BROWN BAG SEMINAR: Viewing estuaries from a ‘macroscope’: How global, regional, and local processes affect the San Francisco Bay and Delta

There has been an ongoing conversation about the importance of thinking about the San Francisco Estuary holistically as a connected system, rather than siloing the Bay, Delta, and watersheds.  The system is connected, after all, and it is important not to ignore the influence they have on each other.

However, the connections just don’t end at the Golden Gate.  The San Francisco Bay and Delta are connected to the ocean and beyond, and as a result, there are global scale processes that can affect the Delta.

Dr. Jim Cloern is a recently retired senior scientist emeritus at the US Geological Service who has spent his career learning how estuaries respond to human activities and variability of the climate system.  In this brown bag seminar, Dr. Cloern gives specific examples of how local, regional, and global scale processes affect the San Francisco Bay and Delta.

Dr. Cloern began by presenting a photograph that was taken off the coast of Israel in the Gulf of Eilat, which is part of the Red Sea.  The Red Sea is a deep, warm, low nutrient region of the ocean that supports a beautiful coral reef system with a diversity of corals and fish.

Coastal systems are changing over time, sometimes in surprising ways, he said.  In 1992, the coral reef system was overwhelmed by a proliferation of algal growth, both microalgae and phytoplankton that completely transformed the system in a short amount of time, killing most of the coral reef.

Algal blooms are oftentimes caused by nutrient enrichment, as was this one, but it wasn’t runoff from land as is usually the case.  The source of nutrients was the deep ocean.  Usually, nutrient concentrations are high on the bottom of the ocean, and are usually isolated from the surface layer by stratification, which occurs when water with different properties such as salinity, density and temperature form layers, acting as a barrier for water mixing. However, there was a climate event that allowed for mixing of the Red Sea that brought deep nutrient-rich ocean water to the surface, where the nutrients were exposed to sunlight, allowing algae to proliferate very quickly.

This mixing event was the result of a climate anomaly over the Middle East that was the response to the volcanic eruption of Mount Pinatubo in the Philippines; the eruption ejected a mass of fine particles in the atmosphere that attenuated light penetration to the land mass and cooled the Middle East.  That in turn caused the surface waters to get cooler, and as the surface waters cooled, they became denser and sank, which allowed for the mixing of the water column that brought nutrients to the surface.

I’m starting with this example to make the one point that I want to make in this talk, and that is that ecosystems like the San Francisco Bay Delta and like this coral reef system can be transformed by events that happen far away,” he said.  “In this particular case, that event was 6000 miles away.  So through the westerly flow of these particles in the atmosphere that originated from this eruption, there was a connection that spanned the continent from Asia to the Middle East.”


The coupled San Francisco Bay Delta system is one of the very best studied estuarine systems in the world, Dr. Cloern said, noting that there are observational records that go back half a century.  Long-term records provide opportunities to observe changes over time and relate them to large scale processes and global scale processes.  And just like the coral reef system was connected, he gave four examples of how the Bay is connected to large scale forcings.

THE WARM BLOB OF 2014-2015

The mass of warm water known as the ‘warm blob’ was an unprecedented climate anomaly that persisted over a large region of the northeast Pacific Ocean.

Dr. Cloern presented a slide with an image of the Pacific Ocean on the west coast of North America, noting that the color of the ocean represents the temperature anomalies; the darker the red, the warmer the anomaly.   The USGS measures temperature in the San Francisco Bay, and during the two years that the warm blob persisted, the USGS measured the highest temperatures in San Francisco Bay.

It’s an illustration of how a large scale process has effects that propagate to the scale of estuaries like San Francisco Bay,” he said.

The plots on the bottom of the slide show temperature and salinity for January, April, and August or winter, spring, and summer.  In each of the plots, the measurements are along the salinity gradient from the Sacramento River to the Central Bay (or from river to the ocean).  The red dots and line represent the mean surface temperature associated with a particular salinity going from the rivers to the ocean, and the graphs show all the observations from 1969 to 2013.  The green line above are the values from 2014 and 2015.

You can see that for every month, every spot along the salinity range, temperatures were warmer, sometimes by as much as three degrees centigrade,” said Dr. Cloern.  “We would have had no clue about why we had unprecedented warm surface waters in the Bay along the entire salinity gradient from the Delta to the coastal ocean without knowing what was going on far away in the northeast Pacific Ocean.”

