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Community assembly has been an important topic in ecological research and theory for over a century. Recently, restoration ecologists have emphasized the use of community assembly rules, such as environmental filtering, to better inform management actions. Although there has been a strong call for the use of community assembly rules in terrestrial restoration ecology, few studies have examined their potential use in providing habitat benefits such as food resources to native species in large‐scale managed aquatic ecosystems. In this study, we found evidence of deterministic community assembly mechanisms in zooplankton communities in floodplain and seasonally inundated off‐channel habitats in California’s Central Valley. Additionally, we found that all sampled off‐channel floodplain habitat types had similar zooplankton communities and that assembly in floodplain habitats was governed by variables associated with increased water residence time. This study is the first to determine community assembly rules in floodplain‐river ecosystems in order to assist managers in providing floodplain food‐web benefits to native fish and wildlife species at the landscape scale.

Floodplains represent critical nursery habitats for a variety of fish species due to their highly productive food webs, yet few tools exist to quantify the extent to which these habitats contribute to ecosystem-level production. Here we conducted a large-scale field experiment to characterize differences in food web composition and stable isotopes (δ¹³C, δ¹⁵N, δ³⁴S) for salmon rearing on a large floodplain and adjacent river in the Central Valley, California, USA. The study covered variable hydrologic conditions including flooding (1999, 2017), average (2016), and drought (2012–2015). In addition, we determined incorporation rates and tissue fractionation between prey and muscle from fish held in enclosed locations (experimental fields, cages) at weekly intervals. Finally, we measured δ³⁴S in otoliths to test if these archival biominerals could be used to reconstruct floodplain use. Floodplain-reared salmon had a different diet composition and lower δ13C and δ³⁴S (δ¹³C = -33.02±2.66‰, δ³⁴S = -3.47±2.28‰; mean±1SD) compared to fish in the adjacent river (δ¹³C = -28.37±1.84‰, δ³⁴S = +2.23±2.25‰). These isotopic differences between habitats persisted across years of extreme droughts and floods. Despite the different diet composition, δ¹⁵N values from prey items on the floodplain (δ¹⁵N = 7.19±1.22‰) and river (δ¹⁵N = 7.25±1.46‰) were similar, suggesting similar trophic levels. The food web differences in δ13C and δ³⁴S between habitats were also reflected in salmon muscle tissue, reaching equilibrium between 24–30 days (2014, δ¹³C = -30.74±0.73‰, δ³⁴S = -4.6±0.68‰; 2016, δ¹³C = -34.74 ±0.49‰, δ³⁴S = -5.18±0.46‰). δ³⁴S measured in sequential growth bands in otoliths recorded a weekly time-series of shifting diet inputs, with the outermost layers recording time spent on the floodplain (δ³⁴S = -5.60±0.16‰) and river (δ³⁴S = 3.73±0.98‰). Our results suggest that δ¹³C and δ³⁴S can be used to differentiate floodplain and river rearing habitats used by native fishes, such as Chinook Salmon, across different hydrologic conditions and tissues. Together these stable isotope analyses provide a toolset to quantify the role of floodplains as fish habitats.

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in California’s Central Valley have emerged as ecologically functioning floodplain rearing habitat for juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods to enhance habitat benefits for fall-run Chinook Salmon reared on winter-flooded rice fields in the Yolo Bypass, a modified floodplain managed for flood control, agriculture, and wildlife habitat in the Sacramento River Valley of California. Investigations included studying the effect of 1) post-harvest field substrate; 2) depth refugia; 3) duration of field drainage; and 4) duration of rearing occupancy on in-situ diet, growth and survival of juvenile salmon. Post-harvest substrate treatment had only a small effect on the lower trophic food web and an insignificant effect on growth rates or survival of rearing hatchery-origin, fall-run Chinook Salmon. Similarly, depth refugia, created by trenches dug to various depths, also had an insignificant effect on survival. Rapid field drainage yielded significantly higher survival compared to drainage methods drawn out over longer periods. A mortality of approximately one third was observed in the first week after fish were released in the floodplain. This initial mortality event was followed by high, stable survival rates for the remainder of the 6-week duration of floodplain rearing study. Across years, in-field survival ranged 7.4–61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in California’s recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant than those sampled concurrently in the adjacent Sacramento River channel. Correspondingly, observed somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater than concurrently and previously observed growth rates in the adjacent Sacramento River. The abundance of food resources and exceptionally high growth rates observed during these experiments illustrate the potential benefits of using existing agricultural infrastructure to approximate the floodplain wetland physical conditions and hydrologic patterns (shallow, long-duration inundation of cool floodplain habitats in mid-winter) under which Chinook Salmon evolved and to which they are adapted.

