Delta nutrients: Sources, sinks, sags, soups, and sensors

Elk SloughDelta Lead Scientist Cliff Dahm discusses sources and effects of nutrients in the Delta

Increasing clarity of waters, the emergence of harmful algal blooms, the proliferation of aquatic water weeds, and altered food webs have brought the issue of nutrient dynamics to the forefront in the Delta.

Nutrients, such as nitrogen (or ammonium) and phosphorus can be beneficial or detrimental to aquatic ecosystems, depending on the type and levels of accumulation.  In the right amount, nutrients can promote healthy plant and animal growth. However, high levels of nutrients can cause water quality concerns and can negatively alter the food web.

Delta Lead Scientist Dr. Cliff Dahm’s career has focused on nutrient biogeochemistry in aquatic ecosystems. bb-dahm_page_01In this Brown Bag Seminar, Dr. Dahm touches on the upcoming chapter in the State of Bay Delta Science 2016, currently in the review stages, and weaves his insights from past research in other aquatic ecosystems with the nutrient studies that are ongoing in the Delta.

Nutrient biogeochemistry has the focus of Dr. Dahm’s research for over 40 years.  He has spent a lot of time at sea, mostly in the Antarctic ocean, but also in the Pacific Ocean and the Atlantic Ocean; he has studied nutrient biogeochemistry at Crater Lake and after the eruption at Mt. St Helens, old growth forests in the Cascades, groundwater to surface water interactions, and the high montaine forest waters in the southwestern US.  Most recently his research has focused on intermittent streams and rivers, which make up about 50% of the waterways worldwide.

Dr. Dahm began the seminar by noting that he would be talking some about the chapter on nutrients for the State of Bay Delta Science, but it is still in the review process and not yet published, but mainly he is going to attempt to weave some of his 40+ years of work on nutrient biogeochemistry and his ideas that might help make progress on nutrients in the Delta.

bb-dahm_page_03The title of the paper under review for the 2016 State of Bay Delta Science is titled, Nutrient Dynamics of the Delta: Effects on Primary Producers.  The State of Bay Delta Science was last published in 2008, but Dr. Dahm noted that out of the many chapters, none of them addressed nutrients.  “I’ve spent some time reading through the two chapters that I thought might have something about nutrients – the water quality chapter and the aquatic ecosystems chapter,” he said.  “If I’m counting right, you’ll find the word nutrient once in the whole document.  So this is a topic that has not been covered in the previous version.”

I thought it was interesting looking at some of the emerging topics that were listed at the end of the chapters on aquatic ecosystems and on water quality, and nutrients certainly weren’t one of them,” he continued.  “In fact, some of the things that they said were emerging issues that should be studied are fire retardants as a contaminant in the system, the legacy effect of PCBs, and multiple mixtures of contaminants and their effects on fish species.  It’s interesting to go back a few years and see what people thought of as emerging topics and then compare it to what is actually coming out in the State of Bay Delta Science 2016.”


bb-dahm_page_05In reviewing the available literature for the State of Bay Delta Science, Dr. Dahm found a few good papers that look at sources of nutrients coming into the Delta, two of which are displayed on the slide.  “The sources of nutrients are certainly scaled to the amount of water that these different systems put into the Delta,” he said.  “From a quantitative perspective, most of the nutrients that enter the Delta from the outside are coming through the Sacramento River system.  Even though the concentrations in the Sacramento are lower than the concentrations in the San Joaquin, the fact that there’s so much water compared to the San Joaquin that for most times of the year, the loads are generally the greatest from the Sacramento River.  There are times of the year, however, that the San Joaquin can become important.”

There is 30 years-plus data and information on nutrient loading from the Sacramento and San Joaquin rivers, and they tend to show that in terms of nutrients entering the Delta, things are actually getting better, not worse, he said.  “In terms of the amount of ammonium, nitrate, of phosphate that’s being loaded into the Delta from external sources, there tends to be some improvement in general, and that improvement seems to be linked to Best Management Practices that are being done within the catchments,” he said.

Dr. Dahm said that we know much less about in-Delta sources of nutrients, such as agricultural drainage from farms within the Delta, or what might be coming from the sediments within the Delta’s aquatic ecosystems.  “Where our gaps are in terms of sources of nutrients are more within the Delta questions, than they are inputs from outside the Delta.  Once these nutrients are within the Delta, what happens to them and what are the things that can occur to the nutrient once in the Delta.”


