This paper was written as part of the 2011 Alaska Oceans Sciences Bowl high school competition. The conclusions in this report are solely those of the student authors.

Hotham Inlet Cyanobacterial Blooms: Cyanobacterial Blooms in the Arctic and Its Potential Effects


Catherine Greene
Chelsea Hadley
Grant Magdanz
Geena Sampson

Team Northern Bullheads

Kotzebue High School
PO Box 264
Kotzebue, AK 99752


Cyanobacteria blooms have become more common in Hotham Inlet. Cyanobacteria are one of the oldest colonizers. They clump together to form filamentous mats, are autotrophic and produce food through photosynthesis.

Due to climate change, water temperatures in Hotham Inlet are increasing, surrounding permafrost is melting, and decomposition rates are rising. The resulting increase in nutrients in the water make cyanobacteria blooms more likely.

Hotham Inlet—with inflows from three major rivers—is brackish and provides a mixing area for many species, which cyanobacteria blooms could easily destroy. In the past two years, four different species of cyanobacteria has been found in Hotham Inlet. Of these four, only two have been known to be toxic. Nevertheless, toxicity is not the only problem. Eutrophication may also be at play. As algae dies, bacteria decompose the algae, use much of the dissolved oxygen in the water, and release phosphate which algae need to survive. This starts a vicious cycle that suffocates many aquatic organisms.

There are many options to slow or stop the formation of cyanobacteria blooms. Low currents and small tides make it more likely for a bloom to occur. To change this, it may be possible to dig a passage in the narrowest part of the peninsula to open a channel between Hotham Inlet and Kotzebue Sound. A recent study has shown that the use of ultrasonic irradiation has successfully reduced the intensity of cyanobacteria blooms. This uses low frequency sound waves and vibrations to destroy the cyanobacteria cells.

Research needs to be done to determine the conditions needed for cyanobacteria to survive. A population estimate for the species the cyanobacteria will affect would help lawmakers determine if seasons need to be shortened or lengthened.


Also known as "blue-green" algae, cyanobacteria are easily found and recognized as one of the earliest colonizers (Bigger, no date). Cyanobacteria are autotrophic (they can take inorganic substances, such as carbon dioxide and produce nutritional organic substances, such as carbohydrates) and produce food though photosynthesis. They are only as large as a single bacterial cell, but can clump together to form filamentous mats. The algae can also look like foam or scum. Most cyanobacteria are unicellular and have multi-layered cell walls larger than that of bacterial cells.

Cyanobacteria can thrive in many different environments including hot springs, salt marshes, moist soils, and even the harsh climates of northern Alaska (Bigger, no date). They reproduce through binary fission. Binary fission is a form of asexual reproduction where the cells divide in half and continue to divide to form colonies at a fast rate if conditions allow.

The cyanobacterial blooms can make clear water become cloudy in a matter of days. It is usually found at the water's surface near the shoreline and can be inches deep depending on the reproduction speed of the cyanobacteria. Cyanobacteria typically grow in late summer or early fall (CDC, no date).

Hotham Inlet

Located north of Kotzebue in Northwest Alaska, Hotham Inlet (locally known as Kobuk Lake) is about 50 miles long and ranges from 5 to 20 miles wide. The inlet is a body of water separated from the Kotzebue Sound by a peninsula about 52 miles long. The Kobuk, Selawik, and Noatak rivers are the inlet's primary contributors of fresh water. As the fresh water is added, storms and tides carry salt water from Kotzebue Sound into the inlet. As a result, the water in Hotham Inlet is a mixture of both salt and fresh water, called brackish water.

The average temperature of Hotham Inlet is about 55°F (13°C) from mid-August to mid-September (See Table 1). During this one-month period, the water temperature is at an average of about 54°F (12°C). Although the water and air temperatures were not taken in the heart of Hotham Inlet, it is located near Kotzebue and the inlet's waters is a part of Kotzebue's coastline. The time period at which these temperatures were taken corresponds to the time of year at which cyanobacterial blooms are observed.

Hotham inlet begins to freeze in October. Due to climate change, the date of which ice starts forming varies. The ice is usually thick enough for safe travel by snow machine in November. Ice coverage throughout Hotham Inlet usually lasts until May.