Author(s): Sommer, Ted; Schreier, Brian; Conrad, J. Louise; Takata, Lynn; Serup, Bjarni; Titus, Rob; Jeffres, Carson; Holmes, Eric; Katz, Jacob | Abstract: Large areas of California’s historic floodplain have been separated from adjacent river channels by levee construction, allowing the development of an extensive agricultural industry. Based on successful partnerships between agriculture and conservation groups to support migrating waterfowl, we examined whether seasonally flooded rice fields could be modified to provide off-channel rearing habitat for juvenile Chinook Salmon Oncorhynchus tshawytscha. During winter and spring of 2012-2017, we conducted a series of experiments in Yolo Bypass and other regions of California’s Central Valley using hatchery Chinook Salmon as a surrogate for wild Chinook Salmon, the management target for our project. Overall, we found that seasonally flooded fields are highly productive, resulting in significantly higher levels of zooplankton and high Chinook Salmon growth rates as compared to the adjacent Sacramento River. We found similar results for multiple geographical areas in the Central Valley, and in different cover types, such as non-rice crops and fallow areas. Although field substrate type did not detectably affect fish growth and survival, connectivity with upstream and downstream areas appeared to drive fish occupancy, because rearing young salmon were generally attracted to inflow in the fields, and not all of the fish successfully emigrated off the fields without efficient drainage. In general, we faced numerous logistic and environmental challenges to complete our research. For example, periodic unmanaged floods in the Yolo Bypass made it difficult to schedule and complete experiments. During severe drought conditions, we found that managed agricultural habitats produced low and variable salmon survival results, likely because of periodically high temperatures and concentrated avian predation. In addition, our project required substantial land-owner time and effort to install and maintain experimental fields. Recent and future infrastructure improvements in Yolo Bypass could substantially improve options for experimental work and broaden efforts to enhance salmon habitat.

Similar to many large river valleys globally, the Sacramento River Valley has been extensively drained and leveed, hydrologically divorcing river channels from most floodplains. Today, the former floodplain is extensively managed for agriculture. Lack of access to inundated floodplains is recognized as a significant contributing factor in the decline of native Chinook Salmon (Oncorhynchus tshawytscha). We observed differences in salmon growth rate, invertebrate density, and carbon source in food webs from three aquatic habitat types—leveed river channels, perennial drainage canals in the floodplain, and agricultural floodplain wetlands. Over 23 days (17 February to 11 March, 2016) food web structure and juvenile Chinook Salmon growth rates were studied within the three aquatic habitat types. Zooplankton densities on the floodplain wetland were 53x more abundant, on average, than in the river. Juvenile Chinook Salmon raised on the floodplain wetland grew at 0.92 mm/day, 5x faster than fish raised in the adjacent river habitat (0.18 mm/day). Two aquatic-ecosystem modeling methods were used to partition the sources of carbon (detrital or photosynthetic) within the different habitats. Both modeling approaches found that carbon in the floodplain wetland food web was sourced primarily from detrital sources through heterotrophic pathways, while carbon in the river was primarily photosynthetic and sourced from in situ autotrophic production. Hydrologic conditions typifying the ephemerally inundated floodplain—shallower depths, warmer water, longer water residence times and predominantly detrital carbon sources compared to deeper, colder, swifter water and a predominantly algal-based carbon source in the adjacent river channel—appear to facilitate the dramatically higher rates of food web production observed in the floodplain. These results suggest that hydrologic patterns associated with seasonal flooding facilitate river food webs to access floodplain carbon sources that contribute to highly productive heterotrophic energy pathways important to the production of fisheries resources.