The key message here is that for in order for us to understand things like temperature variability in the Bay, we need to know what’s going on at a much larger scale – over an ocean basin scale.”


There are natural oscillations of the climate system that effect the Pacific Ocean that have much longer periods, sometimes three or four decades.  The second example is how the San Francisco Bay and its biological communities responded to a big shift in climate forcing over the north Pacific Ocean that happened in 1999.

He presented a graph of the region of North Pacific Ocean from Asia to North America.  The different colors of the Pacific Ocean represent different sea level heights, and he explained that sea level height is important because it controls currents.

There are two different modes of climate forcing of the north Pacific Ocean.  One is called the Pacific Decadal Oscillation or the PDO which is characterized by the one counter-rotating gyre south of Alaska.  The second mode is called the North Pacific Gyre Oscillation or the NPGO, and it has two counter-rotating gyres; the counter-clockwise gyre is pushed to the north, and the below that at mid latitudes is a clockwise-rotating gyre.  This is important because these two different climate modes over the North Pacific Ocean lead to very different patterns of winds, wind-driven currents, and coastal upwelling along the coast of North America, he said.

The PDO pattern is one of relatively weak longshore currents, relatively weak coastal upwelling, relatively small inputs of deep nutrients to the surface, relatively low primary production and low production at higher trophic levels of krill and the seabirds and mammals that feed on them.

The NGPO pattern is very different.  At our latitude, the winds from north to south that drive upwelling are stronger than normal and the upwelling of movement of nutrients to the surface areas is stronger than normal.  Primary productivity is higher than normal along the coast as is productivity at higher trophic levels.

The North Pacific Ocean was in its PDO phase from the mid-1970s until 1999 and then it shifted to the NGPO phase.  This caused a restructuring of biological communities in the San Francisco Bay following that climate shift.  This can be seen in the data from the California Department of Fish and Wildlife’s Bay Studies program that every month, samples a network of 45 sites for all fish species and large crustaceans like fish and shrimp.  The Bay Studies program began in 1980, so there is data for about two decades of the north Pacific Ocean in its PDO phase and then after the abrupt shift to the other phase after 1999.

The upper panel shows monthly variability of the North Pacific Gyre Oscillation, which was mostly in its negative state and then abruptly it shifted to its positive state and stayed mostly in a positive state.  The three bar graphs below this represent indices of the annual population abundance of five different species of demersal fish, including species like English sole.  Below that, three different species of crabs including Dungeness crab, and below that, two different species of shrimp.

You can see the synchrony between the population abundance of these communities with this shift in the NGPO,” Dr. Cloern said.  “These abundances were all below the long term average and then they shifted up to unprecedented high numbers a year or two after this climate shift.”

Although they don’t have observations to support it, the explanation is that when the NGPO is in its positive state, there is strong upwelling, high nutrient concentrations in the coastal ocean, and high biological productivity, including production of larval and juvenile forms of these marine species that are produced in the ocean and then migrate into estuaries like San Francisco Bay, he said.

The basic thought is that when we shifted from the warm, low productivity phase across the ocean to the cool high productivity phase, that generated large numbers of these juveniles that then migrated into the Bay,” he said.  “These are ocean-derived organisms that use the Bay for rearing in the first year or two of their life cycle.”

This was a complete surprise to us, and its pretty compelling observational record showing a connection between the climate state of the northeast Pacific Ocean and biological communities inside San Francisco Bay.  Again, we wouldn’t have a prayer of understanding these record high abundances of all these different species fish and large crustaceans in the Bay without knowing what was going on across the entire north Pacific basin.”


The next example involves the variability of precipitation, runoff, and freshwater inflow to San Francisco Bay.  The bottom graph depicts freshwater inflows to the estuary, showing how highly variable the freshwater flows are from year to year.  Dr. Cloern noted that freshwater inflow to the San Francisco Estuary is much more variable than the freshwater inflows to estuaries on the east coast such as Chesapeake Bay.

One of the important lessons learned in the last decade is that much of this variability of precipitation and fresh water inflow is tied to another large scale, ocean basin scale process – the development of atmospheric rivers of moisture-laden water that are carried to the east.  When they hit North America, the water vapor is condensed into precipitation that then falls on the watershed and generates runoff.

