When cages were used, salmon were PIT tagged to track individual fish growth rates within a specific habitat. We consistently found that salmon growth rates in cages placed in flooded in rice fields were higher than growth rates for juvenile Chinook Salmon of comparative life stage in any of the adjacent riverine habitats and in other regions . Growth rates were also comparatively high when free-swimming salmon were introduced into larger-scale, 0.8-ha flooded agricultural fields. These studies were more representative than those using cages of how migrating salmon might use these habitats under natural flow events. For the multiple years that free-swimming salmon were used , they averaged a mean daily growth rate of 0.98mm d−1. Throughout all study years, caged salmon and free-swimming salmon showed very similar growth rates within the same experimental study units, despite the fact that they likely experienced different micro-habitat conditions . This observation suggests that our salmon growth results were not influenced by cage effects, a well-known issue in enclosure studies . To better understand managed floodplain processes across the region, in 2015, salmon were introduced in fields at a variety of locations in the Central Valley with various vegetative substrates: Sutter Bypass , three locations on the Yolo Bypass , and Dos Rios Ranch at the confluence of the Tuolumne and San Joaquin rivers . At all of the locations,strawberry gutter system juvenile Chinook Salmon grew at rates similar to those observed in experiments conducted at Knaggs Ranch in the Yolo Bypass during previous study years.
These results suggest that multiple geographical regions and substrate types can support high growth rates of juvenile Chinook Salmon. A key objective of our work in flooded fields was to determine whether substrate type has a measurable influence on growth and survival of juvenile Chinook Salmon. Substrate and vegetation can be an important micro-habitat feature for young Chinook Salmon , so we posited that there could potentially be some difference in salmon performance across treatments. In 2013, we examined this question across different substrate types in two ways: telemetry studies using PIT tags; and replicated fields. Both approaches indicated that juvenile salmon did not have a clear preference for different substrates, and grew at similar rates across substrates.We monitored the movements and use of PIT-tagged, hatchery-origin juvenile Chinook Salmon for approximately 1 month over fallowed, disced, and rice stubble substrates in two circular enclosures to determine if there was any preferential use. One enclosure included all three substrates, and one contained only disced substrate .Although growth rates were slightly higher in the enclosure that contained all three substrate types, juvenile salmon grew at very high rates, averaging 1.1mm/d regardless of enclosure. These growth rates were higher than other published growth rates for juvenile Chinook Salmon in the Yolo Bypass, and the region generally .Throughout the 2012–2016 study period, we consistently observed that juvenile Chinook Salmon were attracted to sources of inflow, and that this sometimes became the dominant factor in the distribution of salmon on experimental fields or in enclosures.
In the previously described PITtag observations in 2013, salmon in both enclosures positioned themselves nearest the inflow, regardless of surrounding habitat structure . This result is not surprising, given that juvenile stream salmonids commonly adopt and defend flow oriented positions in stream environments for acquisition of drifting food resources. On flooded agricultural fields, this orientation toward flow may not only be related to feeding behavior but may also serve to keep juvenile salmon in habitat areas that are hydrologically connected and have higher velocities. In fact, analyses of the environmental factors that predict movement of large groups of tagged juvenile Chinook Salmon in the Yolo Bypass found that drainage of flooded areas was a reliable predictor of fish emigration at downstream trapping stations . Although juvenile Chinook Salmon growth rates were consistently high across substrates and study years, we observed highly variable survival of salmon, and available evidence from the studies suggests that this was related, at least in part, to differences among years in drainage rates of the study fields and habitat availability on the floodplain at large. For example, survival in 2013 ranged from 0.0% to 29.3% in the replicated fields containing different agricultural substrates. This variability was likely unrelated to substrate type; instead, these low survival rates were most likely a result of very dry conditions across Yolo Bypass and the Central Valley, generally, when record drought conditions prevailed during 2012–2015, which affected water quantity and quality. In 2013, our replicated field study likely presented one of the only wetted floodplain areas for miles around, and thus presented a prime feeding opportunity for avian predators such as cormorants, herons, and egrets. However, when the same set of fields was used in 2016, survival was much higher . This was generally a wetter period, avian predation pressure was reduced, and we more efficiently opened the flash boards to facilitate faster drainage and fish emigration.