Accurate methods for tracking individuals are crucial to the success of fisheries and aquaculture management. Management of migratory salmonid populations, which are important for the health of many economies, ecosystems, and indigenous cultures, is particularly dependent on data gathered from tagged fish. However, the physical tagging methods currently used have many challenges including cost, variable marker retention, and information limited to tagged individuals. Genetic tracking methods combat many of the problems associated with physical tags, but have their own challenges including high cost, potentially difficult marker design, and incompatibility of markers across species. Here we show the feasibility of a new genotyping method for parent-based tagging (PBT), where individuals are tracked through the inherent genetic relationships with their parents. We found that Rapture sequencing, a combination of restriction-site associated DNA and capture sequencing, provides sufficient data for parentage assignment. Additionally, the same capture bait set, which targets specific restriction-site associated DNA loci, can be used for both Rainbow Trout Oncorhynchus mykiss and Chinook Salmon Oncorhynchus tshawytscha. We input 248 single nucleotide polymorphisms from 1,121 samples to parentage assignment software and compared parent-offspring relationships of the spawning pairs recorded in a hatchery. Interestingly, our results suggest sperm contamination during hatchery spawning occurred in the production of 14% of offspring, further confirming the need for genetic tagging in accurately tracking individuals. PBT with Rapture successfully assigned progeny to parents with a 98.86% accuracy with sufficient genetic data. Cost for this pilot study was approximately $3 USD per sample. As costs vary based on the number of markers used and individuals sequenced, we expect that when implemented at a large-scale, per sample costs could be further decreased. We conclude that Rapture PBT provides a cost-effective and accurate alternative to the physical coded wire tags, and other genetic-based methods.

Differences in basal carbon sources, invertebrate density and salmon growth rate were observed in food webs across a lateral transect of aquatic habitats in the Sacramento River Valley, California. Similar to many large river valleys globally, the Sacramento River Valley has been extensively drained and leveed, hydrologically divorcing most floodplain wetlands and off-channel aquatic habitats from river channels. Today, the former floodplain is extensively managed for agriculture and wildlife habitat. Food web structure and juvenile Chinook Salmon (Oncorhynchus tshawytscha) growth were compared in three aquatic habitat types–river channel, a perennial drainage canal in the floodplain, and agricultural floodplain wetlands, which was seasonally inundated to provide bird and fish habitat during the non-agricultural growth season (late winter). Zooplankton densities on the floodplain wetland were 53 times more abundant, on average, than in the river. Juvenile Chinook Salmon raised on the floodplain wetland grew at mm/day, a rate 5x faster than fish raised in the adjacent river habitat (0.18 mm/day). Mean water residence times calculated for the floodplain agricultural wetland, perennial drainage canal and Sacramento River were 2.15 days, 23.5 seconds, and 1.7 seconds, respectively. Carbon in the floodplain wetland food web was sourced primarily through heterotrophic detrital pathways while carbon in the river was primarily autotrophic and sourced from in situ phytoplankton production. Hydrologic conditions typifying the ephemeral floodplain-shallower depths, warmer water, longer residence times and detrital carbon sources compared to deeper, colder, swifter water and an algal-based carbon source in the adjacent river channel-appear to facilitate the dramatically higher rates of food web production observed in floodplain verses river channel habitats. These results suggest that hydrologic patterns associated with winter flooding provide Mediterranean river systems access to detrital carbon sources that appear to be important energy sources for the production of fisheries and other aquatic resources.

