Tag: strawberry gutter system

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Credible and prediction intervals in the shoot at harvest were similar for both models

However, Southern California, a region that suffers from a similar degree of water shortage, currently uses less than ~3% of municipal wastewater in agriculture, while discharging ~1.5 million acre-feet effluent per year into the Pacific Ocean . Secondary municipal wastewater effluent for ocean discharge is often sufficient to support both the nutrient and water needs for food production. Water reuse in agriculture can bring municipal water reclamation effluent to nearby farms within the city limit, thus promoting local agriculture and also reducing the rate of farmland loss to urban development. While the use of reclaimed water in agriculture offers a multitude of societal and agronomical benefits, broader adoption faces great challenges. One of the important challenges is ensuring the safety of food products in light of a plethora of human pathogens that may be present in recycled wastewater. Past studies have identified risks associated with irrigating food with recycled wastewater through the retention of the irrigation water on edible plant surfaces during overhead irrigation . With the emphasis on water conservation and reduction of evapotranspiration, subsurface drip irrigation is gaining popularity . Since there is lesser contact between water and the plant surface, the chance of surface contamination of pathogens is reduced. However, this new practice presents risk of uptake of microbial pathogens into plants. Such internalized pathogens are of greater concerns as washing, even with disinfectants, may not affect pathogens sheltered in the vasculature. Although pathogen transport through root uptake and subsequent internalization into the plant has been a growing research area, results vary due to differences in experimental design, systems tested, and pathogens and crops examined . Among the array of pathogens causing food borne illness that may be carried by treated wastewater, viruses are of the greatest concern but least studied. According to the CDC, 60% of U.S. food borne outbreaks associated with eating leafy greens were caused by noroviruses ,stacking pots while Salmonella and E. coli only accounted for 10% of the outbreaks . Estimates of global food borne illness prevalence associated with NoV surpass all other pathogens considered.

Viruses are also of concern because they persist in secondary wastewater effluents in high concentrations . They do not settle well in sedimentation basins and are also more resistant to degradation than bacteria . Therefore, in the absence of solid scientific understanding of the risks involved, the public are likely less receptive to adopting treated wastewater for agricultural irrigation. NoV internalization in hydroponic systems has been quantified by DiCaprio et al. . Internalization in crops grown in soil is considered lesser but nevertheless occurs. However, the only risk assessment that considered the possibility of NoV internalization in plants assumed a simple ratio of viruses in the feed water over viruses in produce at harvest to account for internalization. The time dependence of viral loads in lettuce was not explored and such an approach did not permit insights into the key factors influencing viral uptake in plants. In this study, we introduce a viral transport model to predict the viral load in crisp head lettuce at harvest given the viral load in the feed water. It is parameterized for both hydroponic and soil systems. We demonstrate its utility by performing a quantitative microbial risk assessment . Strategies to reduce risk enabled by such a model are explored, and a sensitivity analysis highlights possible factors affecting risk.The plant transpiration rate was adopted as the viral transport rate ) based on: 1) previous reports of passive bacterial transport in plants , 2) the significantly smaller size of viruses compared to bacteria, and 3) the lack of known specific interactions between human viruses and plant hosts . Accordingly, viral transport rate in hydroponically grown lettuce was determined from the previously reported transpiration model , in which the transpiration rate is proportional to the lettuce growth rate and is influenced by cultivar specific factors . These cultivar specific factors used in our model were predicted using the hydroponic crisp head lettuce growth experiment carried out by DiCaprio et al. described in Section 2.3 . Since the transpiration rate in soil grown lettuce is significantly higher than that in the hydroponic system, viral transport rate in soil grown lettuce was obtained directly from the graphs published by Gallardo et al. using WebPlotDigitizer . The shoot growth rate for soil grown lettuce was determined using Eq. 9 . In the absence of a published root growth model for lettuce in soil, a fixed root volume of 100 cm3 was used. In the viral transport model, viral transfer efficiency was used to account for the potential “barrier” between each compartment .

