By: Andrew L. Rypel, Derrick J. Alcott, Paul Buttner, Alex Wampler, Jordan Colby, Parsa Saffarinia, Nann Fangue and Carson A. Jeffres

Long-time followers of this blog may have tracked the evolution of our salmon-rice work for some time. The work originated most strongly with the “The Nigiri Project” in the early 2000s, building from important earlier work by Ted Sommer and colleagues (e.g., Sommer et al. 2001). This blog is a primer on the concept with an update on current studies.

Salmon are in a prolonged state of decline in California. Two of three recognized Chinook salmon runs (Spring-run and Winter-run) are listed under the US Endangered Species Act. The recognized Fall-run and unrecognized Late-Fall-run may not be far behind. These last two populations are notably influenced by a rise in hatchery-origin fish and declines in wild-origin fish, which may mask the Fall-run decline. These trends should not be surprising. 83% of native California fishes are in some form of decline, leading scientists, conservation groups, agriculture, municipal water agencies, and policy makers to search for innovative solutions. One interesting aspect of salmon ecology in the Central Valley is that these fish appear to be floodplain specialists. Before widespread modification of California, water would come off the Sierra Nevada mountains and spread out over the vast Central Valley wetlands. Juvenile salmon would rear in floodplains and feast on abundant food resources. Essentially, salmon used the Central Valley floodplains to ‘gas up’ during their long journey to the Pacific Ocean. Yet today, it is estimated that only ~5% of the original floodplain remains.

One particularly intriguing solution draws from successful conservation practices developed for waterbirds in the Central Valley. During the late 1980s and early 1990s, Pacific flyway birds (many of which overwinter in the Central Valley) were also in decline from a lack of wetland overwintering habitat. These ecological trends overlapped with a need to greatly reduce rice straw burning after harvest in the fall to improve air quality. Thus, the idea was hatched to flood rice fields in winter to decompose the rice straw (when fields would otherwise be fallow). Winter flooding accomplished two goals: 1) massive amounts of wetland habitat for waterbirds, including food; and 2) natural microbial decomposition of rice straw, without smoke! This program was a huge success and almost single-handedly halted Pacific waterbird population declines in California. It was a classic example of ‘reconciliation ecology’, showing how large human-dominated landscapes can be managed to be more wildlife-friendly while still supporting agriculture. What soon followed were even more programs, largely funded by the Natural Resources Conservation Service (NRCS), to do even more to enhance rice fields for waterbird habitat.

Indeed, the bird program was so effective that some people began asking: ‘Hey, if we can do that for birds, why can’t we do that for fish?’

Some of the early work on this question focused on first order questions, like: Do salmon use floodplains? And was followed by the ‘Nigiri Project’ that further asked: Can salmon survive on rice fields?; and do the fish even grow? To make a long story short, salmon do extremely well in seasonally flooded rice fields. They survive at high rates (often 50-80% over the course of a month – excellent for baby fish!), and grow fast (often ~1 mm/day). The secret sauce appears to be their ability to feast on the lush zooplankton communities that develop naturally in winter-flooded fields.

We’ve learned so much more though.  Even without fish, winter-flooded fields can grow fish food (zooplankton) that could be strategically drained to help wild and in-river salmon and other native fishes in the system. Central Valley salmon also may tolerate lower dissolved oxygen levels compared to other salmon populations in the Pacific Northwest, presumably a local evolutionary adaptation to their historic use of floodplains. But temperature and dissolved oxygen conditions can become problematic if fish are held too long (often later into the spring). Finally, there are preliminary indications of an outmigration benefit to rearing on rice fields versus rearing in the river and/or lab. But, this pattern requires replication across more years, and water year types. 

The benefit to salmon from rearing on rice fields can be summed up in two words – big & early. Young salmon from floodplain habitats grow fast and get big, and do so earlier in the season. The resulting outmigrating smolts likely ride higher river flows better, and more reliably, to the ocean. 

