Biology at SCC
Freshwater Ecology & Watershed Research

Cyanobacteria · Chapter 8

Studying Cyanobacteria in the Laboratory

Outline · full text in Phase 2 Last reviewed 2026-11-05

Learning objectives

After studying this chapter, you should be able to:

  1. Prepare and document a wet mount with calibrated measurements.
  2. Record the environmental metadata that make an observation useful.
  3. Explain what pigment, molecular and toxin methods can and cannot tell you.
  4. Apply the safety rules for handling potentially toxic environmental samples.
This chapter is an outline The introduction, planned sections, key terms and references below are reviewed and citable. Full textbook text for each section will be added in Phase 2.

Most of what a student can learn about cyanobacteria starts with a wet mount and a brightfield microscope: growth form, cell dimensions, heterocytes, akinetes, gas vesicles and sheaths are all visible at 400× and 1000× [1]. What turns an observation into data is documentation — calibrated measurements, photographs with scale bars, and the environmental metadata recorded when and where the sample was collected. Pigment measurements, molecular methods and toxin analyses each answer different questions, and each has limits (Chapter 5, Table 5.2) [2, 3].

Laboratory safety Treat environmental samples as potentially hazardous: wear gloves and eye protection, work over a tray, avoid aerosols, and disinfect surfaces afterward. Do not culture, concentrate, aerosolize or freeze–thaw material from a suspected toxic bloom without an approved laboratory protocol and risk assessment. Toxin testing is done by qualified laboratories [4].

Planned sections

8.1 Wet mounts and brightfield microscopy

Preparing mounts from water and biofilm scrapes; India ink for mucilage; magnification choices.

8.2 Morphological identification

Using Chapter 2 and the Atlas; recording provisional morphotypes and confidence; look-alikes [1].

8.3 Microscope calibration and photomicrography

Calibrating the ocular micrometer with a stage micrometer for each objective; scale bars; image metadata and file naming.

8.4 Environmental metadata

Date, time, station, GPS, weather, recent rainfall, temperature, flow and canopy — the fields in the observation data dictionary.

8.5 Water chemistry

Temperature, pH, conductivity, dissolved oxygen, turbidity, nitrate and phosphate; field kits versus laboratory methods; detection limits and quality control.

8.6 Pigment measurements

Chlorophyll a and phycocyanin and what they can and cannot indicate [5, 3].

8.7 Molecular identification concepts

16S rRNA sequencing and toxin-gene qPCR; why genes indicate potential, not production [6, 7].

8.8 Toxin testing through qualified laboratories

ELISA and LC-MS/MS; total versus dissolved toxin; chain of custody [4, 8].

Connection to local research

At Allen Branch and nearby waters

The first Allen Branch laboratory work is descriptive and low-risk: wet mounts of biofilm scrapes, calibrated photomicrographs of each morphotype, and field-kit chemistry with recorded methods and detection limits. See the Field & Laboratory Methods page for protocols as they are written.

Key terms

Wet mount
Specimen in a drop of water under a coverslip.
Ocular micrometer
Scale in the eyepiece, calibrated against a stage micrometer.
Metadata
Information describing when, where and how data were collected.
ELISA
Antibody-based assay that measures a toxin class.
LC-MS/MS
Chromatography–mass spectrometry that measures individual toxin variants.
qPCR
Quantitative PCR; measures gene copies.

References

  1. Rosen, B. H., & St. Amand, A. (2015). Field and laboratory guide to freshwater cyanobacteria harmful algal blooms for Native American and Alaska Native communities. U.S. Geological Survey Open-File Report 2015-1164. https://doi.org/10.3133/ofr20151164
  2. Graham, J. L., Dubrovsky, N. M., & Eberts, S. M. (2016). Cyanobacterial harmful algal blooms and U.S. Geological Survey science capabilities. U.S. Geological Survey Open-File Report 2016-1174. https://doi.org/10.3133/ofr20161174
  3. Chorus, I. (Ed.), & Welker, M. (Ed.) (2021). Toxic Cyanobacteria in Water. CRC Press. https://doi.org/10.1201/9781003081449
  4. U.S. Environmental Protection Agency (n.d.). Laboratories that Analyze for Cyanobacteria and Cyanotoxins. U.S. EPA Harmful Algal Blooms program. https://www.epa.gov/habs/laboratories-analyze-cyanobacteria-and-cyanotoxins (accessed 2026-11-05)
  5. MacColl, R. (1998). Cyanobacterial Phycobilisomes. Journal of Structural Biology, 124(2-3), 311-334. https://doi.org/10.1006/jsbi.1998.4062
  6. Davis, T. W., Berry, D. L., Boyer, G. L., & Gobler, C. J. (2009). The effects of temperature and nutrients on the growth and dynamics of toxic and non-toxic strains of Microcystis during cyanobacteria blooms. Harmful Algae, 8(5), 715-725. https://doi.org/10.1016/j.hal.2009.02.004
  7. Strunecký, O., Ivanova, A. P., & Mareš, J. (2023). An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis. Journal of Phycology, 59(1), 12-51. https://doi.org/10.1111/jpy.13304
  8. Loftin, K. A., Graham, J. L., Hilborn, E. D., Lehmann, S. C., Meyer, M. T., Dietze, J. E., & Griffith, C. B. (2016). Cyanotoxins in inland lakes of the United States: Occurrence and potential recreational health risks in the EPA National Lakes Assessment 2007. Harmful Algae, 56, 77-90. https://doi.org/10.1016/j.hal.2016.04.001