The existence of such a “barrier” is evident from field experiments where some microbial pathogens were internalized in the root but not in the shoot of plants . In addition, viral transfer efficiencies also account for differing observations in pathogen internalization due to the type of pathogen or lettuce. For example, DiCaprio et al. reported the internalization of NoV into lettuce, while Urbanucci et al. did not detect any NoV in another type of lettuce grown in feed water seeded with viruses. The values of ηgr and ηrs were determined by fitting the model to experimental data reported by DiCaprio et al. and is detailed in Section 2.3. The viral removal in the growth medium includes both die-off and AD, while only natural die-off was considered in the lettuce root and shoot. AD kinetic constants as well as the growth medium viral decay constant in the hydroponic case were obtained by fitting the model to the data from DiCaprio et al. . Viral AD in soil has been investigated in both lab scale soil columns and field studies . In our model, viral AD constants in soil were obtained from the experiments of Schijven et al. , who investigated MS2 phage kinetics in sandy soil in field experiments. As the MS2 phage was transported with the water in soil, the AD rates changed with the distance from the source of viruses. To capture the range of AD rates, two scenarios of viral behavior in soils were investigated. Scenario 1 used the AD rates estimated at the site closest to the viral source , while scenario 2 used data from the farthest site . In contrast to lab scale soil column studies, field studies provided more realistic viral removal rates . Using surrogate MS2 phage for NoV provided conservative risk estimates since MS2 attached to a lesser extent than NoV in several soil types . The viral decay rate in the soil determined by Roberts et al. was adopted because the experimental temperature and soil type are more relevant to lettuce growing conditions compared to the other decay study . Decay rates in the root and shoot were used from the hydroponic system predictions.The transport model was fitted to log10 viral concentration data from DiCaprio et al. , extracted from graphs therein using WebPlotDigitizer . In these experiments, NoV of a known concentration was spiked in the feed water of hydroponic lettuce and was monitored in the feed water, the root and shoot over time.

