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At least 145 records · Page 8Linked to original sources
USGS2016

Functional metagenomic selection of RubisCOs from uncultivated bacteria

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a critical yet severely inefficient enzyme that catalyses the fixation of virtually all of the carbon found on Earth. Here, we report a functional metagenomic selection that recovers physiologically active RubisCO molecules directly from uncultivated and largely unknown members of natural microbial communities. Selection is based on CO 2 -dependent growth in a host strain capable of expressing environmental deoxyribonucleic acid (DNA), precluding the need for pure cultures or screening of recombinant clones for enzymatic activity. Seventeen functional RubisCO-encoded sequences were selected using DNA extracted from soil and river autotrophic enrichments, a photosynthetic biofilm and a subsurface groundwater aquifer. Notably, three related form II RubisCOs were recovered which share high sequence similarity with metagenomic scaffolds from uncultivated members of the G allionellaceae family. One of the G allionellaceae RubisCOs was purified and shown to possess CO 2 /O 2 specificity typical of form II enzymes. X-ray crystallography determined that this enzyme is a hexamer, only the second form II multimer ever solved and the first RubisCO structure obtained from an uncultivated bacterium. Functional metagenomic selection leverages natural biological diversity and billions of years of evolution inherent in environmental communities, providing a new window into the discovery of CO 2 -fixing enzymes not previously characterized.

Environmental Microbiology↗
USGS2006

Model weights and the foundations of multimodel inference

Statistical thinking in wildlife biology and ecology has been profoundly influenced by the introduction of AIC (Akaike?s information criterion) as a tool for model selection and as a basis for model averaging. In this paper, we advocate the Bayesian paradigm as a broader framework for multimodel inference, one in which model averaging and model selection are naturally linked, and in which the performance of AIC-based tools is naturally evaluated. Prior model weights implicitly associated with the use of AIC are seen to highly favor complex models: in some cases, all but the most highly parameterized models in the model set are virtually ignored a priori. We suggest the usefulness of the weighted BIC (Bayesian information criterion) as a computationally simple alternative to AIC, based on explicit selection of prior model probabilities rather than acceptance of default priors associated with AIC. We note, however, that both procedures are only approximate to the use of exact Bayes factors. We discuss and illustrate technical difficulties associated with Bayes factors, and suggest approaches to avoiding these difficulties in the context of model selection for a logistic regression. Our example highlights the predisposition of AIC weighting to favor complex models and suggests a need for caution in using the BIC for computing approximate posterior model weights.

Ecology↗
USGS1978

Topographic maps

A topographic map is a line-and-symbol representation of natural and selected man-made features of a part of the Earth's surface plotted to a definite scale. A distinguishing characteristic of a topographic map is the portrayal of the shape and elevation of the terrain by contour lines.

General Information Product↗
USGS1986

Topographic maps

A topographic map is a line-and-symbol representation of natural and selected man-made features of a part of the Earth's surface plotted to a definite scale. A distinguishing characteristic of a topographic map is the portrayal of the shape and elevation of the terrain by contour lines.

Monograph↗
USGS1970

A proposed streamflow data program for Oklahoma

An evaluation of the streamflow data available in Oklahoma has been made to provide guidelines for planning future data-collection programs. The basic steps in the evaluation procedure were (1) definition of the long-terms goals of the streamflow-data program in quantitative form, (2) examination and analysis of streamflow data to determine which goals have been met, and (3) consideration of alternate programs and techniques to meet the remaining goals. The study defines the individual relation between certain statistical streamflow characteristics and selected basin parameters. This relation is a multiple regression equation that could be used on a statewide basis to compute a selected natural-flow characteristic at any site on a stream. The study shows that several streamflow characteristics can be estimated within an accuracy equivalent to 10 years of record by use of a regression related to at least three climatic or basin parameters for any basin of 50 square miles or more. The study indicates that significant changes in the scope and character of the data-collection program would enhance the possibility of attaining the remaining goals. A streamflow-data program based on the guidelines developed in this study is proposed for the future.