Passive integrated transponder (PIT) technology allows passive, individual identification of small fish, making it a potentially useful tool to address an information gap of juvenile salmon habitat use in off-channel environments. We investigated the combined use of field enclosures and PIT technology as a method for studying the habitat preference of juvenile Chinook Salmon Oncorhynchus tshawytscha on a flooded rice field, a potential surrogate for lost floodplain habitat. We stocked two field enclosures (182 m2) with 42 juvenile salmon. One enclosure had equal portions of rice stubble, disced, and fallow habitat treatments, and the second contained only the disced treatment. Fish were tagged with 8- or 12-mm-sized PIT tags, and generated approximately 1 million detections in each enclosure over 14 d. We used a condensing procedure to reduce the data volume while preserving habitat use patterns. The smaller 8-mm tags were only detected along antenna edges, and the 12-mm tags had broader but more ...

When inundated by floodwaters, river floodplains provide critical habitat for many species of fish and wildlife, but many river valleys have been extensively leveed and floodplain wetlands drained for flood control and agriculture. In the Central Valley of California, USA, where less than 5% of floodplain wetland habitats remain, a critical conservation question is how can farmland occupying the historical floodplains be better managed to improve benefits for native fish and wildlife. In this study fields on the Sacramento River floodplain were intentionally flooded after the autumn rice harvest to determine if they could provide shallow-water rearing habitat for Sacramento River fall-run Chinook salmon (Oncorhynchus tshawytscha). Approximately 10,000 juvenile fish (ca. 48 mm, 1.1 g) were reared on two hectares for six weeks (Feb-March) between the fall harvest and spring planting. A subsample of the fish were uniquely tagged to allow tracking of individual growth rates (average 0.76 mm/day) which were among the highest recorded in fresh water in California. Zooplankton sampled from the water column of the fields were compared to fish stomach contents. The primary prey was zooplankton in the order Cladocera, commonly called water fleas. The compatibility, on the same farm fields, of summer crop production and native fish habitat during winter demonstrates that land management combining agriculture with conservation ecology may benefit recovery of native fish species, such as endangered Chinook salmon.

California contains the southernmost native populations of most Pacific Coast salmon and trout, many of which appear to be rapidly headed toward extinction. A quantitative protocol was developed to determine conservation status of all salmonids native to the state. Results indicate that if present trends continue, 25 (78%) of the 32 taxa native to California will likely be extinct or extirpated within the next century,followingthebulltrout(Salvelinus confluentus), which was extirpated in the 1970s. California's salmo- nids are adapted to living in a topographically diverse region with a Mediterranean climate, characterized by extreme seasonal and inter-annual variability in streamflow. Consequently, California salmonids have evolved extraordinary life history diversity to persist in the face of stressful conditions that often approach physiological limits. The spatial distributions of California salmonids vary from wide-ranging anadro- mous forms to endemic inland forms persisting in only a few kilometers of stream. Eighty-one percent of anadromous taxa are threatened with extinction and 73% inland taxa are either threatened or already extinct. Although specific drivers of decline differ across species, major causes of decline are related to increasing competition with humans for water, human degradation of watersheds, and adverse effects of hatchery propagation. Climate change, interacting with the other causes of decline, is increasing the trajectory towards extinction for most populations. Bringing all of California's salmonid fishes back from the brink of extinction may not be possible. If there are bold changes to management policy, however, self-sustaining populations of many species may be possible due to their inherent ability to adapt to changing conditions.

