Delta Smelt Habitat in the San Francisco Estuary: A Reply to Manly, Fullerton, Hendrix, and Burnham’s “Comments on Feyrer et al. Modeling the Effects of Future Outflow on the Abiotic Habitat of an Imperiled Estuarine Fish”

Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can be responsible for detecting or not detecting biological trends. The SmeltCam is an imaging apparatus developed as a potential sampling alternative to long-term trawling gear surveys within the San Francisco Estuary, California, to reduce handling stress on sensitive species like the Delta Smelt (Hypomesus transpacificus). Although believed to be a reliable alternative to closed cod-end trawling surveys, no formal test of sampling efficiency has been implemented using the SmeltCam. We used a paired deployment of the SmeltCam and a conventional closed cod-end trawl within the Napa River and San Pablo Bay, a Bayesian binomial N-mixture model, and data simulations to determine the sampling efficiency of both deployed gear types to capture a Delta Smelt surrogate (Northern Anchovy, Engraulis mordax) and to test potential bias in our modeling framework. We found that retention efficiency—a component of detection efficiency that estimates the probability a fish is retained by the gear, conditional on gear contact—was slightly higher using the SmeltCam (mean = 0.58) than the conventional trawl (mean = 0.47, Probability SmeltCam retention efficiency > trawl retention efficiency = 94%). We also found turbidity did not affect the SmeltCam’s retention efficiency, although total fish density during an individual tow improved the trawl’s retention efficiency. Simulations also showed the binomial model was accurate when model assumptions were met. Collectively, our results suggest the SmeltCam to be a reliable alternative to sampling with conventional trawling gear, but future tests are needed to confirm whether the SmeltCam is as reliable when applied to taxa other than Northern Anchovy over a greater range of conditions.

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Crime Scene San Francisco: Who Is Responsible for the Disappearance of Delta Smelt?

Frontiers for Young Minds ◽

10.3389/frym.2021.612548 ◽

2021 ◽

Vol 9 ◽

Author(s):

Mallory E. Bedwell ◽

Craig Stuart ◽

Melinda R. Baerwald

Keyword(s):

San Francisco ◽

Fish Species ◽

Native Species ◽

Crime Scene ◽

San Francisco Estuary ◽

Invasive Fish ◽

Delta Smelt

Delta smelt are becoming harder and harder to find in the San Francisco Estuary. Some of the suspects in their disappearance are invasive fish species that were introduced from other places into the Estuary. These invasive fish can impact their new habitat by eating the native species that were originally there. However, it is hard to understand what the invasive fish are eating. We found that we can use the DNA in the stomachs of invasive fish to figure out what they have eaten. We caught a common invasive fish in the Estuary, called the Mississippi silverside, and analyzed the DNA from their stomachs to see if it matched delta smelt DNA. We discovered that some Mississippi silversides had delta smelt DNA in their stomachs! We therefore believe that Mississippi silversides are one of the culprits causing the disappearance of delta smelt.

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Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish

PeerJ ◽

10.7717/peerj.12280 ◽

2021 ◽

Vol 9 ◽

pp. e12280

Author(s):

Wilson Xieu ◽

Levi S. Lewis ◽

Feng Zhao ◽

Rachel A. Fichman ◽

Malte Willmes ◽

...

Keyword(s):

San Francisco ◽

Developmental Stages ◽

Critically Endangered ◽

Age And Growth ◽

Estuarine Fish ◽

Fish Length ◽

Life Stages ◽

Vital Rates ◽

Delta Smelt ◽

And Migration

Background The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species’ vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration. However, key methodological assumptions have yet to be validated, thus limiting confidence in otolith-derived metrics that are important for informing major water management decisions in the SFE. Methods Using known-age cultured Delta Smelt and multiple independent otolith analysts, we examined otolith formation, otolith-somatic proportionality, aging accuracy and precision, left-right symmetry, and the effects of image magnification for larval, juvenile, and adult Delta Smelt. Results Overall, otolith size varied linearly with fish size (from 10–60 mm), explaining 99% of the variation in fish length, despite a unique slope for larvae < 10 mm. Otolith-somatic proportionality was similar among wild and cultured specimens. Aging precision among independent analysts was 98% and aging accuracy relative to known ages was 96%, with age estimates exhibiting negligible differences among left and right otoliths. Though error generally increased with age, percent error decreased from 0–30 days-post-hatch, with precision remaining relatively high (≥ 95%) thereafter. Increased magnification (400×) further improved aging accuracy for the oldest, slowest-growing individuals. Together, these results indicate that otolith-based techniques provide reliable age and growth reconstructions for larval, juvenile, and adult Delta Smelt. Such experimental assessments across multiple developmental stages are key steps toward assessing confidence in otolith-derived metrics that are often used to assess the dynamics of wild fish populations.

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Delivering Food to Hungry Fish in the San Francisco Estuary

Frontiers for Young Minds ◽

10.3389/frym.2021.611957 ◽

2021 ◽

Vol 9 ◽

Author(s):

Laura Twardochleb ◽

Leela Dixit ◽

Mallory Bedwell ◽

Brittany Davis ◽

Jared Frantzich

Keyword(s):

Invasive Species ◽

San Francisco ◽

Fish Species ◽

San Francisco Estuary ◽

Fish Food ◽

Yolo Bypass ◽

Delta Smelt ◽

Endangered Fish ◽

The Past

The San Francisco Estuary is home to an important endangered fish called delta smelt. Delta smelt eat small, nutritious animals called zooplankton to survive and grow. In turn, zooplankton grow by eating microscopic plant-like organisms called phytoplankton. In the past, the Estuary was full of plankton and delta smelt. Because people have removed water from the Estuary and invasive species now live there, the Estuary no longer has enough plankton to feed delta smelt, making it difficult for them to survive. Scientists have found a unique place in the Estuary, the Yolo Bypass, that has lots of fish food. The problem is that delta smelt do not live in the Yolo Bypass year-round. Scientists are working to solve this problem by sending river or farm water through the Yolo Bypass, to move fish food downstream to feed the hungry delta smelt and other fish species.

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