Photo by Bruce Barnett/Water Alternatives

BAY-DELTA SCIENCE CONFERENCE: Loss, and Potential Recovery of Primary Production from the Sacramento-San Joaquin Delta

Landscape transformation in the Delta has far-reaching implications, including the loss of primary production that forms the basis for the food web.  A recent study quantified the loss of primary production in the Delta and how much would be restored if all the restoration targets for the Delta were met.  The study, On the Human Appropriation of Primary Production, presents a simple approach for estimating the loss of ecosystem functions from measured habitat losses that can guide conservation plans by establishing historical baselines, projecting functional outcomes of different restoration scenarios, and establishing performance metrics to gauge success.

At the 2021 Bay-Delta Science Conference, Dr. James Cloern, one of twelve scientists from seven different institutions who collaborated on the study, presented the findings. 

Primary productivity is the process of converting the sun’s energy into organic material through photosynthesis.  Primary productivity is important because it forms the foundation of food webs in most ecosystems. So as primary production increases, so does the production of fish and other consumers.

The graph on the slide is from a 1988 paper published by Scott Nixon, which shows that fisheries yield increases as primary production increases across various ecosystem types.

The basic message here is that the magnitude of primary production sets an energetic limit on the capacity of ecosystems to support the production of consumers,” said Dr. Cloern.  “We also know that there’s a strong positive relationship between biological diversity and ecosystem net primary production. So we need to consider the process of primary production as we think about strategies for meeting California’s goal of recovering and enhancing the Delta ecosystem and its native species.”

Humans have played a significant role in reducing the amount of primary production available to all other species on the planet. The concept of human appropriation of primary production was first published by Peter Vitousek and his colleagues at Stanford in 1986. 

It was a revolutionary idea of a mode of human disturbance at the planetary scale,” said Dr. Cloern.  “In this case, we’re talking about net primary production, which is the amount of primary production left for consumers after we subtract the amount of production respired by plants.  The most recent assessment, now almost two decades old, is that we have appropriated about 25% of net primary production in the world’s terrestrial ecosystems.  About half of that is from direct harvests, and about 40% from land use changes, such as the conversion of forests and grasslands into agricultural and urban centers.”

Wetlands have been transformed to an even greater extent than terrestrial ecosystems, but there isn’t a global estimate of the human appropriation of primary production from wetlands.  However, Dr. Cloern pointed out that there is information about landscape changes of some wetland ecosystems that can be used to estimate the losses of primary production.   

The Delta is a great example because there is detailed knowledge of how it has been transformed since the early 1800s.  The maps of the historical and modern Delta landscapes shown on the slide are from the Historical Ecology Study by SFEI.  Many different kinds of historical information were used to determine what the Delta looked like and how it functioned before it was developed for human uses over the last 160 years.

The researchers focused on five wetland habitat types connected by water flows of tides and river inflows, such as tidal and non-tidal marshes, open water habitats, and floodplains.  These connected habitats supported aquatic food webs, but they have largely been disconnected and transformed for agricultural or urban uses.

From the historical ecology study, the area of hydrologically connected habitats was over 2000 square kilometers; it was slightly larger during wet years when floodplains and non-tidal marshes were inundated.  So, the historical ecosystem was a large inland river delta, dominated by tidal and non-tidal marshes, and was about the size of the Chesapeake Bay, the largest estuary in the US.

Today, the area of wetland habitats is now in the range of 300 to 500 square kilometers, varying between dry and wet years.  Dr. Cloern pointed out that the marshes, shown in green, have largely disappeared, while the blue open water habitat has increased in area since the early 1800s.

So, given these quantitative metrics of landscape change, the study asked four questions.

Question 1: What does this magnitude of landscape change mean in terms of ecosystem functions such as primary production?

In this study, researchers considered five different primary producer groups, including two groups of microalgae and three groups of vascular plants, each occupying different habitat types.  The method they used began with scouring the literature to find measurements of primary productivity rates for each of the plant groups and then estimating net primary production as the product of these productivity rates and the area of habitats occupied by each primary producer group.