Note, however, there were some differences in methodology among years, which may have contributed to survival variability. Taken together, these observations of free swimming salmon survival suggest that field drainage rate, and overall floodplain habitat availability, are important factors for improving survival in managed agricultural floodplain habitats. Our observations of juvenile salmon orientation to flow, and the importance of efficient drainage on survival, reinforce observations from natural floodplains that connectivity between perennial channel habitat and seasonal floodplain habitat is an essential attribute of river-floodplain systems . Connectivity of managed floodplain habitats to unmanaged habitats in the river and floodplain is therefore a foundational condition needed to allow volitional migration of juvenile salmon. Further research is needed to identify how to provide sufficient connectivity to maximize rearing and migration opportunities for wild Chinook Salmon.Natural and managed floodplain habitat is subject to a variety of flow and environmental conditions. Variation in flow and temperature dictates when and where managed agricultural habitats may be accessible and suitable for rearing salmonids, with challenges during both wet and dry years, as well as during warm periods. As noted previously, survival in the replicated fields was variable but generally low. We associate these results with the effects of extreme drought conditions that prevailed during the core of our study from 2012 through 2015. Although our field studies were conducted during a time of year when wild salmon have historically used the Yolo Bypass floodplain , the extreme drought made for warm water temperatures, and resulted in our study site being one of the few inundated wetland locations in the region. As such, avian predators were attracted to the experimental fields, exacerbating salmon mortality during drainage. We observed high concentrations of cormorants, herons, and egrets on the experimental fields, and this concentration increased over the study period. As many as 51 wading birds and 23 cormorants were noted during a single survey. The small scale of our project could have further exacerbated predation issues. This situation highlights the importance of the weather dependent,fodder system for sale regional context of environmental conditions, which govern how and when managed floodplains can be beneficial rearing habitats for juvenile salmon. Under certain circumstances, flooded fields can generate high salmon growth but in other scenarios, these habitats can provide poor environmental conditions for salmonids and/or become predation hot spots. Even during wetter conditions, we found that management of agricultural floodplain habitat was challenging. For example, we had hoped to test the idea of using rice field infrastructure to extend the duration of Yolo Bypass inundation events in an attempt to approximate the longer-duration events of more natural floodplains; that is, through flood extension. As noted by Takata et al. , use of the Yolo Bypass by wild Chinook Salmon is strongly tied to hydrology, and salmon quickly leave river-inundated floodplains once drainage begins. We therefore reasoned that flooded rice fields might provide an opportunity to extend the duration of flooding beyond the typical Yolo Bypass hydrograph. In 2015, a flood extension study was planned but not conducted because drought conditions precluded Sacramento River inflow via Fremont Weir. To test the flood extension concept in 2016, we needed substantial landowner cooperation and assistance to install draining structures that allowed maintenance of local flooding after high flow events. Even then, we found it difficult to maintain water levels and field integrity during the tests. In our case, we were fortunate to have the cooperation of willing landowners. Partnership with landowners was key, and would be critical with any future efforts to test the concept of flood extension. We also planned a similar test in 2017, but high and long-duration flood flows prevented the study from occurring.
Over the 6 years of study, except perhaps for 2013 when we focused on other study priorities, we never experienced ideal conditions to adequately test the flood extension concept. We were either in a severe drought, during which the Yolo Bypass did not flood from the river, or we experienced severe and sustained flooding, which made it impossible to contain flood waters within study fields. Based on these experiences, studying the concept of flood extension appears to depend on the occurrence of moderate flood events at the right time of year , provided fields are appropriately designed to hold water and allow efficient immigration and emigration of potentially large numbers of juvenile salmon. However, significant outreach and communication is necessary with landowners to maintain floodwaters on their fields during the natural drainage period. Because these events cannot be predicted well ahead of time, these communications—and availability of robust infrastructure—need to be constantly maintained even outside the flood extension period. As suggested in the previous section, such potential actions would need to be taken in a way that maintains hydrologic connectivity and salmon access, so that salmon can successfully locate potential managed habitats, use them for rearing, and then successfully emigrate from them at the appropriate time. Timing of such potential manipulations is critical because previous sampling has shown that salmon quickly emigrate from the floodplain during large scale drainage events , leaving relatively low densities of salmon in remaining ponded areas to potentially benefit from flood extension. Although our use of hatchery salmon gave us more experimental options during drought conditions, the use of these fish resulted in additional challenges. Our approach relied on a non-traditional use of hatchery salmon, which required a suite of permits and approvals to execute the project. As noted above, the project coincided with a major drought, so access to hatchery salmon was limited as a result of low salmon population levels. In addition, use of hatchery salmon affected the time-period when we could conduct experimental work. We were unable to test salmon response to early season flooding , because the hatchery salmon were too small to receive coded-wire tags as required under our permit conditions. Similarly, the timing of our work was affected by the availability of holding tanks at our partner hatchery , and by the availability of transport staff and vehicles to move salmon to our study site. While we were able to assess many important biological metrics in our study, direct measurement of the population-level effect of floodplain rearing on agricultural habitats proved elusive. A traditional approach to addressing this question involves inserting CWTs into very large numbers of experimental salmon and estimating the population response from expanded CWT recaptures in the ocean fisheries. Recoveries of CWTs in adult salmon from experimental releases made in the Yolo Bypass have generally been very low , making it difficult to get a high level of resolution with which to reliably compare survival rates, including with values in the literature. Although CWT recoveries could potentially be improved by increasing the number of tagged salmon, the effort required even to collect a single data point would be substantial and is limited by the availability of surplus hatchery salmon. A related issue is that it is difficult to design a survival experiment that provides a useful comparison to other management strategies or migration corridors. For example, it is challenging to assess the incremental survival value of flooded agricultural habitat versus adjacent perennial channels . Telemetry can partially address this issue, but current acoustic tagging technology does not allow estimates of survival once smolts emigrate from the estuary, and is also limited in the size of salmon that can be tagged.