Biology at SCC
Freshwater Ecology & Watershed Research

Learn · Unit overview

Cyanobacteria: Biology, Ecology, and Harmful Freshwater Blooms

For students in introductory biology, microbiology and environmental science Overview: about 15 minutes Last reviewed 2026-11-05

In late summer, a farm pond can turn the color of pea soup in a week. Downstream of a reservoir, a river can carry drifting green flecks for hundreds of kilometers. And on the rocks of a clear, cold stream, a dark leathery mat can be quietly producing a nerve toxin. All three are the work of cyanobacteria — an ancient group of photosynthetic bacteria that shaped Earth's atmosphere and still influence water quality, wildlife and human health today [1, 2].

This unit is written as an open textbook. Its ten chapters can be read in order as a course, or used as a reference when a research question comes up in the field or the lab. Each chapter states its learning objectives, defines key terms, cites the sources behind its claims, ends with knowledge checks, and connects the science to research that students at Somerset Community College can do at Allen Branch and other south-central Kentucky waters.

The big ideas

1. Cyanobacteria are bacteria, not algae

Cyanobacteria photosynthesize the way algae and plants do, releasing oxygen, but their cells are prokaryotic: there is no nucleus, no chloroplast and no mitochondrion [3]. "Blue-green algae" is a historical common name that persists in public advisories. Telling a cyanobacterium from a true alga is the first skill in this field, and the comparison table below summarizes it. Chapter 1 develops the cell biology.

2. They changed the planet — and live on in every chloroplast

Cyanobacteria invented oxygenic photosynthesis, and their oxygen accumulated in the atmosphere during the Great Oxidation Event roughly 2.4 billion years ago [4]. Later, a cyanobacterium engulfed by an early eukaryote became the first chloroplast, the ancestor of the plastids in green algae and land plants [5, 6].

3. A few traits explain where they win

Gas vesicles let planktonic species float toward light [7]; heterocytes let some fix atmospheric nitrogen [8]; akinetes let others wait out winter in sediment [9]. Combined with tolerance of warm water and efficient light harvesting, these traits help cyanobacteria outcompete other phytoplankton in warm, calm, nutrient-rich waters [10]. Chapter 2 shows how the same traits are used to identify genera.

4. Blooms have several causes acting together

Excess nutrients are the foundation of most freshwater blooms, but warmth, calm and stratified water, long water residence time and abundant light strongly modulate them [11, 1]. Which nutrient matters most — phosphorus, nitrogen or both — depends on the water body and season; many systems are co-limited [12, 13]. That is why this portal avoids single-cause explanations (Chapter 3, Chapter 4).

5. Not every bloom is toxic, and you cannot tell by looking

Toxin production is a property of particular strains, and toxic and non-toxic strains of the same species look identical under the microscope [14, 15]. Even the dominant genus of a bloom does not reliably predict which toxins are present [16]. Toxins are measured, not inferred, and the U.S. EPA provides health-based guidance values for recreation and drinking water [17, 18]. Chapter 5 covers the toxins and how to interpret results.

6. Streams have their own cyanobacteria

Most public attention goes to scums on lakes, but cyanobacteria also grow as mats and films attached to the bottoms of streams and rivers, and these benthic mats can produce toxins too [19, 20]. A survey of 75 wadeable streams in the southeastern United States detected microcystins in 39% of them [21]. For a shaded creek like Allen Branch, this is the most relevant kind of cyanobacterial ecology.

7. Grazers struggle with cyanobacteria — and can adapt

Cyanobacteria are generally poor food for zooplankton such as Daphnia, because of nutritional deficiencies, awkward colony and filament shapes, toxins and compounds that inhibit digestive enzymes [22, 23]. Yet grazer populations exposed to cyanobacteria can evolve tolerance within decades, and gut microbiomes can contribute [24, 25]. Chapter 6 explores these interactions.

8. Prevention starts in the watershed

Reducing nutrient inputs is the foundation of lasting bloom control; in-lake treatments such as mixing, algaecides or hydrogen peroxide can help in specific situations but treat symptoms, and many marketed products do little [13, 26, 27]. Biological approaches, including grazer-based biomanipulation, are promising but context-dependent [28]. Proposals involving genetically modified organisms remain experimental and would require careful ecological risk assessment before any release [29] (Chapter 7).

9. Kentucky has a bloom history — and big gaps near Somerset

Kentucky's environmental and public-health agencies have issued harmful algal bloom advisories since at least 2013, when the U.S. Army Corps of Engineers identified a bloom on Taylorsville Lake [30, 31], and large blooms on the Ohio River prompted advisories in 2015 and 2019 [32, 33]. Published research on cyanobacteria in the Lake Cumberland basin is scarce; the closest studies come from the Cumberland River system in Tennessee [34, 35]. That gap is an opportunity for SCC students (Chapter 9, Chapter 10).

