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Scientific Investigations Report 2013–5189

Prepared in cooperation with the Ohio Lake Erie Commission

Relations Between DNA- and RNA-Based Molecular Methods for Cyanobacteria and Microcystin Concentration at Maumee Bay State Park Lakeside Beach, Oregon, Ohio, 2012

By Erin A. Stelzer, Keith A. Loftin, and Pamela Struffolino

Thumbnail of and link to report PDF (759 KB)Abstract

Water samples were collected from Maumee Bay State Park Lakeside Beach, Oregon, Ohio, during the 2012 recreational season and analyzed for selected cyanobacteria gene sequences by DNA-based quantitative polymerase chain reaction (qPCR) and RNA-based quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Results from the four DNA assays (for quantifying total cyanobacteria, total Microcystis, and Microcystis and Planktothrix strains that possess the microcystin synthetase E (mcyE) gene) and two RNA assays (for quantifying Microcystis and Planktothrix genera that are expressing the microcystin synthetase E (mcyE) gene) were compared to microcystin concentration results determined by an enzyme-linked immunosorbent assay (ELISA).

Concentrations of the target in replicate analyses were log10 transformed. The average value of differences in log10 concentrations for the replicates that had at least one detection were found to range from 0.05 to >0.37 copy per 100 milliliters (copy/100 mL) for DNA-based methods and from >0.04 to >0.17 copy/100 mL for RNA-based methods.

RNA has a shorter half-life than DNA; consequently, a 24-hour holding-time study was done to determine the effects of holding time on RNA concentrations. Holding-time comparisons for the RNA-based Microcystis toxin mcyE assay showed reductions in the number of copies per 100 milliliters over 24 hours. The log difference between time 2 hours and time 24 hours was >0.37 copy/100 mL, which was higher than the analytical variability (log difference of >0.17 copy/100 mL).

Spearman’s correlation analysis indicated that microcystin toxin concentrations were moderately to highly related to DNA-based assay results for total cyanobacteria (rho=0.69), total Microcystis (rho=0.74), and Microcystis strains that possess the mcyE gene (rho=0.81). Microcystin toxin concentrations were strongly related with RNA-based assay results for Microcystis mcyE gene expression (rho=0.95). Correlation analysis could not be done for Planktothrix mcyE gene expression because of too few detections.

First posted January 7, 2014

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Suggested citation:

Stelzer, E.A., Loftin, K.A., and Struffolino, Pamela, 2013, Relations between DNA- and RNA-based molecular methods for cyanobacteria and microcystin concentration at Maumee Bay State Park Lakeside Beach, Oregon, Ohio, 2012: U.S. Geological Survey Scientific Investigations Report 2013–5189, 9 p., http://dx.doi.org/10.3133/sir20135189.

ISSN 2328–0328 (online)



Contents

Abstact

Introduction

Methods of Study

Quality-Control Considerations for Assessing Molecular Methods for Cyanobacteria

Concentrations of Cyanobacteria by DNA- and RNA-Based Molecular Methods and Their Relations to Toxin Production

Implications for Future Studies

Summary and Conclusions

Acknowledgment

References Cited


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