Jim Cloern looked out of an airplane window one day and saw
red streaks in the water; crimson patches darkening the grey-green shallows
that are San Francisco’s South Bay. A superscientist with the US Geological
Survey, he knew something big was happening.
As soon as the plane landed he called his crew. “You will
not believe the explosion we’re seeing on the surface,” he heard back from his
crew leader Tara Schraga. A quality control freak who sticks to the gold letter
that is attached to everything labeled ‘USGS science,’ Schraga had spent the
morning on their research vessel lowering sensors down into the shallows and
then pulling them out again to log the levels of salt, nutrients, sediment, and
phytoplankton between the surface and the bottom oozes. It turns out that the
tiny drifting plankton visible from the airplane window on that day in 2004 were blooming on
the Bay’s surface in record amounts. The color indicated a red tide, a harmful
algal bloom, like those that closed Florida’s white beaches and made Miamians
cough during the 2018 elections.
I asked Cloern, a humble guy with a big brain who just retired
after 43 years as a scientist specializing in the San Francisco Bay, if he ever
gets tired of plankton? “That would be like asking John Muir if he ever got
tired of trees,” he says.
Spring 2019 finds USGS – the non-partisan, top-of-the-line
federal science service paid for by our tax dollars – in the midst of a
restructuring that includes not hiring someone new to fill Cloern’s supersize shoes.
Word is the agency is thinking of shifting its water division into National Weather
Service style monitoring mode, and cutting coastal research programs like Cloern’s
that make up less than five percent of the national budget. The thing is, it’s
a really bad time for the San Francisco Bay to be in limbo – not knowing if it
will be able to replace this brainpower or sustain USGS’s 50-year-old,
boat-based bay water quality sampling program. As conditions change, more red
tides may be on the way – bad news for shoreline communities, Bay health, the
local economy, and wastewater treatment plants who might be forced to make
significant and costly upgrades to prevent them.
“Regulators have some big decisions pending, such as are we
going to mandate that 37 sewage plants invest in expensive upgrades to treat
and remove nutrients before they enter the Bay?” says Cloern. “Without ongoing
science, those decisions could be costly, ineffective, inefficient, or just plain
Cloern is one of the few that might recognize that red tide
from the air or water and be able to tell you what combination of conditions
produced it. The data his program has collected would reveal how often these
same conditions had occurred in the past 50 years, and a half dozen computer
models supported by this data might be able to predict how often or when they
might occur in the future.
“The system most likely to catch
us with our mouth open by changing dramatically is the South Bay,” says
Cloern’s long time colleague at USGS, Jan Thompson, an expert in the clams and
other invertebrates down in the oozes that eat plankton. She too is due to
retire and not be replaced. “We still don’t know exactly why the South Bay
isn’t pea soup eutrophic today, if it’s something good we should market it and
sell it, but it could be something bad like a contaminant holding blooms in
check,” she says. Putting all the pieces together – conditions plus climate
plus clams plus contaminants, among other estuarine complexities – is the kind
of thing this program has always done best.
“Having the research capacity to receive early indications
of change before it happens is priceless,” says the San Francisco Bay Regional
Water Quality Control Board’s Tom Mumley, who has relied on USGS science to
make sound regulatory decisions for decades. “Absent that think tank, I’m
Decisions higher up in the USGS water division suggest the
program and its lead scientist position could sunset as early as August 2019 or
not at all – the uncertainty is crippling. USGS’s local and state partners in
science are now scrambling to see if they can pick up the slack. And while
making locals pay for coastal estuary research – especially in a flush region
like northern California – may seem like a quick way to free up more bucks for
national initiatives, many prominent people don’t see it that way.
“This is easily the most rigorous long-term science program dealing with estuarine environments on the planet,” says Jeffrey Koseff, an engineer at Stanford University. “It would be a huge loss to the estuarine community and to the science community if it were discontinued.”
Of Chefs and Shifts
When Cloern describes the conditions that led to a red tide
in the South Bay, I can’t help thinking of cooking.