At a glance: telling cyanobacteria from other "algae"
QuestionCyanobacteriaGreen algae, diatoms and other eukaryotic algae
What kind of cell?Prokaryotic (Bacteria)Eukaryotic
Chloroplasts visible?No — pigment is spread through the cellYes — distinct chloroplasts of characteristic shape
Typical color in the fieldBlue-green, olive, brown-black, sometimes redGrass-green (green algae), golden-brown (diatoms)
Special structuresGas vesicles, heterocytes, akinetes, mucilage coloniesNuclei, pyrenoids, flagella, silica walls (diatoms)
Can fix N₂?Some generaNo
Produce cyanotoxins?Some strains of some generaNo (other toxins occur in some marine algae)

Chapters

  1. Chapter 1 What Are Cyanobacteria?

    Photosynthetic bacteria, not algae: cell structure, oxygenic photosynthesis, pigments, and their role in Earth's oxygenation and the origin of chloroplasts.

    Full text 5 learning objectives

  2. Chapter 2 Cyanobacterial Diversity and Identification

    Unicellular, colonial and filamentous forms; heterocytes, akinetes and gas vesicles; eight freshwater genera; why names change; and the limits of identification by microscope.

    Full text 5 learning objectives

  3. Chapter 3 Freshwater Ecology of Cyanobacteria

    Planktonic versus benthic life; light, temperature, mixing and residence time; succession, competition, grazing and microbial partners — from shaded streams to sunlit ponds.

    Outline · full text in Phase 2 4 learning objectives

  4. Chapter 4 Nutrient Cycling and Agricultural Watersheds

    Nitrogen and phosphorus forms, limitation and co-limitation, eutrophication, and how fertilizer, manure, soil, wastewater and stormwater reach water — and when they don't.

    Outline · full text in Phase 2 4 learning objectives

  5. Chapter 5 Harmful Algal Blooms

    What a bloom is, why some are harmful, the four major cyanotoxin groups, oxygen depletion, health effects, U.S. guidance values and how Kentucky issues advisories.

    Full text 5 learning objectives

  6. Chapter 6 Cyanobacteria and Aquatic Food Webs

    How green algae, diatoms, rotifers, copepods, Daphnia, snails, fish and decomposers interact with cyanobacteria — and why cyanobacteria are hard to eat.

    Outline · full text in Phase 2 3 learning objectives

  7. Chapter 7 Bloom Prevention and Biological Control

    Nutrient management, restoration, buffers, mixing, algaecides, biomanipulation, grazer–cyanobacteria coevolution, microbiomes — and a careful look at engineered organisms.

    Outline · full text in Phase 2 4 learning objectives

  8. Chapter 8 Studying Cyanobacteria in the Laboratory

    Wet mounts, brightfield microscopy, calibration and photomicrography, metadata, water chemistry, pigments, molecular concepts and toxin testing — with the limits and safety rules for each.

    Outline · full text in Phase 2 4 learning objectives

  9. Chapter 9 Cyanobacteria in Kentucky

    What is documented about blooms in Kentucky's reservoirs, rivers and ponds since 2013, the agricultural and karst setting, and how much remains unknown near Somerset.

    Outline · full text in Phase 2 3 learning objectives

  10. Chapter 10 Open Research Questions

    Undergraduate-scale research directions for Allen Branch and other south-central Kentucky waters, each linked to background, methods and references.

    Full text 3 learning objectives

How to use this unit

  • Read in order for a course sequence: Chapters 1–2 (organisms), 3–5 (ecology and blooms), 6–7 (food webs and control), 8 (methods), 9–10 (Kentucky and research).
  • Use as a reference from the glossary, the Organism Atlas or the search box.
  • Watch the labels. Statements marked Established reflect broad scientific agreement; Single study marks a finding from one investigation; Preliminary marks observations not yet replicated; Hypothesis and Speculative mark ideas that still need testing. See the evidence standards.
  • Check the sources. Every numbered citation links to a reference list at the end of the page; most also appear, with summaries, in the Research Paper Library.
Status of this unit Chapters 1, 2, 5 and 10 are complete. Chapters 3, 4, 6, 7, 8 and 9 are published as reviewed outlines — learning objectives, a short introduction, the planned sections, key terms and verified references — and will be written in full in Phase 2 of the portal.

Knowledge check

  1. A news story calls a lake bloom "toxic algae." Name two ways that phrase could be inaccurate.

    Show answer and explanation

    The organisms are probably cyanobacteria, which are bacteria rather than algae; and a bloom is not necessarily toxic — toxicity depends on the strains present and must be measured.

  2. Why does this portal avoid saying "phosphorus causes blooms"?

    Show answer and explanation

    Phosphorus is often important, but nitrogen, co-limitation by both nutrients, temperature, light, mixing and residence time also control blooms, and the balance differs among water bodies and seasons.