Hotham Inlet Ecosystem

Hotham Inlet is a brackish estuary that provides a home to a broad variety of aquatic organisms. These include the smallest of bacteria to the heftiest belugas.

Phytoplankton, such as diatoms (multiple species) and the species of cyanobacteria discussed in this paper, make their home in the inlet's waters (See Figure 3). Some examples of zooplankton present in Hotham Inlet include copepods (Eudiaptomus yukonensis), fish larva, and sea star larva. Examples of small invertebrates present are the abundant mysids (multiple species), the Baltic clam (Macoma balthica), brown shrimp (Crangon crangon), flatbottom sea star (Asterias amurensis), and Arctic moon snails (Cryptonatica affinis) also make a living in Hotham Inlet. Some fish species that swim in the waters of the inlet are arctic cod (Boreogadus saida), humpback white fish (Coregonus pidschian), chum salmon (Oncorhynchus keta), and rainbow smelt (Osmerus mordax). Piscivores present include bearded seals (Erignathus barbatus), sheefish (Stenodus leucichthys), and beluga (Delphinapterus leucas).

Cyanobacteria Found in Kotzebue's Waters

Cyanobacterial blooms went from an occasional occurrence to a yearly event within the lifetime of Willie Goodwin, a local Kotzebue elder who is on the Kotzebue Elders' Council. In light of this, cyanobacterial blooms have the potential to become a serious problem in Hotham Inlet as they have in other parts of the world.

According to Alex Whiting (pers. comm.), there were four different species of cyanobacteria found along Kotzebue's coastline within the last two years. The species found last year was Aphanizomenon flos-aquae. The three found this year were Oscillatoria spp., Anabaena spp., and Aphanizomenon spp. Alex has personally observed blooms from 2008 to 2010 in the late summer and early fall.

Oscillatoria spp. cells compress and attach to form long, straight filaments that are either entangled or free-floating. This cyanobacteria typically grows in ponds and treated sewage lagoons (Health, no date). Oscillatoria spp. can be either toxic or non-toxic; they produce the neurotoxin anatoxin-a and the heptoxin microcystin (Stewart, no date).

Anabaena spp. attaches to form strings similar to a string of beads that can be twisted or coiled (Health, no date). Anabaena spp. can produce the same toxins as oscillatoria spp., but have been known to be non-toxic (Schneegurt, no date).

Aphanizomenon spp. is also filamentous; it is usually coiled or tangled. Aphanizomenon flos-aquae thrives in fresh water and is rarely found in salt water (Komarek, 2010).

The cyanobacteria found have a long-term effect on the aquatic ecosystem (See Figure 1). Over time, the abundance of cyanobacteria could increase due to climatic change caused by an increase of carbon dioxide. An increase in temperature leads to hotter days, warmer waters, and less ice coverage. The sun's rays will provide energy for photosynthesis to occur. Photosynthesis is a process where plants take in six molecules of water and carbon dioxide each, then use the sun's rays as an energy source to produce a molecule of sugar for food and six molecules of oxygen to release into the air (Farabee, 2010).

An increase in carbon dioxide in the atmosphere will also cause the permafrost to melt more than it is presently. With the permafrost melting at a more significant rate, higher amounts of nutrients will be released into the waters (Science, no date). The abundance of nutrients will allow the cyanobacteria to grow at a faster rate.

Effects of Cyanobacteria in Hotham Inlet

Over a long period of time, cyanobacteria blooms will result in more toxins in the water and depleted dissolved oxygen and dissolved carbon dioxide levels. The toxins released by the cyanobacteria can be fatal if the animals are exposed to it in large amounts (Gabel, 2010).

The toxins that the cyanobacteria are producing can cause a number of problems. Anatoxin-a (produced by Oscillatoria spp. and Anabaena spp.) can cause "muscle cramps, twitching, paralysis, and cardiac or respiratory failure" if large amounts are consumed (NOAA, 2005). Also, the neurotoxin microcystin can cause "nausea, vomiting, and acute liver failure" (NOAA, 2005). Most cyanobacteria produce the dermatoxins aplysiatoxin, lyngbiatoxin-a, and lipopolysaccharides. These may cause skin irritations, rashes, and gastrointestinal distress (NOAA, 2005).