For example, phytoplankton productivity in the Delta is on the order of about 50 grams of carbon per square meter per year, compared to productivity about ten times higher for marsh vascular plants,” Dr. Cloern said.  “These calculations indicate that annual net primary production was about 1300 kilotons of carbon in the historical landscape, where a kiloton is 1000 tons.”

One kiloton of carbon is the carbon content of about 5 million ears of corn, so the historical Delta produced the carbon equivalent of around 6-7 billion ears of corn and making that production available to support aquatic food webs.

In the modern Delta, net production in hydrologically connected habitats is less than 100 kilotons of carbon,” said Dr. Cloern.  “So our answer to the first question is that over 90% of ecosystem net primary production has been appropriated by our modification of the Delta landscape.”

Question 2: What about shifts in the Delta primary producer communities?

Researchers then asked about shifts in the Delta primary producer communities that resulted from the near-complete loss of marshes and expansion of open water habitat as 98 to 99% of the marshes have been converted to other land uses, while open water habitat has increased by 80%.   

Most – 95% – of net production in the historical landscape was in the marsh, primarily from vascular plants and tules, but also an important component from attached microalgae; net production in open water was a minor component of ecosystem net production – only a few percent,” said Dr. Cloern.  “In the modern Delta landscape, marsh production has been reduced to 30% of the total, while open water production has increased to about half the total. So not only have we reduced the magnitude of net primary production, but we’ve also transformed the marsh fuel ecosystem into one fueled more by aquatic plants, many of which are non-native, and phytoplankton.”

Question 3: How did these changes alter food the food web?

For the third question,  researchers asked how these changes in primary production in the relative contributions of marsh versus open water plants altered food supplies to consumers.  

They considered two important pathways or food supplies to consumers:  conversion of plant biomass, particularly vascular plant biomass, into detritus by microbes; and second, direct consumption by herbivores.  Both of these pathways are considered important in the modern Delta.

The calculations could be done because prior research has found that most vascular plant primary production is converted to detritus, and most algal production is consumed directly by herbivores.  Since the percentages of marsh and floodplain habitats were known, these percentages could then be used to compute the mass carbon.

These calculations indicated that carbon consumption by herbivores has decreased by nearly 90%, and the production of detritus has decreased by more than 90%,” said Dr. Cloern.  “This is essentially the crux of the problem – the primary ecological consequence of land use change has been a 90% reduction in the carbon or energy supply to aquatic consumers, from microbes to copepods to fish and birds.”

Question 4:  What would be the effect on primary production if restoration targets are met?

Continuing population declines of native species have motivated plans to restore lost wetland habitats in the Delta, particularly wetland habitats.  Those plans include restoring over 30,000 acres of tidal wetlands.  So the researchers used the same calculations to estimate increases in primary production if those restoration targets are met.

Dr. Cloern then presented the results, noting that the top bar graph shows increases in habitat areas if restoration targets are met, both in dry and wet years; the bottom bar graph shows the estimates of corresponding increases in net primary production.

So if we are successful at meeting the current habitat area targets, our results suggest that about 12% of lost net primary production could be recovered, the carbon flow to herbivores would double, and detritus production would triple over the rates in the contemporary Delta,” said Dr. Cloern.  “So these are measures of direct benefits to consumers as an outcome of successful habitat restoration.”

Closing thoughts

Coming back to the global problem of lost net primary production of wetlands, I want to end with three general lessons that emerged from our case study of the Delta,” said Dr. Cloern.  “The first lesson is that wetland loss reduces net primary production supporting aquatic food webs. Secondly, some of the net primary production loss to landscape change can be returned with successful habitat restoration. And finally, that simple methods like the methods that we’ve used here can project outcomes of restoration scenarios and establish performance metrics to gauge success.”


QUESTION: Given that the restoration will likely rely heavily on those attached plants and the sewage treatment plant may reduce the biomass of attached plants, how do you see that all playing out in the long run regarding the balance between attached plants and phytoplankton?

