Lookout Slough, part of the Cache Slough Complex. Photo by Florence Low/DWR

DELTA LEAD SCIENTIST: Managed flow pulses as food web support; Synthesis of food web data; Overview of the Science Action Agenda; and more …

At the December meeting of the Delta Stewardship Council, Dr. Laurel Larsen, Delta Lead Scientist, spotlighted an article on the North Delta flow action for Delta smelt, discussed the partnership between the Delta Science Program and the National Center for Ecological Analysis and Synthesis to answer some of the questions surrounding the Delta’s the food web, and highlighted upcoming science symposiums.  Then, Rachel Klopfenstein, a Senior Environmental Science with the Delta Science Program, provided a presentation on the draft Science Action Agenda, which is open for public comment through January 21st.

Article spotlight: Use of a Managed Flow Pulse as Food Web Support for Estuarine Habitat

Dr. Larsen set the stage for the article spotlight by first referring back to other papers she has highlighted during the past year.

In June, she covered Dr. Jim Cloern’s historical analysis of primary productivity in the Delta, which found that the Delta has lost 77% of its wetlands but 89% of its carbon supply to the food web, as wetlands are such abundant suppliers of food. The massive loss of food supply to Delta food webs is one of the factors implicated in the Pelagic Organism Decline, or the steep drop in the populations of four native fish species around the turn of the century.

Last February, Dr. Larsen spotlighted a paper by Dr. Ted Sommer on the Nigiri Project, an ongoing project where rice fields in the Yolo Bypass were inundated to provide rearing habitat for salmon.  This study found that these managed inundation experiments effectively produced abundant zooplankton for rearing fish, given appropriate connectivity to the main channel.

Lookout Slough, part of the Cache Slough Complex. Photo by Florence Low/DWR

The Nigiri project is a great example of a managed flow action that is designed to increase fish access to habitat,” she said.

Another type of managed flow action also designed to promote access to habitat is the operation of the Suisun Marsh salinity control gates to freshen Suisun Marsh, which was touched upon in Dr. Larsen’s overview of the synthesis of drivers of Delta salinity back covered in August.

This month, Dr. Larsen discussed a third type of flow action that, unlike the other two actions previously covered, was not just used to improve habitat locally but was designed to change regional flow and transport patterns, with the intent of transporting more fish food phytoplankton to the lower part of the estuary.

Collectively, flow actions such as these are innovative strategies for potentially enhancing the resilience of species like Delta smelt, to drought, or simply to the poor food conditions that exist in the estuary,” she said.  “These actions often come up in planning discussions.”

However, Dr. Larsen acknowledged that the number of times flow actions have been implemented as adaptive management experiments is relatively small.  This has led to their prioritization in the 2022-2026 Science Action Agenda, under Action 1C, which is to ‘identify and carry out large scale experiments that can address uncertainties in the outcomes of management actions for ecosystem function in the Delta.’

The flow action profiled in the article is the 2016 North Delta Flow Action, which was directed toward Delta smelt, which, like other native fish species, has suffered from a decline in food.  

One part of the Delta that’s known to provide good habitat for the Delta smelt is the Cache Slough Complex in the North Delta, shown on the map. This region retains some of the more complex tidal channels characteristic of the historic Delta, and it’s connected to the Yolo bypass with its higher plankton densities.

While we know that this area generates phytoplankton that contributes to downstream food webs during the wet winter and the spring, this role is repressed during dry summers, when upstream diversions induce a negative upstream flow through the region that directs food resources away from the lower estuary,” said Dr. Larsen.  “2012, however, featured unusually high agricultural flows during the summer through the Yolo Bypass and the Cache Slough complex and did not generate those negative flows. Instead, the high downstream summer flows helped trigger the first fall phytoplankton bloom in the upper estuary in over two decades.”

So in July 2016, a large team of researchers and managers from DWR, USBR, CDFW, NMFS, Fish and Wildlife Service, US Geological Survey, the Natural Resources Agency, and local universities partnered with diverters to generate a summer flow pulse lasting for two weeks as part of the collaborative Delta Smelt Resilience Strategy. The source of water for the flow was agricultural drain water which was rerouted through the Yolo Bypass instead of being directed to the Sacramento River.