We’ve also learned in the last couple of years that much of the variability from year to year in precipitation and runoff into the estuary is associated with the number of atmospheric rivers that hit the continent on an annual basis, he said.  Very wet years such as 1983 were years with large numbers of atmospheric rivers; dry years like the series of dry years in the late 80s and early 90s were years of either no atmospheric rivers forming or just a small number.

Here is an example of an ocean basin scale process having an effect on the watershed, precipitation and runoff in the watershed that then has a downstream effect on the rivers and the estuaries,” he said.  “We know that fish populations in the estuary respond to these global scale processes and again we know this because of the wonderful Bay Studies Program at the California Department of Fish and Wildlife.”

The Bay Studies program has identified 137 different fish species in the estuary over the decades.  The table on the slide is from a paper published by Fred Feyrer that shows that for several species of demersal fish and pelagic fish, there are strong associations between ocean condition, in this case indexed as the NGPO, and population abundance of those species.

In terms of demersal fish, some species like English sole are positively associated with the NGPO; others like croaker are negatively associated.  This probably has to do with the different temperature requirements because one phase is cool and one phase is warm, he said.

Some of the important pelagic fish like northern anchovy and the Pacific herring have low abundances when they are in the NGPO phase while others have high abundance.

There’s a clear connection between population variability of fish in the fish populations in the estuary and this climate mode of the North Pacific that operates over this very large scale,” Dr. Cloern said.  “Then we also know from the Bay Delta Studies program that there are strong connections between freshwater inflow and the population abundances of some fish.  So for example, two different species of demersal fish and two different species of pelagic fish like longfin smelt and striped bass have higher than average population abundances during years of higher than average Delta outflow, so one of these controls on population abundance is tied to biological productivity in the coastal ocean, upwelling in the coastal ocean, winds along the coast, and the other is tied to the number of atmospheric rivers that form over the north Pacific Ocean.


Not all of the global connections are natural processes; the last example Dr. Cloern gave was the ocean-estuary connectivity from transoceanic shipping.

He presented a map of the shipping lines from around the world, noting that the San Francisco Bay is highlighted on the map.

As a ship prepares to traverse the ocean, it takes in ballast water along with whatever living organisms are present at the point of departure; when the ship reaches the port of destination, it discharges the ballast water with whatever is left of those communities that’s still alive.

The San Francisco Bay and Delta has been described as the most invaded estuary with well over 200 species of non-native plants and animals.  Some of those introductions were through discharge of ship ballast.  Many of the animals that are present in plankton and the benthos are indigenous to the estuaries and rivers of the West Pacific.

What this means is the process of moving species along these shipping lanes in ballast water is that all the biological communities of all the world’s coastlines are connected, and this has played a major role in shaping biological communities of San Francisco Bay,” he said.  “Because we have these wonderful observational records, we have a solid understanding of what the ecological consequences of these species introductions have been.”

One compelling example is the restructuring of pelagic communities in the low salinity parts of the estuary after the introduction of a small claim indigenous to Asia species that was almost certainly from discharge of ship ballast.  He presented a slide with graphs showing abundance of the invasive clam, chlorophyll, and three other species from 1975 to 2010.

The invasive clam was first discovered in Suisun Bay in the autumn of 1986, and a year later, it’s population had exploded and it had carpeted the sediments of Suisun Bay and regions downstream.  The clam is a filter feeder and the total volume of water filtered by the population of clams was enough to remove phytoplankton biomass from the overlying water column.

The second graph shows that once the clams were established in Suisun Bay, phytoplankton biomass measured as chlorophyll dropped to low levels and has remained low ever since.  Measurements of primary productivity showed that the primary productivity before and after the clans were introduced decreased by a factor of 5.

A five-fold reduction of primary productivity is a major shock to the ecosystem which had  consequences that ramified throughout the food web.  In particular, species that rely on phytoplankton as their primary food source, such as Synchaeta, Eurytemora, and Neomysus, their populations all collapsed and some of these species have virtually disappeared,” said Dr. Cloern.  “The explanation for that is food limitation and out-competition by this invasive clam for the phytoplankton food resource by the established communities of zooplankton, so the copepod communities in the low-salinity part of the estuary now look very much like the communities in estuaries in rivers of the west Pacific.”

The main point here is that in order for us to understand the variability of things like temperature, water quality, and biological communities in the estuary, we have to have a really good sense at much larger scales, from ocean basin to global scale processes, so there’s connectivity from large-scale to the local scale.”