Open-File Report↗
USGS2012

Sediment transport to and from small impoundments in northeast Kansas, March 2009 through September 2011

The U.S. Geological Survey, in cooperation with the Kansas Water Office, investigated sediment transport to and from three small impoundments (average surface area of 0.1 to 0.8 square miles) in northeast Kansas during March 2009 through September 2011. Streamgages and continuous turbidity sensors were operated upstream and downstream from Atchison County, Banner Creek, and Centralia Lakes to study the effect of varied watershed characteristics and agricultural practices on sediment transport in small watersheds in northeast Kansas. Atchison County Lake is located in a predominantly agricultural basin of row crops, with wide riparian buffers along streams, a substantial amount of tile drainage, and numerous small impoundments (less than 0.05 square miles; hereafter referred to as “ponds”). Banner Creek Lake is a predominantly grassland basin with numerous small ponds located in the watershed, and wide riparian buffers along streams. Centralia Lake is a predominantly agricultural basin of row crops with few ponds, few riparian buffers along streams, and minimal tile drainage. Upstream from Atchison County, Banner Creek, and Centralia Lakes 24, 38, and 32 percent, respectively, of the total load was transported during less than 0.1 percent (approximately 0.9 days) of the time. Despite less streamflow in 2011, larger sediment loads during that year indicate that not all storm events transport the same amount of sediment; larger, extreme storms during the spring may transport much larger sediment loads in small Kansas watersheds. Annual sediment yields were 360, 400, and 970 tons per square mile per year at Atchison County, Banner, and Centralia Lake watersheds, respectively, which were less than estimated yields for this area of Kansas (between 2,000 and 5,000 tons per square mile per year). Although Centralia and Atchison County Lakes had similar percentages of agricultural land use, mean annual sediment yields upstream from Centralia Lake were about 2.7 times those at Atchison County or Banner Creek Lakes. These data indicate larger yields of sediment from watersheds with row crops and those with fewer small ponds, and smaller yields in watersheds which are primarily grassland, or agricultural with substantial tile drainage and riparian buffers along streams. These results also indicated that a cultivated watershed can produce yields similar to those observed under the assumed reference (or natural) condition. Selected small ponds were studied in the Atchison County Lake watershed to characterize the role of small ponds in sediment trapping. Studied ponds trapped about 8 percent of the sediment upstream from the sediment-sampling site. When these results were extrapolated to the other ponds in the watershed, differences in the extent of these ponds was not the primary factor affecting differences in yields among the three watersheds. However, the selected small ponds were both 45 years old at the time of this study, and have reduced capacity because of being filled in with sediments. Additionally, trapping efficiency of these small ponds decreased over five observed storms, indicating that processes that suspended or resuspended sediments in these shallow ponds, such as wind and waves, affected their trapping efficiencies. While small ponds trapped sediments in small storms, they could be a source of sediment in larger or more closely spaced storm events. Channel slope was similar at all three watersheds, 0.40, 0.46, and 0.31 percent at Atchison County, Banner Creek, and Centralia Lake watersheds, respectively. Other factors, such as increased bank and stream erosion, differences in tile drainage, extent of grassland, or riparian buffers, could be the predominant factors affecting sediment yields from these basins. These results show that reference-like sediment yields may be observed in heavily agricultural watersheds through a combination of field-scale management activities and stream channel protection. When computing loads using published erosion rates obtained by single-point survey methodology, streambank contributions from the main stem of Banner Creek are three times more than the sediment load observed by this study at the sediment sampling site at Banner Creek, 2.6 times more than the sediment load observed by this study at the sediment sampling site at Clear Creek (upstream from Atchison County Lake), and are 22 percent of the load observed by this study at the sediment sampling site at Black Vermillion River above Centralia Lake. Comparisons of study sites to similarly sized urban and urbanizing watersheds in Johnson County, Kansas indicated that sediment yields from the Centralia Lake watershed were similar to those in construction-affected watersheds, while much smaller sediment yields in the Atchison County and Banner Creek watersheds were comparable to stable, heavily urbanized watersheds. Comparisons of study sites to larger watersheds upstream from Tuttle Creek Lake indicate the Black Vermillion River watershed continues to have high sediment yields despite 98 percent of sediment from the Centralia watershed (a headwater of the Black Vermillion River) being trapped in Centralia Lake. Estimated trapping efficiencies for the larger watershed lakes indicated that Banner Creek and Centralia Lakes trapped 98 percent of incoming sediment, whereas Atchison County Lake trapped 72 percent of incoming sediment during the 3-year study period.

