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Estuarine Habitat Use by White Sturgeon (Acipenser transmontanus)

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Estuarine Habitat Use by White Sturgeon (Acipenser transmontanus)

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White Sturgeon (Acipenser transmontanus), a species of concern in the San Francisco Estuary, is in relatively low abundance due to a variety of factors. Patton et al. sought identify the estuarine habitat used by White Sturgeon to aid in the conservation and management of the species locally and across its range. By seasonally sampled sub-adult and adult White Sturgeon in the central estuary using setlines across a habitat gradient representative of three primary structural elements, the authors found that the shallow open-water shoal and deep open-water channel habitats were consistently occupied by White Sturgeon in spring, summer, and fall across highly variable water quality conditions, whereas the shallow wetland channel habitat was essentially unoccupied. In summary, sub-adult and adult White Sturgeon inhabit estuaries in at least spring, summer, and fall and small, shallow wetland channels are relatively unoccupied.
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UC Davis
San Francisco Estuary and Watershed Science
Title
Estuarine Habitat Use by White Sturgeon (Acipenser transmontanus)
Permalink
https://escholarship.org/uc/item/50q9h38r
Journal
San Francisco Estuary and Watershed Science, 18(4)
Authors
Patton, Oliver
Larwood, Veronica
Young, Matthew
et al.
Publication Date
2020
DOI
10.15447/sfews.2020v18iss4art4
Copyright Information
Copyright 2020 by the author(s).This work is made available under the terms of a Creative
Commons Attribution License, available at https://creativecommons.org/licenses/by/4.0/
Peer reviewed
eScholarship.org Powered by the California Digital Library
University of California
1
Sponsored by the Delta Science Program and the UC Davis Muir Institute
SFEWS Volume 18 | Issue 4 | Article 4
https://doi.org/10.15447/sfews.2020v18iss4art4
* Corresponding author: vlarwood@usgs.gov
1 US Geological Survey
California Water Science Center
Sacramento CA, 95819 USA
ABSTRACT
White Sturgeon (Acipenser transmontanus), a
species of concern in the San Francisco Estuary,
is in relatively low abundance because of a
variety of factors. The purpose of our study
was to identify the estuarine habitat used by
White Sturgeon to aid in the conservation
and management of the species locally and
across its range. We seasonally sampled sub-
adult and adult White Sturgeon in the central
estuary using setlines across a habitat gradient
representative of three primary structural
elements: shallow wetland channel (mean sample
depth = 2 m), shallow open-water shoal (mean
sample depth = 2 m), and deep open-water channel
(mean sample depth = 7 m). We found that the
shallow open-water shoal and deep open-water
channel habitats were consistently occupied
by White Sturgeon in spring, summer, and fall
across highly variable water quality conditions,
whereas the shallow wetland channel habitat was
essentially unoccupied. We conclude that sub-
adult and adult White Sturgeon inhabit estuaries
in at least spring, summer, and fall and that
small, shallow wetland channels are relatively
unoccupied.
KEY WORDS
White Sturgeon, Acipenser transmontanus,
Habitat, estuary, wetland, conservation,
restoration
INTRODUCTION
Sturgeons are large, long-lived fishes that grow
and mature slowly, ranging throughout North
America, Europe, and Asia (Birstein 1993; Pikitch
et al. 2005). Currently, there are 25 recognized
species in four genera (Birstein 1993; Auer 1996;
Bemis and Kynard 1997; Billard and Lecointre
2000; Pikitch et al. 2005). Sturgeons have
historically been the dominant large fish species
in large rivers in the Northern Hemisphere;
they are highly valued for consumption of their
flesh and roe, and are gaining appreciation as
charismatic megafauna (Chapman et al. 1996;
Pikitch et al. 2005; He et al. 2018). Collectively,
sturgeons are considered one of the most highly
imperiled groups of animals, with 85% of species
at risk of extinction according to the International
Union for Conservation of Nature (IUCN c2020).