In order to be successful, the water level of the Sacramento River needed to be raised, which was accomplished through modified operations of the Keswick Dam, requiring a lot of coordination and planning.  The researchers modeled how flows responded to that action, and then they measured changes in nutrients, zooplankton, and phytoplankton. The results from this 2016 action were recently published in the San Francisco Estuary and Watershed Sciences in a paper led by Jared Frantzich of DWR  and other authors from DWR and Anchor QEA.

The biggest findings were that the action was successful in generating a large volume of downstream flow through that target region, and that flow stimulated a bloom of a beneficial species of phytoplankton downstream,” said Dr. Larsen.  “Now, whether the flow action by itself was sufficient to stimulate this phytoplankton bloom was a bit uncertain, as the species involved in the bloom had been prevalent in the Delta prior to the flow action. So there was abundant seed material for this phytoplankton available in the bottom sediments already.”

She noted that when a similar flow action was undertaken in 2018, which was not covered in this particular paper, a bloom did not result, which has been attributed to the different pre-flow conditions and the lack of a prior bloom in that year.

So the flow action also generated higher numbers of zooplankton in the Cache Slough complex during the flow pulse, but there is little evidence that those zooplankton were exported downstream,” said Dr. Larsen.  “So the North Delta Flow action generated promising results for how we might intervene to enhance Delta smelt resiliency during dry summers, but it also created additional science questions, which subsequent flow actions in 2018 and 2019 were designed to address.”

She noted that the results from the two subsequent experiments are still being analyzed and were not reported on in this paper. “In brief, those experiments revealed that while the food delivery system was less effective than in 2016, there was still more fish food in the lower Yolo Bypass and Cache Slough, then before this action (or this food delivery system) was implemented.”

Dr. Larsen also noted that there is an article about this action in September’s Frontiers for Young Minds.

Councilman Don Nottoli asked if there was a correlation between the wetter years, drought years, and the results of the flow actions.

This is a big part of the question,” said Dr. Larsen.  “Really understanding how the history with respect to how wet it was in the past, what sorts of organisms really populated the food chain in the past year or two years, even in some cases – that is a really big question in terms of how that history impacts responses to flow actions that we might do.  In fact, there’s a big black box when it comes to an understanding of how these food webs work in the Delta.  We have a lot of measurements of phytoplankton; we don’t have very many measurements of zooplankton.  How that lower level or that base of the food web is connected to fish at the top and the influence of other environmental drivers like flows and temperatures is poorly understood. And that’s something that requires really statistically savvy people to put these different data sets together and do that challenging synthesis.”

Note: Article continues below the box.

Use of a Managed Flow Pulse as Food Web Support for Estuarine Habitat

Jared Frantzich, Brittany E. Davis, Michael MacWilliams, Aaron Bever, Ted Sommer

Abstract: While freshwater inf low has been a major focus of resource management in estuaries, including the upper San Francisco Estuary, there is a growing interest in using focused f low actions to maximize benefits for specific regions, habitats, and species. As a test of this concept, in summer 2016, we used a managed f low pulse to target an ecologically important region: a freshwater tidal slough complex (Cache Slough Complex–CSC). Our goal was to improve estuarine habitat by increasing net f lows through CSC to enhance downstream transport of lower trophic-level resources, an important driver for fishes such as the endangered Delta Smelt Hypomesus transpacificus. We used regional water infrastructure to direct 18.5 million m³ of Sacramento River f low into its adjacent Yolo Bypass f loodplain, where the pulse continued through CSC. Simulations using a 3-D hydrodynamic model (UnTRIM) indicated that the managed f low pulse had a large effect on the net f low of water through Yolo Bypass, and between CSC and further downstream. Multiple water quality constituents (specific conductivity, dissolved oxygen, nutrients [NO₃ + NO₂, NH4, PO₄]) varied across the study region, and showed a strong response to the f low pulse. In addition, the lower Sacramento River had increased phytoplankton biomass and improved food quality indices (estimated from long-chain essential fatty acids) after the f low pulse. The managed f low pulse resulted in increased densities of zooplankton (copepods, cladocerans) demonstrating potential advection from upper f loodplain channels into the target CSC and Sacramento River regions. This study was conducted during a single year, which may have had unique characteristics; however, we believe that our study is an instructive example of how a relatively modest change in net f lows can generate measurable changes in ecologically relevant metrics, and how an adaptive management action can help inform resource management.

