CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level
Detecting cyanobacteria in environments is an important concern due to their crucial roles in ecosystems, and they can form blooms with the potential to harm humans and nonhuman entities. However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S...
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description | Detecting cyanobacteria in environments is an important concern due to their crucial roles in ecosystems, and they can form blooms with the potential to harm humans and nonhuman entities. However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S rRNA sequencing, typically provide above-species-level resolution, thereby disregarding intraspecific variation. To address this, we developed a novel DNA microarray tool, termed the CyanoStrainChip, that enables strain-level comprehensive profiling of environmental cyanobacteria. The CyanoStrainChip was designed to target 1277 strains; nearly all major groups of cyanobacteria are included by implementing 43,666 genome-wide, strain-specific probes. It demonstrated strong specificity by in vitro mock community experiments. The high correlation (Pearson’s R > 0.97) between probe fluorescence intensities and the corresponding DNA amounts (ranging from 1–100 ng) indicated excellent quantitative capability. Consistent cyanobacterial profiles of field samples were observed by both the CyanoStrainChip and next-generation sequencing methods. Furthermore, CyanoStrainChip analysis of surface water samples in Lake Chaohu uncovered a high intraspecific variation of abundance change within the genus Microcystis between different severity levels of cyanobacterial blooms, highlighting two toxic Microcystis strains that are of critical concern for Lake Chaohu harmful blooms suppression. Overall, these results suggest a potential for CyanoStrainChip as a valuable tool for cyanobacterial ecological research and harmful bloom monitoring to supplement existing techniques. |
doi_str_mv | 10.1021/acs.est.3c11096 |
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However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S rRNA sequencing, typically provide above-species-level resolution, thereby disregarding intraspecific variation. To address this, we developed a novel DNA microarray tool, termed the CyanoStrainChip, that enables strain-level comprehensive profiling of environmental cyanobacteria. The CyanoStrainChip was designed to target 1277 strains; nearly all major groups of cyanobacteria are included by implementing 43,666 genome-wide, strain-specific probes. It demonstrated strong specificity by in vitro mock community experiments. The high correlation (Pearson’s R > 0.97) between probe fluorescence intensities and the corresponding DNA amounts (ranging from 1–100 ng) indicated excellent quantitative capability. Consistent cyanobacterial profiles of field samples were observed by both the CyanoStrainChip and next-generation sequencing methods. Furthermore, CyanoStrainChip analysis of surface water samples in Lake Chaohu uncovered a high intraspecific variation of abundance change within the genus Microcystis between different severity levels of cyanobacterial blooms, highlighting two toxic Microcystis strains that are of critical concern for Lake Chaohu harmful blooms suppression. Overall, these results suggest a potential for CyanoStrainChip as a valuable tool for cyanobacterial ecological research and harmful bloom monitoring to supplement existing techniques.</description><identifier>ISSN: 0013-936X</identifier><identifier>ISSN: 1520-5851</identifier><identifier>EISSN: 1520-5851</identifier><identifier>DOI: 10.1021/acs.est.3c11096</identifier><identifier>PMID: 38454313</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Bioremediation and Biotechnology ; Cyanobacteria ; Cyanobacteria - genetics ; Deoxyribonucleic acid ; DNA ; DNA chips ; DNA microarrays ; DNA probes ; Ecological research ; Ecosystem ; environmental science ; fluorescence ; Fluorescent indicators ; Genomes ; Harmful Algal Bloom ; Humans ; intraspecific variation ; Lakes ; Lakes - microbiology ; Microcystis ; Microcystis - genetics ; Next-generation sequencing ; Oligonucleotide Array Sequence Analysis ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Surface water ; toxicity ; Water analysis ; Water sampling</subject><ispartof>Environmental science & technology, 2024-03, Vol.58 (11), p.5024-5034</ispartof><rights>2024 The Authors. Published by American Chemical Society</rights><rights>Copyright American Chemical Society Mar 19, 2024</rights><rights>2024 The Authors. Published by American Chemical Society 2024 The