Over-harvest, various forms of habitat loss
RESEARCH
Estuarine Habitat Use by White Sturgeon
(Acipenser transmontanus)
Oliver Patton, Veronica Larwood*1, Matthew Young,1 Frederick Feyrer1
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VOLUME 18, ISSUE 4, ARTICLE 4
and degradation, and other anthropogenic
disturbances are key factors that stress sturgeon
populations worldwide (Birstein 1993).
North America is home to nine species of
sturgeon, all of which have some form of
protection under the US Endangered Species
Act (ESA) (Auer 1996; Haxton et al. 2016).
White Sturgeon (Acipenser transmontanus) is
the largest North American sturgeon and is
distributed along the eastern Pacific Ocean from
central California to Alaska (Birstein 1993;
Jackson et al. 2016), inhabiting rivers, estuaries,
and nearshore coastal environments (Pikitch
et al. 2005). As a group, White Sturgeon are
characterized as amphidromous (Bemis and
Kynard 1997) and endemic to Pacific estuaries
and coastal rivers of North America (Chapman
et al. 1996). Some populations without access to
the sea are critically imperiled, such as the land-
locked population in the middle Snake River in
the Pacif ic Northwest of the United States (Parks
1978; Hildebreand et al. 2016). The San Francisco
Estuary (hereafter the estuary) and its tributaries
contain the largest White Sturgeon population
in California and the southernmost reproducing
population of the species (Chapman et al. 1996;
Pikitch et al. 2005; Hildebrand et al. 2016). The
estuary White Sturgeon population is considered
a species of special management concern by
the state of California (Hildebrand et al. 2016;
Moyle et al. 2016). The estuary population
was nearly extirpated in the late 19th century
from commercial harvest, but now supports a
recreational fishery (Chadwick 1959; Skinner
1962; Parks 1978; Kohlhorst 1980). However,
current harvest levels are unsustainable and,
together with the loss of habitat, represent a
serious threat to the continued existence of the
population (Blackburn et al. 2019).
The estuary White Sturgeon spawn primarily
in the Sacramento River with some evidence of
limited spawning in other tributaries (Kohlhorst
1976; Schaffter 1997; Jackson et al. 2016).
Although adult White Sturgeon use coastal
habitats to some degree, juvenile and adult
White Sturgeon typically remain in the estuary
and lower Sacramento and San Joaquin rivers
for rearing and growth (Kohlhorst et al. 1991;
Bemis and Kynard 1997). White Sturgeon tend
to congregate in deep areas with fine-sediment
substrate and are thought to move into shallow
subtidal habitats to feed during high tides (Moyle
2002); however, little is known about specific
estuarine habitat use. The goal of our study
was to evaluate estuarine foraging habitat use
by sub-adult and adult White Sturgeon to aid
species management and conser vation. This
information can inform managers about how to
prioritize conservation of White Sturgeon across
its geographic range, an approach par ticularly
relevant to the estuary where large-scale habitat
restoration is planned to benefit native fishes.
Actions that are likely to improve habitat in
the estuary include restoring wetlands and
shallow open water habitat; our objective was to
determine how White Sturgeon use these habitats.
METHODS
Study Site and Design
The estuary is located on the Pacific Coast of the
United States in central California (Figure 1A). It
has an open-water surface area of approximately
1,2 35 k m2, a mean depth of 4.6 m, and a volume
of 5.8 10 9 m3. The local Mediterranean climate
is generally characterized by a warm and
dry summer–fall period and a cool and wet
winter–spring period. Our study took place in a
model wetland system (Ryer Island) located in
the central region of the estuary (Figure 1B).
The Ryer Island wetland has a surface area of
approximate ly 3.5 km 2 (347 ha) and is one of the
few remaining natural wetlands in the estuary.
The wetland is f lanked by 0.8 km2 (80 ha) of
shallow shoal habitat, which is in turn flanked
by 1.6 km2 (164 ha) of deep channel habitat. The
wetland’s relatively unaltered state and isolated
location within an expansive open-water region
of the estuar y makes it a natural laboratory to
study the functional ecology of wetlands targeted
for restoration.