Dr. Dahm said one study he worked on was a 10-year study called the Lotic Intersite Nitrogen eXperiment (LINX) which was funded through the National Science Foundation.  The experiment basically looked at the transport, fate, and food web effects in catchments across North America, studying first ammonium and then nitrate.  For the ammonium experiments, they were six week continuous measurements of what happened to ammonium in stream and small river systems; for the nitrate study, they studied 72 streams done over a 24 hour period.

What was innovative about these studies and what made them highly published and highly acknowledged studies that helped inform transport, fate, and food web effects of nutrients was that the study used a ‘true tracer,’ said Dr. Dahm.  He explained what that meant:  “A true tracer means that we didn’t change the concentration of the nutrients in the system we working.  What we did was simply change the ratio of the stabilized isotope N15 to stabilized isotope N14.  In natural systems it’s overwhelmingly N14 with a little bit of N15.  What we did is just change that ratio; you can change that ratio and have almost no effect on concentration.”

bb-dahm_page_06With the ammonium study, we changed the ratio so that we had much heavier N15 enriched ammonium, and you could then follow that and what happened to the ammonium,” he said, pointing to the diagram which is an attempt to show how this actually works.  “So a tracer is added, it’s enriched in N15, and then a number of things can happen to that ammonium.  It can be transported through the system and you can watch how much gets transported out of the system.  It could be taken by a variety of biological processes, such as taken up by aquatic plants, benthic algae, phytoplankton, or decomposing detritus.   So by sampling all of those compartments and making measurements, you can actually then follow where that ammonium is going within the system you are studying.  By using this same technique on systems all over North America, we could then compare between the systems because we used exactly the same methodology at each site.”

He noted that by using mass spectrometry, you can get very accurate measurements of stable isotopes very inexpensively.

The studies with ammonium were very informative, one example being the importance of nitrification or the conversion of ammonium to nitrate by microbial processes.  “All systems, even with ammonium levels at near detection, had measurable nitrification rates,” he said.  “A lot of people had thought that the process would outcompeted by biotic uptake, but the chemosynthetic pathway of nitrification was actually important in all systems.”

With the ammonium tracer experiments, they were also able to look at both abiotic and biotic pathways, he said, explaining that ammonium is positively charged, so it can stick to a negatively charged clay; in addition, ammonium in high pH environments becomes a ammonia, a gas, and that can volatize out through the water into the atmosphere.  “We were able to quantify that process, so this was a methodology that worked well enough that the National Science Foundation was willing to give us a few million dollars more to do exactly the same thing, only to use nitrate.”

Why the interest in nitrate?  “The interest in nitrate was because the loading of nitrate into coastal ocean systems worldwide had become a serious problem; in particular, it was serious problem in the Mississippi River drainage, and we needed to know whether or not small streams and rivers were effective in retaining or processing some of that nitrate,” he said.  “So the studies basically used this N15 tracer approach, and because of it, we were able to very sensitively measure these processes in these aquatic systems.  We started in the small streams and small rivers, it’s been extended now to some larger rivers.  The costs goes up, the more of the isotope you have to add, and actually now people are doing similar kinds of work in some coastal ocean and some estuarine systems.”

bb-dahm_page_07Dr. Dahm then further explained the study.  After the enriched isotope is added, if you take the sample moving downstream from the point of introduction, the stable isotope begins to disappear from the water; it can disappear because it gets absorbed, volatilized, goes into detrital pathways, or goes into algae or aquatic plants.  “You can sample all of those, you can figure out what all that is, and what you also get is an uptake rate,” he said, noting that the chart on the right is basically the natural log of the N15 tracer as a function of distance downstream,” he said.  “One of things you can then get is an uptake length, so how far do you have to downstream before this ammonium is taken up.”

For ammonium, these small streams and small rivers we were working in, I don’t think there was a site anywhere where the ammonium was not taken up on average in less than 1000 meters, and in most cases it was less than 100 meters, so very effective processing of the ammonium,” he continued.  “For the nitrate, it stayed in the water longer.  For some systems that were very nitrogen-limited, those distances again were short, in the tens to hundreds of meters, but in systems that had tons of nitrate, ie row crop agriculture in the Midwest, there was basically no uptake length.  It was being transported through the system just like the water.  It was basically a conservative solute.”

These processes allowed us to measure a lot of key rates, such as nitrification, denitrification, or uptake into some of the key biotic components in the system, and so this is something that has some utility.  In this case, we enriched the N15, but there’s also the potential of using just natural abundances in certain systems, and so I’m actively encouraging us to see if that might work in some areas within the Delta.”