Next, Dr. Cloern gave some examples of regional-scale processes that drive variability in the estuary, noting that in this context, he is talking about the watershed and the immediate connection of the Bay to the Gulf of Farallones or the boundaries between the estuary and the ocean and the watershed.


One regional-scale process that occurred in the watershed that had a downstream effect on the Bay was hydraulic mining, a process that went on for almost three and half decades in the late 1800s which used high pressure water jets to tear down hillsides on the western slope of the Sierra to make ores available for extraction of gold.  The process mobilized large quantities of boulders, gravels, sand, and fine sediments that were carried downstream and settled in the river systems and downstream into San Francisco Bay.  G. K. Gilbert, a USGS geologist in the early 1900s did a number of different kinds of measurements and came to the conclusion that hydraulic mining led to the deposition of a billion cubic meters of sediment in San Francisco Bay.

Here’s an example of connectivity that was hundreds of miles away from San Francisco Bay that had a big effect on the sediment supply to the Bay and its geomorphology,” he said.

Bruce Jaffe at the USGS and his colleagues have tried to reconstruct what the effects of hydraulic gold mining were on the shape of the bay floor.  They took all of the bathymetric surveys that have ever been done for the San Francisco Bay and digitized them.  The first survey was done was in 1856, which was before hydraulic mining began.  The second survey was done in 1887, a couple of years after the process had ended.

The map on the slide is showing San Pablo Bay and the difference between water depths from those two surveys, with the areas in red representing there was deposition of sediments and the water became shallower; the dark red represents the areas that filled in 3 meters.  Bruce Jaffe and his colleagues did this for all the embayments of the system, added them up, and miraculously, they added up to number of pretty close to a billion cubic meters.

This guy, a century and a half ago, was smart enough to figure out what that number was, and he was pretty damn close,” Dr. Cloern noted.

The era of hydraulic mining which increased sediment supply to the rivers and to the estuary was followed by a very different era in the early 20th century where we began to dam all of the large rivers.   The graph shows the time series and the total cumulative storage capacity of reservoirs after new dams were built and went online; he pointed out the step up when Shasta went online in the mid-1940s.  By around 1980, all of the large rivers had been dammed.

We now have a capacity to store fifty cubic kilometers of water, and to put that in perspective, that’s double the median precipitation over the entire watershed, so we obviously have the capability of capturing large volumes of water,” he said.

One of the downstream consequences of damming rivers is that the sediment generated by the erosion of land is held back by the dams rather than being transported downstream, and so as we entered this era of dam construction and reservoirs going online, the sediment supply from the watershed to the estuary has been decreasing.

He presented a plot showing the suspended particulate matter in Suisun Bay over a 35 year period, noting that there’s been a significant decline of suspended particulate matter or sediments over time.

Human activities in the watershed generated an era where we filled in the Bay, it got shallower, and that was replaced by a different activity, a new era, where the Bay is now losing more sediments to the ocean than it’s receiving from the rivers, and it’s deepening,” he said.  “So two examples of how human activities in the watershed have effects on the downstream Bay.


The Central Valley is an area of intense agricultural production.  One of the outcomes of that agricultural production is mobilization and addition of nutrients, nitrogen and phosphorous as fertilizers, some of which runs off into the rivers and is carried into the estuary.

The time series on the slide shows nitrate concentrations in the San Joaquin River beginning in the 1950s, which shows the steady increase in nitrate after the intense agriculturalization of the Central Valley began.

To put it in perspective, the units here are micro-moles, and 100 micro-moles of nitrate is a very, very big number in terms of regulating algal growth,” Dr. Cloern said.  “So Central Valley agriculture is another activity in the watershed that has downstream effects on the Bay.  The Bay is enriched in nutrients in part because of runoff from farm fields.”


Dr. Cloern next turned to the topic of algal toxins in San Francisco Bay.  He presented a chart showing concentrations of two different algal toxins: the black bar is domoic acid which causes paralytic shellfish poisoning; the red bar is microcystin, a toxin produced by the freshwater cyanobacteria microcystis.  The values are values measured at different locations in San Francisco Bay; the study took mussels from Tomales Bay, placed them in San Francisco Bay, and then harvested them later and measured their tissue concentrations of domoic acid and microcystin.