A quantitative protocol was developed to determine conservation status of all 129 freshwater fishes native to California. Seven (5%) were extinct; 33 (26%) were found to be in danger of extinction in the near future (endangered); 33 (26%) were rated as sufficiently threatened to be on a trajectory towards extinction if present trends continue (vulnerable); 34 (26%) were rated as declining species but not in immediate danger of extinction. Only 22 (17%) species were found to be of least concern. Of 31 species officially listed under federal and state endangered species acts (ESAs), 17 (55%) were rated as endangered by our criteria, while 12 (39%) were rated vulnerable. Conversely, of the 33 species that received our endangered rating, only 17 (51%) were officially listed under the ESAs. Among the seven metrics used to assess extinction threat, climate change, area occupied and anthropogenic threats had the largest negative impacts on status. Of 15 categories of causes of decline, those most likely to diminish status were alien species, agriculture, and dams. Overall, 83% of California’s freshwater fishes are extinct or at risk of becoming so, a 16% increase since 1995 and a 21% increase since 1989. The rapid decline of California’s inland fishes is probably typical of declines in other regions that are less well documented, indicating a strong need for improved conservation of freshwater ecosystems.

The ranges and abundances of species that depend on freshwater habitats are declining worldwide. Efforts to counteract those trends are often hampered by a lack of information about species distribution and conservation status and are often strongly biased toward a few well-studied groups. We identified the 3,906 vascular plants, macroinvertebrates, and vertebrates native to California, USA, that depend on fresh water for at least one stage of their life history. We evaluated the conservation status for these taxa using existing government and non-governmental organization assessments (e.g., endangered species act, NatureServe), created a spatial database of locality observations or distribution information from ~400 data sources, and mapped patterns of richness, endemism, and vulnerability. Although nearly half of all taxa with conservation status (n = 1,939) are vulnerable to extinction, only 114 (6%) of those vulnerable taxa have a legal mandate for protection in the form of formal inclusion on a state or federal endangered species list. Endemic taxa are at greater risk than non-endemics, with 90% of the 927 endemic taxa vulnerable to extinction. Records with spatial data were available for a total of 2,276 species (61%). The patterns of species richness differ depending on the taxonomic group analyzed, but are similar across taxonomic level. No particular taxonomic group represents an umbrella for all species, but hotspots of high richness for listed species cover 40% of the hotspots for all other species and 58% of the hotspots for vulnerable freshwater species. By mapping freshwater species hotspots we show locations that represent the top priority for conservation action in the state. This study identifies opportunities to fill gaps in the evaluation of conservation status for freshwater taxa in California, to address the lack of occurrence information for nearly 40% of freshwater taxa and nearly 40% of watersheds in the state, and to implement adequate protections for freshwater taxa where they are currently lacking.

The Kobuk River runs west along the southern Brooks Range from Gates of the Arctic National Park in Alaska, USA, to the Chukchi Sea. It is highly vulnerable to changes in climate due to its sub-Arctic location, unique geography, and permafrost foundation. Combined with its pristine condition, these qualities make the Kobuk an ideal system upon which to build a conceptual model for predicting ecosystem effects of climate change. We constructed a conceptual ecosystem model for the Kobuk River synthesizing surveyed baseline hydrologic, geomorphic and biotic conditions with literature on Arctic rivers. While the mainstem Kobuk has limited biological productivity, it provides spawning habitat and connectivity for large resident and migratory fish that rely upon off-channel habitat for food resources. System function is dependent largely on intermittent pulse flows that connect riverine habitats, allowing periods of late summer high productivity in off-channel habitat. Spring break-up and hill slope processes are critically important for maintaining habitat complexity and inter-connectivity. Climate change models predict the region will experience a disproportionate increase in average winter air temperature relative to summer temperatures, in the number of ice-free days, and in annual rainfall. Our conceptual model predicts that changes to fish and invertebrate populations on the Kobuk River will result not from physiological responses to increased temperatures, but rather to shifts in two main physical drivers: 1) spring break-up intensity, resulting in changes to scour rate and sediment deposition; and 2) discontinuous permafrost melt, resulting in widespread heterogeneous zones of active layer thickening and thermokarsting. The interaction of these two drivers offers four potential scenarios of geomorphic change in the system and four dramatically different biological outcomes. This model should help managers and scientists evaluate the magnitude and direction of ecosystem changes as they occur within the Kobuk system and potentially other sub-Arctic river systems.