Dr. Dahm then gave his thoughts about nutrient sinks within the Delta.  “When I arrived here in 2008, I had this nice tour of the Delta, and they were telling me that the Delta is a low productivity system, there’s almost no primary production,” he said.  “But I kept seeing all these aquatic plants everywhere in the Delta.  It didn’t look like a low productivity system to me, so I had to wonder about that.”

A group of scientists came together for the Delta Primary Production Workshop in October of 2015, and this was one of the topics of discussion.  “There’s been some nice studies of annual phytoplankton primary production within the Delta,” he said.  “The Jassby, Cole, and Cloern paper is a nice example of that.  The number in that paper is about 70 grams of carbon per meter squared per year of phytoplankton production with a factor of about 5 between low and high values.  70 is the average, so low years it might be down 20 or 30, in high years in might up over 100, so those are the kind of numbers for phytoplankton primary production.”

bb-dahm_page_08Dr. Dahm wondered about the primary production for the extensive amount of aquatic plants that are out there.  “There are two groups of aquatic plants that dominate the Delta waterways,” he said.  “One group is the submersed aquatic macrophytes, and in particular Egeria densa or Brazilian water weed.  I went out started to try and find information on rates of primary production for Brazilian water weed … What I did find is in Wetzel’s spec book a nice summary of submerged aquatic macrophyte primary production worldwide, and the numbers that he gave for places where nutrients are in abundance were anywhere from 200 to 1500 grams of carbon per meter squared per year for submerged aquatic macarophytes of which Egeria densa is an example.  So that’s kind of the dynamic range that he’s found worldwide for these kinds of submerged aquatic macrophytes.”

The other group of organisms are the free floating forms that dominate and particularly water hyacinth,” he said.  “Water hyacinth is a highly productive plant, and in fact, the rates of production in Wetzel’s book for water hyacinth range from 1500 to 4400 grams of carbon per meter squared per year.”

In a recent presentation to the Interagency Ecological program, Dr. Ted Sommer pointed out that in 2015, about 30% of the waterways in the Delta were covered with aquatic macrophytes, mostly invasive aquatic macrophytes.  “So with these rates of primary production, it’s verified in the Delta, and then linking them to the elemental stoichiometry of how much nitrogen and how much phosphorous are in these plants could give us a pretty good idea for demand for nitrogen and the demand for phosphorous from this group of organisms,” he said.  “My initial calculations would suggest that when we have these big water weed problems that we’ve been having of late, I think there’s as much nutrients going into those plants as there is going into phytoplankton – and maybe more.”

I think that is a worthwhile endeavor to begin to think about and potentially analyze,” Dr. Dahm said.  “You would need to collect these plants in various places around the Delta, you would need to measure the carbon, nitrogen, and phophorous content of these plants, and begin to look at the potential for these to be one of the major sinks.”

bb-dahm_page_09The free floating forms, you know they are sourcing it out of the water,” he pointed out.  “With the Egeria, with the rooted submerged aquatic macrophytes, there’s always this question of how much is coming from the sediment versus how much is coming from the water, and that would also have to be determined.”

The slide has a map of Frank’s Tract in 2014 and another from September of 2015 that shows the coverage of aquatic macrophytes.  “With this kind of coverage of aquatic macrophytes, there’s got to be a lot of nutrients going into these systems, and I think this is something worth doing research on and getting better numbers concerning how much nutrient is being sources out of the water.”


We’ve had some interesting phytoplankton dynamics in the Delta this year, some of that is desirable and some of this is less desirable,” he said.

bb-dahm_page_11He began with the desirable soup.  In March of this year, the Yolo Bypass spilled and there was a lot of water moving through the Bypass; it then began to drain.  Later on in April, there was a large bloom that extended well into May.

This is an organism that had a very extensive bloom in the northern part of the Delta for a few weeks to a month,” he said.  “People scrambled to get researchers out to the site and so quite a bit of information has been collected, both continuous sensor data and nutrient data.  That nutrient data is being analyzed, and it will be very interesting to see what form of nitrogen is driving this bloom.  Is it a nitrate driven bloom or an ammonium driven bloom?  Or did we need to see the ammonium down to a low level before the nitrate started to be utilized? So I think we have an opportunity to look at some of the dynamics of bloom formation and nutrient biogeochemistry as this process proceeded within the Delta.”

bb-dahm_page_12Then in July of this year, a similar experimental study was done through the collaborative effort of many individuals and organizations to move water through the Yolo Bypass to see if another bloom would occur.  “That experiment was also nicely designed into a sampling protocol and sampling scheme, so we had a number of good measurement science, a lot of sensor data was being collected throughout this movement of water through the lower Yolo Bypass into the north Delta, and a bloom again occurred.”

bb-dahm_page_13He presented a graph of chlorophyll data, pointing out the start and the development of the bloom that again lasted for multiple weeks.  “It’s the same organism as the bloom that occurred earlier from the natural spill of the Yolo Bypass that occurred in the late spring, early summer.  So it’s very interesting that we can potentially manage this system for this kind of primary production.”

