scholarly journals Optimizing an eDNA protocol for monitoring endangered Chinook Salmon in the San Francisco Estuary: balancing sensitivity, cost and time

2019 ◽  
Author(s):  
Thiago M. Sanches ◽  
Andrea M. Schreier
Keyword(s):  
Dna Extraction ◽  
San Francisco ◽  
Chinook Salmon ◽  
Magnetic Beads ◽  
Oncorhynchus Tshawytscha ◽  
Environmental Dna ◽  
San Francisco Estuary ◽  
Time Cost ◽  
Dna Yield ◽  
Pcr Inhibitor

AbstractEnvironmental DNA (eDNA) analysis has gained traction as a precise and cost effective method for species and waterways management. To date, publications on eDNA protocol optimization have focused primarily on DNA yield. Therefore, it has not been possible to evaluate the cost and speed of specific components of the eDNA protocol, such as water filtration and DNA extraction method when designing or choosing an eDNA pipeline. At the same time, these two parameters are essential for the experimental design of a project. Here we evaluate and rank different eDNA protocols in the context of Chinook salmon (Oncorhynchus tshawytscha) eDNA detection in an aquatic environment, the San Francisco Estuary. We present a comprehensive evaluation of multiple eDNA protocol parameters, balancing time, cost and DNA yield. For estuarine waters, which are challenging for eDNA studies due to high turbidity, variable salinity, and the presence of PCR inhibitors, we find that a protocol combining glass filters and magnetic beads, along with an extra step for PCR inhibitor removal, is the method that best balances time, cost, and yield. In addition, we provide a generalized decision tree for determining the optimal eDNA protocol for other studies on aquatic systems. Our findings should be applicable to most aquatic environments and provide a clear guide for determining which eDNA pipeline should be used for a given environmental condition.Author SummaryThe use of environmental DNA (eDNA) analysis for monitoring wildlife has steadily grown in recent years. Though, due to differences in the ecology of the environment studied and the novelty of the technique, eDNA currently shows a lack of standards compared to other fields. Here we take a deep look into each step of an eDNA assay, looking at common protocols and comparing their efficiencies in terms of time to process the samples, cost and how much DNA is recovered. We then analyze the data to provide a concise interpretation of best practices given different project constraints. For the conditions of the San Francisco Estuary we suggest the use of glass fiber filtration, the use of paramagnetic beads for DNA extraction and the use of a secondary inhibitor removal. We expect our findings to provide better support for managers to decide their standards ahead of project submission not only for estuarine conditions but for other waterine conditions alike.

scholarly journals Managed Wetlands Can Benefit Juvenile Chinook Salmon in a Tidal Marsh

2021 ◽  
Author(s):  
Nicole M. Aha ◽  
Peter B. Moyle ◽  
Nann A. Fangue ◽  
Andrew L. Rypel ◽  
John R. Durand
Keyword(s):  
San Francisco ◽  
Growth Rates ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Nursery Habitat ◽  
San Francisco Estuary ◽  
Rice Fields ◽  
Fish Growth ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook

AbstractLoss of estuarine and coastal habitats worldwide has reduced nursery habitat and function for diverse fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Underutilized off-channel habitats such as flooded rice fields and managed ponds present opportunities for improving rearing conditions and increasing habitat diversity along migratory corridors. While experiments in rice fields have shown enhanced growth rates of juvenile fishes, managed ponds are less studied. To evaluate the potential of these ponds as a nursery habitat, juvenile Chinook salmon (~ 2.8 g, 63 mm FL) were reared in cages in four contrasting locations within Suisun Marsh, a large wetland in the San Francisco Estuary. The locations included a natural tidal slough, a leveed tidal slough, and the inlet and outlet of a tidally muted managed pond established for waterfowl hunting. Fish growth rates differed significantly among locations, with the fastest growth occurring near the outlet in the managed pond. High zooplankton biomass at the managed pond outlet was the best correlate of salmon growth. Water temperatures in the managed pond were also cooler and less variable compared to sloughs, reducing thermal stress. The stress of low dissolved oxygen concentrations within the managed pond was likely mediated by high concentrations of zooplankton and favorable temperatures. Our findings suggest that muted tidal habitats in the San Francisco Estuary and elsewhere could be managed to promote growth and survival of juvenile salmon and other native fishes.

scholarly journals Ancient DNA Analysis of Archaeological Specimens Extends Chinook Salmon’s Known Historic Range to San Francisco Bay and Its Southernmost Watershed