  3. Where in a shaded stream would you look first for cyanobacteria, and why?

    Show answer and explanation

    On submerged surfaces — rocks, wood, sediment — as attached biofilms or mats. Flowing water flushes plankton downstream, so benthic growth is more typical of streams than floating scums.

References

  1. Huisman, J., Codd, G. A., Paerl, H. W., Ibelings, B. W., Verspagen, J. M. H., & Visser, P. M. (2018). Cyanobacterial blooms. Nature Reviews Microbiology, 16(8), 471-483. https://doi.org/10.1038/s41579-018-0040-1
  2. Paerl, H. W., & Otten, T. G. (2013). Harmful Cyanobacterial Blooms: Causes, Consequences, and Controls. Microbial Ecology, 65(4), 995-1010. https://doi.org/10.1007/s00248-012-0159-y
  3. Parker, N., Schneegurt, M., Thi Tu, A.-H., Lister, P., & Forster, B. M. (2016). 4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria. In Microbiology (OpenStax). OpenStax, Rice University. https://openstax.org/books/microbiology/pages/4-3-nonproteobacteria-gram-negative-bacteria-and-phototrophic-bacteria Open textbook (CC BY 4.0).
  4. Lyons, T. W., Reinhard, C. T., & Planavsky, N. J. (2014). The rise of oxygen in Earth’s early ocean and atmosphere. Nature, 506(7488), 307-315. https://doi.org/10.1038/nature13068
  5. Archibald, J. M. (2015). Endosymbiosis and Eukaryotic Cell Evolution. Current Biology, 25(19), R911-R921. https://doi.org/10.1016/j.cub.2015.07.055
  6. Ponce-Toledo, R. I., Deschamps, P., López-García, P., Zivanovic, Y., Benzerara, K., & Moreira, D. (2017). An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids. Current Biology, 27(3), 386-391. https://doi.org/10.1016/j.cub.2016.11.056
  7. Walsby, A. E. (1994). Gas vesicles. Microbiological Reviews, 58(1), 94-144. https://doi.org/10.1128/mr.58.1.94-144.1994
  8. Kumar, K., Mella-Herrera, R. A., & Golden, J. W. (2010). Cyanobacterial Heterocysts. Cold Spring Harbor Perspectives in Biology, 2(4), a000315-a000315. https://doi.org/10.1101/cshperspect.a000315
  9. Kaplan-Levy, R. N., Hadas, O., Summers, M. L., Rücker, J., & Sukenik, A. (2010). Akinetes: Dormant Cells of Cyanobacteria. In Topics in Current Genetics (pp. 5-27). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-12422-8_2
  10. Carey, C. C., Ibelings, B. W., Hoffmann, E. P., Hamilton, D. P., & Brookes, J. D. (2012). Eco-physiological adaptations that favour freshwater cyanobacteria in a changing climate. Water Research, 46(5), 1394-1407. https://doi.org/10.1016/j.watres.2011.12.016
  11. Paerl, H. W., & Huisman, J. (2008). Blooms Like It Hot. Science, 320(5872), 57-58. https://doi.org/10.1126/science.1155398
  12. Elser, J. J., Bracken, M. E. S., Cleland, E. E., Gruner, D. S., Harpole, W. S., Hillebrand, H., Ngai, J. T., et al. (2007). Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems. Ecology Letters, 10(12), 1135-1142. https://doi.org/10.1111/j.1461-0248.2007.01113.x
  13. Paerl, H. W., Scott, J. T., McCarthy, M. J., Newell, S. E., Gardner, W. S., Havens, K. E., Hoffman, D. K., et al. (2016). It Takes Two to Tango: When and Where Dual Nutrient (N & P) Reductions Are Needed to Protect Lakes and Downstream Ecosystems. Environmental Science & Technology, 50(20), 10805-10813. https://doi.org/10.1021/acs.est.6b02575
  14. Kurmayer, R., Christiansen, G., & Chorus, I. (2003). The Abundance of Microcystin-Producing Genotypes Correlates Positively with Colony Size in Microcystis sp. and Determines Its Microcystin Net Production in Lake Wannsee. Applied and Environmental Microbiology, 69(2), 787-795. https://doi.org/10.1128/aem.69.2.787-795.2003
  15. 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
  16. Graham, J. L., Loftin, K. A., Meyer, M. T., & Ziegler, A. C. (2010). Cyanotoxin Mixtures and Taste-and-Odor Compounds in Cyanobacterial Blooms from the Midwestern United States. Environmental Science & Technology, 44(19), 7361-7368. https://doi.org/10.1021/es1008938
  17. U.S. Environmental Protection Agency (2019). Protecting Human Health from Cyanotoxin Exposure During Recreation. U.S. EPA Harmful Algal Blooms program. https://www.epa.gov/habs/protecting-human-health-cyanotoxin-exposure-during-recreation (accessed 2026-11-05) States EPA's 2019 recommended recreational criteria/swimming advisory values: microcystins 8 µg/L, cylindrospermopsin 15 µg/L.