To answer that question, we’re going to have to make some projections of what the treatment processes are going to do in terms of nitrogen and phosphorus loadings and concentrations in the estuary,” said Dr. Cloern.  “It’s very unlikely that phosphorus will ever become limiting here because it’s present in such high concentrations, so the essential question is, will biologically available forms of nitrogen be reduced to levels that ultimately limit the biomass production of either vascular plants or phytoplankton? I think that’s unlikely. But I think it’s the kind of question that we can assess with models and probably some pretty simple models.”

We also have to think about the differences between floating vascular plants and submerged rooted vascular plants because the rooted vascular plants have the advantage of having access to nitrogen and phosphorus pools stored in the sediments. So if we do reach a state where nitrogen in concentrations in water becomes limiting, that doesn’t necessarily mean that this reduction in nutrient inputs in concentrations is going to reduce the production of rooted vascular plants.

Another thing that it means is, is there going to change the ecosystem back to a state of where vascular plant production, and in particular marsh vascular plant production, becomes more important than it is now? So recovering a form of production from a community that has largely been lost.”

Bottom line, to answer your question is, how far are we going to reduce N & P inputs to the estuary as a result of upgraded sewage treatment practices in this one sewage treatment plant,” continued Dr. Cloern.  “I think I think the answer to the P part of that is hardly any. But I also wonder how big the sediment N pool is to be drawn down? Because it would eventually be drawn down to a level commensurate with the ambient inputs.”

We actually answered that question for the whole base system, so if you read the paper, the answer to that question is in there,” said Dr. Cloern.  “But in the process of putting this paper together, I did a lot of reading on the legacy nutrients in the sediments of estuaries. And the general rule seems to be for eutrophic estuaries that have been enriched over periods of decades, that the pool is going to be present and available to be converted into plant biomass for multiple decades.”

QUESTION:  How do the results change with the climate enhancement of cyanobacteria which create chlorophyll but not desirable food?

We didn’t consider changes in the plant communities in any way in this analysis,” said Dr. Cloern.  “That’s a question that is separate from the questions that we asked in our study. But it’s a question that could be built on the answers to these questions that we’ve answered in our study. If we think in a very general sense, one of the outcomes will be a reduction in the relative importance of production in open water habitats as we increase the aerial extent of marshes. So the relative contributions of the complete aquatic producer community are going to decrease as a result of increasing contributions from the marsh vascular plants.”

But what this means in terms of shifts in phytoplankton communities, we didn’t consider that question at all. We just considered primary production by phytoplankton based on measured rates of productivity in the contemporary Delta. And in terms of projections of responses to climate change, I think it’s really important for people to understand is that what we have attempted here is not to compute what historical product production in the Delta was, but rather, what would the primary production in the Delta have been in today’s environmental conditions, the presence of clams, today’s turbidity, today’s flows, today’s nutrients, but in the historical landscape, so what we tried to do was think about contemporary conditions, and answer the question, what would the potential production be in today’s world but in yesterday’s landscape configuration.”

It’s the same thing for the projections of responses to changes in climatic forcing of the Delta. We didn’t consider changes and things like seasonal timing of flows or heat waves or temperature or salinity increases. We only ask the question, if we think about today’s environment and increase the acreage is of tidal marshes and non-tidal marshes and floodplains that are part of our restoration plan, what would the expected outcome be? So we tried to isolate the effects of the landscape from all these other forces that drive variability of primary production.” 

PAPER: On the human appropriation of wetland primary production

James E. Cloern, Samuel M. Safran, Lydia Smith Vaughn, April Robinson, Alison A.Whipple, Katharyn E.Boyer, Judith Z.Drexler, Robert J.Naiman, James L.Pinckney, Emily R.Howe, Elizabeth A.Canuel, Letitia Grenier


    • Landscape modification reduces net primary production (NPP) supporting other species.
    • Wetlands are being lost faster than forests but the associated loss of NPP is unknown.
    • We show that 77% loss of habitats from a large wetland ecosystem reduced NPP by 94%.
    • Success at meeting habitat restoration targets could recover 12% of lost NPP.
    • Estimated losses of ecosystem functions from habitat loss can guide restoration plans.

Click here to read/download this paper.

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