Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria
The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds. In eutrophic fresh and brackish waters, their mass occurrences (water looms) are often toxic an...
Published in: | Applied and Environmental Microbiology |
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American Society for Microbiology.
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Online Access: | http://hdl.handle.net/2434/10682 https://doi.org/10.1128/AEM.70.12.7161-7172.2004 |
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ftunivmilanoair:oai:air.unimi.it:2434/10682 2024-02-11T09:57:30+01:00 Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria B. Castiglioni K. Sivonen P. Rajaniemi A. Rantala M. A. Mugnai S. Ventura A. Wilmotte C. Boutte S. Grubisic P. Balthasart A. Mezzelani G. De Bellis E. Rizzi A. Frosini C. Consolandi R. Bordoni C. Battaglia B. Castiglioni E. Rizzi A. Frosini K. Sivonen P. Rajaniemi A. Rantala M.A. Mugnai S. Ventura A. Wilmotte C. Boutte S. Grubisic P. Balthasart C. Consolandi R. Bordoni A. Mezzelani C. Battaglia G. De Bellis 2004-12 http://hdl.handle.net/2434/10682 https://doi.org/10.1128/AEM.70.12.7161-7172.2004 eng eng American Society for Microbiology. info:eu-repo/semantics/altIdentifier/pmid/15574913 info:eu-repo/semantics/altIdentifier/wos/WOS:000225719300028 volume:70 issue:12 firstpage:7161 lastpage:7162 journal:APPLIED AND ENVIRONMENTAL MICROBIOLOGY http://hdl.handle.net/2434/10682 doi:10.1128/AEM.70.12.7161-7172.2004 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-10444235787 Cyanobacteriaa ligases metabolism rna ribosomal 16s genetics Settore BIO/10 - Biochimica info:eu-repo/semantics/article 2004 ftunivmilanoair https://doi.org/10.1128/AEM.70.12.7161-7172.2004 2024-01-23T23:16:45Z The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds. In eutrophic fresh and brackish waters, their mass occurrences (water looms) are often toxic and constitute a high potential risk for human health. Therefore, rapid and reliable identification of cyanobacterial species in complex environmental samples is important. Here we describe the development and validation of a microarray for the identification of cyanobacteria in aquatic environments. Our approach is based on the use of a ligation detection reaction coupled to a universal array. Probes were designed for detecting 19 cyanobacterial groups including Anabaena/Aphanizomenon, Calothrix, Cylindrospermopsis, Cylindrospermum, Gloeothece, halotolerants, Leptolyngbya, Palau Lyngbya, Microcystis, Nodularia, Nostoc, Planktothrix, Antarctic Phormidium, Prochlorococcus, Spirulina, Synechococcus, Synechocystis, Trichodesmium, and Woronichinia. These groups were identified based on an alignment of over 300 cyanobacterial 16S rRNA sequences. For validation of the microarrays, 95 samples (24 axenic strains from culture collections, 27 isolated strains, and 44 cloned fragments recovered from environmental samples) were tested. The results demonstrated a high discriminative power and sensitivity to 1 fmol of the PCR-amplified 16S rRNA gene. Accurate identification of target strains was also achieved with unbalanced mixes of PCR amplicons from different cyanobacteria and an environmental sample. Our universal array method shows great potential for rapid and reliable identification of cyanobacteria. It can be easily adapted to future development and could thus be applied both in research and environmental monitoring. Article in Journal/Newspaper Antarc* Antarctic The University of Milan: Archivio Istituzionale della Ricerca (AIR) Antarctic Applied and Environmental Microbiology 70 12 7161 7172 |
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Open Polar |
collection |
The University of Milan: Archivio Istituzionale della Ricerca (AIR) |
op_collection_id |
ftunivmilanoair |
language |
English |
topic |
Cyanobacteriaa ligases metabolism rna ribosomal 16s genetics Settore BIO/10 - Biochimica |
spellingShingle |
