Pollution & the West

When red tide smothered an urban lake, citizen scientists sounded the alarm

Private citizens were first on the scene to document a massive die-off in Oakland’s Lake Merritt. Their contributions were enabled by the crowd-source observation tool iNaturalist.

Shifting tides Lake Merritt in downtown Oakland in cleaner times, above left, and after a devastating algal bloom brought fish-killing red tide to the lake in the summer of 2022. Mike D via Flickr and Damon Tighe

By Bhumikorn Kongtaveelert

It was the morning of August 28, 2022 and Lake Merritt’s red tide outbreak had made it a graveyard. The shore sediments were covered with silver dashes of goby fish and tiny dead sea life covered the edges of the Oakland estuary. Sturgeon and a large bat ray drifted lifeless to the surface; when living they tended to brood unseen underneath the quiet ecosystem. When the water was still, you might have mistaken Lake Merritt  for an amber incarnation of its former self, capturing thousands of fish suspended in water, a tessellation of white-eyed creatures, blankly staring in bewilderment.

Within a day, the mild fishy smell had grown into a pungent foul odor. Navigating the lake, Damon Tighe, a self-described citizen scientist, was shocked at the unfamiliar and alarming sights: lifeless clams, their shells wide open as if to surrender their vitality; carcasses of countless aquatic animals embedded in the mud; in the water, schools of smelts and gobies frantically swimming towards the surface seeking oxygen as the bottom of the lake grew increasingly hypoxic.

Clockwise from upper left, dead creatures on the shores of Lake Merritt included a striped bass, green crab, anchovies and a flatfish. Damon Tighe

Crowd-sourced observations document an unfolding crisis

The magnitude of this massive die-off led Tighe to launch a campaign to crowd-source efforts to document the loss of biodiversity. His key tool was iNaturalist — an online platform that aggregates users’ pictures of flora and fauna and the observed location.


What Tighe initially thought was a localized disaster had, in fact, permeated the entire San Francisco Bay Area estuaries. “By the time I woke up in the morning, there [were] already like 100 observations in there. And I was like, ‘Oh, crap, this is way bigger,’” he said. 

The work of citizen scientists like Tighe and his new network is increasingly intertwined with the work of research scientists at public agencies and research institutions like the United States Geological Survey (USGS), San Francisco Estuary Institute (SFEI) and San Francisco Baykeeper. Researchers from these groups are analyzing data from Tighe’s campaign and their own formal observations to guess at possible causes for the die-off. 

“By the time I woke up in the morning, there [were] already like 100 observations in there. And I was like, ‘Oh, crap, this is way bigger.’”

Damon Tighe, citizen scientist

Online citizen-science communities helped researchers get a more complete picture of the local ecology under crisis, but their role might be enhanced as scientists streamline their investigations. Jon Rosenfeld, the senior scientist at SF Baykeeper, said that formal research to test their hypotheses “will require more advanced planning, asking the right questions, and then setting up citizen scientists to collect data that will help answer the particular questions.”  Citizen scientists’ efforts are pivotal in helping scientists monitor the loss of biodiversity. Researchers at the Estuary Institute say that volunteers are crucial to surmount the daunting challenges of monitoring the 1600-square-mile shoreline of the San Francisco Bay.

Warnings from citizen observers went unheard

Last summer, the spread of harmful algae Heterosigma akashiwo across the estuary led to more than 10,000 fish kills, including more than 400 dead sturgeon — a protected species close to extinction. It was first documented almost two months earlier in mid-July by citizen reports to Baykeeper’s pollution hotline. They saw that the water had turned brown — the result of  the phytoplankton’s quick spread thanks to increased access to nutrients and sunlight. Eventually, when the surge of these nutrients is exhausted, the bloom disappears

Tighe was not alone in noticing what happened. Local residents like Katie Noonan and sent additional samples. Some explained the science to general audiences in places like Jim Ervin’s Fish In The Bay blog and Luis A. Solórzano’s video essay. These contributions were pivotal in documenting the bloom as it unfolded, as evidenced by Baykeepers’ timeline.

Video by Luis A. Solórzano

But the sightings and sampling by Tighe and others could have been better used, said Ervin, a volunteer researcher at the Olith Geochemistry and Fish Ecology Lab at the University of California, Davis. He believes that the early warnings could have led agencies to “shut the tide gates at Lake Merritt and possibly prevented the explosive bloom of akashiwo.” 