Partnership between Delta Science Program and the National Center for Ecological Analysis and Synthesis

Next, Dr. Larsen discussed the partnership between the Delta Science Program and the National Center for Ecological Analysis and Synthesis to answer some of the questions surrounding the Delta’s the food web.

This month’s article spotlight discussed how flow actions are being used to generate food for fish and how different flow actions in the North Delta over the years had fairly varied results.  The results underscore how we don’t really understand how to generate more food for native fishes because the food web is a bit of a black box, she said.

The Collaborative Adaptive Management Team (or CAMT) and other collaborative groups in the Delta have identified the need for developing predictive tools or models to help anticipate the outcome of a given flow action, which can help decide whether and when to implement these costly high-effort endeavors. These calls for food web models echo a call from the Delta Independent Science Board in their invasive species report released in early 2021, which also identified food web models as a critical need.  In particular, the report demonstrates how these models can help us make connections in advance between habitat restoration or flow actions and benefits for native fishes.

For decades, through the Interagency Ecological Program and other entities, we’ve collected monitoring data on phytoplankton and environmental drivers and fish species,” said Dr. Larsen.  “This really constitutes a big data set in the classical sense. But individual data collection efforts are typically focused on individual species or groups of species, but there’s not necessarily coordination across the different components of the food web. And similarly, funding for data collection does not often extend to funding for analysis.”

Dr. Larsen noted that these issues are not unique to the Delta but are pervasive across the environmental sciences. It’s challenging, costly, and time-consuming to use existing data to address holistic questions about the system because data sets are often not compatible, or at least not readily compatible. For instance, they might have different formats, timestamps, and assumptions used in the data processing.  And up until recently, many of them may not have been accessible, though she acknowledged AB 1755 is changing that for the better.

She noted that another challenge is that the techniques for analyzing big data are also evolving rapidly. Scientists trained as subject matter experts often don’t have the skills to do this analysis to answer the big questions regarding complex systems.

These challenges often can thwart seeing the return on scientific investment because, without those big picture analyses, we really can’t answer some of the biggest questions relevant to management needs,” said Dr. Larsen.  “Synthesis is the answer here. It’s an approach to scientific discovery that allows us to look across individual data collection efforts and answer big picture questions about the whole system. So synthesis is an increasingly critical science need, and it’s also one of the core functions of the Delta science program.

However, synthesis needs are far bigger than any one agency can tackle, said Dr. Larsen.  Former Delta Lead Scientist Dr. Peter Goodwin used to say that solutions for managing the Delta more sustainably lie in the data that’s already been collected; it just needs to be unlocked. So the Delta Science Program engaged in its partnership with the National Center for Ecological Analysis and Synthesis to provide training to the broader community of scientists to enable far more agencies and scientists to perform this needed synthesis.

Through that NCEAS-DSP partnership, a working group of 19 participants from nine agencies and universities convened for three weeks of training and collaborative work, which took place at UC Davis in person in September, October, and November.  Given the urgent need for synthesis to understand controls on the estuarine food web, the working group focused on applying their training to address that challenge. Through the summer, Delta Science Program staff and NCEAS pulled together the data needed to analyze relationships between these different components of the food web and environmental factors to produce a database that will also be accessible to others outside the working group as one of their products.

The 19 participants continue to work with this dataset in two working subgroups, which are focused on understanding the effect of flood management on estuary health and on identifying drivers of food web dynamics on an estuary scale. The preliminary results will be presented internally in January, and a series of work products is expected in mid to late 2022, including peer-reviewed publications, presentations, and fact sheets that translate the scientific analyses to meet management needs.  They will also be producing broadly accessible data and models that others can use.

This work is really important because I think that synthesis, in general, is not well understood,” said Dr. Larsen.  “It’s one of the aspects of the science that we do that has the greatest potential to address some of the biggest management questions.”


Environmental Justice Initiative

The council’s 2019 Five Year Review report identified environmental justice as a priority issue and recommended the preparation of an issue paper to investigate the need for additional strategies or responses to address environmental justice within the Delta Plan, summarize the best available science, and identify future policy options for the council to consider.