While fitting the model, an initial feed volume of 800 mL was adopted and parameters producing final volumes of b200 mL were rejected. To fit the model while accounting for uncertainty in the data, a Bayesian approach was used to maximize the likelihood of the data given the parameters. A posterior distribution of the parameters was obtained by the differential evolution Markov chain  algorithm,strawberry gutter system which can be parallelized and can handle multi-modality of the posteriors distribution without fine tuning the jumping distribution. Computation was carried out on MATLAB R2016a and its ParCompTool running on the High Performance Computing facility at UC Irvine.Table 3 lists the parameters estimated by model fitting and their search bounds. Fitting data from DiCaprio et al. without including viral AD to the tank walls was attempted but the results were not used in the risk estimates due to the poor fit of model to the data. The rationale behind the model fitting procedure and diagnostics are discussed in Supplementary section S1H.A summary of the model fitting exercise for viral transport in hydroponic grown lettuce is presented in Fig. 2. Under the assumption of first order viral decay, NoV loads in water at two time points did not fall in the credible region of model predictions, indicating that mere first order decay was unsuitable to capture the observed viral concentration data. The addition of the AD factor into the model addressed this inadequacy and importantly supported the curvature observed in the experimental data. This result indicates the AD of viruses to hydroponic tank wall is an important factor to include in predicting viral concentration in all three compartments .The adequacy of model fit was also revealed by the credible intervals of the predicted parameters for the model with AD . Four of the predicted parameters: at, bt, kdec, s and kp, were restricted to a smaller subset of the search bounds, indicating that they were identifiable. In contrast, the viral transfer efficiency η and the kinetic parameters spanned the entirety of their search space and were poorly identifiable. However, this does not suggest that each parameter can independently take any value in its range because the joint distributions of the parameters indicate how fixing one parameter influences the likelihood of another parameter . Hence, despite the large range of an individual parameter, the coordination between the parameters constrained the model predictions to produce reliable outcomes . Therefore, the performance of the model with AD was considered adequate for estimating parameters used for risk prediction.Risk estimates for lettuce grown in the hydroponic tank or soil are presented in Fig. 4. Across these systems, the FP model predicted the highest risk while the 1F1 model predicted the lowest risk. For a given risk model, higher risk was predicted in the hydroponic system than in the soil. This is a consequence of the very low detachment rates in soil compared to the attachment rates. Comparison of results from Sc1 and Sc2 of soil grown lettuce indicated lower risks and disease burdens under Sc1 . Comparing with the safety guidelines, the lowest risk predicted in the hydroponic system is higher than the U.S. EPA defined acceptable annual drinking water risk of 10−4 for each risk model. The annual burdens are also above the 10−6 benchmark recommended by the WHO . In the case of soil grown lettuce, neither Sc1 nor Sc2 met the U.S. EPA safety benchmark. Two risk models predicted borderline disease burden according to the WHO benchmark, for soil grown lettuce in Sc1, but under Sc2 the risk still did not meet the safety guideline. Neither increasing holding time of the lettuce to two days after harvesting nor using bigger tanks significantly altered the predicted risk . In comparison, the risk estimates of Sales-Ortells et al. are higher than range of soil grown lettuce outcomes presented here for 2 of 3 models. The SCSA sensitivity indices are presented in Fig. 5. For hydroponically grown lettuce, the top 3 factors influencing daily risk are amount of lettuce consumed, time since last irrigation and the term involving consumption and ρshoot. Also, the risk estimates are robust to the fitted parameters despite low identifiability of some model parameters . For soil grown lettuce, kp appears to be the major influential parameter, followed by the input viral concentration in irrigation water and the lettuce harvest time. Scorr is near zero, suggesting lesser influence of correlation in the input parameters.In this study, we modeled the internalization and transport of NoV from irrigation water to the lettuce using ordinary differential equations to capture the dynamic processes of viral transport in lettuce. This first attempt is aimed at underscoring the importance of the effect of time in determining the final risk outcome. The modeling approach from this study may be customized for other scenarios for the management of water reuse practices and for developing new guidelines for food safety. Moreover, this study identifies critical gaps in the current knowledge of pathogen transport in plants and calls for further lab and field studies to better understand risk of water reuse.

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The main reason was a reduction in direct and indirect nitrous oxide emissions

Phase I also considered agricultural adaptation strategies that addressed regional issues such as hydrology, growers’ attitudes toward climate change, and urbanization versus preservation of farmland. These topics are explored in more quantitative ways here.Since 1960, total crop acreage in Yolo County has been declining. Vegetable and orchard crop areas have increased, while field crop acreage has declined . There has been an increase in higher‐revenue‐per‐acre crops, especially a shift out of barley, and a shift into more processing tomatoes, wine grapes, and walnuts. Many factors affect changes in acreage, including changes in market conditions , input supplies, and climate. Among factors affecting acreage decisions, we investigated whether changes in climate have affected acreage allocations across crops. If responses to climate changes in the past continue to hold in the future, we can use hisorical information to learn more about how crop acreages are likely to change in response to the forecasted Yolo County climate changes from 2010 to 2050. We developed econometric models that relate acreages of each major crop to relative prices and key climate variables . The models are applied to the data including 60 years of acreage for major crops and 100 years of local climate history. Our climate history indicates that during the past century, the increase in annual temperature appears to be mainly due to warmer winters rather than to warmer summers . There was a decrease of about 150 winter chill hours in the last 100 years. Using historical reationships between climate and acreage allows investigation of how forecasted climate changes in Yolo County may affect Yolo acreage patterns. Acreage projections use climate projections for the B1 and A2 scenarios from 2010 to 2050 with GCM data from GFDL‐BCCA. Acreage projections hold constant relevant drivers of crop acreage, except for local climate variables. Among field crops,planting gutter warmer winter temperatures were projected to cause wheat acreage to decline and alfalfa acreage to rise . Thus, future decisions to increase alfalfa acreage present an interesting implication for water use: wheat uses little irrigation; whereas, alfalfa is one of the more intense water users.