The question now is how the expanding work of community volunteers will be integrated into formal efforts to monitor the health of the Bay. While there is still no precise definition of “citizen scientist,” researchers largely agree that they are volunteers who generate new data for scientists

More than a hobby: citizen science’s role grows in collecting data and sounding alerts

Damon Tighe in a self-portrait at Mare Island. Damon Tighe

Unlike traditional collaborations where citizen scientists volunteer their time to help researchers on designated inquiries, Tighe’s independent data collection efforts demonstrated potential for citizen science to be more autonomous and generate unexpected leads. Citizen science monitoring biodiversity is not merely a hobbyist pursuit; more than 80 percent of biodiversity data in Europe was recorded by citizen scientists, according to a 2015 paper.

Just as nutrient spikes accelerate harmful blooms in the Bay, the internet has accelerated the impact of citizen scientists. What Tighe and his online community did using a mobile application to coordinate their observations meant that their autonomous efforts paralleled the work of research scientists. Their archive of ecological damage enabled scientists to to potentially learn more about the conditions behind the bloom. 

For Rosenfield, citizen scientists are “an early warning system”; the integration of volunteer observations increases the chance of detecting irregular events that institutional sampling efforts might not have the flexibility to detect. “The data are very valuable in this observational stage,” Rosenfield said. 

iNaturalist rides a wave of internet-based observation platforms

As Tighe’s iNaturalist campaign demonstrated, the internet plays a pivotal role in documenting changes in local ecology. Founded in 2008, iNaturalist now has more than 3.2 million users globally; they have become a community of naturalists keeping track of changes in their local ecologies. The platforms connect occasional observers with dedicated taxonomers and scientists, who have expertise in classifying different species and local biodiversity.

Similar platforms like eBird and GBIF—the Global Biodiversity Information Facility—preceded iNaturalist and have been embraced by birders and researchers, respectively.

Smartphone apps and mobile web access enable volunteers to record observations efficiently. Through the ‘project’ function of iNaturalist, Tighe’s campaign let users coordinate their observations, and so it gained traction. By the end of the algal bloom, more than 130 volunteers put 1,100 distinct observations on a map spanning the distance from Bodega Beach to Santa Cruz. 

Via smartphones, a running tally of observations

Volunteer data contributed to Damon Tighe’s iNaturalist project “SF Bay Harmful Algae Bloom” eventually numbered over 1,110 by the end of November 2022.

Sources: iNaturalist; ESRI (satellite imagery); CalTrans (streets and roads); NASA (terrain);

Geoff McGhee

“I could see where the data was coming from and say, ‘Hey, nobody’s been over here, can you put time there?’

Damon Tighe

The app lets users see their observations populating a real-time map, which is different from normal reporting where agencies compile and verify the data elsewhere. This map helped Tighe coordinate efforts to monitor the estuary more efficiently. “I could see where the data was coming from and say, ‘Hey, nobody’s been over here, can you put time there?’” he said. As fish began to decay, any delay meant losing data points. The ad hoc efforts led to a broader archive as observers raced against the clock.

Mobile apps like this also allow for precision in geolocating data. As Lauren Gilespie, a fourth-year Ph.D. in Computer Science at Stanford who relies on biodiversity data from citizen science platforms, explained,  “GPS signaling is so accurate on phones these days that we get down to 10-30 meter accuracy.”


“It’s really neat [to see that] people are actually using the platform, not just to create observations but actually to coordinate activities around a particular problem,” said Scott Loarie, the co-director of iNaturalist. “That kind of crowdsourcing of the identification is really different from what was possible before the internet.”

Fast-moving citizen science augments and backstops formal monitoring projects

It’s not that the Bay’s ecosystem is understudied. Since 1969, USGS’s Water Quality of San Francisco Bay Research and Monitoring Project, has been using submersible sensors to collect and analyze water samples. But even with these monthly analyses across 37 locations, rapid algal blooms and busts are missed. 

A monthly data collection initiative from the U.C. Davis lab expanded monitoring in southern San Francisco Bay and Coyote Creek estuary but last summer, the lab’s timing was off. It had its trawl in early July, just before volunteers recorded the algal bloom. Another trawl came  in August, just before the fish die-off. “We were blissfully trawling in lower South Bay,” Ervin recalled. “We saw no trace of [the bloom] …. If you’re not sampling it frequently enough, you’ll never catch the next red tide.” 