Our study design examined White Sturgeon
abundance across a physical habitat gradient
characteristic of the three major structural
habitats present in the estuary: shallow wetland
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https://doi.org/10.15447/sfews.2020v18iss4art4
channel, shallow open-water shoal, and deep
open-water channel (Atwater et al. 1979; Moyle
et al. 2010; Whipple et al. 2012). The deep open-
water channel habitat was characterized as a
broad, deep (average sample depth = 7 m) non-
vegetated channel, which conveys most of the
tidal flow volume in the estuary. The shallow
open-water shoal habitat was characterized as
shallow (average sample depth = 2 m) subtidal
habitat that seasonally supports sparsely
distributed and variably dense submersed aquatic
vegetation (SAV). The dominant SAV species
was sago pondweed (Stuckenia spp.) (Borgnis
and Boyer 2016). The shallow wetland habitat
was characterized as shallow (average sample
depth = 2 m), sma ll (average widt h = 6 m) cha nnels
within the heavily vegetated tidal marsh. Primary
emergent vegetation included common reeds
(Phragmites australis) and tules (Scirpus spp.).
The Ryer Island wetland is typical of a historical,
natural (i.e., non-leveed) wetland in the estuary
in that water inundates the vegetated marsh plain
on high tides and then drains into a network of
subtidal channels on low tides; wetland sampling
took place in the small channels. Substrate in
each habitat was not characterized quantitatively
but was generally comprised of variable mixtures
of mud, sand, and peat.
Data Collection
To collect data over a broad range of
environmental conditions, we sampled for
White Sturgeon in each habitat from May 2017
through October 2018. We conducted a total of
Figure 1 Study area showing the locations
of (A) the San Francisco Estuary and the Ryer
Island wetland in central California, USA, (B)
California Department of Water Resources’ water
quality and outflow measurement sites (see
Data Availability) relative to Ryer Island (in dark
gray), and (C) each individual setline deployment.
4
VOLUME 18, ISSUE 4, ARTICLE 4
six sampling events, one each in May, August,
and November 2017 and March, July, and October
2018. During each sampling event, we deployed
three individual setlines in each habitat, totaling
nine per sampling event. Setlines were generally
similar in form to those previously used in White
Sturgeon studies in the estuary by the California
Department of Fish and Wildlife (Dubois et al.
2010). The setlines were 120 m in length and
possessed a total of 18 circle hooks (six each of
size 2/0, 4/0, and 6/0) baited with commercially
available cut lamprey. Hook gangions were placed
approximately 4 m apart, consisted of 1 m of
60-kg test-braided Dacron line, and were attached
to the main line with halibut clips (Elliott and
Beamesderfer 1990). The main line was composed
of 5/16-in tarred, twisted nylon rope and
stretched in place by heavy anchors attached to
each end. We deployed setlines at midday and
retrieved them approximately 24 hrs later; we
recorded total hours deployed as sampling effort.
In total, 54 setlines with 970 hooks (one setline
possessed 16 hooks) were deployed across the six
sampling events and were collectively fished for
1,315 hours.
Specific setline deployment sites were determined
using satellite imagery and bathymetry to create
polygons for each habitat type and random points
were generated using the “create random points”
tool in geographic information system (GIS)
software (ESRI, Redlands, CA). Upon retrieval, we
assigned each hook a condition for the presence or
absence of White Sturgeon, measured all hooked
White Sturgeon for total length (mm), and then
released them alive.
Environmental conditions during the study period
were characterized from freshwater outflow,
water temperature, and specific conductance
(a surrogate for salinity) data obtained from
the California Department of Water Resources
(CDWR). CDWR estimates daily average
freshwater outf low through the estuary using a
mass–balance calculation, and we calculated daily
average values for the water-qualit y parameters
from continuous measurements taken every 15
minutes at a gaging station located within the
study site (Fig u r e 1C).
Data Analysis
We used Bayesian generalized linear mixed
modeling (GLMM) to examine variability in White
Sturgeon counts in relation to each sampled
habitat. The overall modeling objective was to
elucidate patterns of White Sturgeon abundance
across the three habitats. The response variable
for our model was counts of White Sturgeon
caught in each setline. For modeling purposes,
White Sturgeon counts were not structured by
size or estimated age of individuals because there
was no statistically significant difference in total
length of White Sturgeon captured across habitats
or sampling events (generalized linear model,
p-value 0. 81).