By 2050, tomato acreage is projected to increase compared to the current level . This is also related to the increase in growing degree days in the winter months. A warmer climate in late winter/early spring has allowed early planting and provided favorable conditions for establishment. The forecasted climate changes have only moderate impacts on projected tree and vine crop acreage, in part because the climate changes that have occurred have not yet affected key variables enough to induce a significant change in the acreage of perennials when market conditions have been favorable. Almond acreage is projected to increase slightly with warmer temperatures in 2035–2050 . Almonds have a relatively low winter chill hour requirement. Walnut acreage, however, would decline slightly ; it has a higher winter chill requirement. This is consistent with the finding that surveyed orchard growers express concern about a decrease in winter chill hours . These projections rely on using historical relationships between acreage change and climate variables change. They are based actual past responses of acreage to climate. However, no attempt is made to forecast the relative prices, technical changes, new markets, or other factors that will also affect acreage. Water supply vulnerabilities for agriculture and other sectors can be mediated through traditional infrastructure improvements or alternative water policies . Local stewardship that is implemented by water managers and agricultural users tends to be more economical and have less environmental impact than developing new supplies. One tool that has helped water resource managers integrate climate change projections into their decision making process is the Water Evaluation and Planning system . WEAP, a modeling platform that enables integrated assessment of a watershed’s climate, hydrology, land use, infrastructure, and water management priorities , is used here for the Yolo County Flood Control and Water Conservation District service area. It covers 41 percent of the county’s irrigated area and is located in the western and central portion of the county .Recognizing the key role that land‐use planning will play in achieving the goals of AB 32, legislators passed Senate Bill 375 in 2008, requiring sustainable land‐use plans that are aligned with AB 32 .

Local governments must address GHG mitigation in the environmental impact report that accompanies any update to their general plan or carry out a specific “climate action plan” . Emissions of GHG from agriculture are often missing from existing inventory tools geared to local planners. The local government of Yolo County was among the first in California to pass a climate action plan . This project contributed to this climate action plan, and developed a set of guidelines to estimate GHG emissions from agriculture within a local inventory framework . The Tier 1 methods used here have been adapted for local activity data largely from three main sources: the California Air Resources Board Technical Support Document for the 1990–2004 California GHG Emissions Inventory ; the U.S. Environmental Protection Agency Emissions Inventory Improvement Program Guidelines ; and the 2006 IPCC Guidelines for National GHG Inventories . In Yolo County, total agricultural emissions declined by 10.4 percent between 1990 and 2008 .Lower fertilizer use was driven by two important land use trends: a 6 percent reduction in the county’s irrigated cropland; and a general shift away from crops that have high N rates coupled with an expansion in alfalfa and grape area, which require less fertilizer . In both years, emissions of CO2, N2O, and methane from diesel‐powered mobile farm equipment were responsible for 20.0 to 23.0 percent of total agricultural emissions in Yolo County between 1990 and 2008 . Fuel consumption per unit area for several important crops offset the small decline in irrigated cropland. Using the Tier 1 method prescribed by ARB, emissions of CH4 from rice cultivation were estimated to increase from 25.9 to 31.2 kilotons carbon dioxide equivalent between 1990 and 2008, entirely due to an expansion in the area under rice cultivation. Studies also suggest that cultivation practices that combine straw incorporation and winter flooding tend to generate more CH4 emissions than burning rice straw . Thus, estimates generated using the DeNitrification‐DeComposition model showed a larger increase in emissions over the study period because the Tier 3 method accounted for changes in residue and water management made in compliance with the state air quality regulations that have phased out rice straw burning, and the increase in cultivated area . 

