Studying rare and sensitive species is a challenge in conservation biology. The problem is exemplified by the case of the imperiled delta smelt Hypomesus transpacificus, a small delicate fish species endemic to the San Francisco Estuary, California. Persistent record-low levels of abundance and relatively high sensitivity to handling stress pose considerable challenges to studying delta smelt in the wild. To attempt to overcome these and other challenges we have developed the SmeltCam, an underwater video camera codend for trawled nets. The SmeltCam functions as an open-ended codend that automatically collects information on the number and species of fishes that pass freely through a trawled net without handling. We applied the SmeltCam to study the fine-scale distribution of juvenile delta smelt in the water column in the upper San Francisco Estuary. We learned that during flood tides delta smelt were relatively abundant throughout the water column and that during ebb tides delta smelt were significantly less abundant and occurred only in the lower half and sides of the water column. The results suggest that delta smelt manipulate their position in the water column to facilitate retention in favorable habitats. With the application of the SmeltCam we increased the survival of individual delta smelt by 72% compared to using a traditional codend, where all of the fish would have likely died due to handling stress. The SmeltCam improves upon similar previously developed silhouette photography or video recording devices and demonstrates how new technology can be developed to address important questions in conservation biology as well as lessen the negative effects associated with traditional sampling methods on imperiled species.

Restored tidal wetlands may provide important food web support for at-risk fish species in the Sacramento-San Joaquin Delta (Delta) of California, including Delta Smelt (Hypomesus transpacificus) and Chinook Salmon (Oncorhynchus tshawytscha). Since many tidal wetland restoration projects are planned or have recently been constructed in the Delta, understanding the diversity and variability of wetland invertebrates that are fish prey items is of increasing importance. During this study, two different invertebrate sampling techniques were tested (leaf packs and sweep nets) in four habitat types within three different wetland areas to evaluate which sampling technique provided the most reliable metric of invertebrate abundance and community composition. Sweep nets provided a better measure of fish food availability than leaf packs and were better able to differentiate between habitat types. Generalized linear models showed submerged and floating vegetation had higher abundance and taxa richness than channel habitats or emergent vegetation. Permutational multivariate analysis of variance showed significantly different communities of invertebrates in different habitat types and in different wetlands, and point-biserial correlation coefficients found a greater number of mobile taxa associated with sweep nets. There were more taxa associated with vegetated habitats than channel habitats, and one area had more taxa associated with it than the other two areas. These results suggest that restoration sites that contain multiple habitat types may enhance fish invertebrate prey diversity and resilience. However, the effect of habitat diversity must be monitored as restoration sites develop to assess actual benefits to at-risk fish species.

