Improved detection of mcyA genes and their phylogenetic origins in harmful algal blooms

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Lee, Jaejin
Choi, Jinlyung
Fatka, Micah
Liang, Xuewei
Leung, Tania
Major Professor
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Swanner, Elizabeth
Associate Professor
Ikuma, Kaoru
Associate Professor
Howe, Adina
Associate Professor
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Civil, Construction and Environmental Engineering

The Department of Civil, Construction, and Environmental Engineering seeks to apply knowledge of the laws, forces, and materials of nature to the construction, planning, design, and maintenance of public and private facilities. The Civil Engineering option focuses on transportation systems, bridges, roads, water systems and dams, pollution control, etc. The Construction Engineering option focuses on construction project engineering, design, management, etc.

The Department of Civil Engineering was founded in 1889. In 1987 it changed its name to the Department of Civil and Construction Engineering. In 2003 it changed its name to the Department of Civil, Construction and Environmental Engineering.

Dates of Existence

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  • Department of Civil Engineering (1889-1987)
  • Department of Civil and Construction Engineering (1987-2003)
  • Department of Civil, Construction and Environmental Engineering (2003–present)

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Geological and Atmospheric Sciences
Bioinformatics and Computational Biology
Agricultural and Biosystems Engineering
Agricultural and Biosystems Engineering
Bioinformatics and Computational Biology

Microcystins, a group of cyanotoxins produced by cyanobacterial strains, have become a significant microbial hazard to human and animal health due to increases in the frequency and intensity of cyanobacterial harmful algal blooms (CyanoHABs). Many studies have explored the correlation between microcystin concentrations and abundances of toxin-producing genes (e.g., mcyA genes) measured using quantitative PCR, and discrepancies between toxin concentrations and gene abundances are often observed. In this study, the results show that these discrepancies are at least partially due to primer sets that do not capture the phylogenetic diversity of naturally present toxin-producers. We designed three novel primer gene probes based on known mcyA genes to improve the detection and quantification of these genes in environmental samples. These primers were shown to improve the identification of mcyA genes compared to previously published primers in freshwater metagenomes, cyanobacterial isolates, and lake water samples. Unlike previously published primers, our primer sets could selectively amplify and resolve Microcystis, Anabaena, and Planktothrix mcyA genes. In lake water samples, abundance estimations of mcyA genes were found to correlate strongly with microcystin concentrations. Based on our results, these primers offer significant improvements over previously published probes to accurately identify and quantify mcyA genes in the environment. There is an increasing need to develop models based on microbial information and environmental factors to predict CyanoHABs, and improved primers will play an important role in aiding monitoring efforts to collect reliable and consistent data on toxicity risks.


This is a manuscript of an article published as Lee, Jaejin, Jinlyung Choi, Micah Fatka, Elizabeth Swanner, Kaoru Ikuma, Xuewei Liang, Tania Leung, and Adina Howe. "Improved detection of mcyA genes and their phylogenetic origins in harmful algal blooms." Water Research (2020): 115730. DOI: 10.1016/j.watres.2020.115730. Posted with permission.

Wed Jan 01 00:00:00 UTC 2020