The basic GLMM structure was:
[count] ~ log(Effort(H *h)i) + b1Habitati + aEvent[k]
Sampling effort (Effort) was included as an offset
to standardize counts and was characterized
as hours (H)*hooks (h); hooks was included to
account for one setline which had 16 hooks
instead of 18. Habitat (i.e., wetland, shoal,
channel) was included as a categorical variable.
Sampling event was included as a random factor
variable to allow intercepts to vary across each
of the six sampling events. This enabled the
model to account for several important factors,
including any variation in abundance, water
quality conditions, water elevation and tide stage/
velocity variables that we could not logistically
accommodate in the study design, as well as
any other unmeasured factors that could have
conceivably influenced catches and varied among
the individual sampling events. The sampling
event random variable accounted for the effect of
water-quality variables on counts.
Modeling was implemented using the “brms”
package (Bürkner 2017) in the R statistical
computing environment (R Core Team 2019).
We used widely applicable information criteria
(WAIC) to examine the fit of models, with and
without the event variable, constructed with
several different distributions suitable for count
data: Poisson, zero-inf lated Poisson, negative
binomial, and zero-inf lated negative binomial
5
https://doi.org/10.15447/sfews.2020v18iss4art4
(Zuur et al. 2009). We assessed the predictive
accuracy of the top models by examining the
mean (average error) and the standard error (root
mean square error or RMSE) of the difference
between the model's predictions and the
original data set. The closer average error and
RMSE values are to zero the more accurate the
predictions. Fixed effects were assigned weakly
informative (μ = 0, σ = 10), nor mally di stribute d
priors while random effects were assigned weakly
informative (μ = 0, σ = 10) Cauc hy-distr ibuted
priors. Models were implemented with default
values of four chains with 4,000 iterations,
proceeded by 1,000 warmup iterations.
Data Availability
Freshwater outflow data were obtained from
CDWR and are available at http://cdec.water.
ca.gov/cdecstation2/?sta=DTO. Water temperature
and specific conductance data were obtained
from the CDWR and are available at http://cdec.
water.ca.gov/cdecstation2/?sta=RYC. Original
data collected for this study are available in the
US Geological Survey’s ScienceBase Catalog at
https://doi.org/10.5066/P9087XOC (Steinke et al.
2019).
RESULTS
Environmental conditions exhibited substantial
variabilit y over the study period (Table 1 and
Figure 2). Freshwater outf low values ranged
from 99 to 3,384 m3 sec–1 (mea n = 471, sta ndard
deviation = 525). Temperature values ranged from
9 to 24 °C (mean = 17, standard deviation = 4).
Specific conductance values ranged from
1 to 22,791 μs cm1 (mea n = 8,959, standa rd
deviation = 5,700). For reference, these specific
conductance values translate to salinity values
of approximately 0 to 16 ppt (mean = 6, standard
devi ation = 5).
We captured total of 111 White Sturgeon. Of
this total, 54 were captured in the deep open-
water channel, 56 were captured in the shallow
open-water shoal, and one was captured in
the shallow wetland. Overall, the number of
individuals caught per setline ranged from zero
to seven (mean = 2, standard deviation = 2). Total
lengths of the individuals captured ranged
from 675 to 1,604 mm (mean = 1,111, standard
deviation = 186). Bycatch for this study consisted
of only 12 individual f ishes: ten Striped Bass
(Morone saxatilis), one Jacksmelt (Atherinopsis
californiensis), and one White Catfish (Ameiurus
catus). The overall frequency of retrieving
damaged or missing hooks was 2% and the
overall frequency of hooks with no bait was 10%.
Modeling results indicated, regardless of
statistical sampling distribution, that physical
habitat strongly affected White Sturgeon counts
(Table 2). Counts of White Sturgeon in the deep
open-water channel and the shallow open-water
shoal were statistically indistinguishable from
each other but were substantially higher than
Table 1 Summary of environmental conditions and White Sturgeon catches across sampling events. Water temperature, specific
conductance, and freshwater outflow data were obtained from the California Department of Water Resources (see Methods) and
the values in the table are means of the five days preceding and including the sampling date. Sampling hours is the total amount
of time the nine setlines were deployed during each sampling event. Total length refers to the mean total length and standard
deviation of all sturgeon captured during that sampling event.