Some of these values, especially the highest values, are alarming – high enough to trigger closure of shellfisheries if there were commercial shellfisheries in the Bay, he said.  The big question is where are the origins of these toxins accumulating in the mussels?

One question that has become a priority question for us, is the ocean the source of domoic acid that’s accumulated in mussels in San Francisco Bay?  He presented a map of the coast of North America showing the regions of the coastal zone that are considered hot spots because of large production of Pseudo-nitzschia biomass and their large excretion of domoic acid.

Specifically, the question is, is the domoic acid that’s accumulating inside San Francisco Bay, did it originate in the coastal ocean and then get carried into Bay?  Or were the Pseudo-nitzschia cells produced in the coastal ocean and carried into the Bay that then produced domoic acid?  Or is there a resident population of Pseudo-nitzschia that’s the origin of this domoic acid?

We have some real fundamental questions about the source of domoic acid and other algal toxins that are produced by marine phytoplankton species and it’s relevant to this theme of regional scale forcing,” he said.  “This could be a regional scale process that is having an effect on water quality in the Bay.”

Similarly, at the other end of the estuary, they were surprised to see high levels of microcystin in the Bay because as far as they know, this organism doesn’t grow and produce microcystis in salty water.

We’re finding it in salt water organisms at high salinities,” he said.  “Is the source the microcystin that’s produced upstream during these microcystis blooms that develop in the Delta or in urban reservoirs around the shoreline of the Bay.  So we need to figure out what the source of microcystin is in the Bay and it’s going to require us to look at a regional scale, because it’s unlikely that this toxin in particular is produced in the Bay.”


The last scale Dr. Cloern talked about was how processes on the local scale affect the Delta.


The San Francisco Bay is a highly urbanized area with a population of 7.5 million people.  Treated wastewater is discharged into the Bay from 42 different sewage treatment plants.  Sewage disposal is the largest source of both nitrogen and phosphorus to San Francisco Bay.

To put that in a global perspective, he presented a chart showing a measurement or an estimate of the total loading rate of nitrogen to individual estuaries around the world, including places such as Venice Lagoon in Italy, Chesapeake Bay, and Long Island on the East Coast.

These are all places where water quality degradation has clearly been a response to large nutrient inputs, and the units here are mass of nitrogen per square meter of estuary per year,” he said.  “When we put San Francisco Bay in this global perspective, it’s in the 87 percentile, so in terms of sewage inputs of nitrogen to San Francisco Bay, it’s one of the highest in the world.  This is an example of a local scale process from the urbanized landscape, and the Bay is enriched and the water quality changed as a result of this local process.”


There are numerous examples of how diverting freshwater from the Delta has effects on the interior part of the Delta.  Dr. Cloern’s example used measurements made on Mildred Island, a flooded island in the center of the Delta; the state and federal export pumps are in the south Delta and as those pumps operate, water is drawn from the north to the south, which has an effect on the relative proportion of Sacramento and San Joaquin water in the interior Delta which in turn affects water quality.

He presented data from the month of October back in 2001 that was from a sensor in the middle of Mildred Island measuring salinity continuously; he noted that the oscillations are tidal oscillations.

You see this trend of increasing salinity that occurred over a period of a month and this puzzled us,” he said.  “We didn’t understand what this increasing salinity was while we were taking measurements, and later we found out that this period of increasing salinity was a period when the pumping was reduced for a month.  The idea here is that as pumping was reduced, there was a smaller fraction of low salinity Sacramento water in the central Delta; it was replaced by a higher fraction of higher salinity San Joaquin water.  So here’s another example of how a local activity, in this case, pumping water from the south Delta, has an effect on the flow path and water quality in the interior of the Delta.”


Dr. Cloern acknowledged that he has shown a lot of data, but there’s really one message here.  “When we think about the San Francisco Bay Delta system, how it’s changing, why it’s changing, and how it might change in the future, we have no prayer of answering those questions if we’re only thinking locally,” he said.  “We need to broaden our thinking into a perspective that recognizes the importance of watershed scale processes and ocean basin scale and global scale processes.”

The word ‘macroscopic view’ was coined by Scott Nixon who was trying to explain to people that if you are trying to understand the eutrophication problem of estuaries, you can’t just think locally; there are large-scale processes that play an important role in shaping how nutrients are turned into algal biomass in estuaries.  From the observational programs in San Francisco Bay and the Delta, we know that the many of the transformations that have taken place in the Delta and its ecosystem and in the Bay are the result of activities that are hundreds of miles away or thousands of miles away, he said.