A study was conducted in California concerning sea otters and cyanobacteria (Gabel, 2010). Researchers say that there was a link between the algal toxins and the deaths of the sea otters. The cyanobacteria first grew in fresh water then traveled down a stream or other waterways into the ocean where the oysters, mussels, and clams ingested it and became contaminated. The sea otters then consumed the toxic oysters, mussels, and clams with a fatal result.

In Hotham Inlet's physical ecosystem, the cyanobacteria toxins would affect the zooplankton first after consumption of the cyanobacteria. The zooplankton would be infected with toxins and once eaten by the small invertebrates, they in turn, would be contaminated. The herring and other fish that feed on the small invertebrates would also be contaminated with the toxins if consumed, as will the piscivores if they consume the fish.

Another negative effect that could affect the goal of our management plan (which will be described later) is eutrophication. Eutrophication is the emission of a high amount of nutrition in a body of water over a long period of time by a natural phenomena like permafrost melt, or by human activities such as untreated sewage runoff (Science, no date).

The process of eutrophication starts when the algae dies. Bacteria in the water need a lot of oxygen to decompose the algae. While the bacteria use the dissolved oxygen, it releases phosphate back into the water to feed more algae. Most aquatic animals will die as a result of the lack of oxygen in the water (Science, no date).

Eutrophication can also be considered pollution (USGS, 2010). This process gradually destroys lakes and rivers and kills smaller sea life. Eventually, the body of water is overwhelmed with dead plants and animals that sink to the bottom and decrease the dissolved oxygen level. For example, in the 1960s Lake Erie was named the "Dead Lake" because it underwent this process and still has not fully recovered(" Science, no date).

Management Plan

Willie Goodwin (pers. comm.) has noticed that cyanobacteria most likely occur in places with little current. If this theory is true, Hotham Inlet, which has areas of very low current, would make a great place for cyanobacteria to grow. One idea to eliminate the process of cyanobacterial growth in Hotham Inlet is to dig into the narrowest part of the peninsula, which is about half a mile wide, to create an additional passage from Hotham Inlet to Kotzebue Sound. According to Vera Alexander, a professor and scientist at the University of Alaska Fairbanks, said that she has not heard of cyanobacterial blooms in Alaska's marine waters. Therefore, this idea would create salt water currents that flow throughout the inlet and could potentially keep the cyanobacteria from growing in oversized colonies. Ideally a structure would be installed to control the water flow through this area.

Another solution would be a process called ultrasonic irradiation (Lenntech, 2009). Using a combination of very low frequency sound waves (21.5 kHz) and vibrations, this creates cavitation that produces free radicals which damage the algal cells. The free radicals then react with the potassium iodide in the water which then separates the bond between the potassium and iodide to make the iodine free. The ratio of iodine to cavitation is then calculated to estimate the damage to the algal cells. The more iodine that is present, the faster it kills the algal blooms. The damaged algae is unable to photosynthesize properly and lessens the amount of toxins being released.

Researchers tested algae in test tubes with 120 watts of electricity and a frequency of 28kHz at 1, 3, 5, 10, 15, and 30 seconds of exposure to ultrasonic irradiation (Lenntech, 2009).

A third plausible solution is limiting the subsistence hunting and gathering of local residents. Although it is a traditional way of life, only about half of the locals harvest fish and seals in Kotzebue Sound and Hotham Inlet. The subsistence hunting of bearded seals is unlimited for local residents that are part Alaska coastal native. To maintain sufficient numbers of sea life in Kotzebue's waters we propose that limiting the subsistence harvest within a specific time frame would help keep the populations stable.

Also, such activities as commercial and sport fishing that already have a season, can be shortened if needed to maintain sufficient populations of salmon and sheefish. Although the periods are not long, this gives the populations of fish and other species that feed on the fish time to keep a stable population.

The fourth proposal is to create a culvert or construct an opening and closing gate south of the airport near the treated sewage lagoon. Kotzebue is located on a peninsula so it appears to be an island (See Figure 5). There is a lagoon southeast of the town where currents are fairly low. Also, there is a landing strip that stretches into the middle of the lagoon which makes it appear as two separate lakes. These lakes (known locally as the lagoon) are connected to Hotham Inlet, and will provide an ideal place for cyanobacteria to grow. The opening would provide more currents and circulation in Kotzebue Sound's waters and may slow or halt the growth of cyanobacteria due to the introduction of salt and cooler water temperatures. Another possible effect that may inhibit cyanobacteria growth would be that nutrients that propagate cyanobacteria blooms would be diluted. This procedure would be similar to removing the narrowest part of the Baldwin Peninsula.

