Freshwater Ecology & Watershed Research

Cyanobacteria · Chapter 3

Freshwater Ecology of Cyanobacteria

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

Learning objectives

After studying this chapter, you should be able to:

  1. Contrast planktonic and benthic cyanobacteria and the habitats each occupies.
  2. Explain how light, temperature, stratification and water residence time favor or limit cyanobacteria.
  3. Predict how a shaded, flowing stream and an open, still pond differ in their likely cyanobacterial communities.
  4. Describe seasonal succession and the roles of competition, grazing and microbial interactions.
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.

Whether cyanobacteria thrive in a body of water depends less on whether they are present — they almost always are — than on whether conditions let them outgrow their competitors and outlast their losses. Warm temperatures, calm and stratified water, long water residence times and ample light favor the planktonic bloom-formers; buoyancy, efficient light harvesting, phosphorus storage and nitrogen fixation are the traits that let them exploit those conditions [1, 2, 3]. Warm summers can tip the balance strongly: modeling and observations from a European lake showed that a heatwave summer promoted cyanobacterial dominance [4].

Streams and rivers work differently. Flow flushes plankton downstream, so in small streams cyanobacteria are mostly benthic: films, mats and colonies attached to rocks, wood and sediment, sharing the surface with diatoms, green algae, bacteria and fungi [5, 6]. Large, slow rivers sit in between; cyanobacteria are routine members of their phytoplankton even when they do not dominate [7]. The contrast between a shaded, flowing stream such as Allen Branch and an open, sunlit farm pond is therefore a contrast between two different ecological games.

Planned sections

3.1 Planktonic versus benthic cyanobacteria

Life in the water column versus life on surfaces; buoyancy regulation by gas vesicles in plankton [8]; mat formation, detachment and downstream dispersal in rivers [9, 6].

3.2 Lakes, reservoirs, ponds, wetlands, streams and rivers

How depth, mixing, flow and residence time differ among habitats, and which cyanobacteria each tends to support. Reservoirs combine river inflow with lake-like stratification.

3.3 Light availability and shading

Light as a control on both planktonic and benthic producers; efficient light harvesting by phycobilisomes in turbid water [2]; canopy shading in small streams.

3.4 Water temperature

Higher optimal growth temperatures of many bloom-forming cyanobacteria; heatwaves and climate warming [1, 4, 10].

3.5 Mixing and stratification

Thermal stratification, buoyant species at the surface, and why artificial mixing can suppress cyanobacteria in some deep lakes but not shallow ones [11].

3.6 Water residence time

Slow-growing populations need time; flushing in streams and at high flows removes plankton. Low, slow flows set the stage for river blooms such as those on the Ohio River [12].

3.7 Seasonal succession

The seasonal sequence of phytoplankton and zooplankton in lakes and the mechanisms behind it [13]; overwintering akinetes and colonies on sediments [14].

3.8 Competition with other phytoplankton

Nutrient affinity, storage and nitrogen fixation as competitive traits [2]; ratios of nitrogen to phosphorus [15].

3.9 Grazing by zooplankton

How grazing pressure shapes plankton and why cyanobacteria often escape it (developed in Chapter 6) [16].

3.10 Microbial interactions

Bacteria associated with colonies and mats, viruses and parasites, and the microbial community of stream biofilms.

Connection to local research

At Allen Branch and nearby waters

Hypothesis In shaded reaches of Allen Branch, benthic diatoms and bacteria will dominate biofilms, and cyanobacterial mats, if present, will be more common where the canopy opens. A sunlit farm pond, in contrast, is the habitat where planktonic bloom-formers such as Microcystis would be expected in summer. Both are predictions to test.

Related: shaded versus sunlit reaches, seasonal biofilms.

Key terms

Planktonic
Suspended in the water column.
Benthic
Attached to or living on the bottom.
Biofilm
Microbial community in a slime matrix on a surface.
Stratification
Layering of a lake by temperature and density.
Residence time
Average time water spends in a water body or reach.
Succession
Predictable seasonal change in community composition.

References

  1. Paerl, H. W., & Huisman, J. (2008). Blooms Like It Hot. Science, 320(5872), 57-58. https://doi.org/10.1126/science.1155398 (external site, opens in a new tab)
  2. 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 (external site, opens in a new tab)
  3. 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 (external site, opens in a new tab)
  4. Jöhnk, K. D., Huisman, J., Sharples, J., Sommeijer, B., Visser, P. M., & Stroom, J. M. (2008). Summer heatwaves promote blooms of harmful cyanobacteria. Global Change Biology, 14(3), 495-512. https://doi.org/10.1111/j.1365-2486.2007.01510.x (external site, opens in a new tab)
  5. 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 (external site, opens in a new tab)
  6. 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 (external site, opens in a new tab)
  7. Graham, J. L., Dubrovsky, N. M., Foster, G. M., King, L. R., Loftin, K. A., Rosen, B. H., & Stelzer, E. A. (2020). Cyanotoxin occurrence in large rivers of the United States. Inland Waters, 10(1), 109-117. https://doi.org/10.1080/20442041.2019.1700749 (external site, opens in a new tab)
  8. Walsby, A. E. (1994). Gas vesicles. Microbiological Reviews, 58(1), 94-144. https://doi.org/10.1128/mr.58.1.94-144.1994 (external site, opens in a new tab)
  9. Bouma-Gregson, K., Power, M. E., & Bormans, M. (2017). Rise and fall of toxic benthic freshwater cyanobacteria (Anabaena spp.) in the Eel river: Buoyancy and dispersal. Harmful Algae, 66, 79-87. https://doi.org/10.1016/j.hal.2017.05.007 (external site, opens in a new tab)
  10. Mantzouki, E., Lürling, M., Fastner, J., De Senerpont Domis, L., Wilk-Woźniak, E., Koreivienė, J., Seelen, L., et al. (2018). Temperature Effects Explain Continental Scale Distribution of Cyanobacterial Toxins. Toxins, 10(4), 156. https://doi.org/10.3390/toxins10040156 (external site, opens in a new tab)
  11. 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 (external site, opens in a new tab)
  12. Nietch, C. T., Gains-Germain, L., Lazorchak, J., Keely, S. P., Youngstrom, G., Urichich, E. M., Astifan, B., et al. (2022). Development of a Risk Characterization Tool for Harmful Cyanobacteria Blooms on the Ohio River. Water, 14(4), 644. https://doi.org/10.3390/w14040644 (external site, opens in a new tab)
  13. Sommer, U., Adrian, R., De Senerpont Domis, L., Elser, J. J., Gaedke, U., Ibelings, B., Jeppesen, E., et al. (2012). Beyond the Plankton Ecology Group (PEG) Model: Mechanisms Driving Plankton Succession. Annual Review of Ecology, Evolution, and Systematics, 43(1), 429-448. https://doi.org/10.1146/annurev-ecolsys-110411-160251 (external site, opens in a new tab)
  14. 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 (external site, opens in a new tab)
  15. Smith, V. H. (1983). Low Nitrogen to Phosphorus Ratios Favor Dominance by Blue-Green Algae in Lake Phytoplankton. Science, 221(4611), 669-671. https://doi.org/10.1126/science.221.4611.669 (external site, opens in a new tab)
  16. Ger, K. A., Hansson, L., & Lürling, M. (2014). Understanding cyanobacteria‐zooplankton interactions in a more eutrophic world. Freshwater Biology, 59(9), 1783-1798. https://doi.org/10.1111/fwb.12393 (external site, opens in a new tab)