Many agricultural practices to mitigate GHG emissions offer agricultural co‐benefits. For example, economic factors are prompting local farmers to shift more of their land to crops that happen to require less N fertilizer and diesel fuel, and to adopt practices that reduce these inputs. Growers cite rising cost and market volatility of inputs, rather than mitigation per se, as a more immediate motivation to use fertilizer and fuel more efficiently. In 1990, emissions sources associated with urban areas accounted for approximately 86 percent of the total GHG emissions countywide,gutter berries while unincorporated areas supporting agriculture were responsible for 14 percent . If calculated on an area‐wide basis the county’s urban areas emitted approximately 152.0 tons CO2e per hectare per year . By contrast, this inventory results indicates that in 1990 Yolo County’s irrigated cropland averaged 2.16 t CO2e ha‐1 yr‐1 and that livestock in rangelands emitted only 0.70 t CO2e ha‐1 yr‐1 . This 70‐fold difference in the annual rate of emissions between urbanized land and irrigated cropland suggests that land‐use policies that protect existing farmland from urban development are likely to help stabilize and or reduce future GHG emissions, particularly if they are coupled with “smart growth” policies that prioritize urban infill over expansion .Many factors affect farmers’ perceptions and response to climate change; for example, characteristics of the individual farmer and their farm; social networks and involvement in programs run by local institutions, agricultural organizations, and extension services; and views on government programs and environmental policies. The goal of this sub-project is to: examine Yolo County farmers’ perceptions of climate change and its risks to agriculture; and develop a better understanding of how such factors might influence farmers’ adoption of proposed adaptation and mitigation practices. We conducted semi‐structured interviews with eleven farmers and two agricultural extension workers in the fall of 2010. The sampling strategy recruited respondents from a cross section of farm sizes, local cropping systems, and market orientations. Interviewers followed a set of open‐ended questions to minimize prompting and interviewer bias, and were used to develop a quantitative survey which was mailed to farmers in Yolo County during February and March of 2011. The survey sample was drawn from a list of 572 individuals who have submitted conventional or certified organic pesticide use permits to the Yolo County Agriculture Commissioner’s office. The final response rate was 34.0 percent. Results of the survey indicated that 54.4 percent of farmers agreed to some extent with the statement “the global climate is changing” . A minority indicated that local summer temperatures had decreased over time, while only 5.6 percent observed an increase. While contrary to statewide mean temperatures, this corresponds with local climate records which show little change in maximum summer temperature over the last century . A majority of farmers indicated that rainfall, drought, and flooding had not changed over the course of their career, but a sizable minority reported water availability had decreased and <1 percent said it had increased. In 1976, the newly constructed Indian Valley Reservoir began supplementing the District’s surface water supplies to local growers.

However, a recent drought in 2009 and 2010 reduced water releases in those years to less than 40 percent of the average for the preceding decade . The memory of this recent a drought may therefore occupy a central place in farmers’ perception of water related trends. Respondents with greater concern for drought and less reliable water were more likely to pump groundwater, drill new wells, and adopt drip irrigation . A farmer’s views on climate change affected the inclination to implement voluntary mitigation practices. More specifically, farmers who disagreed with the statement “The global climate is changing” were less likely to adopt mitigation practices than those who agreed with the statement. Likewise, skepticism that human activities are an important cause of climate change meant less inclination to adopt mitigation practices. Farmers who had frequent contact with local agricultural organizations were more likely to implement mitigation strategies Farmers are often more concerned about the future impact of government regulations than they are about the direct impacts of climate change. This ranking of concern is not surprising given the gradual nature of climate change. However, it does underscore the importance of understanding how farmers view environmental regulations and the information needed to influence their likelihood to adopt mitigation and adaptation practices. Strategies to expand the reach of local agricultural organizations and government conservation programs by improving farmer participation in their activities are thus seen as an important way to strengthen adaptation and mitigation efforts.UPlan relies on a number of demographic inputs . Attractors are given a positive value . Discouragements are given negative values . A system of weights is used to rank the attractive or discouraging property of each variable. We modified UPlan to allow development within existing urban areas, on the assumption that a significant urban redevelopment is likely within the 2010–2050 time frame. The A2 scenario loses two times more acreage of high quality soils to urbanization compared to B1 . One of the most striking findings is just how little land is required to house future populations at higher densities. The B1 and AB 32+ scenarios require 44 percent and 7 percent of the urbanized land of the A2 scenario, respectively. Even holding population increase constant at B1 levels, these scenarios use 63 percent and 38 percent of the land of the A2 scenario, most or all of it within existing urban areas, and also greatly reduce GHG emissions from transportation. These results suggest that the most important climate change mitigation policy that Yolo County could adopt would be to restrict urban development to infill locations within existing cities, and to keep existing farmland in agriculture.

