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USGS2018

Understanding how microbiomes influence the systems they inhabit

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Nature Microbiology↗

USGS2025

Wave driven cross shore and alongshore transport reveal more extreme projections of shoreline change in island environments

Coastal erosion, intensified by sea level rise, poses significant threats to coastal communities in Hawaiʻi and similar island communities. This study projects long-term shoreline change on the Hawaiian Island of O‘ahu using the data-assimilated CoSMoS-COAST shoreline change model. CoSMoS-COAST models four key shoreline processes: (1) Alongshore transport, (2) Recession due to sea level rise, (3) Cross-shore transport due to waves, and (4) Residual processes represented by a linear trend term. This study marks the first application of CoSMoS-COAST for an oceanic equatorial island with narrow beaches and a dynamic wave climate. The model is informed with a novel combination of shoreline data derived from high-resolution imagery from Planet, Sentinel-2, and Landsat satellites, wave-climate hindcasts specific to Hawai‘i, and regional beach-slope surveys. On a dynamic northern Oʻahu beach, the model achieved a root mean square error of 9.4 m between observations and model output. CoSMoS-COAST predicts that 81% of O‘ahu’s sandy beach coastline could experience beach loss by 2100; with 39.8% of this loss happening by 2030. This represents an increase, 43.3%, in net landward shoreline change compared to previous erosion forecasts, for 0.3 m of sea level rise (2050). Additionally, dynamic processes such as cross-shore equilibrium processes and alongshore sediment transport, play a large contribution to gross shoreline change within the next decade, particularly on O ‘ahu’s north and west shores. In the long term, we find that recession due to sea level rise and residual processes dominate, but dynamic, wave-driven processes (longshore and cross-shore transport) still account for 34% of shoreline change between present and 2100. We assert dynamic, wave-driven processes are a crucial addition for accurate modeling of island sandy beach environments. These findings have implications for O‘ahu’s coastal planning and development, suggesting updates to shoreline policies that rely upon erosion forecasting, and highlights the importance of incorporating wave and alongshore transport in erosion models for other Pacific islands.

Hawaii↗

USGS2010

Coupled arsenotrophy in a hot spring photosynthetic biofilm at Mono Lake, California

