Callen Hyland, UC San Diego research scientist and La Jolla Library Wet Lab volunteer, gave a talk May 7 at the library to release the preliminary data of a crowdfunded study that looked at the microbial diversity of La Jolla Cove and other beaches.
She opened her talk with a word of caution: “These findings are preliminary and by no means complete. … I know that a lot of people have supported this in hopes of having answers to a specific question, but those answers might not be here. You can never know, going into a scientific project, what the exact results are going to be.”
To complete the study, Hyland collected samples at Children’s Pool, La Jolla Cove, La Jolla Shores and (on one day only) Scripps Pier each month from June to November 2016 and sent the samples to a lab for DNA sequencing, paid for by the crowdfunding. She said she is still analyzing the data and there would be another talk offered when more conclusions can be drawn.
What speculations she could make, however, were: 1) The Cove and Children’s Pool have more microbial diversity than La Jolla Shores and Scripps Pier, 2) it could be a combination of marine mammals, geographic features, humans and plant life causing it; and 3) while fecal indicator bacteria does appear to have increased in recent years, she said: “I saw no smoking gun that the water is dangerous — that doesn’t mean it isn’t there, but I haven’t found it.”
Over the course of her talk, Hyland went into the scientific nitty-gritty about gene sequencing methods (she used 16S rRNA gene sequencing), components analysis, showed data graphs, the Alpha Diversity and Beta Diversity results, the various methods against which this data was measured, and more.
But for those less scientifically minded, she explained that, in this study, “microbial” means bacteria and archaea (single-celled organisms once thought to be bacteria), and is measured in Operational Taxonomic Units (OTUs), which is the way to describe the “species” of bacteria.
“In La Jolla, we are lucky to live in very close proximity to nature,” Hyland said. “It’s an urban environment with all the modern conveniences, but close to a variety of wildlife. There are birds and an unprecedented proximity to marine mammals. There aren’t many situations where humans and marine mammals share such a close environment. We have the Children’s Pool, which has a harbor seal colony; and La Jolla Cove, which has a sea lion colony and is also popular with swimmers and snorkelers — not to mention the fish and seagrass underwater.”
To carry out her study, Hyland said she collected water samples in sterile bags (the same ones used to collect forensic information), stored the bags in coolers to maintain the correct temperature, processed the samples by sterilizing the stored materials and filtering the water, and stored the processed samples. The storage tubes were kept on dry ice and then, a negative-80 degree Celsius freezer. From there, they were sent to a lab for DNA sequencing.
She was sent the raw data, and classified the distinct sequences.
“We’re capturing enough diversity that we can see a difference between sampling sites,” Hyland explained. “The Shores and Scripps Pier grouped together, and La Jolla Cove and Children’s Pool grouped together. We have two sites that are much more diverse than the other two.”
She added that the Children’s Pool and La Jolla Cove have “statistically significantly higher” observed OTUs than La Jolla Shores, and that number did not change over the sampling months.
As to why Children’s Pool and La Jolla Cove were more diverse, Hyland posed: “The marine mammal populations are different, and with the more diversity, the more opportunity there is for those OTUs to be present. Whether the seals and sea lions have anything to do with that, I don’t know. There could be geological features that change the water currents.
“You also see sea grass and kelp in The Cove and Children’s Pool, but not so much in The Shores. We have different bird populations and human activities, too. Let me tell you, at some times of the year, humans are the dominant form of wildlife! I don’t know what is driving it … and which factors are causal, but these are very distinct environments.”
In terms of harmful OTUs, she said, she pulled up the Centers for Disease Control data for waterborne pathogens, and did not find them in her data. “That doesn’t mean they are not there, because pathogens do not have to be present in high numbers to cause disease,” she said.
Further, she pulled similar data for pinniped zoonotic diseases (ones that can travel from pinnipeds to humans) and only one was present and at a low level.
As a next step, Hyland said she will explore source tracking.
“We could look at The Cove and look at human fecal matter, sea lion fecal matter, and see to what extent these sources contribute to the overall data,” she said. “I’m thinking about ways to make this available to the public so people could review the data themselves and see what conclusions they draw. I would also like to upload the information to a public database.”
Hyland is further looking to adapt a similar project and make it a citizen science initiative, such as sampling one site at different tidal times. Additional talks are planned, but have not been scheduled.