue>2</issue><spage>103</spage><epage>110</epage><pages>103-110</pages><issn>1342-6311</issn><eissn>1347-4405</eissn><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. 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| subjects | Base Sequence Cylindrospermopsis - classification Cylindrospermopsis - genetics Cylindrospermopsis raciborskii DNA Primers - genetics DNA, Bacterial - isolation & purification DNA, Ribosomal - chemistry DNA, Ribosomal - genetics DNA, Ribosomal Spacer - genetics Fresh Water - microbiology Genetic Variation HOPE Molecular Sequence Data Molecular Typing - methods Phylogeny Polymerase Chain Reaction - methods relative abundance RNA, Ribosomal, 16S - genetics RNA, Ribosomal, 23S - genetics Sequence Analysis, DNA Taiwan Water Microbiology |
| title | Development of a Hierarchical Oligonucleotide Primer Extension Assay for the Qualitative and Quantitative Analysis of Cylindrospermopsis raciborskii Subspecies in Freshwater |
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