The next big question is what effects did this bloom have on up the food web, so how much of this material moved into zooplankton communities and did it get up into an effect on the fish community, so I think there are exciting and well designed research and important implications moving forward as we think about how to manage places like the Yolo Bypass.”

He then turned to the second and undesirable soup, the harmful algal blooms that have been problematic worldwide, as well as in California.  “A number of different harmful algal blooms are involved, but the one that seems to be dominant in many sites is microcystis, and microcystis is showing up in a number of locations throughout California, including the Delta,” he said.  “The concern with these kinds of harmful algal blooms are not only the ecological effects of these blooms on the food web, but also there’s a direct human health issue that has to be addressed.

A variety of toxins are produced by these harmful algal blooms, including neurotoxins and levels of cyanotoxins that are significant concern.  “The Delta effects from microcystis, the worst blooms this year have been in the south Delta.  There’s some very clear water quality effects that come with these blooms, including large swings in pH and dissolved oxygen in some of the channels so there’s another one of the sags.  Ammonium has been shown to be the preferred nitrogen source for these harmful algal blooms, so this issue of ammonium interacting with harmful algal blooms is another area that I think is deserving of some attention.”


bb-dahm_page_16Dr. Dahm then discussed other sags.  He presented a slide with information from a 1956 paper by H.T. Odum in the inaugural issue of Limnology and Oceanography.  “This is a paper where Howard T. Odom basically pointed out that if you make regular repeated measurements of dissolved oxygen and couple that with some information on the light field, temperature, and barometric pressure, you can do calculations that would allow you to estimate rates of primary production in the aquatic system that you are studying,” he said.

There’s one other important kicker in this and it’s the biggest challenge in using this method and that is you also need to know something about the exchange of oxygen between the water and the atmosphere, and that exchange process is called a reaeration coefficient,” he continued.  “There are some direct ways of measuring it and there are some model based mechanisms estimating it.  Most commonly now, people are using these model-based tools to estimate reaeration, but most of the good studies will couple it with direct measurements to make sure the models are well calibrated to it.”

So this is the paper written a long time ago by a very smart man who basically said hey, if you make these kinds of measurements, and you get some of the ancillary data that goes along with these kinds of measurements, you can estimate not only rates of primary production, but you can also estimate how much respiratory activity is going, or in other words, how much oxygen demand is in the system, chemical and biological,” he said.

bb-dahm_page_17We’ve made a few additions to this as time has gone on; we basically now are able to measure dissolved oxygen continuously with all of our new optically based sensors,” he said.  “One person I’ve had a great opportunity to work with closely on this is Matt Cohen, he’s at the University of Florida, he’s been making these kinds of measurements in large rivers in Florida, and he utilizes the new generations of sensors that are able to measure a lot of these variables continuously.”

He’s added another important wrinkle, so not only are you able to measure rates of primary production and rates of respiration, you can also measure rates of nutrient uptake,” said Dr. Dahm.  He explained that Matt Cohen and Jim Heffernan at Duke have developed a method that uses daily sags in nutrients linked to the daily sags in oxygen to figure how much nutrient uptake is occurring within an aquatic system on a daily time step, such as the amount of milligrams of nitrogen or phosphorous per day.

bb-dahm_page_18Dr. Dahm said that they’ve utilized sensors that can continuously measure nutrients which are coupled to sensors that continuously measure oxygen.  “By looking at the day-night cycle, or at the drawdown during the day and the build back up at night, you can use that information to generate rates of primary production on the x axis and rates of nutrient uptake on the y axis, and you can actually do a regression line on that, and you can actually look at the ratio at which these nutrients are being taken up.  This is an example with nitrogen; same thing could be done with phosphorous.”

Dr. Dahm said what was interesting was the study in this Florida river had a carbon to nitrogen ratio of 24.  He explained that red field ratio is the atomic ratio of carbon, nitrogen and phosphorus found in phytoplankton and throughout the deep oceans, and it’s remarkably constant throughout all of the oceans of the world, as well as big lakes, also. The carbon to nitrogen to phosphorous ratio in the red field ratio is 106 moles of carbon, 16 moles of nitrogen, 1 mole of phosphorous.