In February of 2021, the preparation of the issue paper began.  Recently, Council staff have been conducting outreach to environmental justice organizations and community-based organizations to arrange for interviews from a broad set of groups working across many different EJ issues and in different regions of the Delta.  For more information, check out the Delta Stewardship Council’s Environmental Justice webpage.

Delta Interagency Invasive Species Symposium

Aerial view of invasive hyacinth clogging channels in the Delta. Photo by Paul Hames / DWR

The Delta Interagency Invasive Species Coordination Team held its biennial symposium on December 15.  The Coordination Team was formed to foster communication and collaboration among California state agencies that detect, prevent and manage invasive species and restore invaded habitats in the Sacramento San Joaquin Delta.  The goals of the Coordination Team are to establish a framework for strategic planning; coordinate implementation, education, and outreach; identify data management research needs; and funding.  Participants include state agency program managers and scientists, research and conservation groups, federal agencies, and other stakeholders.  The Delta Stewardship Council is a co-chair of that team.

The symposium focused on the challenge of early detection and rapid response (or EDRR) to species invasions once they’re detected. EDRR is a second line of defense for our system once prevention measures have failed.  Eradication at the early stages before the species has had a chance to get established and spread is the most cost-effective and efficient way to protect our system from the ongoing threat of invasive species, Dr. Larsen said.

Sessions at the symposium focused on lessons learned from EDRR efforts and other systems, successes, and setbacks in EDRR efforts in the Delta, and emerging EDRR tools and challenges. Council staff participated in several ways, including moderating sessions and serving on the planning committee. 

The symposium laid a great foundation for developing a framework for implementing EDRR in a systematic way in the Delta,” said Dr. Larsen.  “This helps advance action 3d of the 2022 to 2026 Science Action Agenda, which is to synthesize existing knowledge and conduct applied interdisciplinary research to evaluate the costs and benefits of different strategies for minimizing introduction and spread of invasive species and to inform early detection and rapid response strategies.”

Upcoming science events

Adapting Restoration for a Changing Climate symposium will be held February 2-3.  Registration is now open, and a full agenda will be posted on December 20 on the Delta Science Program’s adaptive management webpage.

Upcoming salinity management workshops will be held April 26-27 and October 11-12 of 2022.  The workshops are designed to lay the groundwork for the collaborative development of a suite of scenarios to evaluate alternative salinity management strategies.  These strategies include using salinity barriers, modifying water operations, implementing restoration in the face of a changing climate, and identifying the impacts on Delta communities, ecosystems, and water supply.

The Delta Science Fellows Program RFA will be released on January 25.  It is a great opportunity for master’s students, Ph.D. students, and postdoctoral scholars. This year, one new feature of the RFA will have a separate track devoted to social science projects.

Science Action Agenda

At the December meeting of the Delta Stewardship Council, Rachel Klopfenstein, a Senior Environmental Science with the Delta Science Program, provided a presentation on the 2022 to 2026 Science Action Agenda update. 

The Science Action Agenda is widely recognized as a collaborative document developed by the scientific community for the scientific community that helps align science priorities with key management needs.  The Science Action Agenda is also called out in Governor Newsom 2020 Water resilient portfolio as a potential statewide model for prioritizing science relating to water supply, water quality, and flood risk.

The Science Action Agenda provides a unique service to the council and the Delta science program, as well as to the broader Delta science community,” said Ms. Klopfenstein.  “No other document elevates a list of shared science priorities for the Delta quite like the Science Action Agenda.  And while the Delta science program facilitates the process, the science action agenda is coproduced with stakeholder input and encompasses priorities from different collaborative venues and entities, thereby advancing shared interests and promoting transparency and collaboration.”

COVID made meeting in person challenging, but nonetheless, they engaged with over 30 collaborative groups, heard from over 125 workshop participants, and gathered over 150 survey responses across multiple surveys.

The Science Action Agenda is used by the Delta Science Program and other agencies as a guide for science funding. For example, the 2017-2021 Science action agenda was used by the US Bureau of Reclamation, the California Department of Fish and Wildlife, and the State Water Contractors to allocate over $35 million for competitive research projects and graduate student fellowships over the last five years.

While the Delta Science Program primarily leads these funding opportunities, we’re always looking to form partnerships and continue those we’ve already made,” said Ms. Klopfenstein.