28Restored tidal wetlands may provide important food web support for at-risk fish species in the 29 Sacramento-San Joaquin Delta (Delta) of California, including Delta Smelt (Hypomesus 30 transpacificus) and Chinook Salmon (Oncorhynchus tshawytscha). Since many tidal wetland 31 restoration projects are planned or have recently been constructed in the Delta, understanding the 32 diversity and variability of wetland invertebrates that are fish prey items is of increasing 33 importance. During this study, two different invertebrate sampling techniques were tested (leaf 34 packs and sweep nets) in four habitat types within three different wetland sites to evaluate which 35 sampling technique provided the most reliable metric of invertebrate abundance and community 36 composition. Sweep nets provided a better measure of fish food availability than leaf packs and 37 were better able to differentiate between habitat types. Generalized linear models showed 38 submerged and floating vegetation had higher abundance and species richness than channel 39 habitats or emergent vegetation. Permutational multivariate analysis of variance showed 40 significantly different communities of invertebrates in different habitat types and in different 41 wetlands, and point-biserial correlation coefficients found a greater number of mobile taxa 42 associated with sweep nets. There were more taxa associated with vegetated habitats than 43 channel habitats, and one region had more taxa associated with it than the other two regions. 44These results suggest that restoration sites that contain multiple habitat types may enhance fish 45 invertebrate prey diversity and resilience. However, the effect of habitat diversity must be 46 monitored as restoration sites develop to assess actual benefits to at-risk fish species. 47 48 3 49Tidal wetlands provide an important source of productivity to many estuaries worldwide, 50 subsidizing the surrounding open-water areas with vascular plant detritus, phytoplankton, 51 zooplankton, and nekton biomass [1][2][3][4][5]. Productive freshwater tidal wetlands dominated the 52 landscape of California's Sacramento-San Joaquin Delta (Delta) prior to the Gold Rush, but, by 53 1930, the vast majority of wetlands were reclaimed, primarily for agriculture [6] (see Fig 1A). 54While there is currently no quantitative estimate of the impact of wetland loss on aquatic primary 55 productivity, production most likely declined drastically post-reclamation [7]. 56 57 Figure 1. A) Map of California (USA) with the San Francisco Bay-Delta watershed. The inset is 58 a finer-scale map of the Legal Delta, with the focal area in the Cache Slough Complex outlined 59 with a dashed box. B) The Cache Slough complex, with sampling regions circled. Each region 60 contained four sampling sites with different habitat types: SAV, FAV, EAV, and channel. 61 62 Restoration of tidal wetland habitat in the Delta may increase overall primary and secondary 63 production, and thus multiple regulatory mandates now include tidal wetland restoratio...

Biological invasion by non-native species has been identified as one of the major threats to native fish communities worldwide. The fish community of San Francisco Estuary is no exception, as the estuary has been recognized as one of the most invaded on the planet and the system has been impacted significantly by these invasions. Here, we summarize the introduction and probable establishment of a new species in the Sacramento–San Joaquin Delta, the Bluefin Killifish (Lucania goodei), as discovered by the US Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP). The DJFMP has conducted a large-scale beach seine survey since 1976, and it is the longest-running monitoring program in the San Francisco Estuary that extensively monitors the shallow-water nearshore habitat. Possibly introduced as discarded aquarium fish within the vicinity of the Delta Cross Channel, Bluefin Killifish is a close relative of the Rainwater Killifish (Lucania parva), another non-native fish species that has been present in the San Francisco Estuary system for decades. Studies in their native range suggest that Bluefin Killifish will fill a similar niche to Rainwater Killifish, albeit with a more freshwater distribution. The potential ecological impact of Bluefin Killifish remains unclear in the absence of additional studies. However, we have been able to track the spread of the species within the Sacramento–San Joaquin Delta through the existence of long-term monitoring programs. Our findings demonstrate the value of monitoring across various habitats for the early detection and proactive management of invasive species.

Studying rare and sensitive species is a challenge in conservation biology. The problem is exemplified by the case of the imperiled delta smelt Hypomesus transpacificus, a small delicate fish species endemic to the San Francisco Estuary, California. Persistent record-low levels of abundance and relatively high sensitivity to handling stress pose considerable challenges to studying delta smelt in the wild. To attempt to overcome these and other challenges we have developed the SmeltCam, an underwater video camera codend for trawled nets. The SmeltCam functions as an open-ended codend that automatically collects information on the number and species of fishes that pass freely through a trawled net without handling. We applied the SmeltCam to study the fine-scale distribution of juvenile delta smelt in the water column in the upper San Francisco Estuary. We learned that during flood tides delta smelt were relatively abundant throughout the water column and that during ebb tides delta smelt were significantly less abundant and occurred only in the lower half and sides of the water column. The results suggest that delta smelt manipulate their position in the water column to facilitate retention in favorable habitats. With the application of the SmeltCam we increased the survival of individual delta smelt by 72% compared to using a traditional codend, where all of the fish would have likely died due to handling stress. The SmeltCam improves upon similar previously developed silhouette photography or video recording devices and demonstrates how new technology can be developed to address important questions in conservation biology as well as lessen the negative effects associated with traditional sampling methods on imperiled species.