Providing a mosaic of growth and outmigration conditions is essentially similar to a diversified stock portfolio and provides a buffer for adverse conditions which also takes advantage of good conditions. Most studies that release fish into the river in the late spring have low outmigration survival. Flows in late spring and into summer tend to have clear water with low food abundance and more active predators. Thus, imagine a riverine food desert – but one where fish are also at constant risk of being eaten – not a great situation for baby salmon.

There is much potential for novel conservation practices, but we still need more science. We are currently collaborating with the California Rice Commission, NRCS, California Trout, state and federal agencies, and others to develop a draft a new management practice for how rice farmers could make their fields salmon-friendly during winter months. Currently, this practice involves prescribed flooding instructions, installing modified boards (boards with a v-notch and a hole, see schematic) for the salmon to swim through, and monitoring of water levels and aquatic habitat conditions. We have focused the draft practice on rice fields in the Sutter and Yolo bypass where salmon could enter rice fields during flood events and leave the fields volitionally. Some of the major science questions we currently have are: 1) What is the rate at which natural-origin salmon are entrained into these fields? 2) How well do juvenile salmon swim through a modified board system? 3) Can we replicate the promising potential outmigration benefit in additional years?

This year we are working primarily on a production-scale test field in the Sutter Bypass. The test field was prepared in accordance with a developing draft NRCS management practice. 8000 fertilized salmon eggs were acquired from Coleman National Fish Hatchery and reared at UC Davis. A subsample of these reared juvenile fish were implanted with PIT tags at UC Davis – essentially a FasTrak transponder injected into the fish. After placing PIT antennae (toll plaza) on the rice boxes, the hatchery fish were released into the test field to grow, eat zooplankton and presumably benefit from rearing in this naturalized floodplain system. PIT tagged fish will tell us how well juvenile salmon navigate the system of boards and checks, when they choose to exit the field, and how many ultimately pass out of the bottom check (i.e., in-field survival). We also have salmon growing in cages which allow us to track growth of individual fish, and to protect some fish for JSAT tagging. JSAT tags (an acoustic tag) produces high frequency sounds. Listening devices (receivers) in the Sacramento River and Delta allow us to listen for and track individual fish as they migrate to the ocean. Our goal is to tag 600 of our rice- and lab-reared fish and to conduct a side-by-side comparison of outmigration survival.

Yet research projects in actual floodplains need to be prepared for actual flooding and drought. If the bypass and study plots flood, our hatchery fish would leave the study plots, but natural fish could theoretically also come in. Indeed we actually selected the study fields partially because they had a high tendency to flood. In this scenario, our experiment changes. We would now be studying the entrainment rates of natural fish to the test plots, working with the grower to continue managing the field for salmon, and continue with our planned JSAT side-by-side experiment using caged fish. With or without natural floods, the rice fields must be drained by March 1st to allow rice planting and prevent poor temperature-oxygen conditions as spring arrives. Oh, we also have temperature-oxygen sensors in the fields to monitor habitat conditions 24-7, and time lapse trail cameras to study wading bird visitation and avian predation risk. 

There’s a lot going on! It is hard and important work, and there is no shortcut to high quality science. Ultimately, it’s a prime example of the type of thinking needed to solve environmental challenges in California (and elsewhere). Flooded rice fields are also just part of the solution for native fish. Wetland restoration and holistic/flexible flow and land management will also be needed to create sustainable solutions. An important and differentiating characteristic of the work is that, while fish and farms have often been pitted against each other in California, here there is real collaboration with potential for success. With 40 million people on the landscape, and too few wetlands, we must learn to use and expand wetland functions in smarter ways, even if they are agricultural wetlands.

Andrew Rypel is a Professor and the Peter B. Moyle & California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and a Co-Director of the Center for Watershed Sciences. Derrick Alcott and Parsa Saffarinia are postdoctoral scholars at University of California, Davis and the Center for Watershed Sciences. Paul Buttner is Manager of Environmental Affairs for the California Rice Commission. Alex Wampler is a Master’s student in the Animal Biology Graduate Group at University of California, Davis. Jordan Colby is a Junior Specialist in the Department of Wildlife, Fish & Conservation Biology at University of California, Davis. Nann Fangue is a professor and Chair of the Department of Wildlife, Fish & Conservation Biology at University of California, Davis. Carson Jeffres is a Senior Researcher and the Field and Laboratory Director at the Center for Watershed Sciences at University of California, Davis.