So I’d like to make the point that we need to change the way in which we view the Delta and the coupled Bay Delta system and teach ourselves, and learn how to take this macroscopic view, both when we’re doing science and when we’re thinking about policies and regulations to protect resources,” he said.

Estuaries are among the most complex ecosystems on the planet because they have many different forcings: the atmosphere over the ocean, the ocean itself, the atmosphere over the watershed, the watershed itself, these local processes – there’s connectivity across all of these boundaries and it’s a reasonable question to ask if we have the intellectual capacity and the tools to deal with this complexity.

I tend to be an optimist, so yes I think this is coming,” said Dr. Cloern.  “We need to put much more effort individually and collectively into taking the macroscopic view, but I want to give you one last example that illustrates how we can view ecosystems from this macroscopic lens.”

He presented one last example, this from a recently published paper by NOAA’s Santa Cruz office; they are trying to answer the question of what regulates the number of adult chinook salmon that return to the rivers after they’ve completed their maturation in the coastal ocean, and specifically the fall run of chinook salmon.

The diagram represents the complicated life cycle of salmon that begins with spawning, fertilization of eggs that develop into redds that eventually hatch into larva and juveniles that eventually migrate through the Delta, through the Bay and then into the Pacific Ocean where they spend four years maturing before they return. So the question was what determines the number of adults that return to the river to spawn after this four year cycle?

They did a really interesting analysis with this model, he said.  They asked the model, what are the few essential steps in this life cycle that determine how many adults return to the rivers at the end of the cycle?

What they found was that there are three important steps in this life cycle that play unusually large roles in determining the success of fall run chinook salmon,” said Dr. Cloern.  “Those three things are first, the temperature of the rivers where the eggs are incubating because it has an effect on egg survival; the second is freshwater inflow because it affects survival of the juveniles that are migrating to the ocean; and the third one is ocean condition, because it affects both the predation on juvenile salmon in the ocean as well as their food supply.  Interestingly, they used the NGPO as their index of ocean condition.”

This is a beautiful example of applying the macroscopic view, and you have to do that with a species that has a life cycle between rivers and oceans,” he said.  “In this particular case, the three important components that determine success were a process in the rivers which is water temperature that’s determined by both global scale and regional scale processes; freshwater inflow which is determined by global scale processes as well as regional and local scale processes; and then ocean condition, which is determined things like atmospheric pressure distributions over the north Pacific Ocean.”

To me, this is good news,” he said.  “I think it’s a beautiful example of how we can apply the macroscopic view, and if I had one piece of advice, it’s that I think we need to make sure that we are thinking from a macroscopic lens when we are studying the Bay and Delta and when we are trying to figure out the best ways to sustain its resources.”


Question: What would you say about our ability to be predictive?  Is ecology rooted in explaining what we’ve seen, or if we take the proper perspective, do you think there’s a chance at understanding what is coming at a fundamental level, like predicting the number of returning fish, for example?

Dr. Cloern:  “A couple of things I want to say about this.  One, I think a logical response to my talk is, OK we get it Jim, so what?  And there’s a lot to the ‘so what’ question, and this makes it crystal clear to me that if we think about all the factors that influence the things that we’re trying to preserve or recover, there are some processes that are important that we just can’t control.  We have no control over whether the Pacific Ocean is going to be in its PDO phase or it’s NGPO phase.  We have no control over, as far as we know, about the number of atmospheric rivers that are going to hit North America in a year.  So what that tells us is that there are limitations to what we can accomplish through regulations and policies, because there are so many forces that are out of our control.  I think the way that we can deal with that is we acknowledge it and we embrace it.

One of the ways we can deal with that is if we’re thinking about a specific regulatory action and a specific policy, it’s important for us to plan those regulations or those policies around scenarios that expand the range of conditions that exist across the Pacific Ocean, so rather than making a prediction, do a scenario.  If we implemented this policy and the north Pacific Ocean was in its PDO phase, what does that mean for the estuary?  If we implement this policy and it was in the other phase, what would that mean for the estuary?  We need different policies depending upon what state that the coastal ocean is in.”

