We start our field work with observing the surrounding riparian native trees (often Western sycamores, willows, California coastal live oaks, and Pacific poison oaks) and the aquatic vegetation (Broadleaf cattails, Watercress). Then, we measure stream canopy cover, substrate type, water depth and velocity, water temperature, pH, conductivity, salinity, and total dissolved solids using different field instruments, such as the Extech EC500 Waterproof ExStik® II pH/Conductivity Meter. The physical habitat and water chemistry conditions are very important factors, which determine the algal composition and the functioning of the entire stream ecosystem. During our multiple field trips to Escondido Creek, we noticed that in the spring, the stream bottom is covered by large, green, branched, algal filaments, while in the fall, they are replaced by long, golden-brown, diatom colonies. These filaments are firmly attached to hard substrates, but sometimes may detach and float on the water surface. We use simple sampling tools to remove the attached algae and collect them in carefully labeled plastic bags or tubes. The fresh algal samples are transported to the laboratory on ice in a cooler.

When collecting bottom (called also benthic) algae it is a good idea to use gloves to avoid skin contact with possible toxic cyanobacteria or other potentially harmful bacteria.

We use light microscopes to magnify the tiny algae 100 to 1000 times, and use taxonomic literature and websites to identify the species. In the spring, the bottom of Escondido Creek is nearly completely covered by large grass-green filaments, which look branched even macroscopically. When magnifying the filaments 100 to 200 times with a microscope, we see that they are composed of a single row of long, cylindrical cells with side branches. This is the green alga Cladophora (the Latin name means “bearing branches”). Different species of Cladophora are commonly distributed in fresh or marine habitats. Cladophora is tolerant to pollution and its excess growth indicates increased nutrient and organic load.

When we look at the filaments at higher magnification (400 times) we see small, golden, elliptical cells and round, bluish-reddish cells attached to the wall of Cladophora. These algae are epiphytes because they grow on other algae or plants but are not parasitic. These golden-colored epiphytes on Cladophora are diatoms, and the reddish cells are cyanobacteria.

Diatoms are beautiful single-celled algae with golden chloroplasts and symmetrical walls made of silica. We clean the diatom silica shells in the lab with oxidizers to observe it better and to identify the species. The epiphytic cyanobacteria form colonies with numerous reddish cells embedded in colorless polysaccharide mucilage. Note that the photomicrographs have a scale bar at the right bottom corner which is helpful to get the size of the cells.

We use electron microscopy to view algae under even higher magnification and see the ultrastructure of the algal cells better. The electron microscope uses a beam of electrons as a source of illumination, in contrast to light. To identify the diatom species, we often need a scanning electron microscope's view of the detailed, silica walls, which are finely perforated. Transmission electron microscopy is very helpful to display intracellular structures, such as membranes and storage granules in cyanobacteria.

We isolated the cyanobacterial epiphyte from Cladophora grown in laboratory cultures. Cladophora grows well both in a liquid culturing medium and on the top of a solid agar medium. These cultures allow us to investigate the alga in more detail. REU undergraduate students pictured the cellular ultrastructure with a transmission electron microscope (see the images in the previous section) and extracted DNA from the culture. Molecular analysis showed that the cyanobacterium in the culture grows and works together in a mutualistic relationship with another non-photosynthetic bacterium, which we published as species that are new to science . 2023 REU students are continuing their studies on the molecular taxonomic identity of the cyanobacterium, which is currently unresolved. Molecular analysis also provides information about functional genes related to the synthesis of biologically active compounds, such as toxins or pigments.

Scientific communication and data presentation are important parts of our work and student training. NSF REU undergraduate student researchers presented posters with their findings from Escondido Creek during the final summer showcase and published their results in a peer-reviewed journal.

If you are interested to learn more about using benthic algae as bioindicators of stream water quality, check out the second publication (Benthic soft-bodied algae as bioindicators of streamwater quality). The California State Water Resources Control Board has an extensive Surface Water Ambient Monitoring Program, which uses algae in stream bioassessment and provided funding for our algal research.