2020 ◽  
Author(s):  
Richard B. Lanman ◽  
Linda Hylkema ◽  
Cristie M. Boone ◽  
Brian Alleé ◽  
Roger O. Castillo ◽  
...  
Keyword(s):  
Native American ◽  
San Francisco ◽  
Ancient Dna ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Dna Analysis ◽  
Oncorhynchus Tshawytscha ◽  
San Francisco Bay ◽  
Bay Area ◽  
Guadalupe River

Understanding a species’ historic range guides contemporary management and habitat restoration. Chinook salmon ( Oncorhynchus tshawytscha ) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropomorphic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Using ichthyofaunal analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara circa 1781-1834 CE, 86 salmonid vertebrae were identified. Ancient DNA sequencing identified three of these as from Chinook salmon and the remainder from steelhead trout. These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their historic range to include San Francisco Bay’s southernmost watershed.

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

2004 ◽  
Keyword(s):  
Life History ◽  
San Francisco ◽  
Early Life ◽  
Oncorhynchus Tshawytscha ◽  
San Francisco Estuary ◽  
Sacramento River ◽  
Yolo Bypass ◽  
Species Abundances ◽  
Native Fishes ◽  
Rotary Screw

<em>Abstract.</em>—We examined assemblage patterns of early life stages of fishes for two major tributaries of the upper San Francisco Estuary: (1) Sacramento River channel, and (2) Yolo Bypass, the river’s seasonal floodplain. Over four hydrologically diverse years (1999–2002), we collected 15 species in Yolo Bypass egg and larval samples, 18 species in Yolo Bypass rotary screw trap samples, and 10 species in Sacramento River egg and larval samples. Fishes captured included federally listed species (delta smelt <em>Hypomesus transpacificus </em>and splittail <em>Pogonichthys macrolepidotus</em>) and several game species (American shad <em>Alosa sapidissima</em>, striped bass <em>Morone saxatilis</em>, crappie <em>Pomoxis </em>spp., and Chinook salmon <em>Oncorhynchus tshawytscha</em>). As in other regions of the estuary, alien fish comprised a large portion of the individuals collected in Yolo Bypass (40–93% for egg and larval net samples; 84–98% for rotary screw trap samples) and Sacramento River (80–99% for egg and larval net samples). Overall ranks of species abundances were significantly correlated for Yolo Bypass and Sacramento River, suggesting that each assemblage was controlled by similar major environmental factors. However, species diversity and richness were higher in Yolo Bypass, likely because of a wider variety of habitat types and greater hydrologic variation in the floodplain. In both landscapes, we found evidence that timing of occurrence of native fishes was earlier than aliens, consistent with their life history and our data on adult migration patterns. We hypothesize that Yolo Bypass favors native fishes because the inundation of seasonal floodplain typically occurs early in the calendar year, providing access to vast areas of spawning and rearing habitat with an enhanced food web. Conclusions from this analysis have implications for the management of aquatic biodiversity of tributaries to the San Francisco Estuary and perhaps to other lowland rivers.

scholarly journals Reconsidering the Estimation of Salmon Mortality Caused by the State and Federal Water Export Facilities in the Sacramento–San Joaquin Delta, San Francisco Estuary

2020 ◽  
Vol 18 (3) ◽  
Author(s):  
Andrew Jahn ◽  
William Kier
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Near Field ◽  
San Francisco Estuary ◽  
The State ◽  
Juvenile Salmon ◽  
Small Fish ◽  
Accuracy And Precision ◽  
Behavioral Barriers ◽  
Existing Data

Combined water exports from Old River in the south end of California’s San Francisco Estuary (estuary) by state and federal pumping facilities entrain small fishes, including out-migrating juvenile salmon. Both export projects have fish salvage facilities that use behavioral barriers (louvers) in combination with screens to guide fish into collection areas from which they are trucked to release points in the western Delta. Sacramento River-origin Chinook Salmon are regularly taken in the projects’ fish salvage operations. Survival has been estimated within the boundaries of both intake structures, but not in Old River. Prevailing methods for estimating fish losses are based on studies of louver efficiency, near-field survival at the state facility, and assumed survival at the federal facility. The efficiency of the fish salvage operations is affected by several factors, including intake velocity, debris build-up on the louvers and trash racks, and by the omnipresence of predators in front of and within the fish guidance structures. Analysis of existing data suggests that under average conditions, juvenile salmon survive entrainment into the forebay of the state facility at a rate of less than 10%. There is no evidence for better survival at the federal facility. We found no data on predation outside of either the state’s forebay or the federal trash boom, structures which are separated by an approximately 2-km reach of Old River where predation on small fish is thought to be intense. We suggest an improvement to the existing loss estimation, and discuss some features of the studies needed to increase its accuracy and precision.

