scholarly journals Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary

2020 ◽  
Author(s):  
Michelle J. Jungbluth ◽  
Jillian Burns ◽  
Lenny Grimaldo ◽  
Anne Slaughter ◽  
Aspen Katla ◽  
...  
Keyword(s):  
San Francisco ◽  
Feeding Habits ◽  
Food Limitation ◽  
Alpha Diversity ◽  
Larval Survival ◽  
San Francisco Estuary ◽  
Feeding Strategies ◽  
Larval Fishes ◽  
Dna Metabarcoding ◽  
Longfin Smelt

AbstractFood limitation can dampen survival and growth of fish during early development. To investigate prey diversity important to the planktivorous larval longfin smelt (Spirinchus thaleichthys) and Pacific herring (Clupea pallasii) from the San Francisco Estuary, we used DNA metabarcoding analysis of the cytochrome oxidase I gene on the guts of these fishes and on environmental zooplankton samples. Differential abundance analysis suggested that both species consumed the most abundant zooplankton at a lower rate than their availability in the environment. Both fish consumed the prey that were commonly available and relatively abundant. Prey taxa substantially overlapped between the two species (Schoener’s index = 0.66), and alpha diversity analysis suggested high variability in the content of individual guts. Abundant prey taxa in both fish species included the copepods Eurytemora carolleeae, Acanthocyclops americanus, and A. robustus; the Acanthocyclops spp. are difficult to identify morphologically. A few uncommon prey in the diets hint at variable feeding strategies, such as herring (presumably egg) DNA in the longfin smelt diets, which suggests feeding near substrates. Herring consumed the small (<0.5 mm) copepod Limnoithona tetraspina more frequently (30%) than did smelt (2%), possibly indicating differences in foraging behavior or sensory abilities. Among the unexpected prey found in the diets was the cnidarian Hydra oligactis, the polychaete Dasybranchus sp., and a newly identified species Mesocyclops pehpeiensis. “Unknown” DNA was in 56% of longfin smelt diets and 57% of herring diets, and made up 17% and 21% of the relative read abundance in the two species, respectively. Our results suggest that these two fishes, which overlap in nursery habitat, also largely overlap in food resources necessary for larval survival.

scholarly journals Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary

2021 ◽  
Author(s):  
Michelle J. Jungbluth ◽  
Jillian Burns ◽  
Lenny Grimaldo ◽  
Anne Slaughter ◽  
Aspen Katla ◽  
...  
Keyword(s):  
San Francisco ◽  
Feeding Habits ◽  
San Francisco Estuary ◽  
Larval Fishes

scholarly journals Forage Fish Larvae Distribution and Habitat Use During Contrasting Years of Low and High Freshwater Flow in the San Francisco Estuary

2020 ◽  
Vol 18 (3) ◽  
Author(s):  
Lenny Grimaldo ◽  
Jillian Burns ◽  
Robert E. Miller ◽  
Andrew Kalmbach ◽  
April Smith ◽  
...  
Keyword(s):  
Habitat Use ◽  
San Francisco ◽  
Fish Larvae ◽  
San Francisco Estuary ◽  
High Flow ◽  
Low Flow ◽  
Forage Fish ◽  
Pacific Herring ◽  
Freshwater Flow ◽  
Longfin Smelt