Event Date
Temperature (°C)
mean ± SD
Mean specific
conductance
(µs cm1 ± SD)
Mean freshwater
outflow
(m³s–1 ± SD
Total sampling
hours
Total White
Sturgeon
captured
Total length (mm)
mean ± SD
1 25-May-2017 19 ± 1 261 ± 168 1740 ± 143 213 30 1101 ± 156
2 29-Aug-2017 21 ± 1 7863 ± 2165 330 ± 13 256 25 1105 ± 172
3 29-Nov-2017 15 ± 1 12254 ± 2223 214 ± 27 203 27 1081 ± 198
4 20-Mar-2018 18 ± 1 6958 ± 2403 723 ± 164 217 7 1142 ± 172
5 05-Jul-2018 21 ± 1 13125 ± 2569 159 ± 20 213 9 1033 ± 173
6 10-Oct-2018 21 ± 1 14313 ± 2913 233 ± 96 213 13 1257 ± 217
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VOLUME 18, ISSUE 4, ARTICLE 4
Figure 2 Time series plots of water temperature (°C), specific conductance (µs cm–1), and freshwater outflow (m3 sec–1) in the
study area, from May 2017 to November 2018. Black points superimposed on the time series show when the six individual sampling
events took place.
Figure 3. Marginal effects for each habitat type based on the best-fitting model identified in Table 2. Each point signifies the mean
expected White Sturgeon count per setline and the whiskers represent the 95% confidence interval for each habitat.
7
https://doi.org/10.15447/sfews.2020v18iss4art4
in the shallow wetland (Figure 2). Regarding the
different statistical distributions examined, WAIC
values demonstrated that models which included
habitat and event fit the data better than models
that excluded those parameters, indicating that
each distribution generated generally similar
results. However, Poisson models had the lowest
RMSE (Poisson
1.44, Zero-inf lated Poisson
1.49;
Negative binomial
1.53, Zero-inflated negative
binomial
1.54) and best fit the data.
DISCUSSION
Our study improves the understanding of White
Sturgeon estuarine habitat utilization over a
range of environmental conditions in the San
Francisco Estuar y (estuar y). Ryer Island contains
three major habitats that White Sturgeon
encounter throughout the estuar y. This knowledge
can help contextualize White Sturgeon habitat
use and movement within the estuar y, as well as
inform resource managers of essential sturgeon
habitat when they plan restoration sites.
Of the three habitats at Ryer Island, sub-adult and
adult White Sturgeon were relatively abundant in
the deep open-water channel and shallow open-
water shoal habitats but were largely absent in the
wetland habitat. Interestingly, White Sturgeon are
found in the larger sloughs of Suisun Marsh, a
large, expansive wetland located near Ryer Island
(Matern et al. 2002; Moyle et al. 1986). We posit
that White Sturgeon did not occupy the wetland
habitat at Ryer Island because of its smaller,
shallower channels compared to the larger sloughs
in Suisun Marsh, which are more comparable in
size and depth to the deep open-water channel
in this study. In general, the presence or absence
of White Sturgeon in wetland habitats may be
driven by habitat size and configuration, food
and prey availability, and substrate type. We did
observe one White Sturgeon within the wetland
habitat at Ryer Island. The location of this catch
was near the wetland breach, adjacent to shoal
habitat. A study on Lake Sturgeon (Acipenser
fulvescens) has shown that they tend to aggregate
near a wetland complex when another suitable
habitat is present (Damstra and Galarowicz
2013). It is uncertain if this White Sturgeon was
utilizing the wetland habitat for foraging or was
baited into the wetland from the shoal habitat.