So if you have a system dominated by phytoplankton, that carbon to nitrogen ratio should be 7, or approximately 7.  This one is 24.  What does that tell you?  Lots of aquatic plants in the system; this is a system that has most of its production going to aquatic plants.  Wouldn’t that be interesting to know in the Delta what phytoplankton is dominant versus where some of these aquatic plants are dominant?  Here is a method that works.”


Dr. Dahm then turned to his last subject, sensors.  He noted that one of his colleagues who is with the Monterey Bay Aquarium Research Institute has been developing sensors for the oceans which are starting to be used in freshwater systems now.

There are now continuous sensors for measuring phosphate and nitrate; sensors that measure algal pigments, some of the organic carbon components of water, and sensors that measure different aspects of the sediment composition and sediment types.  There are many other sensors in the development stages.

He then presented a pair of slides from Brian Pellerin that illustrate the difference between taking grab samples and using a continuous sensor.

On the left is an example of taking grab samples in an aquatic system every few hours, and in this case they measured nitrate over a three-day period.  “If you looked at this data, you’d say concentrations of nitrate are increasing, maybe 20% over that three-day period – this would be probably what you would report out if you had analyzed these data, but when you take a continuous sensor in this system, this was what was going on in that same time frame.”

There are two things to note, he said.  “First is that the continuous sensors agree very well with the lab analyzed data, and second, there’s a whole lot more structure and a whole lot more going on than just the grab samples would allow.  So these sensors I think are really helping us understand nutrients everywhere, and we have a lot of these sensors deployed in the Delta.”

bb-dahm_page_23Dr. Dahm then presented a graph showing continuous measurement of discharge and nitrate at 2 locations in the Delta from August 2013 to October 2014; the black line is tidally averaged flow, and the green and yellow are the two stations within the Delta.  “A couple things jump out at me when I see this,” said Dr. Dahm.  “The first one is the very important role that big flow events play.  This is from 2013-14 data, so these flows are up in the order of 30,000 cfs, so not the spill type-flows that would get water into the Yolo Bypass currently.  You can see that the nutrients respond quite strongly to these flow events, and nitrate in particular is enriched, so it’s probably not surprising that when you get flow events that spill into the Yolo Bypass, you are probably putting out quite a bit of nutrients out into the system, and how those are processed and how they are utilized I think is another area well worth considering as a major research area.  It also helps to explain some of the phenomenal productivity that connecting these floodplains with the river seem to generate.”

bb-dahm_page_24He then presented a slide from the Australian Rivers Institute about a study done in Morton Bay and the rivers that drain into it.  “The Australian Rivers Institute was the lead in developing for what I have seen worldwide, one of the best monitoring programs done anywhere to basically help make decisions on adaptive management and experimentation to deal with water quality in Morton Bay, and so the initial program focused on the bay.  After a couple of years of that, it became clear they had better start measuring what’s going on the rivers so they expanded that and they used that then to make decisions how to invest finite resources in various kinds of aspects to try to improve the health of aquatic ecosystems in this area round southeast Queensland.”

Early on, they worked to assess the source of nutrients getting into Morton Bay, so they did a number of studies, one of which used stabilized isotopes.  “It turned out that the ammonium that is part of the effluent being discharged by some of the wastewater treatment plants in this part of Australia is enriched in the heavy isotope and it provided a natural tracer, and that natural tracer then moved into various parts of the food web,” he said.  “In this series of diagrams is the condition that existed in 1998; the areas in red are areas that have substantive effluent sourced nitrogen.  What they used actually to look for this for either macro-algae or aquatic plants, both of which we could utilize similarly, and this is what they found.  So it was pretty clear that they had some point sources that were important, they invested $400 million in upgrading those plants, and as you can see during the plant upgrades and the continuing to monitor, here’s 2001, 2002, and then 2008, that they were largely able to eliminate this source of effluent derived nitrogen from the Morton Bay ecosystem.”

“This was a way of showing the efficacy of the upgrade in improving the condition relative to nutrient availability for the primary producers within this aquatic system,” he said.


Dr. Dahm pointed out that this might have some applicability here in the California Delta with the Regional San facility’s upgrade.  “These are things that if we do the right kind of experimentation and measurements beforehand, it might prove as a good mechanism to look at the effectiveness after the upgrade and see if some of the hypotheses that various people are putting forward actually come to be true.  That’s one of my little pet projects that I’m going to work on up until I really retire six to nine months from now, maybe a year.”


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