Red-pigmented biofilms grow on rock and cobble surfaces present in anoxic hot springs located on Paoha Island in Mono Lake. The bacterial community was dominated (∼ 85% of 16S rRNA gene clones) by sequences from the photosynthetic Ectothiorhodospira genus. Scraped biofilm materials incubated under anoxic conditions rapidly oxidized As(III) to As(V) in the light via anoxygenic photosynthesis but could also readily reduce As(V) to As(III) in the dark at comparable rates. Back-labeling experiments with 73 As(V) demonstrated that reduction to 73 As(III) also occurred in the light, thereby illustrating the cooccurrence of these two anaerobic processes as an example of closely coupled arsenotrophy. Oxic biofilms also oxidized As(III) to As(V). Biofilms incubated with [ 14 C]acetate oxidized the radiolabel to 14 CO 2 in the light but not the dark, indicating a capacity for photoheterotrophy but not chemoheterotrophy. Anoxic, dark-incubated samples demonstrated As(V) reduction linked to additions of hydrogen or sulfide but not acetate. Chemoautotrophy linked to As(V) as measured by dark fixation of [ 14 C]bicarbonate into cell material was stimulated by either H 2 or HS − . Functional genes for the arsenate respiratory reductase ( arrA ) and arsenic resistance ( arsB ) were detected in sequenced amplicons of extracted DNA, with about half of the arrA sequences closely related (∼98% translated amino acid identity) to those from the family Ectothiorhodospiraceae . Surprisingly, no authentic PCR products for arsenite oxidase ( aoxB ) were obtained, despite observing aerobic arsenite oxidation activity. Collectively, these results demonstrate close linkages of these arsenic redox processes occurring within these biofilms. Oxyanions of the group 15 element arsenic, arsenate [As(V)] and arsenite [As(III)], have been known for millennia to be potent poisons. Despite its well-established toxicity to life, the phenomenon of arsenic resistance was discovered whereby some microorganisms maintain an otherwise “normal” existence in the presence of high concentrations of As(V) or As(III) (17, 29, 31). More recently it has become recognized that certain representatives from the bacterial and archaeal domains can actually exploit the electrochemical potential of the As(V)/As(III) redox couple (+130 mV) to gain energy for growth. This can be achieved either by employing As(III) as an autotrophic electron donor or by using As(V) as a respiratory electron acceptor (18, 21, 34). The latter phenomenon, although most commonly associated with chemoheterotrophy, can also employ inorganic substances like sulfide or H 2 . Indeed, As(V)-respiring anaerobes displaying a capacity for chemoautotrophy with these electron donors have been isolated and described (5, 7, 16). We recently reported that photoautotrophy is supported by As(III) in anoxic biofilms located in hot springs on Paoha Island in Mono Lake, CA (15). This process represented a novel means of As(III) oxidation achieved via anoxygenic photosynthesis occurring in certain photosynthetic bacteria (i.e., Ectothiorhodospira ) and possibly within some cyanobacteria as well (e.g., “ Oscillatoria ”). Whether or not a microbial habitat is overtly oxic or anoxic, or temporally shifts between these two states over a diel cycle, critical energy linkages between aerobes and anaerobes have long been known for the biogeochemical cycles of key elements, such as sulfur, iron, and nitrogen. Most prominently studied is the case of nitrogen, whereby an ecological coupling exists between the processes of nitrification and denitrification (9, 10, 28). The former process provides energy to aerobic nitrifiers, while the latter process consumes the nitrate produced by this reaction, thereby meeting the energy needs of the denitrifiers. For arsenic, the detection of both As(III) oxidation and As(V) reduction in oxic and anoxic incubations of freshly collected periphyton suggested that an analogous coupled process may also occur for this element (12). Similarly, several uncontaminated soils in Japan displayed a capacity for either As(V) reduction or As(III) oxidation upon arsenic oxyanion amendment and whether they were incubated under oxic or anoxic conditions (39). A defined coculture consisting of an aerobic As(III) oxidizer (strain OL1) and an anaerobic As(V) respirer (strain Y5) was shown to function in this fashion under manipulated laboratory conditions of oxygen tension (26). We pursued the phenomenon of coupled arsenic metabolism further by using materials collected from the hot spring biofilms in Mono Lake, but we focused on examination of the cycling of arsenic under anoxic conditions. In this paper we report results obtained by manipulated incubations of red-pigmented biofilms found in the hot springs of Paoha Island. Preliminary community characterizations of these biofilms show that they are dominated by B acteria from the genus Ectothiorhodospira but also harbor an assemblage of Archaea related to the Halobacteriacaea . Incubation results have demonstrated the presence of the following arsenic metabolic activities: respiratory As(V) reduction, photosynthetic anaerobic As(III) oxidation, and aerobic As(III) oxidation, along with the ecophysiological conditions under which they occur. Surprisingly, we were unable to obtain authentic PCR products for arsenite oxidase genes ( aoxB ), despite observing aerobic As(III) oxidation activity. These biofilms serve as a model system for how anaerobic cycling of arsenic can be sustained with oxidation of As(III) by anoxygenic photosynthesis coupled to regeneration of this electron donor via dissimilatory As(V) reduction. The significance that such a light-driven anaerobic ecosystem may have played in the Archean Earth is discussed.