He says unusual weather, calm winds, stagnant water, and
record high air temperatures “stratified” the bay into layers of fresh and
salty, warm and cold water. The layers enabled the phytoplankton to swim up to
the surface and stay there, rather than sinking to the bottom to be scarfed by
filter feeding clams. Up there in the sunlight, away from consumers, they
bloomed and bloomed. Some blooming is great for the food chain; too much can be
Most people looking at the Bay would not see all this
variety hidden under the milky surface. In fact the Bay is more like a complex
stew than a basic broth. To understand how all the textures and flavors affect
each other, let alone what happens when you add salt or sugar, lower the heat, or
overstir, you have to be a kind of master chef. The way Cloern talks, you can
hear the little grey cells processing decades of data, observations,
experiments, and wisdom to conjure the red tide recipe. No one is a master chef
or superscientist (an actual USGS classification) overnight.
In Cloern’s long career, the Bay has “flipped,” as some
scientists call it, a number of times. First came the invasion of the Asian
overbite clam in the 1980s, a creature that can filter the entire water column
within a day. The second time occurred in 1999, when the Bay’s phytoplankton suddenly
began blooming in autumn rather than spring. “I thought we’d made a mistake, we
went back and double checked everything,” says Cloern, who had recorded spring
blooms for 22 years prior. But that flip – which he later figured out was the result
of a change out in the Pacific Ocean that produced more flatfish, crabs and
shrimp than in past years, species that then migrated into the Bay and ate a
lot of clams, clams that in turn stopped scarfing plankton — is just one more
example of the ever changing nature of estuaries.
“Most of the things I’ve worked on I couldn’t have
anticipated,” says Cloern.
USGS’s national budget for research has declined in real dollars
from around $700 million in 1996 to $650 million in 2017. Cloern’s coastal
research and bay monitoring program is down to a mere $760,000 per year in cost
today. All scraps compared to a $5 billion border fence or a $13 billion space
force. Yet this USGS science serves Americans every day – tracking storms,
measuring snowpack, steering airplanes, saving salmon, monitoring water
quality, modeling the cascade of effects that occur with climate change, namely
interpreting our changing world – as
the USGS slogan goes.
Nationally, while total
research and development spending by the federal government is at an
all-time high, it has steadily declined as a percentage of the country’s total GDP,
from 1.05 percent in 1980 to 0.615 percent in 2016, according to articles in Scientific American and analysis by the
National Association for the Advancement of Science.
For the last 10 years, there’s been a shift to short term,
soft money funding for science that makes it difficult to monitor the
environment over the long term, as the Bay program has. “If resource agencies cannot rely on
long-term funding, they cannot implement long-term monitoring programs, which
means we cannot track long-term trends. And if we cannot track trends we won’t
know if our ecosystems are changing — and that seems to be the intent of the
federal bureaucracy these days,” says Ian Wren, a staff scientist
with the nonprofit San Francisco Baykeeper. “The administration has pushed for
cuts to USGS, NOAA and EPA in an attempt to shield themselves from unfavorable
science outcomes. In the Bay Area, we’ve always welcomed scientific insight
into our planning and business conversations, and been willing to pay for it.”
Needless to say, the costs of doing sound science have climbed
over the two decades that funding levels for USGS programs have remained stuck between
$600 and $700 million. Gone is the golden era of USGS science that built the
beautiful, modern headquarters for the Bay program in Menlo Park. Completed in
1996, the building housed seven full time, permanent position scientists and
their assistants, technicians, post-docs, and students. “Every lab was
customized to the kind of science we do,” says Cloern. He remembers popping in
and out of colleague’s labs to decipher estuary mysteries, never worrying about
raising a dime, the feds were so fully vested in this venture. “If you visited
our building now, you’d see quiet hallways, empty offices, state-of-the-science
laboratories with lights off. It’s a ghost town.”
