拉伤
蓝藻
环境DNA
吞吐量
微阵列
计算生物学
DNA
生物
计算机科学
基因
遗传学
细菌
生态学
基因表达
生物多样性
电信
解剖
无线
作者
Haoyue Shu,Lei Zhao,Yanyan Jia,Feifei Liu,Jiang Chen,Ching S. Chang,Tengchuan Jin,Jian Yang,Wen‐Sheng Shu
标识
DOI:10.1021/acs.est.3c11096
摘要
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.
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