Photo by Liam Rubin.

Benthic Cyanobacteria

What are Benthic Cyanobacteria?

Benthic cyanobacteria are tiny, plant-like organisms that grow on the bottom of lakes and rivers, attached to rocks, sediment, and aquatic plants. 

Unlike the floating “pea soup” blooms you might see on the surface, these cyanobacteria can form mats that stay underwater. These mats can sometimes break loose and float to the surface and accumulate on the shore.

Even though they grow out of sight, benthic cyanobacteria can still be harmful. Some produce toxins that can affect people, pets, and wildlife. Because they’re underwater, they often go unnoticed. They don’t need nutrient-rich water to thrive and are becoming more common as climate and water conditions change.

Detection Challenges

Benthic cyanobacteria can thrive in clear water and are hard to detect without close inspection, requiring public awareness.

Here’s what to look for:

  • Slimy or leathery patches stuck to rocks, logs, or plants
  • Dark green, brown, black, or reddish mats
  • Fuzzy or jelly-like blobs that may float or stay submerged
  • Mats with bubbles trapped underneath
  • Musty or earthy smells, especially when mats are thick or decaying
  • Detached mats that float to the surface or wash up on shore

They can be thin and patchy or thick and rubbery, and sometimes they cling to aquatic plants or form gelatinous colonies that look like grapes or marbles underwater.

Examples of Benthic Cyanobacteria

Globules

There are several types of benthic cyanobacteria (or cyanobacteria that grows on the bottom of lakes and rivers) that form small rounded colonies, or globules, that can look very similar in the field. 

What you may observe:

  • Small colonies with gelatinous or leathery textures and a round or elongated shape.
  • Colonies attached directly to rocks, sediment, or other substrates (can detach and float to the surface).
  • Colors ranging from green to yellow, brown, or black, sometimes with multiple colors present within the same colony.
  • Forms pea- to egg-sized gelatinous spherical colonies.

Floating Mats

Some benthic cyanobacteria can detach from the bottom and form floating mats, which may resemble other algae or organic debris in the field. 

What you may observe:

  • Loose mats or clumps floating at the water surface or just below it, often accumulating along shorelines or in calm areas
  • Colors ranging from dark green and olive to brown, yellow, or black, sometimes with multiple colors within the same mat
  • Typically darker, thicker, and more clumped together when picked up with a stick compared to green algae, which usually appear bright green and grow as loose filaments or hair-like strands rather than cohesive mats.

Attached Mats

There are several types of benthic cyanobacteria that grow attached to the bottom and form a carpet like mat.

What you may observe:

  • Dark brown, black, olive, or deep green mats attached to cobbles, boulders, or other submerged surfaces
  • Velvety, slimy, or felt-like coatings that spread across rocks and may form patchy or continuous carpets
  • Typically darker, thicker, and more clumped together when picked up with a stick compared to green algae, which usually appear bright green and grow as loose filaments or hair-like strands rather than cohesive mats.

Benthic Monitoring Program

The Lake Champlain Committee has partnered with TetraTech to expand monitoring efforts to include benthic cyanobacteria. These organisms are often overlooked in traditional surface bloom monitoring, yet they can play an important role in lake ecology and may produce toxins under certain conditions.

This work is integrated into our broader cyanobacteria monitoring program, helping us better understand the distribution, extent, and ecological presence of benthic cyanobacteria throughout the Lake Champlain watershed. In addition to visual monitoring, samples are also being collected to support identification efforts and improve our understanding of where and when these organisms are occurring.

Funding

Funding for this project is provided by the United States Environmental Protection Agency under assistance agreement to NEIWPCC in partnership with the Lake Champlain Basin Program.