Sure, the national federal funding stream may have declined,
but one big contributor to the local uncertainty has to do with one federal
agency shafting another. Since Silicon Valley’s state-of-the-technology and
bio-med labs for the likes of Google, Genetech and Stanford flourish all around,
the feds very own GSA (General Services Agency) insists on charging USGS commercial
rate rent for the Menlo Park building. Last I checked, nobody could afford
commercial rates in Silicon Valley except the one percent. Where Cloern once
worked with more than half a dozen full time scientists, his current permanent staff
amounts to a single part-timer.
Personally, all this makes me depressed. When I was a little
girl, my Dad and I used to climb around Yosemite using maps sketched,
ground-truthed, printed, and waxed by USGS. The minute detail of a drainage dip
or rocky promontory on each map saved us from getting lost countless times.
When I grew up to be an environmental writer, I always found
USGS scientists and studies at the frontiers of understanding how we as humans
were fouling our own nest. When I shifted to science journalism, I learned that
any USGS source was golden: fact checked, peer reviewed, decorated with so many
caveats, footnotes, and citations it drove those of us trying to simplify the
story for common consumption crazy. This science, to me, was a true mark of the
greatness of government. My science, paid for by my tax dollars, free of faith
and unsullied by dark money.
The Three-Legged Chair
Here in the watershed of San Francisco Bay, USGS science is
the fourth leg of dozens of chairs at the head table. The 50 years of Bay monitoring
data and observations, interpreted by Cloern and his team for decisionmakers
and regulators, has become an integral part of the regional science enterprise.
Removing that leg from each of those chairs for less than a million bucks would
topple dozens of ongoing programs that underpin management of California’s
water supply, economy, endangered species, fires, floods, wastewater treatment
services, and more.
Take for example the Interagency
Ecological Program for the Delta, which relies on USGS to cover the lower
watershed. “Our authorities here in the Delta may be circumscribed, but as
scientists we know we can’t really limit ourselves to one area of a very large
watershed, it’s all connected,” says Steve Culberson, lead scientist for the
“Losing this program would create a major hole in our understanding
of the Bay-Delta region,” says Ted Sommer, a fish biologist with the powerful
California Department of Water Resources, a key partner in the IEP with other
federal and local programs that need science to help manage conflicts between
water use and endangered fish. “It’s been a great template for large,
interdisciplinary projects and how to use long-term monitoring data to provide
insights into major ecological patterns and processes.”
Culberson says the IEP might
never have noticed the pattern of decline among multiple pelagic fish species
in the Delta all at once (aka the “POD”) without this kind of mindset. “Cloern’s
program helped teach us how to tease out those patterns with analytical
methods, methods that were then borrowed and applied by people up here,” says
To sum up, the degree of collaboration and integration among the region’s monitoring systems, though far from perfect, risks a domino effect from the loss of the USGS leg. At a minimum, locals are hoping for a basement level investment in Bay monitoring from the feds, but what they’d really like to see is a renewed commitment to coastal research and science staff.
HABs and HABnots
The Bay stank in the 1960s, and it could stink again if
we’re not careful. Rotten egg fumes wafting into the Google courtyard at lunch
hour might not mix well with the organic greens, cilantro chicken, and artisan
The main driver of that potential stink up is nutrients.
These nitrogen-containing compounds run off our hillsides, streets, and farms
into Bay and Delta waters, but in San Francisco Bay the majority comes from the
wastewater discharges. There’s a lot in most estuaries, and Cloern says the Bay
is in the top 10 percent worldwide for nutrient loadings.
For decades, however, something has prevented nutrients from
sparking and fueling the kind of plankton growth that robs the water of oxygen
and produces toxins. Toxic algae blooms affect many waters of world and have
been especially problematic in places like the East Coast’s Chesapeake Bay and,
more recently, Florida’s Atlantic beachline. There last fall’s toxic bloom killed
manatees, dolphins, sea turtles and at least one whale shark.
Former Florida Republican Governor Rick Scott received blame
for previously cutting the state’s water management budget and, by some
allegations, contributing to the conditions that caused the algal explosion.