“We saw no trace of [the bloom] …. If you’re not sampling it frequently enough, you’ll never catch the next red tide.”

Jim Ervin, retired environmental engineer, author, Fish in the Bay blog

Integrating citizen science in research can reduce costs, important for organizations like the U.C. Davis lab, which has a shoestring budget. A 2015 meta-analysis of 388 research projects with citizen science participation, relying on a total of 1.3 million volunteers, found citizen science provided $700 million to $2.5 billion worth of free labor annually — the equivalent of at least 11 percent of the National Science Foundation’s annual budget.

Volunteers’ observations can help pinpoint the sources of nutrient overloads in the water. Tighe and his network helped document an unusually fierce episode of the red tide, a problem that has afflicted the Bay for years. Experts believe culprits are the region’s 37 sewage plant operations whose runoff likely allowed these algae to grow dramatically in the estuary.

Algal blooms expected to remain a chronic problem in the Bay

David Senn, senior scientist at the San Francisco Estuary Institute and lead scientist at the San Francisco Bay Nutrient Management Program thinks the algal bloom will remain a chronic problem in the Bay. “Maybe it’s going to be here forever,” he said in an interview with Bay Nature. “There’s one way of at least reducing the magnitude of an event like this. And that’s if the nutrient levels were lower in San Francisco Bay.”

Satellite imagery over the San Francisco Bay Area shows the telltale glow of chlorophyll concentrations associated with algal blooms in August and September 2022. European Space Agency via Sentinelhub

Researchers agree that citizen science allows them to test hypotheses at a far broader scale. In an interview with Bay Nature, Levi Lewis, a fisheries biologist at UC Davis, said that labs lack resources to conduct thorough postmortem examinations for every fish kill. Public reports enabled researchers to accurately assess the magnitude of fish kills. As Rosenfeld said, “relying on a principal investigator and their grad students to go out and document everything in an ecosystem as large as San Francisco Bay is just not going to work.”

“Relying on a principal investigator and their grad students to go out and document everything in an ecosystem as large as San Francisco Bay is just not going to work.”

Jon Rosenfeld, SF Baykeeper

While Tighe’s and fellow volunteers’ rapid response was helpful in archiving the magnitude of the biodiversity crisis, Rosenfield acknowledged that as scientific investigation becomes more specific, citizen scientists would need more training to provide useful measurements; Baykeepers and research partners are awaiting funding to train their volunteers. 

Despite possible biases and duplicative data, citizen science enables a “big picture” view of ecosystems

Now, data from citizen science platforms gathered with looser protocols are less reliable. Before being able to conduct analysis, research partners in USGS, SFEI and Baykeeper have to clean the data first.“You can have multiple sightings and recordings of possibly the same kind of carcass that’s on a beach,” explained Aundi Mevoli, a field investigator at Baykeeper. “So sometimes we had multiple locations from iNaturalist, but we’re looking at the same specimen that has washed up.” 

Online citizen science platforms may also amplify traditional biases in traditional citizen-science practices; there are more observations made from regions that are easy to reach and of species that are most recognizable. For example, Tighe’s campaign saw a large scope of regions surveyed, but most observations are clustered around the Bay near urban environments; there is sparse sampling near the beach areas. Similarly, we would expect there to be less observations of sturgeon, since there are rare species in the bay, but because they are easy to identify. However, we saw a disproportionately high count of dead sturgeon recorded on Tighe’s iNaturalist campaign, compared to other fish. 
These built-in biases ensure that some regions have more observations on iNaturalist. This has consequences. “If you then naively assume the number of unique species seen on iNaturalist in a given area is the actual underlying biodiversity, then you would be biased to thinking areas with a higher sampling effort are more biodiverse,” Gillespie said.

“Science begins with observation.”

Jon Rosenfeld, SF Baykeeper

Despite its shortcomings, online citizen science platforms enable open-ended observations. Compared to traditional scientific biodiversity surveys that focus on specific organisms, these citizen science efforts provide a more holistic observation of ecosystems. “Science begins with observation,” Rosenfield said. With more vigilant, dedicated hands monitoring the health of the bay, citizen science provides a new pathway  ecological surveys in the midst of climate uncertainty. 


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