California↗

USGS2023

Introduction to the digitization of seismic data: A user’s guide

Modern seismic data are collected, distributed, and analyzed using digital formats, and this has become a standard for the field. Although most modern seismometers still make use of analog electronic circuits, their data are converted from an analog voltage output to time‐tagged counts by way of digitization. Although much of the digitization process is not complicated to conceptualize, there is a fair bit of jargon in digitizer specifications, and a few pitfalls that can arise in the processes of recording and analyzing ground‐motion data. In this article, we review some of the fundamental physical properties of data acquisition systems and the basic steps in digitizing data from an analog instrument (specifically a seismometer). We then briefly discuss the digitization process and some of the key properties needed to make these data useful for seismological applications. Finally, we discuss some of the filtering processes that naturally arise from digitization and how it can affect the processing workflow. The end goal is to provide a user guide that will enable seismologists to have a working knowledge of the digitization process. We focus on aspects central to seismological applications and have tried to avoid getting bogged down in signal processing formalism.

Seismological Research Letters↗

USGS2004

Archive of Digital Boomer Seismic Reflection Data Collected During USGS Field Activities 93LCA01 and 94LCA01 in Kingsley, Orange, and Lowry Lakes, Northeast Florida, 1993 and 1994

In August and September of 1993 and January of 1994, the U.S. Geological Survey, under a cooperative agreement with the St. Johns River Water Management District (SJRWMD), conducted geophysical surveys of Kingsley Lake, Orange Lake, and Lowry Lake in northeast Florida. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, GIS information, observer's logbook, Field Activity Collection System (FACS) logs, and formal FGDC metadata. A filtered and gained GIF image of each seismic profile is also provided. Refer to the Acronyms page for expansion of acronyms and abbreviations used in this report. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Examples of SU processing scripts and in-house (USGS) software for viewing SEG-Y files (Zihlman, 1992) are also provided. The data archived here were collected under a cooperative agreement with the St. Johns River Water Management District as part of the USGS Lakes and Coastal Aquifers (LCA) Project. For further information about this study, refer to http://coastal.er.usgs.gov/stjohns, Kindinger and others (1994), and Kindinger and others (2000). The USGS Florida Integrated Science Center (FISC) - Coastal and Watershed Studies in St. Petersburg, Florida, assigns a unique identifier to each cruise or field activity. For example, 93LCA01 tells us the data were collected in 1993 for the Lakes and Coastal Aquifers (LCA) Project and the data were collected during the first field activity for that project in that calendar year. For a detailed description of the method used to assign the field activity ID, see http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html. The boomer is an acoustic energy source that consists of capacitors charged to a high voltage and discharged through a transducer in the water. The transducer is towed on a sled at the sea surface and when discharged emits a short acoustic pulse, or shot, that propagates through the water and sediment column. The acoustic energy is reflected at density boundaries (such as the seafloor or sediment layers beneath the seafloor), detected by the receiver, and recorded by a PC-based seismic acquisition system. This process is repeated at timed intervals (e.g., 0.5 s) and recorded for specific intervals of time (e.g., 100 ms). In this way, a two-dimensional vertical image of the shallow geologic structure beneath the ship track is produced. Acquisition geometery for 94LCA01 is recorded in the operations logbook. No logbook exists for 93LCA01. Table 1 displays acquisition parameters for both field activities. For more information about the acquisition equipment used, refer to the FACS equipment logs. The unprocessed seismic data are stored in SEG-Y format (Barry and others, 1975). For a detailed description of the data format, refer to the SEG-Y Format page. See the How To Download SEG-Y Data page for more information about these files. Processed profiles can be viewed as GIF images from the Profiles page. Refer to the Software page for details about the processing and examples of the processing scripts. Detailed information about the navigation systems used for each field activity can be found in Table 1 and the FACS equipment logs. To view the trackline maps and navigation files, and for more information about these items, see the Navigation page. The original trace files were recorded in nonstandard ELICS format and later converted to standard SEG-Y format. The original trace files for 94LCA01 lines ORJ127_1, ORJ127_3, and ORJ131_1 were divided into two or more trace files (e.g., ORJ127_1 became ORJ127_1a and ORJ127_1b) because the original total number of traces exceeded the maximum allowed by the processing system. Digital data were not recoverable for 93LCA