His actions as governor included relaxing requirements on septic system
inspections, which may have allowed a surge of sewage-tainted runoff to enter
waterways, feeding the toxin-producing algae. The state’s new governor, Republican
Ron DeSantis, has vowed to turn the tide. Two days after being sworn in in
January, he signed an order that will seek $2.5 billion over four for better
management and protection of water resources. The order will empower local
agencies to curb nutrient loading of waterways and hopefully prevent more ecological
crises like that occurred under Scott’s watch.
San Francisco Bay has not experienced the magnitude of harmful
algae bloom (HAB) seen recently in Florida. Cloern, Thompson, and their USGS
and regional colleagues have all attempted to understand the Bay’s resistance
to these eutrophic blooms, and tried to figure out if and when that resistance
might time out. It all has to do with subtle shifts in temperature, waning
turbidity (as gold mining era debris washes out of the system), estuarine
mixing, and climate. A combination of unidentified factors is likely at play.
“We’re just now learning both how
nutrient rich this estuary is and how fortunate we are to have some natural resilience
to this condition,” says the SF Bay Regional Board’s Tom Mumley. “USGS gave us
early warning that this was waning.”
It may not be long now.
HABs increasingly appear in California headlines associated with toxins
in the crab catch, domoic acid sickening seals, and dead fish.
“As turbidity clears sunlight may penetrate further, and
increase productivity in ways we haven’t been used to,” says IEP’s Steve
Culberson. “While we may initially see some boost in productivity to support
native species, these new conditions, and the warmer water temperatures we’re
seeing in the Delta, may trigger more HABs, which will create problems meeting
requirements of biological opinions.”
Monitoring has already established that microcystin toxins from
Delta HABs are ending up in the Bay. Downstream, meanwhile, UC Santa Cruz
scientist Raphe Kudela, who collects samples from the Peterson, has established that similar toxins originating from
Pacific Ocean HABs can be found in the Central Bay.
These kinds of early warnings from USGS and its
collaborators led the water quality control board to launch strategic planning
around nutrient management for the San Francisco Estuary in 2012. “After five
years of capacity building, we’re now diving deeply into answering targeted
management and science questions,” says the San Francisco Estuary Institute’s
David Senn, lead scientist for the strategy.
Regulators need to decide, and dischargers need to know, if
they will be required to invest in expensive new treatment systems to remove
nutrients. Such an upgrade of the region’s POTWs (publicly owned treatment works)
was estimated to cost $5-$10 billion in a recent, exhaustive engineering
analysis conducted by HDR consultants (see margin graphic). With other pending
pressures on end-of-the-pipe systems, such as emerging concerns about pass-through
pharmaceuticals and microplastics, not to mention increasing flood threat to shoreline
pipelines and settling ponds from rising sea levels, the importance of good science
to tease out priorities is critical.
“Instead of slamming the POTWs
with costly responses to problems once they happen, we’ve had the benefit of
eight years of dialogue and additional studies,” says the water quality board’s
Mumley. “We’re all working together to create scientific basis for action.”
Cloudy Above and Below
With its gunmetal grey flanks, from afar the R/V Petersen looks like a military patrol boat. But instead of guns, flares, and sirens, it’s equipped with a special crane to lower a CTD in and out of the water. (CTD refers to a high-tech, sensor-loaded device that gathers samples on conductivity/ salinity, temperature and depth). Every month the Peterson visits 32 stations on the water, from south of Redwood City to the Delta’s Rio Vista, and lowers and retrieves the device and all its data. Other onboard bells and whistles include a benthic grab to scoop up bottom samples, sophisticated computers, and a laboratory for processing what comes up on board rather than back in Menlo Park.
One of the latest and greatest instruments on board is an Imaging Flow Cytobot, used on the USGS sampling cruises by Raphe Kudela. Bay water passes through the instrument, and each time a plankton cell is detected it takes a photo (see below). “This new technology is opening up brand new perspectives for measuring and understanding changes in this microscopic, but essential, biological community,” says Cloern.
With such exciting leaps and bounds in technology, one can’t
help wondering if we could do all this Bay monitoring remotely, with satellites
and sensors strapped to bridge stanchions and shoreline moorings. Wouldn’t it be cheaper and more efficient?