Kansas↗
USGS1986

Manual for estimating selected streamflow characteristics of natural-flow streams in the Colorado River basin in Utah

Methods are presented for estimating 10 streamflow characteristics at three types of sites on natural flow streams in the Colorado River Basin in Utah. The streamflow characteristics include average discharge and annual maximum 1-, 7-, and 15-day mean discharges for recurrence intervals of 10, 50 and 100 years. At or near gaged sites, two methods weight gaging station data with regression equation values to estimate streamflow characteristics. At sites on ungaged streams, a method estimates streamflow characteristics using regression equations. The regression equations relate the streamflow characteristics to the following basin and climatic characteristics: contributing drainage area, mean basin elevation, mean annual precipitation, main channel slope, and forested area. Separate regression equations were developed for four hydrologically distinct regions in the study area. The standard error of estimate for the 10 streamflow characteristics ranges from 13% to 87%. Basin, climatic, and streamflow characteristics, available as of September 30, 1981, are presented for 135 gaging stations in Utah, Arizona, Colorado, and Wyoming. In addition, weighted estimates of the streamflow characteristics based on station data and the regression equation estimates are provided for most gaging stations. (Author 's abstract)

Water-Resources Investigations Report↗
USGS2011

USGS invasive species solutions

Land managers must meet the invasive species challenge every day, starting with identification of problem species, then the collection of best practices for their control, and finally the implementation of a plan to remove the problem. At each step of the process, the availability of reliable information is essential to success. The U.S. Geological Survey (USGS) has developed a suite of resources for early detection and rapid response, along with data management and sharing.

Natural Selections↗
USGS2020

The impacts of a changing climate to DOD coastal facilities in the tropical Pacific Ocean

The USGS, the National Oceanic and Atmospheric Administration (NOAA), Deltares, and the University of Hawaii (UH) recently completed a study investigating the impact of a changing climate and sea-level rise on Roi-Namur Island on Kwajalein Atoll in the Republic of the Marshall Islands, which is part of the Ronald Reagan Ballistic Missile Defense Test Site (RTS). The isolated location of RTS makes it uniquely suited to support realistic testing of missiles and intercept scenarios with minimal safety and environmental concerns. In addition, this unique location supports research and development for space and missile programs and space reconnaissance and surveillance operations. RTS has been a critical component of the Pacific Range, with the world’s most advanced telemetry, optics, and radar instrumentation used to collect metric and signature data on missiles.

Kwajalein Atoll↗
USGS2002

Seasonal and diel habitat selection by bluegills in a shallow natural lake

Habitat use by bluegill Lepomis macrochirus may be dictated by the avoidance of predators and the availability of prey. Previous work suggests that bluegills large enough to avoid predators will select habitats based on foraging profitability. However, these studies focused on smaller fish (<150 mm standard length) in laboratory experiments or in natural systems with distinct vegetated and open-water habitats. Our objective was to use radio telemetry to determine monthly and diel vegetation selection by larger (>200 mm total length [TL]) bluegills in a shallow (mean depth = 1.2 m), 332-ha, natural lake (Pelican Lake, Nebraska) with both emergent and submergent vegetation distributed throughout. A total of 78 bluegills (200-273 mm TL) were implanted with radio transmitters and relocated daily for 6 d per month (April-September); up to 20 of the tagged fish were relocated every 2 h for a 24-h period once each month. Regardless of diel period, bluegills used open-water, emergent vegetation, submergent vegetation, and mixed emergent - submergent vegetation habitat types in similar proportions. During April, June, and July, male bluegills positively selected emergent vegetation, whereas female bluegills showed no vegetation selection preference during any month. Throughout the study period, bluegills never avoided open-water habitats, suggesting that larger individuals may continue to use open-water habitats in proportion to their availability. In addition, emergent vegetation appeared to be important, particularly for male bluegills. Although the mechanism for the positive selection of emergent vegetation by males was unclear, the protection or enhancement of such habitats may facilitate the preservation of quality bluegill populations in shallow lakes.

Transactions of the American Fisheries Society↗
USGS2011

Habitat diversity in the Northeastern Gulf of Mexico: Selected video clips from the Gulfstream Natural Gas Pipeline digital archive

This project combines underwater video with maps and descriptions to illustrate diverse seafloor habitats from Tampa Bay, Florida, to Mobile Bay, Alabama. A swath of seafloor was surveyed with underwater video to 100 meters (m) water depth in 1999 and 2000 as part of the Gulfstream Natural Gas System Survey. The U.S. Geological Survey (USGS) in St. Petersburg, Florida, in cooperation with Eckerd College and the Florida Department of Environmental Protection (FDEP), produced an archive of analog-to-digital underwater movies. Representative clips of seafloor habitats were selected from hundreds of hours of underwater footage. The locations of video clips were mapped to show the distribution of habitat and habitat transitions. The numerous benthic habitats in the northeastern Gulf of Mexico play a vital role in the region's economy, providing essential resources for tourism, natural gas, recreational water sports (fishing, boating, scuba diving), materials, fresh food, energy, a source of sand for beach renourishment, and more. These submerged natural resources are important to the economy but are often invisible to the general public. This product provides a glimpse of the seafloor with sample underwater video, maps, and habitat descriptions. It was developed to depict the range and location of seafloor habitats in the region but is limited by depth and by the survey track. It should not be viewed as comprehensive, but rather as a point of departure for inquiries and appreciation of marine resources and seafloor habitats. Further information is provided in the Resources section.

