Datasets of High-throughput DNA Sequencing, Genetic Fingerprinting, and Quantitative PCR from Upper Klamath Lake, Oregon, 2013-14

Dates

Publication Date: 2017-06-05
Start Date: 2013-07-09
End Date: 2014-09-15

Citation

Eldridge, S.L., Driscoll, Connor, and Dreher, T.W., 2017, Datasets of high-throughput DNA sequencing, genetic fingerprinting, and quantitative PCR from Upper Klamath Lake, Oregon, 2013-14: U.S. Geological Survey data release, https://doi.org/10.5066/F7C53J3V.

Summary

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 [...]

Summary

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 under different conditions. Additionally, with some modifications, the same techniques can be applied to different sample types, including water, sediment, and tissue.

Contacts

Point of Contact :: Sara Eldridge
Originator :: Sara Eldridge, Connor Driscoll, Theo Dreher
Metadata Contact :: Sara Eldridge
Publisher :: U.S. Geological Survey
Distributor :: U.S. Geological Survey - ScienceBase
USGS Mission Area :: Water Resources
SDC Data Owner :: Oregon Water Science Center

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High-throughput DNA sequencing results.csv “HTS Data”		574 KB
Microscopy data_2013.csv “Microscopy Data”		8.76 KB
qPCR Results.csv “qPCR Data”		2 KB
QC Data.xlsx “QC Data”		134.95 KB
Metadata.xml “Metadata” Original FGDC Metadata	View	12.65 KB

Related External Resources

Type: Publication that references this resource

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.	https://doi.org/10.3133/sir20175026

Purpose

Data were collected to (1) characterize the microbial community at one site in Upper Klamath Lake and determine changes in the community through time using high-throughput DNA sequencing of the total bacterial community based on a single gene target in comparison with traditional light microscopy; (2) to determine the abundances of potentially toxigenic and non-toxigenic strains of Microcystis and the changes through time of these abundances using qPCR; and (3) to determine the abundances of Aphanizomenon, Microcystis, and total cyanobacteria and the changes through time of these abundances using qPCR.

Datasets of High-throughput DNA Sequencing, Genetic Fingerprinting, and Quantitative PCR from Upper Klamath Lake, Oregon, 2013-14

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