Wouldn’t it be more modern that noodling around the Bay in a boat?
“The truth is the technology is
just not there yet,” says USGS’ Tara Schraga who’s crew regularly test runs the
latest sensors and protocols on the Petersen
against the quality of the data coming out of the Bay. “It’s tough to use
satellites to see San Francisco Bay year round because of the fog and the
turbidity – you can’t see the tell-tale pigments in the plankton that help us
identify the size and species.”
One boat and a crew covering a big
estuary once a month can also cost a lot less than installing stationary
sensors where there are no pilings, adding them to buoys, or fixing them onto
bridge stanchions and shorelines. It’s labor intensive to get quality data from
these stationary devices, which also only measure one place in the Bay and
depth in the water column. According to Schraga: “Without the boat samples, you’re
missing spatial coverage of where things are happening, both horizontally and
vertically, top to bottom, in the water.”
Once installed, these stationary sensors also invite all
manner of Bay life to colonize them – clamping on with suction feet, sliming
surfaces with a green film. “Left unattended, things grow on the instrument housings and
sensors themselves, and fine particles clog various parts needed to take
measurements,” says Senn.
Senn knows from experience. The region’s nutrient management group manages an array of stationary sensors in the South Bay. “The longest we’ve been able to go is three weeks before sensor fouling starts to kick in to an extent that data quality suffers tremendously. Then we have to send someone out to clean them off and recalibrate them,” says Senn. (The Bay hosts a network of other stationary sensors managed by the Regional Monitoring Program and the Estuary and Ocean Science Center — see map, side column).
Grabbing samples from the Bay bottom is another thing best
done from a boat. These samples get carried back to the Menlo Park lab where
graduate students and lab rats sift through the muck, sorting the aliens from
the natives, the worms from the slugs, the Asian overbite clams from the native
filter feeders that siphon the water for drifting plankton. Yet this benthic
ecology component of the Bay’s coastal research program is also slated to end.
Thompson is managing a few remaining grants and a skeleton program until she
finishes a phased retirement.
“For our Delta biogeochemical
model development, I had expected Jan Thompson would be an [ongoing] resource
for grazing rates and benthic processes,” says Janis Cooke, a senior scientist
with the state’s Central Valley Water Quality Control Board. Cooke needs to
understand how these processes affect where and how much food is left in the
system for native fish. “Any decision to eliminate their positions and
associated research programs would be shortsighted.”
The best future program, everyone
agrees, is some combination of stationary sensors, a boat and crew, and a lead
scientist or two with the chops to turn concentration levels into management
“Without someone interpreting the data it’s not useful,” says Schraga.
Shooting in the Dark
So just imagine taking a jog with
your dog on that new stretch of Bay Trail you like – the one with the pretty
purple flowers dancing in the breeze and the steps leading down to the beach.
It’s high tide. Your dog chases a ball in and out of the water, upchucks in the
back seat of your car on the way home, and dies that night for no apparent
reason. While this may sound alarmist, it could happen.
Bay Area residents have come to
expect a beautiful bayshore and safe, non-sticky, non-stinky water for their
pets and children to play in. That cleanliness is a point of pride, another
couple of zeroes on your property value, or benefit of your waterfront
workplace. That cleanliness, and the science and long term monitoring that contributed
to it, is an international, not local resource.
Indeed conditions from year to
year, as posted and made available to all on the USGS Bay water quality
monitoring web site, serve a much broader audience than just local residents.
In 2019, the web site with its downloadable data was getting more than 2,000
visits a day, with users from 90 different countries, ranging from Andorra to
Zimbabwe at last look. Could this invaluable resource soon be parked on some
obscure federal server?
“Most scientists are trained to look at the own backyard
estuary, but it is essential to understand and appreciate differences among
systems across the world to produce better science,” says Jacob Carstensten of Denmark,
one of an international group of scientists who have benefitted from Cloern’s
global scholarship comparing Bay results with other estuaries. “The San
Francisco Bay monitoring program is unique for the US West Coast – no other
program has delivered so much science [or so] broadened our views on coastal
ecology. Environmental policies should be informed by people actually working
in coastal science, and scientists in government research institutions are best
to give that advice.”