The physical configuration of the Ryer Island
complex provided a unique natural laboratory to
test how abundance varies across major structural
habitat elements. Limitations of our study
included that it was conducted at a single location
and that the sampling gear targeted a limited size
range of actively feeding fish. While Ryer Island
represents a single location, we have no reason
to believe that the broad habitat preferences we
identified would vary across the estuar y. The
specific hook sizes and baits used in our study
may have contributed to the predominance of
sub-adult and adult White Sturgeon obser ved in
the catches. Future research that incorporates a
wider selection of hook sizes and baits, or other
observational tools such as telemetr y, could be
conducted to more thoroughly examine habitat
usage and movements of all life stages of White
Sturgeon. Higher resolution sampling in space and
time could potentially increase our understanding
of White Sturgeon movement and foraging in
the estuary, including evaluating the effects of
day vs. night and tidal cycle on White Sturgeon
foraging behavior.
Understanding how White Sturgeon, of all life
stages, utilize the estuarine environment is an
important consideration for habitat restoration
projects. Attainable habitat actions include the
restoration of shallow inundated habitat, which
we have shown to support actively foraging
Table 2 Parameter coefficients and 95% credible intervals
generated from the best fitting generalized linear mixed
models on White Sturgeon counts (see Methods for details).
Variables with credible intervals not overlapping zero were
deemed significant and highlighted in bold.
Response variable = count, Distribution = Poisson
Coefficient ± SE
Lower
95% CI
Upper
95% CI
Intercept 5.11 ± 0.38 – 5.85 – 4.38
Wetland
(relative to channel) 4.51 ± 1.28 – 7.72 – 2.65
Shoal
(relative to channel) 0.05 ± 0.19 – 0.33 0.42
8
VOLUME 18, ISSUE 4, ARTICLE 4
sub-adult and adult White Sturgeon within the
estuary. Further research on all life stages of
White Sturgeon in estuarine habitats would help
better inform sturgeon management and the
potential role of estuarine habitat restoration.
ACKNOWLEDGEMENTS
Funding was provided by the Bureau of
Reclamation (IA# R15PG00085). Dave Ayers,
Ethan Clark, Justin Clause, Ethan Enos, Mary
Jade Farruggia, Emerson Gusto, Jessie Kathan,
Robert Spankowski, and Dennis Steinke assisted
with field work. Chris Vallee provided invaluable
support and infectious enthusiasm. Field sampling
was authorized by California Department of Fish
and Wildlife Scientific Collecting Permit SC-3602,
National Marine Fisheries Service Scientific
Research Permit 19121, California Endangered
Species Act (CESA) Memorandum of Understanding
for the take of threatened and endangered species
issued by the California Department of Fish and
Wildlife, and take authority obtained through the
Interagency Ecological Program (IEP). Any use
of trade, firm, or product names is for descriptive
purposes only and does not imply endorsement by
the US Government.
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... We quantified life-long variation in exposure to salinity concentrations in White Sturgeon to reconstruct movements and habitat use in the SFE using fin ray Sr isotope ( 87 Sr/ 86 Sr) geochemistry. Although previous studies have described habitat use of White Sturgeon in the SFE using baited hooks, telemetry, and mark recapture techniques (Nelson et al., 2013;Miller et al., 2020;Patton et al., 2020), our study is the first to employ a natural geochemical tracer to examine the ontogenetic movements and habitat use patterns of over 100 individual White Sturgeon over their lifespan prior to capture. Our results largely corroborated prior observations of amphidromous migratory behaviors (Bemis and Kynard, 1997;Patton et al., 2020) with prolonged periods of estuarine residence (DeVore et al., 1999;Miller et al., 2020). ...
... Although previous studies have described habitat use of White Sturgeon in the SFE using baited hooks, telemetry, and mark recapture techniques (Nelson et al., 2013;Miller et al., 2020;Patton et al., 2020), our study is the first to employ a natural geochemical tracer to examine the ontogenetic movements and habitat use patterns of over 100 individual White Sturgeon over their lifespan prior to capture. Our results largely corroborated prior observations of amphidromous migratory behaviors (Bemis and Kynard, 1997;Patton et al., 2020) with prolonged periods of estuarine residence (DeVore et al., 1999;Miller et al., 2020). However, we also observed broad variation among individual fish. ...
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