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Each enclosure contained an array of six rectangular PIT antennas arranged in the same orientation

Given that the proposed California threshold is 0%, a scenario in which both GM and non-GM products are offered side-by-side in the market seems unlikely. Some non-GM products may remain unlabeled if food companies are able to find substituting ingredients that are not at any risk of containing GM. But certified non-GM products will mostly disappear. As U.S. corn, canola, and soybean production uses primarily GM varieties, Prop 37 labeling standards will force change in the composition of retail products offered. As the initiative applies only to California, it may not be profitable to undergo a reduction of GM inputs for one state. If this is the case, then the vast majority of food products that are not completely GM-free will bear the new label. As a consequence, a fraction of consumers now wary of the label may shift their consumption towards organic. Such a transition implies potential gains for organic growers but potential losses for conventional growers. Today, a move towards “non-GM” or “naturally grown” labels is underway, especially with natural grocers. Some organic corn and soybean growers in the U.S. have converted back to conventional with non-GM seeds, thereby saving labor and other costs, while still getting similar price premia. The “non-GM” or “natural” products are the closest competition for organic products now; but they will be reduced or eliminated with Prop 37 due to forced relabeling and the prohibition of terms such as “naturally grown” on food labels . Table 4 outlines the likely impacts of Prop 37 on various categories of food and beverages.conducted a series of field studies during 2012-2017. To test fish and food web responses within different land-management scenarios, we conducted our project on standard rice and winter wheat fields, adjacent fallow lands,stackable planters and rice fields with different harvest practices or other experimental modifications. This work yielded several publications that provided insight into habitat conditions in flooded rice fields for fish and invertebrates . The focus of our effort was on rearing habitat for young Chinook Salmon, but this work may also be relevant to other native fishes.

The goal of this paper is to summarize the key lessons learned from 6 years of research on the feasibility of using farm fields as rearing habitat for juvenile Chinook Salmon in the Yolo Bypass and other Central Valley locations. Our hope is that our summary will provide guidance to future researchers, as well as inform managers as they evaluate potential management approaches. An important caveat is that our studies were not intended as a proof of concept for any specific management actions. Rather, our research was intended to examine some of the attributes that could reduce limitations to rearing conditions identified in early research, and gain insight into some of the key considerations for potential future agricultural floodplain management. A second major caveat is that we had to rely on juvenile hatchery Chinook Salmon as a surrogate for wild Chinook Salmon, our ultimate target for habitat restoration. We recognize that there are several potential differences in the behavior of hatchery and wild Chinook Salmon . However, hatchery salmon were the only feasible alternative in this case since downstream migrating wild juvenile Chinook Salmon were mostly cut off from the Yolo Bypass because of extreme drought conditions. Nonetheless, hatchery salmon have been used successfully as a research tool in many types of ecological studies, so many of the lessons learned here should have at least some relevance to wild Sacramento River Chinook Salmon. Finally, our project was separate from a number of other fish management research projects in agricultural parcels, such as current efforts to investigate whether invertebrates grown on flooded rice fields can be used as a food subsidy for adjacent river channels . The Yolo Bypass is a 24,000-ha, partially leveed flood basin that is used to safely convey floodwaters away from Sacramento Valley communities . The Yolo Bypass contains a suite of habitats including agricultural lands, managed wetlands, upland habitat, and perennial ponds and channels, with broad open-water tidal wetlands at its downstream end where it joins the Sacramento-San Joaquin Delta .