Cyanobacteriaa ligases metabolism rna ribosomal 16s genetics Settore BIO/10 - Biochimica B. Castiglioni K. Sivonen P. Rajaniemi A. Rantala M. A. Mugnai S. Ventura A. Wilmotte C. Boutte S. Grubisic P. Balthasart A. Mezzelani G. De Bellis E. Rizzi A. Frosini C. Consolandi R. Bordoni C. Battaglia Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria |
topic_facet |
Cyanobacteriaa ligases metabolism rna ribosomal 16s genetics Settore BIO/10 - Biochimica |
description |
The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds. In eutrophic fresh and brackish waters, their mass occurrences (water looms) are often toxic and constitute a high potential risk for human health. Therefore, rapid and reliable identification of cyanobacterial species in complex environmental samples is important. Here we describe the development and validation of a microarray for the identification of cyanobacteria in aquatic environments. Our approach is based on the use of a ligation detection reaction coupled to a universal array. Probes were designed for detecting 19 cyanobacterial groups including Anabaena/Aphanizomenon, Calothrix, Cylindrospermopsis, Cylindrospermum, Gloeothece, halotolerants, Leptolyngbya, Palau Lyngbya, Microcystis, Nodularia, Nostoc, Planktothrix, Antarctic Phormidium, Prochlorococcus, Spirulina, Synechococcus, Synechocystis, Trichodesmium, and Woronichinia. These groups were identified based on an alignment of over 300 cyanobacterial 16S rRNA sequences. For validation of the microarrays, 95 samples (24 axenic strains from culture collections, 27 isolated strains, and 44 cloned fragments recovered from environmental samples) were tested. The results demonstrated a high discriminative power and sensitivity to 1 fmol of the PCR-amplified 16S rRNA gene. Accurate identification of target strains was also achieved with unbalanced mixes of PCR amplicons from different cyanobacteria and an environmental sample. Our universal array method shows great potential for rapid and reliable identification of cyanobacteria. It can be easily adapted to future development and could thus be applied both in research and environmental monitoring. |
author2 |
B. Castiglioni E. Rizzi A. Frosini K. Sivonen P. Rajaniemi A. Rantala M.A. Mugnai S. Ventura A. Wilmotte C. Boutte S. Grubisic P. Balthasart C. Consolandi R. Bordoni A. Mezzelani C. Battaglia G. De Bellis |
format |
Article in Journal/Newspaper |
author |
B. Castiglioni K. Sivonen P. Rajaniemi A. Rantala M. A. Mugnai S. Ventura A. Wilmotte C. Boutte S. Grubisic P. Balthasart A. Mezzelani G. De Bellis E. Rizzi A. Frosini C. Consolandi R. Bordoni C. Battaglia |
author_facet |
B. Castiglioni K. Sivonen P. Rajaniemi A. Rantala M. A. Mugnai S. Ventura A. Wilmotte C. Boutte S. Grubisic P. Balthasart A. Mezzelani G. De Bellis E. Rizzi A. Frosini C. Consolandi R. Bordoni C. Battaglia |
author_sort |
B. Castiglioni |
title |
Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria |
title_short |
Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria |
title_full |
Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria |
title_fullStr |
Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria |
title_full_unstemmed |
Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria |
title_sort |
development of a universal microarray based on the ligation detection reaction and 16s rrna gene polymorphism to target diversity of cyanobacteria |
publisher |
American Society for Microbiology. |
publishDate |
2004 |
url |
http://hdl.handle.net/2434/10682 https://doi.org/10.1128/AEM.70.12.7161-7172.2004 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/15574913 info:eu-repo/semantics/altIdentifier/wos/WOS:000225719300028 volume:70 issue:12 firstpage:7161 lastpage:7162 journal:APPLIED AND ENVIRONMENTAL MICROBIOLOGY http://hdl.handle.net/2434/10682 doi:10.1128/AEM.70.12.7161-7172.2004 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-10444235787 |
op_doi |
https://doi.org/10.1128/AEM.70.12.7161-7172.2004 |
container_title |
Applied and Environmental Microbiology |
container_volume |
70 |
container_issue |
12 |
container_start_page |
7161 |
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7172 |
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1790609792975241216 |