Use of the SmeltCam as an Efficient Fish Sampling Alternative Within the San Francisco Estuary

Huntsman, Brock M.; Feyrer, Fredrick; Young, Matthew J.

doi:10.15447/sfews.2021v19iss2art6

Cited by 3 publications

(4 citation statements)

References 27 publications

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“…Although standardized protocols were used to sample during this study, issues of catchability are potentially a significant source of bias in our and other fish community analyses. Recent efforts in the San Francisco Estuary have demonstrated significant differences among fish species in their catchability using common surveying gears, and these differences can also be detected using the same gear types for similar fish species depending on fish life stage and the habitat types sampled (Huntsman et al, 2022; Huntsman, Feyrer, & Young, 2021; Huntsman, Feyrer, Young, Hobbs, et al, 2021; Mitchell et al, 2017; Mitchell & Baxter, 2021). We used gill nets during our sampling, which target active fishes and potentially bias our sampling toward fishes with active life‐history traits (Feyrer & Healey, 2002).…”

Section: Discussionmentioning

confidence: 99%

Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta

et al. 2023

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Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are a defining feature in tidal terminal channel ecosystems from which native aquatic communities have evolved.However, few studies have explored the relationship between fish community structure and hydrodynamics in these tidal terminal channel ecosystems. We sampled fish communities throughout a network of terminal channels within the northeasternmost region of the San Francisco Estuary to determine the relationship between fish community structure and hydrodynamics within these environments. We collected two years (2017 and 2018) of fish community samples using gill nets and analyzed data using multivariate community analyses and count models. We found metrics of fish diversity and counts of native fishes to be greatest upstream (farthest from tidal influence) of the tidal excursion within terminal channels. Counts of non-native fishes were less affected by this hydrodynamic feature of terminal channels and more tightly correlated to local habitat conditions (e.g., water temperature, depth). Our results suggest that channel hydrodynamics plays a role in structuring fish communities within terminal channels, particularly native fishes. These results indicate that hydrodynamics in tidal delta ecosystems may be able to be altered in ways that benefit native fishes without the cost of water pumping.K E Y W O R D S backwater slough, Cache Slough complex, multivariate, San Francisco Estuary, spatial scale, tidal excursion, tidal marsh † Deceased

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Section: Discussionmentioning

confidence: 99%

Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta

et al. 2023

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“…First, our study did not account for how total fish biomass within the trawl affected gear efficiency in the cod end of trawls. Higher biomass in the trawl is positively correlated to gear efficiency because of the reduction in mesh openings (usually toward the cod end), which prevents smaller fishes from passing through the net (Mitchell et al 2017;Peterson and Barajas 2018;Huntsman et al 2021b). This may explain some of the variability in relative catchability observed for some fish species captured by similarly operated gears (e.g., small Striped Bass between the FMWT and BSMT).…”

Section: Discussionmentioning

confidence: 99%

“…A substantial amount of work has been done to account for observation error from differences in catchability and to provide measures of uncertainty (Walsh 1997;Royle 2004;MacKenzie and Royle 2005;Kéry and Royle 2016). Yet, work to estimate catchability in the estuary to date has either included a select few species (Perry et al 2016;Mitchell et al 2017;Mitchell et al 2019;Huntsman et al 2021aHuntsman et al , 2021b or focused on occupancy rather than abundance (Mahardja et al 2017;Peterson and Barajas 2018).…”

Section: Introductionmentioning

confidence: 99%

Relative Bias in Catch Among Long-Term Fish Monitoring Surveys Within the San Francisco Estuary

Huntsman¹,

Mahardja²,

Bashevkin³

2022

SFEWS

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Fish monitoring gears rarely capture all available fish, an inherent bias in monitoring programs referred to as catchability. Catchability is a source of bias that can be affected by numerous aspects of gear deployment (e.g., deployment speed, mesh size, and avoidance behavior). Thus, care must be taken when multiple surveys—especially those using different sampling methods—are combined to answer spatio-temporal questions about population and community dynamics. We assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary: the Bay Study Otter Trawl (BSOT), the Bay Study Midwater Trawl (BSMT), the Fall Midwater Trawl (FMWT), and the Suisun Marsh Otter Trawl (SMOT). We used generalized additive models with a spatio-temporal smoother and survey as a fixed effect to predict gear-specific estimates of catch for 45 different fish species within large and small size classes. We used estimates of the fixed effect coefficients for each survey (e.g., BSOT) relative to the reference gear (FMWT) to develop relative measures of catchability among taxa, surveys, and fish-size classes, termed the catch-ratio. We found higher relative catchability of 27%, 22%, and 57% of fish species in large size classes from the FMWT than in the BSMT, BSOT, or SMOT, respectively. In the small size class, relative catchability was higher in the FMWT than the BSMT, BSOT, or SMOT for 50%, 18%, and 25% of fish species, respectively. As expected, relative catchability of demersal species was higher in the otter trawls (BSOT, SMOT) while relative catchability of pelagic species was higher in the midwater trawls (FMWT, BSMT). Our results demonstrate that catchability is a source of bias among monitoring efforts within the San Francisco Estuary, and assuming equal catchability among surveys, species, and size classes could result in significant bias when describing spatio-temporal patterns in catch if ignored.

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“…Complementary approaches like eDNA could supplement and support this gear-based data. For listed species like delta smelt, regulatory limits on incidental take associated with gear-based monitoring could be circumvented with non-invasive approaches like eDNA detection (Holmes et al, 2024) or underwater video imaging (Huntsman et al, 2021). With the decline in the delta smelt population, the ability to detect their presence by gear-based monitoring has become increasingly difficult, limiting managers' ability to evaluate the effectiveness of actions targeting delta smelt recovery, having a comprehensive understanding of distribution patterns, and subsequently conducting targeted sampling in regions where smelt are present.…”

mentioning

confidence: 99%

CRISPR‐based environmental DNA detection for a rare endangered estuarine species

Nagarajan,

Sanders,

Kolm

et al. 2024

Environmental DNA

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Environmental DNA (eDNA) methods complement traditional aquatic monitoring surveys and are especially advantageous for rare and listed species to detect spatial and temporal distribution patterns. However, improvements in ease of use and portability could increase the utility of eDNA methods, leading to more widespread application, including expanding its role in management decision‐making processes. We describe the development of an eDNA detection assay for delta smelt (Hypomesus transpacificus), an endangered fish in the San Francisco Estuary, using SHERLOCK (Specific High‐Sensitivity Enzymatic Reporter Unlocking). SHERLOCK is a clustered regularly interspaced short palindromic repeats (CRISPR)‐based diagnostic tool with the ability to detect species‐specific genetic variants, making it ideal for genetic‐based taxonomic identification of any organism. Because of its high sensitivity and specificity, SHERLOCK is adaptable to eDNA detection in water samples. Here, we describe adaptation of a delta smelt SHERLOCK assay for use with estuarine water eDNA samples. This version of the assay exhibits increased sensitivity compared to the original delta smelt SHERLOCK protocol (new limit of detection approximately three copies per reaction compared to ~300 in original assay) and successfully detected delta smelt eDNA in both experimental and natural contexts. Overall, our results demonstrate that SHERLOCK eDNA detection offers managers an alternative, isothermal methodology, and highlights some challenges for detection of rare, endangered species at low abundance.

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Use of the SmeltCam as an Efficient Fish Sampling Alternative Within the San Francisco Estuary

Cited by 3 publications

References 27 publications

Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta

Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta

Relative Bias in Catch Among Long-Term Fish Monitoring Surveys Within the San Francisco Estuary

CRISPR‐based environmental DNA detection for a rare endangered estuarine species

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