The basin receives seasonal inflow from the Sacramento River, Colusa Basin , Cache Creek, and Putah Creek, as well as substantial perennial tidal flow from the San Francisco Estuary via the lower Sacramento River at the downstream end of the floodplain . The Yolo Bypass floods to various degrees in approximately 80% of water years, but inundation events are often relatively short and sometimes driven entirely by inflow from the west-side tributaries. The most substantial flow events come from the Sacramento River, which enters the Yolo Bypass via Fremont Weir and Sacramento Weir. However, in drought periods, such as during 2012-2015, there is little or no flooding.For each year, we evaluated water quality , food web responses , and fish growth and condition . Water temperature in fields was recorded continuously at 10- to 15-minute intervals with Onset HOBO® loggers, and a suite of other water-quality parameters was measured and recorded using handheld and continuously installed multi-parameter sondes. We included plankton sampling with the broad goal of characterizing the communities and densities of phytoplankton and zooplankton in the study fields. Because long-term monitoring of the Yolo Bypass includes weekly plankton sampling in both the perennial Yolo Bypass channel of the Toe Drain and the Sacramento River, we could compare our experimental fields to productivity across habitats. Because the study fields were shallow compared to canal and riverine channel environments, sampling methods had to be slightly modified compared to the Toe Drain and Sacramento River. As a result, we used hand-tosses of a smaller 30-cm zooplankton net , recording the length of the toss, and the relative percent of the net mouth that was submerged during net retrieval. Detailed methods for zooplankton sampling are described in Corline et al. . Fish used in the experiments were primarily fall-run Chinook Salmon parr obtained from Feather River Fish Hatchery; however, small numbers of wild Sacramento River Chinook Salmon were also studied in 2013 and 2013, 2015, and 2016 . The majority of the study fish were free swimming throughout the flooded fields, but mesh cages were also used as a tool to compare hatchery salmon growth and survival across substrates in 2012 or habitats in 2016 and 2017. The initial study year was a pilot effort to evaluate whether managed flooding of a rice field could provide suitable habitat for juvenile salmon rearing, and to assess associated growth and survival. A single 2-ha field contained a patchwork of four agricultural substrate types, including disced , short rice stubble , high rice stubble , and fallow vegetation. Approximately 10,200 juvenile salmon were released in the field, with a subset implanted with passive integrated transponder tags, so individuals could be identified, and individual growth rates could be measured. Twenty PIT-tagged fish were also released in each of eight enclosures placed over patches of the different substrate types, to determine if growth rates differed .Substrates in flooded rice fields differ from those that juvenile salmon may encounter in natural floodplains or riverine systems. Thus, the goal of the second study year was to investigate whether juvenile salmon had differential growth and survival rates across agricultural substrates,stacking pots and whether they would preferentially use a specific substrate type when given a choice. Our logic was that understanding these responses could provide insight into whether some agricultural practices provide more suitable salmon rearing conditions than others.