Prioritizing Research

In order to follow through with all of the proposals for managing a stable population of the target species, data need to be collected. First of all, what causes a cyanobacterial bloom (weather conditions, water temperature, salinity, dissolved nutrients, oxygen levels, etc.) needs to be known. That way it would be easier to predict when blooms will occur so the appropriate parts of the management plan can be implemented.

Other data that should be known are the populations of fish and piscivores in Hotham Inlet and Kotzebue Sound. This could be done by tagging the animals with either plastic or radio tags. By using the plastic tags, researchers would probably use the process called "mark and recapture". This means that the fish would be tagged (record location tag number, weight of fish, estimate age, etc.) and released back into the water. Over a certain period, the researchers would return back to the same spot and capture the same species of fish to record how many were captured again. If a large amount of tagged fish were captured, it would mean that the populations are relatively small. If a small amount of tagged fish were captured, it would mean that the population is relatively large.

The seal population can be monitored by using radio tags. These tags would send and receive satellite signals and information about the seal would constantly be sent to a computer and recorded. Using radio tags would help researchers understand the paths of the seals, if the seals are directly in or near a cyanobacterial bloom, and it would make recapturing the species easier to assess health.

Funding for this project would probably be provided by the federal government if it were to become a major problem within Kotzebue. Local residents with some knowledge of cyanobacteria (i.e., Alex Whiting) would conduct the experiments for the most part and observe the populations of the aquatic species over time. Because the cyanobacteria typically occur at the end of summer, the projects would probably be put on hold until then but this would provide more information for locals.

More research would include the type of help Kotzebue would be able to get. Kotzebue is located on a peninsula and costs quite a bit to be transported there. Also, the instruments and materials that would be needed to construct a culvert, a gate, or to dig through the narrowest part of the peninsula, or to experiment with ultra irradiation would have to be transported here on a barge, which also costs a lot of money.

In conclusion, there are plausible ways to reduce the growth of cyanobacteria, but we have no evidence that the increase of present algae has started to cause problems in Kotzebue at this time.

Figures and Tables


Air Temperature

Water Temperature







1.013, 18 ppt

WNW 25mph

Heavy overcast, rain—at times heavy and strong SSE winds for the last few days. Temps in the 60's for 3 days dropping into the 50's yesterday and today.




1.014, 19 ppt

NNW 10mph

Water level dropped lots, strong winds subsided.




1.004, 5 ppt

NW 5mph

NW winds the last few days, partly sunny, med Water height, no precipitation.




1.005, 6 ppt

E 10mph

No rain the last few days, generally light winds.




1.006, 6 ppt

WNW 20mph

Sunny with clear skies.




1.006, 9 ppt

SSE 13mph





1.009, 13 ppt

SSE 23mph

Rain and high water.




1.004, 5 ppt

E 5mph

Light winds, calm at times from last night through this morning. A bloom happened sometimes between yesterday afternoon and this morning, Kobuk Lake had algae patches an Selawik Lake had heavy bloom covering most of the lake. The bloom near Kotzebue happened in the lagoon bordering the ESE side of town and not in front on the Sound side this year.

Table 1. Data collected by Alex Whiting and the Field Biology class.
Location: lat: 66.903086°N lon: -162.586017°

climate change effects on cyanobacteria

Figure 1. A chart illustrating the effects of climate change on cyanobacteria.

graph of salmon releases and herring spawning biomass in Lynn Canal

Figure 2. Illustration of potential negative effects of cyanobacteria blooms on the Hotham Inlet ecosystem.between the species.

food web illustration

Figure 3. Food web illustration.

map of Hotham Inlet including Kotzebue

Figure 4. Map of Hotham Inlet and Kotzebue.

map of Kotzebue including the lagoon and surrounding waters

Figure 5. Map of Kotzebue; a visual of the lagoon and surrounding waters.