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Using high-throughput DNA sequencing, genetic fingerprinting, and quantitative PCR as tools for monitoring bloom-forming and toxigenic cyanobacteria in Upper Klamath Lake, Oregon, 2013 and 2014

Scientific Investigations Report 2017-5026
By: , , and 
https://doi.org/10.3133/sir20175026

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Abstract

Monitoring the community structure and metabolic activities of cyanobacterial blooms in Upper Klamath Lake, Oregon, is critical to lake management because these blooms degrade water quality and produce toxic microcystins that are harmful to humans, domestic animals, and wildlife. Genetic tools, such as DNA fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analysis, high-throughput DNA sequencing (HTS), and real-time, quantitative polymerase chain reaction (qPCR), provide more sensitive and rapid assessments of bloom ecology than traditional techniques. The objectives of this study were (1) to characterize the microbial community at one site in Upper Klamath Lake and determine changes in the cyanobacterial community through time using T-RFLP and HTS in comparison with traditional light microscopy; (2) to determine relative abundances and changes in abundance over time of toxigenic Microcystis using qPCR; and (3) to determine relative abundances and changes in abundance over time of Aphanizomenon, Microcystis, and total cyanobacteria using qPCR. T-RFLP analysis of total cyanobacteria showed a dominance of only one or two distinct genotypes in samples from 2013, but results of HTS in 2013 and 2014 showed more variations in the bloom cycle that fit with the previous understanding of bloom dynamics in Upper Klamath Lake and indicated that potentially toxigenic Microcystis was more prevalent in 2014 than in years prior. The qPCR-estimated copy numbers of all target genes were higher in 2014 than in 2013, when microcystin concentrations also were higher. Total Microcystis density was shown with qPCR to be a better predictor of late-season increases in microcystin concentrations than the relative proportions of potentially toxigenic cells. In addition, qPCR targeting Aphanizomenon at one site in Upper Klamath Lake indicated a moderate bloom of this species (corresponding to chlorophyll a concentrations between approximately 75 and 200 micrograms per liter) from mid-June to mid-August, 2014. After August 18, the Aphanizomenon bloom was overtaken by Microcystis late in the season as microcystin concentrations peaked. Overall, results of this study showed how DNA-based, genetic methods may provide rapid and sensitive diagnoses for the presence of toxigenic cyanobacteria and that they are useful for general monitoring or ecological studies and identification of cyanobacterial community members in complex aquatic habitats. These same methods can also be used to simultaneously address spatial (horizontal and vertical) and temporal variation and under different conditions. Additionally, with some modifications, the same techniques can be applied to different sample types, including water, sediment, and tissue.

Suggested Citation

Eldridge, S.L.C., Driscoll, Connor, and Dreher, T.W., 2017, Using high-throughput DNA sequencing, genetic fingerprinting, and quantitative PCR as tools for monitoring bloom-forming and toxigenic cyanobacteria in Upper Klamath Lake, Oregon, 2013 and 2014: U.S. Geological Survey Scientific Investigations Report 2017–5026, 50 p., https://doi.org/10.3133/sir20175026.

ISSN: 2328-0328 (online)

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Table of Contents

  • Abstract
  • Introduction
  • Genetic Fingerprinting and High-Throughput DNA Sequencing to Characterize Community Structure
  • qPCR for Quantitative Analysis of Toxin-Producing and Bloom-Forming Cyanobacteria
  • Quality Control for Bias and Variability in Sampling and Analysis
  • Summary
  • Acknowledgments
  • References Cited
  • Glossary
Publication type Report
Publication Subtype USGS Numbered Series
Title Using high-throughput DNA sequencing, genetic fingerprinting, and quantitative PCR as tools for monitoring bloom-forming and toxigenic cyanobacteria in Upper Klamath Lake, Oregon, 2013 and 2014
Series title Scientific Investigations Report
Series number 2017-5026
DOI 10.3133/sir20175026
Year Published 2017
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Oregon Water Science Center
Description Report: vi, 50 p.; Data Release
Country United States
State Oregon
Other Geospatial Upper Klamath Lake
Online Only (Y/N) Y
Google Analytic Metrics Metrics page
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