In addition to guiding funding calls, the agenda has other uses.  For example, a scientist in the system can use the Science Action Agenda to see what science activities to fund or what actions are of shared interest in the community. Likewise, a manager can look at the Science Action Agenda to see what priorities are shared with other entities.

The 2022-2026 Science Action Agenda is the second full iteration, although there were two similar efforts in the past.  Ms. Klopfenstein said all of these previous efforts provide an opportunity to learn what works and what could be improved, resulting in some changes in the development process.

One of those changes, a recommendation from the Delta Plan Interagency Implementation Committee’s Science Funding and Governance Initiative in 2019, was to add management questions with the goal of better linking science actions to the broader management needs.  

This update also involved many more stakeholders and interests than the previous iteration, which was in response to calls for more coproduction.  There were many opportunities for engagement, including multiple online surveys and public workshops. 

The 2022 Science Action Agenda was also informed by the funded research from the previous funding solicitations and an assessment and tracking of progress made on the 2017-2021 Science Action Agenda that was summarized in a report.

The progress summary step, in particular, served to be really critical to the development process,” said Ms. Klopfenstein.  “In addition to determining the amount of funding that was allocated based on the last science action agenda, we reviewed all activities that contributed to addressing the 25 Science actions in the previous science action agenda and sought public input on the progress summary. We released the final progress summary in the spring of this year.  The existing gaps and what did not get addressed were used to inform the development of new science actions that are in our draft now.  We will continue to adaptively manage the Science Action Agenda update process and welcome input.”

The 2022-2026 Science Action Agenda document and process have been organized into three hierarchical components, as shown by the pyramid diagram, to ensure that the science actions are grounded in the management context.  

The six identified management needs are at the top of the pyramid and are the broadest component. Below are the management questions, which are new for this iteration and offer slightly more resolution on key management issues across the Delta and broader estuary. Public outreach and input identified 65 management questions, though not all directly related to priority science actions in the draft.  Twenty-five science actions are prioritized in the draft, based on input for funding in the near term.

We had so many good suggestions for science actions that we chose to preserve 75 of them in the appendix of the document, so folks can see which ones were proposed but not prioritized for funding right now, but are still important,” said Ms. Klopfenstein.

With the help of public input, six management needs were identified:

  • Improve coordination and integration of large-scale experiments, data collection, and evaluation across scales and institutions
  • Enhance monitoring and model interoperability, integration, and forecasting
  • Expand multi-benefit approaches to managing the Delta as a social-ecological system
  • Build and integrate knowledge on social process and behavior of Delta communities and residents to support effective and equitable management
  • Acquire new knowledge and synthesize existing knowledge of interacting stressors to support species recovery
  • Assess and anticipate climate change impacts to support successful adaptation strategies

These six needs highlight information that’s needed to inform decision making, assessing scenarios, and enhancing Delta governance,” said Ms. Klopfenstein.  “Many of these needs relate to existing Council priorities, including Delta Adapts and our efforts to enhance social science integration.”

Twenty-five science actions have been proposed as a priority for funding, which are responsive to the management needs and the management questions.

These include:

  • enhancing forecasting and monitoring efforts to be more nimble, effective, and forward-looking;
  • understanding impacts and management of contaminants and harmful algal blooms, which can have detrimental effects to people and the ecosystem;
  • increasing knowledge of the Delta as an interconnected social-ecological system with particular emphasis on understanding values, equity, and resilience; improving invasive species management, such as detecting and responding to invasions earlier;
  • better anticipating and addressing climate change impacts that threaten the Delta; and
  • evaluating social and ecological trade-offs of drought management actions.

It’s worth noting that in incorporating input, and crafting the science actions, we sought to strike a balance between specific and broad; broad enough to be inclusive of the input that we received, but also responsive to the recognition in the system that we have management gaps that relate maybe less to individual processes and resources, but rather connections between processes and resources,” said Ms. Klopfenstein.  “We also have some science actions that are quite specific to advance key gaps in the system like for species recovery.”

The Science Action Agenda is available for public review through January 21, 2022.  They are seeking input from the Delta Independent Science Board, various collaborative groups, workshop participants, those that have participated in the process, and other interested members of the public. After considering comments, the final Science Action Agenda is anticipated to be released in the spring of 2022.

To access the draft Science Action Agenda for 2022-2026 and other related documents, click here.
Print Friendly, PDF & Email