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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Veröffentlicht in:Environmental science & technology 2024-03, Vol.58 (11), p.5024-5034
Hauptverfasser: Shu, Hao-Yue, Zhao, Liang, Jia, Yanyan, Liu, Fei-Fei, Chen, Jiang, Chang, Chih-Min, Jin, Tao, Yang, Jian, Shu, Wen-Sheng
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container_end_page 5034
container_issue 11
container_start_page 5024
container_title Environmental science & technology
container_volume 58
creator Shu, Hao-Yue
Zhao, Liang
Jia, Yanyan
Liu, Fei-Fei
Chen, Jiang
Chang, Chih-Min
Jin, Tao
Yang, Jian
Shu, Wen-Sheng
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 &gt; 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. 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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. 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source ACS Publications; MEDLINE
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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