Sequencing the Mysterious Microbes of the San Francisco Estuary

Digging for DNA

Lui is proud to be contributing knowledge that agencies like DWR and her other collaborator, the United States Geological Survey (USGS), can use to better manage the estuary's natural resources. Still, these partnerships are far from one-sided. She wouldn't have access to a boat, for starters, let alone one specially equipped to conduct biological monitoring. Along with the chemical reagents and neatly labeled glass beakers one would find in any wet lab, the Sentinel boasts a special intake that pumps water directly from the river into a customized laboratory where it is analyzed and collected in an on-board sink. After arriving at the day's first stop on Grizzly Bay near Suisun Slough, Lui collects her first samples from this faucet. While the water filling her plastic containers looks clear, it is full of microscopic bacteria, archaea, and viruses whose DNA will give Lui a snapshot of the microbial communities inhabiting this site.

Out on the deck, the crew deploys a crane that scoops up sediment from the river bottom and deposits it into a large filtering container. Lui and DWR's benthic specialist, Betsy Wells, peer excitedly into the wooden box now filled with precious mud.

While Wells focuses on the clams and other invertebrate animals inhabiting the sediment, Lui pursues the microscopic life hidden between particles of sand, silt, and other debris in the mud itself.

"This is awesome," said Lui as she scraped a layer of dark brown silt off the top of the mud pile before going back with another collection tube to grab material from farther down. Besides the water samples she's already collected, Lui will sequence each layer of sediment separately to zero in on the microorganisms living in different strata with distinct ecological roles.

From Mud to Models

Back at Berkeley Lab, Lui prepares the samples for long-read sequencing, the first step in assembling those genome puzzles. This approach involves repeated sequencing of as many long pieces of DNA as possible to compile complete genomes for each organism.

"Getting complete genomes rather than just fragments is crucial for understanding the full capabilities, functionality, and survival requirements for each organism," Lui said. "And the more overlapping pieces you have, the more confident you are that your genome is correct."

Once Lui knows which genes different species have in their genomes, she can hunt for clues about how those organisms may be functioning. Lui might look out for genes related to processing nitrogen, for example, because the amount of nitrogen circulating in an environment is linked to algal blooms.

Right now, Lui is focused on setting up a baseline database of the microorganisms present in the estuary. Future samples can then be matched to intact genomes in the database, significantly reducing the sequencing and computing power required to piece them together. This initial groundwork will make it more feasible for Lui to track microbial populations over time and across different locations to see how they adapt to environmental changes.

"How the microbes are responding to climate change or the salinity increasing because of drought farther up the Delta - these are all things that we can track with sequencing," said Lui.

Genomes can also provide insight as to how or why microbes are evolving.

"How species interact with each other and the environment impacts which traits are passed on, and then we can see those changes in the genome," she said. "Microbial evolution can happen on the timescale of days or weeks, especially under extreme conditions. We don't understand how what we're doing - either with climate change or what we're dumping in the water - is affecting them."

This understanding of who's there, what they're doing, and how they're responding to a changing environment will help create more detailed predictive models of estuary dynamics. Ultimately, such models could inform policy decisions that cap agricultural inputs or other sources of nutrient pollution at different times of year, or enable agencies to adjust other parameters like salinity to compensate in high-risk time periods.

"I would hope in 10 to 20 years we would be able to take a few measurements and predict where and when a harmful algal bloom will happen, where the water quality might be bad, and know what the levers are for mitigating those events," Lui said. "Doing research that's important for this area where I grew up means a lot to me. Being out on the boat, seeing the water - we take it for granted, but once the water gets bad, it could be gone. We have to take care of it."

Public link

Please use the above public link if you want to share this noodl on another website.