Authors</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a491t-1da7bb114c5d6afb6c50d753bf490be07eb79b91d722c5a18bdca8e5574723633</citedby><cites>FETCH-LOGICAL-a491t-1da7bb114c5d6afb6c50d753bf490be07eb79b91d722c5a18bdca8e5574723633</cites><orcidid>0000-0001-8784-8968</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/acs.est.3c11096$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/acs.est.3c11096$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>230,314,776,780,881,2752,27055,27903,27904,56716,56766</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38454313$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shu, Hao-Yue</creatorcontrib><creatorcontrib>Zhao, Liang</creatorcontrib><creatorcontrib>Jia, Yanyan</creatorcontrib><creatorcontrib>Liu, Fei-Fei</creatorcontrib><creatorcontrib>Chen, Jiang</creatorcontrib><creatorcontrib>Chang, Chih-Min</creatorcontrib><creatorcontrib>Jin, Tao</creatorcontrib><creatorcontrib>Yang, Jian</creatorcontrib><creatorcontrib>Shu, Wen-Sheng</creatorcontrib><title>CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level</title><title>Environmental science & technology</title><addtitle>Environ. Sci. Technol</addtitle><description>Detecting cyanobacteria in environments is an important concern due to their crucial roles in ecosystems, and they can form blooms with the potential to harm humans and nonhuman entities. However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S rRNA sequencing, typically provide above-species-level resolution, thereby disregarding intraspecific variation. To address this, we developed a novel DNA microarray tool, termed the CyanoStrainChip, that enables strain-level comprehensive profiling of environmental cyanobacteria. The CyanoStrainChip was designed to target 1277 strains; nearly all major groups of cyanobacteria are included by implementing 43,666 genome-wide, strain-specific probes. It demonstrated strong specificity by in vitro mock community experiments. The high correlation (Pearson’s R > 0.97) between probe fluorescence intensities and the corresponding DNA amounts (ranging from 1–100 ng) indicated excellent quantitative capability. Consistent cyanobacterial profiles of field samples were observed by both the CyanoStrainChip and next-generation sequencing methods. Furthermore, CyanoStrainChip analysis of surface water samples in Lake Chaohu uncovered a high intraspecific variation of abundance change within the genus Microcystis between different severity levels of cyanobacterial blooms, highlighting two toxic Microcystis strains that are of critical concern for Lake Chaohu harmful blooms suppression. Overall, these results suggest a potential for CyanoStrainChip as a valuable tool for cyanobacterial ecological research and harmful bloom monitoring to supplement existing techniques.</description><subject>Bioremediation and Biotechnology</subject><subject>Cyanobacteria</subject><subject>Cyanobacteria - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA chips</subject><subject>DNA microarrays</subject><subject>DNA probes</subject><subject>Ecological research</subject><subject>Ecosystem</subject><subject>environmental science</subject><subject>fluorescence</subject><subject>Fluorescent indicators</subject><subject>Genomes</subject><subject>Harmful Algal Bloom</subject><subject>Humans</subject><subject>intraspecific variation</subject><subject>Lakes</subject><subject>Lakes - microbiology</subject><subject>Microcystis</subject><subject>Microcystis - genetics</subject><subject>Next-generation sequencing</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA 16S</subject><subject>Surface water</subject><subject>toxicity</subject><subject>Water analysis</subject><subject>Water sampling</subject><issn>0013-936X</issn><issn>1520-5851</issn><issn>1520-5851</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFks1vEzEQxS1ERUPgzA1Z4oKENh2v7f3ggqK0UKTQHhokbpbt9WZdbdap1xspB_53vE0aARLi5IN_783Mm0HoDYEZgZRcSN3PTB9mVBMCZfYMTQhPIeEFJ8_RBIDQpKTZj3P0su_vASClULxA57RgnFFCJ-jnYi87dxe8tN2isduPeI5v3M60-PJmjr9Z7Z30Xu7xyrkW187ja7tuklXj3bButkPAlyYYHazrsKvxVbez3nUb0wXZ4kdvJXUw3kosAw6NwYdaeGlikVforJZtb14f3yn6_vlqtbhOlrdfvi7my0SykoSEVDJXihCmeZXJWmWaQ5VzqmpWgjKQG5WXqiRVnqaaS1KoSsvCcJ6zPKUZpVP06eC7HdTGVDq252Urtt5upN8LJ63486ezjVi7nYih8mxMaoreHx28exhi5GJje23aVnbGDb2gwIBRoGnxXzQtOctz4Ono-u4v9N4NvotRRKosSQHssfuLAxWX0ffe1KfGCYjxDEQ8AzGqj2cQFW9_n_fEP-09Ah8OwKg81fyX3S_oLb7d</recordid><startdate>20240319</startdate><enddate>20240319</enddate><creator>Shu, Hao-Yue</creator><creator>Zhao, Liang</creator><creator>Jia, Yanyan</creator><creator>Liu, Fei-Fei</creator><creator>Chen, Jiang</creator><creator>Chang, Chih-Min</creator><creator>Jin, Tao</creator><creator>Yang, Jian</creator><creator>Shu, Wen-Sheng</creator><general>American Chemical Society</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>7QO</scope><scope>7ST</scope><scope>7T7</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>SOI</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-8784-8968</orcidid></search><sort><creationdate>20240319</creationdate><title>CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level</title><author>Shu, Hao-Yue ; Zhao, Liang ; Jia, Yanyan ; Liu, Fei-Fei ; Chen, Jiang ; Chang, Chih-Min ; Jin, Tao ; Yang, Jian ; Shu, Wen-Sheng</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a491t-1da7bb114c5d6afb6c50d753bf490be07eb79b91d722c5a18bdca8e5574723633</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Bioremediation and Biotechnology</topic><topic>Cyanobacteria</topic><topic>Cyanobacteria - genetics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA chips</topic><topic>DNA microarrays</topic><topic>DNA probes</topic><topic>Ecological research</topic><topic>Ecosystem</topic><topic>environmental science</topic><topic>fluorescence</topic><topic>Fluorescent indicators</topic><topic>Genomes</topic><topic>Harmful Algal Bloom</topic><topic>Humans</topic><topic>intraspecific variation</topic><topic>Lakes</topic><topic>Lakes - microbiology</topic><topic>Microcystis</topic><topic>Microcystis - genetics</topic><topic>Next-generation sequencing</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rRNA 16S</topic><topic>Surface water</topic><topic>toxicity</topic><topic>Water analysis</topic><topic>Water sampling</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shu, Hao-Yue</creatorcontrib><creatorcontrib>Zhao, Liang</creatorcontrib><creatorcontrib>Jia, Yanyan</creatorcontrib><creatorcontrib>Liu, Fei-Fei</creatorcontrib><creatorcontrib>Chen, Jiang</creatorcontrib><creatorcontrib>Chang, Chih-Min</creatorcontrib><creatorcontrib>Jin, Tao</creatorcontrib><creatorcontrib>Yang, Jian</creatorcontrib><creatorcontrib>Shu, Wen-Sheng</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Environmental science & technology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shu, Hao-Yue</au><au>Zhao, Liang</au><au>Jia, Yanyan</au><au>Liu, Fei-Fei</au><au>Chen, Jiang</au><au>Chang, Chih-Min</au><au>Jin, Tao</au><au>Yang, Jian</au><au>Shu, Wen-Sheng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level</atitle><jtitle>Environmental science & technology</jtitle><addtitle>Environ. Sci. Technol</addtitle><date>2024-03-19</date><risdate>2024</risdate><volume>58</volume><issue>11</issue><spage>5024</spage><epage>5034</epage><pages>5024-5034</pages><issn>0013-936X</issn><issn>1520-5851</issn><eissn>1520-5851</eissn><abstract>Detecting cyanobacteria in environments is an important concern due to their crucial roles in ecosystems, and they can form blooms with the potential to harm humans and nonhuman entities. However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S rRNA sequencing, typically provide above-species-level resolution, thereby disregarding intraspecific variation. To address this, we developed a novel DNA microarray tool, termed the CyanoStrainChip, that enables strain-level comprehensive profiling of environmental cyanobacteria. The CyanoStrainChip was designed to target 1277 strains; nearly all major groups of cyanobacteria are included by implementing 43,666 genome-wide, strain-specific probes. It demonstrated strong specificity by in vitro mock community experiments. The high correlation (Pearson’s R > 0.97) between probe fluorescence intensities and the corresponding DNA amounts (ranging from 1–100 ng) indicated excellent quantitative capability. Consistent cyanobacterial profiles of field samples were observed by both the CyanoStrainChip and next-generation sequencing methods. Furthermore, CyanoStrainChip analysis of surface water samples in Lake Chaohu uncovered a high intraspecific variation of abundance change within the genus Microcystis between different severity levels of cyanobacterial blooms, highlighting two toxic Microcystis strains that are of critical concern for Lake Chaohu harmful blooms suppression. Overall, these results suggest a potential for CyanoStrainChip as a valuable tool for cyanobacterial ecological research and harmful bloom monitoring to supplement existing techniques.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>38454313</pmid><doi>10.1021/acs.est.3c11096</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0001-8784-8968</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Bioremediation and Biotechnology Cyanobacteria Cyanobacteria - genetics Deoxyribonucleic acid DNA DNA chips DNA microarrays DNA probes Ecological research Ecosystem environmental science fluorescence Fluorescent indicators Genomes Harmful Algal Bloom Humans intraspecific variation Lakes Lakes - microbiology Microcystis Microcystis - genetics Next-generation sequencing Oligonucleotide Array Sequence Analysis RNA, Ribosomal, 16S - genetics rRNA 16S Surface water toxicity Water analysis Water sampling |
title | CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level |
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