Florida;Alabama;Mississippi;Louisiana↗
USGS2006

Concentrations of elements in sediments and selective fractions of sediments, and in natural waters in contact with sediments from Lake Roosevelt, Washington, September 2004

Twenty-eight composite and replicate sediment samples from 8 Lake Roosevelt sites were collected and analyzed for 10 alkali and alkaline earth elements, 2 non-metals, 20 metals, and 4 lanthanide and actinide elements. All elements were detected in all sediment samples except for silver (95 percent of the elements detected for 1,008 analyses), which was detected only in 4 samples. Sequential selective extraction procedures were performed on single composite samples from the eight sites. The percentage of detections for the 31 elements analyzed ranged from 76 percent for the first extraction fraction using a weak extractant to 93 percent for the four-acid dissolution of the sediments remaining after the third sequential selective extraction. Water samples in various degrees of contact with the sediment were analyzed for 10 alkali and alkaline earth elements, 5 non-metals, 25 metals, and 16 lanthanide and actinide elements. The filtered water samples included 10 samples from the reservoir water column at 8 sites, 32 samples of porewater, 55 samples from reservoir water overlying sediments in 8 cores from the site incubated in a field laboratory, and 24 water samples that were filtered after being tumbled with sediments from 8 sites. Overall, the concentrations of only 37 percent of the 6,776 analyses of the 121 water samples were greater than the reporting limit. Selenium, bismuth, chromium, niobium, silver, and zirconium were not detected in any water samples. The percentage of concentrations for the water samples that were above the reporting limit ranged from 14 percent for the lanthanide and actinide elements to 77 percent for the alkali and alkaline earth elements. Concentrations were greater than reporting limits in only 23 percent of the analyses of reservoir water and 29 percent of the analyses of reservoir water overlying incubation cores. In contrast, 47 and 48 percent of the concentrations of porewater and water samples tumbled with sediments, respectively, were greater than the reporting limit.

Washington↗
USGS2016

Estimating peak-flow frequency statistics for selected gaged and ungaged sites in naturally flowing streams and rivers in Idaho