It’s important to remember how much this long legacy of
water quality monitoring has paid off economically and for the health of the
Bay Area and the nation. What ends up in the Bay comes from a vast watershed
and an equally vast Pacific Ocean, not just one small region. “USGS is gathering
data coming from more than 40 percent of the land mass of California through a
major river system and estuary, with essentially a statewide effect, not to
mention a nationwide effect on the agricultural economy. That’s why the Bay
Area shouldn’t be paying for it all,” says Dave Williams, executive director of
the Bay Area Clean Water Agencies, an association of publicly- owned wastewater
treatment plants that serve more than seven million residents of the Bay Area.
The Bay Area has already started
paying. When earlier shortfalls threatened the USGS program, the Regional
Monitoring Program and those managing the water board’s Nutrient Management
Strategy stepped up. Together, they managed to bankroll the conversion of the former
police boat to a floating science lab when the aging Polaris had to be replaced. They also funded essential crew
“We had to,” says SFEI’s Senn. “The
community has relied on this information for a long time.”
“Good science always saves us
money,” says Dave Williams. “The good news is that some traditional problems
like biological oxygen demand, suspended solids, and metals like copper and
nickel in the water are now thankfully in the rearview mirror, to some extent
due to all the monitoring and understanding of the Bay we’ve been able to tap.
The bad news is that we are now facing all these new challenges, and if we
don’t have the same data to continue to understand our receiving waters we’re
going to be shooting in the dark or making overly conservative decisions.”
Funding partnerships have worked in the past to support
collaborative monitoring programs, and will work in the future, but local and
state agencies don’t want to let the feds entirely off the hook.
“For almost anything we do these
days, it’s hard to have single payer anymore, but it does seem like the federal
government’s whole purpose is to spend money wisely that can benefit large
groups of people or places or estuaries like ours,” says Dave Williams.
The benefits of continued tracking of nutrients, blooms, red
tides, invaders, and emerging contaminants are obvious. For one thing, with its
foundation in past conditions, the USGS Bay program could also help us confront
major changes to the Bay’s tidal prism from sea level rise – which is slated
for 3-6 feet by 2100.
“Change in overall depth is going to be a big one, given
that it is a major parameter in phytoplankton growth,” says Thompson. “If the
South Bay becomes as deep as the Central Bay, two things will happen: vertical
turnover rates will go down, and less phytoplankton will be lost to Bay bottom consumers.”
The advancing ocean will also submerge Bay mudflats and
lessen turbidity, another limit on bloom rates. More and bigger sea walls,
built to protect major shoreline infrastructure, will exacerbate circulation problems.
“The Bay will be more like a big bath tub, not a good result if you’re worried
about HABs,” says Thompson.
“Having this research program has helped us adapt, helped us
create a healthy bay and healthy economy,” says Tom Mumley. “What could be a
better use of public resources?”
“In a day and age where children are suing the government for environmental harm, it is absolutely the state’s responsibility to continue this amazing bay research program,” says one of its graduates, Misty Peacock, director of the Salish Sea Research Center in Bellingham, Washington.
“If I was to keep going for another 10 years, I expect by then I’d be working on something I can’t even imagine right now,” says Jim Cloern. “I’ll feel comfortable about stopping as soon as the Bay stops changing.”
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Ariel Rubissow Okamoto is both today’s editor-in-chief and the founding editor of ESTUARY magazine (1992-2001). She enjoys writing in-depth, silo-crossing stories about water, restoration, and science. She’s a co-author of a Natural History of San Francisco Bay (UC Press 2011), frequent contributor of climate change stories to Bay Nature magazine, and occasional essayist for publications like the San Francisco Chronicle (see her Portfolio here). In other lives, she has been a vintner, soccer mom, and waitress. She lives in San Francisco close to the Bay with her architect husband Paul Okamoto.