To compare growth and survival rates across rice stubble, disced, and fallow substrates, we created a series of nine 0.8-ha experimental fields with individual inlets and outlets, with three replicates of each substrate . We placed approximately 4,600 hatchery origin juvenile Chinook Salmon in each field for 40 days and measured weekly during the study period to estimate average growth rates. To examine substrate preference, we used PIT-tag technology to track individual fish in two large circular enclosures . In addition to examining the potential for preference among agricultural substrates, this study also investigated whether newer and smaller PIT tags were viable for detecting juvenile salmon movements in these habitats. One enclosure included three habitat treatments , and the other served as a comparison with only the disced treatment.Fish remained in the enclosures for 14 days, during which occupancy data were collected. Detailed methods can be found in Conrad et al. .As an engineered floodplain, the Yolo Bypass is designed to drain efficiently. During moderate inundation events, availability of floodplain habitat can be brief—persisting for a week or less. In 2016, our focus was to test the feasibility of using agricultural infrastructure to extend the duration of a small to moderate flood event, increasing the length of time flooded habitat was available to fish. We called this idea “flood extension.” We planned similar studies in other study years, but extreme weather events prevented implementation . Landowner partners in the Yolo Bypass at Knaggs Ranch, Conaway Ranch, and Swanston Ranch agreed to maintain shallow inundation for 3 to 4 weeks in a designated experimental field after a natural flood event. At Knaggs Ranch, the landowner made modest to extensive modifications to the drainage infrastructure to allow more control over the drainage rate from the inundated field to the Toe Drain. At Swanston and Conaway ranches, inundation was maintained with flash boards, which could be removed once it was time to drain the field. During the first week of flood extension, we held stocked hatchery salmon and any entrained natural-origin salmon, allowing us to estimate growth and survival rates upon drainage. Thereafter, we allowed salmon to leave fields if they chose to do so. We outfitted field drains with a plastic mesh live-car trap, where we captured and measured emigrating individuals before they proceeded downstream. In 2016, the attempt to test a “flood extension” concept was unsuccessful because inundation occurred late in the season, resulting in unsuitably warm water temperatures for juvenile salmon in our experimental fields. We therefore made a second attempt to conduct a flood extension pilot in 2017 at Knaggs Ranch, Conaway Ranch, and Swanston Ranch, and at a new site in the Yolo Bypass Wildlife Area located south of Interstate 80 between the cities of Davis and Sacramento . Field infrastructure was identical to 2016, with the YBWA utilizing flash boards to hold water in similar fashion to Conaway and Swanston ranches. As we describe below, high flows made it infeasible to complete the flood extension work, although we were still able to conduct water-quality and food-web sampling, along with the use of experimental cages to evaluate salmon growth comparatively across experimental sites.Previous research has shown that inundated Yolo Bypass floodplain habitat typically has substantially higher densities of phytoplankton, zooplankton, and drift invertebrates than the adjacent Sacramento River across a suite of water year types . Our studies consistently showed that managed inundation of agricultural fields supported statistically higher levels of phytoplankton and invertebrates than the Sacramento River . Also notable was that phytoplankton and zooplankton densities in our flooded experimental fields in Yolo Bypass were higher than those measured during river inundated flood events and in the Toe Drain, a perennial tidal channel . In addition, the invertebrate community in flooded rice fields was completely dominated by zooplankton , particularly Cladocera, whereas drift invertebrates such as Diptera were found in higher concentrations in study sites at Conaway Ranch and Dos Rios. Drift invertebrates are often a more substantial part of the food web in natural flood events in Yolo Bypass . Nonetheless, zooplankton densities can be relatively high in Yolo Bypass during dry seasons and drought years . The specific reasons for these differences include longer residence time and shallower depths in the Yolo Bypass than in adjacent perennial river channels . Water source also may have been important for quantity and composition of invertebrates, including zooplankton, since all the managed flooding work was conducted using water from Knights Landing Ridge Cut, not the Sacramento River.Given the high densities of prey in the flooded fields, along with the low metabolic costs of maintaining position in a relatively low-velocity environment, it is not surprising that growth rates of juvenile salmon were comparatively high . This result was consistent across approaches used: cages, enclosures open to the substrate, and free-swimming fish.