The U.S. Geological Survey, in cooperation with the Idaho Transportation Department, updated regional regression equations to estimate peak-flow statistics at ungaged sites on Idaho streams using recent streamflow (flow) data and new statistical techniques. Peak-flow statistics with 80-, 67-, 50-, 43-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities (1.25-, 1.50-, 2.00-, 2.33-, 5.00-, 10.0-, 25.0-, 50.0-, 100-, 200-, and 500-year recurrence intervals, respectively) were estimated for 192 streamgages in Idaho and bordering States with at least 10 years of annual peak-flow record through water year 2013. The streamgages were selected from drainage basins with little or no flow diversion or regulation. The peak-flow statistics were estimated by fitting a log-Pearson type III distribution to records of annual peak flows and applying two additional statistical methods: (1) the Expected Moments Algorithm to help describe uncertainty in annual peak flows and to better represent missing and historical record; and (2) the generalized Multiple Grubbs Beck Test to screen out potentially influential low outliers and to better fit the upper end of the peak-flow distribution. Additionally, a new regional skew was estimated for the Pacific Northwest and used to weight at-station skew at most streamgages. The streamgages were grouped into six regions (numbered 1_2, 3, 4, 5, 6_8, and 7, to maintain consistency in region numbering with a previous study), and the estimated peak-flow statistics were related to basin and climatic characteristics to develop regional regression equations using a generalized least squares procedure. Four out of 24 evaluated basin and climatic characteristics were selected for use in the final regional peak-flow regression equations. Overall, the standard error of prediction for the regional peak-flow regression equations ranged from 22 to 132 percent. Among all regions, regression model fit was best for region 4 in west-central Idaho (average standard error of prediction=46.4 percent; pseudo-R 2 >92 percent) and region 5 in central Idaho (average standard error of prediction=30.3 percent; pseudo-R 2 >95 percent). Regression model fit was poor for region 7 in southern Idaho (average standard error of prediction=103 percent; pseudo-R 2 <78 percent) compared to other regions because few streamgages in region 7 met the criteria for inclusion in the study, and the region’s semi-arid climate and associated variability in precipitation patterns causes substantial variability in peak flows. A drainage area ratio-adjustment method, using ratio exponents estimated using generalized least-squares regression, was presented as an alternative to the regional regression equations if peak-flow estimates are desired at an ungaged site that is close to a streamgage selected for inclusion in this study. The alternative drainage area ratio-adjustment method is appropriate for use when the drainage area ratio between the ungaged and gaged sites is between 0.5 and 1.5. The updated regional peak-flow regression equations had lower total error (standard error of prediction) than all regression equations presented in a 1982 study and in four of six regions presented in 2002 and 2003 studies in Idaho. A more extensive streamgage screening process used in the current study resulted in fewer streamgages used in the current study than in the 1982, 2002, and 2003 studies. Fewer streamgages used and the selection of different explanatory variables were likely causes of increased error in some regions compared to previous studies, but overall, regional peak‑flow regression model fit was generally improved for Idaho. The revised statistical procedures and increased streamgage screening applied in the current study most likely resulted in a more accurate representation of natural peak-flow conditions. The updated, regional peak-flow regression equations will be integrated in the U.S. Geological Survey StreamStats program to allow users to estimate basin and climatic characteristics and peak-flow statistics at ungaged locations of interest. StreamStats estimates peak-flow statistics with quantifiable certainty only when used at sites with basin and climatic characteristics within the range of input variables used to develop the regional regression equations. Both the regional regression equations and StreamStats should be used to estimate peak-flow statistics only in naturally flowing, relatively unregulated streams without substantial local influences to flow, such as large seeps, springs, or other groundwater-surface water interactions that are not widespread or characteristic of the respective region.

Idaho↗
USGS2005

Development of regional curves relating bankfull-channel geometry and discharge to drainage area for streams in Pennsylvania and selected areas of Maryland

Natural-stream designs are commonly based on the dimensions of the bankfull channel, which is capable of conveying discharges that transport sediment without excessive erosion or deposition. Regional curves relate bankfull-channel geometry and discharge to drainage area in watersheds with similar runoff characteristics and commonly are utilized by practitioners of natural-stream design to confirm or refute selection of the field-identified bankfull channel. Data collected from 66 streamflow-gaging stations and associated stream reaches between December 1999 and December 2003 were used in one-variable ordinary least-squares regression analyses to develop regional curves relating drainage area to cross-sectional area, discharge, width, and mean depth of the bankfull channel. Watersheds draining to these stations are predominantly within the Piedmont, Ridge and Valley, and Appalachian Plateaus Physiographic Provinces of Pennsylvania and northern Maryland. Statistical analyses of physiography, percentage of watershed area underlain by carbonate bedrock, and percentage of watershed area that is glaciated indicate that carbonate bedrock, not physiography or glaciation, has a controlling influence on the slope of regional curves. Regional curves developed from stations in watersheds underlain by 30 percent or less carbonate bedrock generally had steeper slopes than the corresponding relations developed from watersheds underlain by greater than 30 percent carbonate bedrock. In contrast, there is little evidence to suggest that regional curves developed from stations in the Piedmont or Ridge and Valley Physiographic Province are different from the corresponding relations developed from stations in the Appalachian Plateaus Physiographic Province. On the basis of these findings, regional curves are presented to represent two settings that are independent of physiography: (1) noncarbonate settings characterized by watersheds with carbonate bedrock underlying 30 percent or less of watershed area, and (2) carbonate settings characterized by watersheds with carbonate bedrock underlying greater than 30 percent of watershed area. All regional curves presented in this report have slopes that are significantly different from zero and normally distributed residuals that vary randomly with drainage area. Drainage area explains the most variability in bankfull cross-sectional area and bankfull discharge in the noncarbonate setting (R2 = 0.92 for both). Less variability is explained in bankfull width and depth (R2 = 0.81 and 0.72, respectively). Regional curves representing the carbonate setting are generally not as statistically robust as the corresponding noncarbonate relations because there were only 11 stations available to develop these curves and drainage area cannot explain variance resulting from karst features. The carbonate regional curves generally are characterized by less confidence, lower R2 values, and higher residual standard errors. Poor representation by watersheds less than 40 mi2 causes the carbonate regional curves for bankfull discharge, cross-sectional area, and mean depth to be disproportionately influenced by the smallest watershed (values of Cook's Distance range from 3.6 to 8.4). Additional bankfull discharge and channel-geometry data from small watersheds might reduce this influence, increase confidence, and generally improve regional curves representing the carbonate setting. Limitations associated with streamflow-gaging station selection and development of the curves result in some constraints for the application of regional curves presented in this report. These curves apply only to streams within the study area in watersheds having land use, streamflow regulation, and drainage areas that are consistent with the criteria used for station selection. Regardless of the setting, the regional curves presented here are not intended for use as the sole method for estimation of bankfull characteristics; however, th