Energy dynamics and growth of Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California during the estuarine phase and first ocean year

2010 ◽  
Vol 67 (10) ◽  
pp. 1549-1565 ◽  
Author(s):  
R. Bruce MacFarlane
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Climate Models ◽  
Oncorhynchus Tshawytscha ◽  
Energy Content ◽  
Central Valley ◽  
Energy Dynamics ◽  
Period Data ◽  
Energy Gains ◽  
Engraulis Mordax

The greatest rates of energy accumulation and growth in subyearling Chinook salmon ( Oncorhynchus tshawytscha ) occurred during the first month following ocean entry, supporting the importance of this critical period. Data from an 11-year study in the coastal ocean off California and the San Francisco Estuary revealed that juvenile salmon gained 3.2 kJ·day–1 and 0.8 g·day–1, representing 4.3%·day–1 and 5.2% day–1, respectively, relative to estuary exit values. Little gain in energy (0.28 kJ·day–1) or size (0.07 g·day–1) occurred in the estuary, indicating that the nursery function typically ascribed to estuaries can be deferred to initial ocean residence. Calculated northern anchovies ( Engraulis mordax ) equivalents to meet energy gains were one anchovy per day in the estuary (8% body weight·day–1) and about three per day immediately following ocean entry (15% body weight·day–1). Energy content in the estuary was positively related to higher salinity and lower freshwater outflow, whereas in the ocean, cooler temperatures, lower sea level, and greater upwelling resulted in greater gains. These results suggest that greater freshwater flows, warmer sea temperatures, and reduced or delayed upwelling, all of which are indicated by some (but not all) climate models, will likely decrease growth of juvenile Chinook salmon, leading to reduced survival.

scholarly journals Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10231
Author(s):  
John K. Pearman ◽  
Nigel B. Keeley ◽  
Susanna A. Wood ◽  
Olivier Laroche ◽  
Anastasija Zaiko ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Community Composition ◽  
Oncorhynchus Tshawytscha ◽  
Environmental Dna ◽  
Illumina Miseq ◽  
Ecological Impacts ◽  
Biotic Index ◽  
Soil Dna ◽  
Additional Advantage ◽  
Marine Aquaculture

Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between “distance” from the farm and “kit” in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.

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

2004 ◽  
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Reference Group ◽  
Central Valley ◽  
Study Groups ◽  
San Francisco Estuary ◽  
Study Group ◽  
First Feeding ◽  
Back Calculation ◽  
Juvenile Chinook

<em>Abstract.</em>—We compared two approaches to back-calculation with otolith microstructure to develop a method for accurately estimating growth rates of juvenile fall-run Chinook salmon <em>Oncorhynchus tshawytscha </em>in California’s Central Valley. Total otolith width was a strong determinant of fork length (FL) in linear regressions used to determine the <em>y</em>-intercept in the fish size–otolith size relationship in two study groups of Chinook salmon. The Fraser-Lee back-calculation model estimated FL at first feeding in both study groups that did not differ significantly from lengths of first-feeding Chinook salmon in a reference group. In comparison, the biological-intercept method produced back-calculated lengths that were significantly greater in one study group than lengths of first-feeding Chinook salmon in the reference group. Chinook salmon emergence dates, estimated from counts of daily growth increments beyond the first-feeding check, corresponded with observed emergence periods in the river and hatchery populations from which the study groups were sampled. Size-at-age relationships were well described by a power function in both study groups, where mean FL over time approached an apparent asymptote at approximately 80 mm after 90 d postemergence. Growth rate estimates, using back-calculated size from the Fraser-Lee model, averaged 0.50 mm/d in one study group and 0.43 mm/d in the other study group. These estimates fell within the range of previous growth rate estimates for juvenile Chinook salmon in Central Valley riverine, floodplain, and delta environments and were about 2.5 times higher on average than an estimate for the San Francisco Estuary and about 2.3 times lower on average than estimates from the Strait of Georgia. We discuss the utility of otolith microstructure to not only estimate growth rates, but also to reconstruct emergence-date distributions in cohorts of emigrating juvenile Chinook salmon for stock identification purposes.

scholarly journals The expansion of exotic Chinook salmon (Oncorhynchus tshawytscha) in the extreme south of Patagonia: an environmental DNA approach

2019 ◽  
Vol 21 (4) ◽  
pp. 1415-1425 ◽  
Author(s):  
Cristina Fernanda Nardi ◽  
Daniel Alfredo Fernández ◽  
Fabián Alberto Vanella ◽  
Tomás Chalde
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Environmental Dna
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