Dr. Cloern said that through his work in the San Francisco Bay, they’ve known for decades that the Bay is highly enriched in nitrogen and phosphorus, much more highly enriched than Chesapeake Bay or Long Island Sound.  Those estuaries are clearly impaired by high nutrient levels – large algal blooms, large productivity, and anoxia in the summertime.

San Francisco Bay doesn’t, and we’ve explained historically why that is,” he said.  “The Bay has inherent resistance mechanisms, and so for decades because of our work, the regional board and others didn’t really care much about nutrients.  We know nitrates are high but we’re not seeing anoxia or harmful algal blooms.  Then things started changing, and after the 1999 climate shift, we started measuring significant increases in phytoplankton biomass in the south Bay and the Central Bay and it was tied to this restructuring of biological communities.  We also started making it clear to ourselves and the regional board that in the community of phytoplankton, there are about a dozen or a couple dozen species that are toxin producing, sometimes at levels of concern.”

After these things started happening, we saw a big red tide event in 2004 that was tied to a heat wave,” Dr. Cloern said.  “After these events accumulated over a period of time, the regional board started taking a real interest in the nutrient issue.  So here’s an example of where our understanding of the bay and the issues that rise to the top of the priority list for regulatory agencies like the regional board, changed in response to this shift in climate forcing over the north Pacific.  It’s also an example of how our policies need to be adaptive to things like long-term droughts, major floods, what the level of productivity is in the coastal ocean, and what’s the temperature distribution in the coastal ocean.”

I don’t think we should throw our hands up; I think we should accept the fact that these large scale processes are important and we don’t have any control over them, but we do have control over the kinds of policies that we develop, the regulatory actions that we try to develop, and make them adaptable to the range of scenarios that we’ve seen in the coastal ocean or in the watershed.”

I think the key lesson here for policy making is the lesson that we have to be adaptable to these forces that we can’t control.  Within the watershed, it’s a mix of things.  There are some things and some of these processes in the watershed we do have control over and some we don’t.  At the local scale, that’s where the control is tightest and we can have the greatest confidence in the outcomes of the policies that we develop.”

Question: Given the challenges of these issues, but there are opportunities and we can think about things we can manage.  How can we use science to prioritize issues and to really identify what are the critical uncertainties or also what are the critical issues where we do have opportunities to manage things and really have an effect?

Dr. Cloern: “One of the lessons about uncertainties is that we should expect that the bigger the scale of variability that we’re looking at, the bigger the uncertainties are going to be, so I think we should accept that.   We should accept the fact that the Delta is going to continue to be driven by large scale regional and local scale processes.  It’s important for us to pay attention to all three of them.  In terms of monitoring, we have these great monitoring programs in the Bay and in the Delta.  We also need equally good monitoring systems in the atmosphere and in the watersheds.  So I don’t know where the big data gaps and the uncertainties are in terms of data in the watershed and across the ocean and atmospherically, but I think paying attention is really important.”

I could imagine the value of an office whose responsibility it is to pay attention to what’s going on in the watershed and what’s going on in the Pacific and what’s going on in the Bay and the Delta with the idea of alerting people when new developments arise, and also start building the depth of our understanding of this connectivity.”

I’ll give you an example of why this would be helpful from a scientist’s perspective.  A couple years ago, our ship goes from San Jose up to Rio Vista, and we were sampling in Rio Vista in the summertime, and one year, we measured really, really high chlorophyll concentrations in the lower Sacramento River.  We’d never seen that before.  What the heck is this?  We looked at it under the microscope and it was a big bloom of a freshwater diatom.  I found out later that this was the result of an experiment to flood Yolo Bypass to generate blooms.  I had no idea that this was going on.  If there was a clearinghouse that says this experiment is going on.”

If there was a clearinghouse, an office where somebody or some group of people are paying close attention to things like there’s an atmospheric river developing, we’re projecting that next week is going to be a major rainfall event, or this levee is about to break, we’re going to open this gate for this period and then close it for this period, or we’re going to flood this floodplain, so it would be really valuable for the monitoring and research communities to know those things in advance.   This is shaping up to be a wet year, what does that mean for water management, what does that mean for stratification of the south Bay?  We get big blooms during wet years.  What does that mean for these fish communities that seem to be tied to precipitation and runoff?  Maybe that’s more than can be accomplished, or is even feasible, I just know it’d be an office that would be very useful.”


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