Scientific Investigations Report↗
USGS2008

Selecting remediation goals by assessing the natural attenuation capacity of groundwater systems

Remediation goals for the source areas of a chlorinated ethene‐contaminated groundwater plume were identified by assessing the natural attenuation capacity of the aquifer system. The redox chemistry of the site indicates that sulfate‐reducing (H 2 ∼ 2 nanomoles [nM]) per liter conditions near the contaminant source grade to Fe(III)‐reducing conditions (H 2 ∼ 0.5 nM) downgradient of the source. Sulfate‐reducing conditions facilitate the initial reduction of perchloroethene (PCE) to trichloroethene (TCE), cis ‐dichloroethene ( cis ‐DCE), and vinyl chloride (VC). Subsequently, the Fe(III)‐reducing conditions drive the oxidation of cis ‐DCE and VC to carbon dioxide and chloride. This sequence gives the aquifer a substantial capacity for biodegrading chlorinated ethenes. Natural attenuation capacity (the slope of the steady‐state contaminant concentration profile along a groundwater flowpath) is a function of biodegradation rates, aquifer dispersive characteristics, and groundwater flow velocity. The natural attenuation capacity at the Kings Bay, Georgia site was assessed by estimating groundwater flowrates (∼0.23 ± 0.12 m/d) and aquifer dispersivity (∼1 m) from hydrologic and scale considerations. Apparent biodegradation rate constants (PCE and TCE ∼ 0.01 d −1 ; cis ‐DCE and VC ∼ 0.025 d −1 ) were estimated from observed contaminant concentration changes along aquifer flowpaths. A boundary‐value problem approach was used to estimate levels to which contaminant concentrations in the source areas must be lowered (by engineered removal), or groundwater flow velocities lowered (by pumping) for the natural attenuation capacity to achieve maximum concentration limits (MCLs) prior to reaching a predetermined regulatory point of compliance.

Bioremediation Journal↗
USGS1989

Guide for selecting Manning's roughness coefficients for natural channels and flood plains

Although much research has been done on Manning's roughness coefficient, n, for stream channels, very little has been done concerning the roughness values for densely vegetated flood plains. The n value is determined from the values of the factors that affect the roughness of channels and flood plains. In densely vegetated flood plains, the major roughness is caused by trees, vines, and brush. The n value for this type of flood plain can be determined by measuring the vegetation density of the flood plain. Photographs of flood-plain segments where n values have been verified can be used as a comparison standard to aid in assigning n values to similar flood plains.

Water Supply Paper↗
USGS2020

Nowhere to hide: The importance of instream cover for stream‐living Coastal Cutthroat Trout during seasonal low flow

Through their multiple functions, refuges may be important for stream‐living fishes, particularly during stressful events such as seasonal low flow or drought. Coastal Cutthroat Trout Oncorhynchus clarkii clarkii is an ideal study organism to understand the importance of refuge. During seasonal low flow, lower water levels limit access to refuge and emigration, survival of fish is low, and predation risk is high. Under these conditions, we studied patterns of cover use from field observations and tested predictions from multiple hypotheses about cover use in a semi‐natural experiment. Boulders were the main cover selected by trout in natural streams. Trout disproportionately used cover near deeper water, and they selected larger‐sized cover in shallower water. Trout showed plasticity to switch among behaviours, concealing under cover and emigrating as first options, followed by grouping, and then habitat shifting. Lack of feeding and growth suggested that perceived threat of predation was a more important driver of behaviour than foraging. Emigration was also linked to cover, with higher levels of emigration associated with less cover availability, revealing a potential link between refuge and demography through emigration. Except for feeding, the intensity of alternative behaviours can increase or decrease depending on refuge availability. Collectively, findings of this work indicate that cover can be considered a critical limiting resource along with other fundamental resources of food and space for stream‐living fish.

Ecology of Freshwater Fish↗