  18. U.S. Environmental Protection Agency (2015). EPA Drinking Water Health Advisories for Cyanotoxins. U.S. EPA Harmful Algal Blooms program. https://www.epa.gov/habs/epa-drinking-water-health-advisories-cyanotoxins (accessed 2026-11-05) 10-day health advisories (2015): microcystins 0.3 µg/L (bottle-fed infants and pre-school children) and 1.6 µg/L (school-age children and adults); cylindrospermopsin 0.7 and 3.0 µg/L.
  19. Quiblier, C., Wood, S., Echenique-Subiabre, I., Heath, M., Villeneuve, A., & Humbert, J.-F. (2013). A review of current knowledge on toxic benthic freshwater cyanobacteria – Ecology, toxin production and risk management. Water Research, 47(15), 5464-5479. https://doi.org/10.1016/j.watres.2013.06.042
  20. Wood, S. A., Kelly, L. T., Bouma‐Gregson, K., Humbert, J., Laughinghouse, H. D., Lazorchak, J., McAllister, T. G., et al. (2020). Toxic benthic freshwater cyanobacterial proliferations: Challenges and solutions for enhancing knowledge and improving monitoring and mitigation. Freshwater Biology, 65(10), 1824-1842. https://doi.org/10.1111/fwb.13532
  21. Loftin, K. A., Clark, J. M., Journey, C. A., Kolpin, D. W., Van Metre, P. C., Carlisle, D., & Bradley, P. M. (2016). Spatial and temporal variation in microcystin occurrence in wadeable streams in the southeastern United States. Environmental Toxicology and Chemistry, 35(9), 2281-2287. https://doi.org/10.1002/etc.3391
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  26. Lürling, M., & Mucci, M. (2020). Mitigating eutrophication nuisance: in-lake measures are becoming inevitable in eutrophic waters in the Netherlands. Hydrobiologia, 847(21), 4447-4467. https://doi.org/10.1007/s10750-020-04297-9
  27. Visser, P. M., Ibelings, B. W., Bormans, M., & Huisman, J. (2016). Artificial mixing to control cyanobacterial blooms: a review. Aquatic Ecology, 50(3), 423-441. https://doi.org/10.1007/s10452-015-9537-0
  28. Jeppesen, E., Søndergaard, M., Lauridsen, T. L., Davidson, T. A., Liu, Z., Mazzeo, N., Trochine, C., et al. (2012). Biomanipulation as a Restoration Tool to Combat Eutrophication. In Advances in Ecological Research (pp. 411-488). Elsevier. https://doi.org/10.1016/b978-0-12-398315-2.00006-5
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  30. Kentucky Energy and Environment Cabinet (2013). Public Advised of Potential Health Risks with Exposure to Water in Taylorsville Lake. Naturally Connected (Cabinet news). https://kydep.wordpress.com/2013/06/28/public-advised-of-potential-health-risks-with-exposure-to-water-in-taylorsville-lake/ (accessed 2026-11-05)
  31. Kentucky Energy and Environment Cabinet (2013). Harmful algal blooms found at four more Kentucky lakes. Naturally Connected (Cabinet news). https://kydep.wordpress.com/2013/10/21/harmful-algal-blooms-found-at-four-more-kentucky-lakes/ (accessed 2026-11-05)
  32. Kentucky Energy and Environment Cabinet (2015). Recreational advisory issued for Ohio River due to harmful algal bloom. Naturally Connected (Cabinet news). https://kydep.wordpress.com/2015/09/18/recreational-advisory-issued-for-ohio-river-due-to-armful-algal-bloom/ (accessed 2026-11-05)
  33. Kentucky Energy and Environment Cabinet (2019). Harmful Algal Bloom Recreational Public Health Advisory Issued. Naturally Connected (Cabinet news). https://kydep.wordpress.com/2019/09/26/harmful-algal-bloom-recreational-public-health-advisory-issued/ (accessed 2026-11-05)
  34. Hill, K. L., Jaegge, A. C., Moore, D. M., & Byl, T. D. (2026). Tracking Toxins: A Pilot Investigation of Cyanotoxins in North-Central Tennessee’s Surface Waters and Wells. Toxins, 18(6), 239. https://doi.org/10.3390/toxins18060239
  35. Li, J., & Murdock, J. (2025). Nutrient concentration, stoichiometry, and timing of delivery can regulate cyanobacterial dominance and microcystin production in rivers. Journal of Environmental Management, 377, 124714. https://doi.org/10.1016/j.jenvman.2025.124714