Recruitment of estuarine organisms can vary dramatically from year to year with abiotic and biotic conditions. The San Francisco Estuary (California, USA) supports a dynamic ecosystem that receives freshwater flow from numerous tributaries that drain one of the largest watersheds in western North America. In this study, we examined distribution and habitat use of two forage fish larvae of management interest, Longfin Smelt Spirinchus thaleichthys and Pacific Herring Clupea pallasii, during a low-flow and a high-flow year to better understand how their rearing locations (region and habitat) may affect their annual recruitment variability. During the low-flow year, larval and post-larval Longfin Smelt were distributed landward, where suitable salinity overlapped with spawning habitats. During the high-flow year, larval Longfin Smelt were distributed seaward, with many collected in smaller tributaries and shallow habitats of San Francisco Bay. Local spawning and advection from seaward habitats were speculated to be the primary mechanisms that underlie larval Longfin Smelt distribution during the high-flow year. Larval Pacific Herring were more abundant seaward in both years, but a modest number of larvae were also found landward during the low-flow year. Larval Pacific Herring abundance was lower overall in the high-flow year, suggesting advection out of the area or poor recruitment. Future monitoring and conservation efforts for Longfin Smelt and Pacific Herring should recognize that potential mechanisms underlying their recruitment can vary broadly across the San Francisco Estuary in any given year, which suggests that monitoring and research of these two species expand accordingly with hydrologic conditions that are likely to affect their spawning and larval rearing distributions.

Sampling Uncharted Waters: Examining Rearing Habitat of Larval Longfin Smelt (Spirinchus thaleichthys) in the Upper San Francisco Estuary

2017 ◽  
Vol 40 (6) ◽  
pp. 1771-1784 ◽  
Author(s):  
Lenny Grimaldo ◽  
Fred Feyrer ◽  
Jillian Burns ◽  
Donna Maniscalco
Keyword(s):  
San Francisco ◽  
San Francisco Estuary ◽  
Longfin Smelt

scholarly journals The value of long-term monitoring of the San Francisco Estuary for Delta Smelt and Longfin Smelt

2021 ◽  
pp. 148-171
Author(s):  
Trishelle L. Tempel ◽  
Timothy D. Malinich ◽  
Jillian Burns ◽  
Arthur Barros ◽  
Christina E. Burdi ◽  
...  
Keyword(s):  
San Francisco ◽  
San Francisco Estuary ◽  
Delta Smelt ◽  
Long Term Monitoring ◽  
Term Monitoring ◽  
Longfin Smelt

Chronic food limitation of egg production in populations of copepods of the genusAcartia in the San Francisco estuary

Estuaries ◽  
2005 ◽  
Vol 28 (4) ◽  
pp. 541-550 ◽  
Author(s):  
Wim J. Kimmerer ◽  
Nissa Ferm ◽  
Mary Helen Nicolini ◽  
Carolina Peñalva
Keyword(s):  
San Francisco ◽  
Egg Production ◽  
Food Limitation ◽  
San Francisco Estuary

Early Life History of Fishes in the San Francisco Estuary and Watershed

2004 ◽  
Keyword(s):  
Life History ◽  
San Francisco ◽  
Striped Bass ◽  
Early Life ◽  
Early Life History ◽  
San Francisco Estuary ◽  
Delta Smelt ◽  
History Of ◽  
Acanthogobius Flavimanus ◽  
Longfin Smelt

<em>Abstract.</em>—We analyzed data on spring and summertime larval and juvenile fish distribution and abundance in the upper San Francisco Estuary (SFE), California between 1995 and 2001. The upper SFE includes the tidal freshwater areas of the Sacramento–San Joaquin Delta downstream to the euryhaline environment of San Pablo Bay. The sampling period included years with a variety of outflow conditions. Fifty taxa were collected using a larval tow net. Two common native species, delta smelt <em>Hypomesus transpacificus </em>and longfin smelt <em>Spirinchus thaleichthys</em>, and four common alien taxa, striped bass <em>Morone saxatilis</em>, threadfin shad <em>Dorosoma petenense</em>, gobies of the genus <em>Tridentiger</em>, and yellowfin goby <em>Acanthogobius flavimanus</em>, were selected for detailed analysis. Outflow conditions had a strong influence on the geographic distribution of most of the species, but distribution with respect to the 2 psu isohaline (X2) was not affected. The distribution patterns of delta smelt, longfin smelt, and striped bass were consistent with larvae moving from upstream freshwater spawning areas to downstream estuarine rearing areas. There were no obvious relationships of outflow with annual abundance indices. Our results support the idea of using X2 as an organizing principle in understanding the ecology of larval fishes in the upper SFE. Additional years of sampling will likely lead to additional insights into the early life history of upper SFE fishes.

