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PUBLICATION NOTICE: A High-throughput Method for Counting Cyanobacteria Using Fluorescence Microscopy

US Army Engineer Research and Development Center
Published Aug. 28, 2019

The US Army Engineer Research and Development Center has published the report/note described and linked below. Approved for public release; distribution is unlimited.

Report Number:

ERDC TR-19-21


A High-throughput Method for Counting Cyanobacteria Using Fluorescence Microscopy


Kaytee Pokrzywinski, Brandon Boyd, and Jarrell Smith


Harmful algal blooms (HABs) occur all over the world naturally, but are increasing in frequency largely due to eutrophication. The U.S. Army Corps of Engineers (USACE) manages over 400 freshwater waterways making cyanobacteria HABs (cyanoHABs) a significant threat to water quality. CyanoHABs have been identified as a significant problem in USACE managed waterways where districts have reported associated fish kills and waterway closures. For USACE districts, when contracted out, the return time for cyanobacterial enumeration is approximately 30 days, therefore, there is a need to provide a better approach to counting cyanobacteria. However, counting cyanobacteria is notoriously difficult due to large filaments that make conventional counting methods impractical. It is anticipated that the application of this method for routine counting of field samples will greatly reduce analysis time, and therefore, will enhance the ability to combat HABs. In addition to cyanoHAB monitoring, cell densities are required for various down-stream techniques, including nucleic acid extractions where overloading of solid phase extraction columns can cause a loss of sample. This study developed automated image processing routines that enable rapid and accurate cell counting. The results of this method compared favorably with manual counting of single-cell and filamentous cyanobacteria cultures at a fraction of the analysis time.

41 pgs / 2.5 mb


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