Acknowledgements: We thank a large number of people, agencies, growers, project funders, landowners and agencies that have helped along the way. We especially thank landowners we are currently working with, especially Steve and the rest of the Neader family, John Brennan, and Montna Farms. We thank Coleman National Fish Hatchery and USFWS for providing the hatchery eggs for this work. We thank Dennis Cocherell for technical and logistical support and Rachelle Tallman, Mattea Berglund Ken Zillig, and Cassidy Cooper for past and current assistance with the project. We also thank past farms we have directly worked with who have contributed to where we are today, especially Conaway Ranch and River Garden Farms. We thank staff and leadership at NOAA (Kimberly Clements, Maria Rea, Brian Ellrott, Kristin Begun, Garwin Yip), NRCS (Timmie Mandish and Jennifer Cavanaugh), CDFW (Jonathan Nelson, Bjarni Serup, Dan Kratville, Lee Scheffler) and California Trout (especially Jacob Katz and Jacob Montgomery). And finally our major sponsors, notably USDA NRCS, California Rice Commission, Syngenta, State Water Contractors, along with many supporting partners including Valent, Grow West, Corteva, The California Rice Research Board, American Commodity Company, California Family Foods, Lundberg Family Farms, the Almond Board of California, the S.D. Bechtel Jr. Foundation and other valued sponsors. 

Further Reading

California conservationists and farmers unite to protect salmon https://www.reuters.com/business/environment/california-conservationists-farmers-unite-protect-salmon-2022-02-09/

Raised in rice fields. https://www.biographic.com/raised-in-rice-fields/

The nigiri concept https://caltrout.org/regions/central-california-region/the-nigiri-concept

Helping fins and feathers https://podcast.calrice.org/episode-29-helping-fins-and-feathers/

Bellido-Leiva, F., R.L. Lusardi, and J.R. Lund. 2021. Modeling the effect of habitat availability and quality on endangered winter-run Chinook salmon (Oncorhynchus tshawystscha) production in the Sacramento Valley. Ecological Modelling 447:109511.

Bellido-Leiva, F., R.L. Lusardi, and J.R. Lund. 2021. Assessing portfolios of actions for winter-run salmon in the Sacramento Valley. https://californiawaterblog.com/2021/05/29/assessing-portfolios-of-actions-for-winter-run-salmon-in-the-sacramento-valley/

Corline, N.J., R.A. Peek, J. Montgomery, J.V.E. Katz, and C.A. Jeffres. 2021. Understanding community assembly rules in managed floodplain food webs. Ecosphere 12: e03330.

Holmes, E.J., P. Saffarinia, A.L. Rypel, M.N. Bell-Tilcock, J.V. Katz, and C.A. Jeffres. 2021. Reconciling fish and farms: Methods for managing California rice fields as salmon habitat. PLoS ONE 16(2): e0237686.

Jeffres, C.A., E.J. Holmes, T.R. SOmmer, and J.V.E. Katz. 2020. Detrital food web contributes to aquatic ecosystem productivity and rapid salmon growth in a managed floodplain. PLoS ONE 15(9): e0216019.

Katz, J.V.E., C. Jeffres, J.L. Conrad, T.R. Sommer, J. Martinez, S. Brumbaugh, N. Corline, and P.B. Moyle. 2017. Floodplain farm fields provide novel rearing habitat for Chinook salmon. PLoS ONE 12(6): e0177409.

Sommer, T.R., M.L. Nobriga, W.C. HArrell, W. Batham, and W.J. Kimmerer. 2001. Floodplain rearing of juvenile Chinook salmon: evidence of enhanced growth and survival. Canadian Journal of Fisheries and Aquatic Sciences 58: 325-333.
Sommer, T., B. Harrell, M. Nobringa, R. Brown, P. Moyle, W. Kimmerer, and L. Schemel. 2001. California’s Yolo Bypass: evidence that flood control can be compatible with fisheries, wetlands, wildlife, and agriculture. Fisheries 26: 6-16.