scholarly journals Fewer and Farther between: Changes in the Timing of Longfin Smelt (Spirinchus thaleichthys) Movements in the San Francisco Estuary

2021 ◽  
Author(s):  
Vanessa Tobias ◽  
Randall Baxter
Keyword(s):  
San Francisco ◽  
Additive Model ◽  
San Francisco Estuary ◽  
Estuarine Fish ◽  
Data Set ◽  
Midwater Trawl ◽  
Recovery Planning ◽  
Monitoring Study ◽  
Longfin Smelt

Abundance of estuarine fish species has declined globally. In the San Francisco Estuary (SFE), long-term monitoring documented declines of many species including the anadromous species Longfin Smelt (Spirinchus thaleichthys). To improve management and recovery planning, we identified patterns in the timing, seasonal occupancy, and distribution of Longfin Smelt in a monitoring study (San Francisco Bay Study) for five regions of the SFE using a generalized additive model. We then investigated the year-to-year variability in the shape of the seasonal relationships using functional data analysis (FDA). FDA separated the variability due to population size from variability due to differences in occupancy timing. We found that Longfin Smelt have a consistent seasonal distribution pattern, that two trawl types were needed to accurately describe the pattern, and that the pattern is largely consistent with the hypothesized conceptual model. After accounting for variability in occupancy due to year-class strength, the timing of occupancy has shifted in three regions. The most variable period for the upstream regions Suisun Bay and Confluence was age-0 summer and for the downstream region Central Bay, was age-0 late fall. This manifested as a recent delay in the typical fall re-occupation of upstream regions, reducing Longfin Smelt abundance as calculated by another monitoring study (Fall Midwater Trawl); thus, a portion of recent reductions in Fall Midwater Trawl abundance of Longfin Smelt result from changes in behavior rather than a decline in abundance. The presence of multiple monitoring surveys allowed analysis of distribution from one data set to interpret patterns in abundance of another. Future investigations will examine environmental conditions as covariates during these periods and could improve our understanding of what conditions contribute to the shifting occupancy timing of Longfin Smelt, and possibly provide insight into the long-term quality of the San Francisco Estuary as habitat.

Environmental DNA

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Graduate Students ◽  
Feeding Habits ◽  
Environmental Dna ◽  
Research Field ◽  
Background Information ◽  
Ecological Processes ◽  
Biodiversity Research ◽  
Dna Metabarcoding ◽  
Standard Information

Environmental DNA (eDNA), i.e. DNA released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on the distribution or feeding habits of species. It has therefore great potential for applications in ecology and biodiversity management. However, this research field is fast-moving, involves different areas of expertise and currently lacks standard approaches, which calls for an up-to-date and comprehensive synthesis. Environmental DNA for biodiversity research and monitoring covers current methods based on eDNA, with a particular focus on “eDNA metabarcoding”. Intended for scientists and managers, it provides the background information to allow the design of sound experiments. It revisits all steps necessary to produce high-quality metabarcoding data such as sampling, metabarcode design, optimization of PCR and sequencing protocols, as well as analysis of large sequencing datasets. All these different steps are presented by discussing the potential and current challenges of eDNA-based approaches to infer parameters on biodiversity or ecological processes. The last chapters of this book review how DNA metabarcoding has been used so far to unravel novel patterns of diversity in space and time, to detect particular species, and to answer new ecological questions in various ecosystems and for various organisms. Environmental DNA for biodiversity research and monitoring constitutes an essential reading for all graduate students, researchers and practitioners who do not have a strong background in molecular genetics and who are willing to use eDNA approaches in ecology and biomonitoring.

Sign in / Sign up

Export Citation Format

Share Document