Data Series↗

USGS2001

The STRATAFORM Project: U.S. Geological Survey geotechnical studies

This report presents physical property logs of core samples from an offshore area near Eureka, CA. The cores were obtained as part of the STRATAFORM Program (Nittrouer and Kravitz, 1995, 1996), a study investigating how present sedimentation and sediment transport processes influence long-term stratigraphic sequences preserved in the geologic record. The core samples were collected during four separate research cruises to the northern California study area, and data shown in the logs of the cores were collected using a multi-sensor whole core logger. The physical properties collected are useful in identifying stratigraphic units, ground-truthing acoustic imagery and sub-bottom profiles, and in understanding mass movement processes. STRATA FOR mation on M argins was initiated in 1994 by the Office of Naval Research, Marine Geology and Geophysics Department as a coordinated multi-investigator study of continental-margin sediment transport processes and stratigraphy (Nittrouer and Kravitz, 1996). The program is investigating the stratigraphic signature of the shelf and slope parts of the continental margins, and is designed to provide a better understanding of the sedimentary record and a better prediction of strata. Specifically, the goals of the STRATAFORM Program are to (Nittrouer and Kravitz, 1995): - determine the geological relevance of short-term physical processes that erode, transport, and deposit particles and those processes that subsequently rework the seabed over time scales <10 2 years. - improve capabilities for identifying the processes that form the strata observed within the upper ~100 m of the seabed commonly representing 104-106 years of sedimentation. - synthesize this knowledge and bridge the gap between time scales of sedimentary processes and those of sequence stratigraphy. The STRATAFORM Program is divided into studies of the continental shelf and the continental slope; the geotechnical group within the U.S. Geological Survey provides support to both parts of the project.

California↗

USGS2004

Incorporating uncertainty into mercury-offset decisions with a probabilistic network for National Pollutant Discharge Elimination System permit holders: An interim report

This interim report describes an alternative approach for evaluating the efficacy of using mercury (Hg) offsets to improve water quality. Hg-offset programs may allow dischargers facing higher-pollution control costs to meet their regulatory obligations by making more cost effective pollutant-reduction decisions. Efficient Hg management requires methods to translate that science and economics into a regulatory decision framework. This report documents the work in progress by the U.S. Geological Survey’s Western Geographic Science Center in collaboration with Stanford University toward developing this decision framework to help managers, regulators, and other stakeholders decide whether offsets can cost effectively meet the Hg total maximum daily load (TMDL) requirements in the Sacramento River watershed. Two key approaches being considered are: (1) a probabilistic approach that explicitly incorporates scientific uncertainty, cost information, and value judgments; and (2) a quantitative approach that captures uncertainty in testing the feasibility of Hg offsets. Current fate and transport-process models commonly attempt to predict chemical transformations and transport pathways deterministically. However, the physical, chemical, and biologic processes controlling the fate and transport of Hg in aquatic environments are complex and poorly understood. Deterministic models of Hg environmental behavior contain large uncertainties, reflecting this lack of understanding. The uncertainty in these underlying physical processes may produce similarly large uncertainties in the decisionmaking process. However, decisions about control strategies are still being made despite the large uncertainties in current Hg loadings, the relations between total Hg (HgT) loading and methylmercury (MeHg) formation, and the relations between control efforts and Hg content in fish. The research presented here focuses on an alternative analytical approach to the current use of safety factors and deterministic methods for Hg TMDL decision support, one that is fully compatible with an adaptive management approach. This alternative approach uses empirical data and informed judgment to provide a scientific and technical basis for helping National Pollutant Discharge Elimination System (NPDES) permit holders make management decisions. An Hg-offset system would be an option if a wastewater-treatment plant could not achieve NPDES permit requirements for HgT reduction. We develop a probabilistic decision-analytical model consisting of three submodels for HgT loading, MeHg, and cost mitigation within a Bayesian network that integrates information of varying rigor and detail into a simple model of a complex system. Hg processes are identified and quantified by using a combination of historical data, statistical models, and expert judgment. Such an integrated approach to uncertainty analysis allows easy updating of prediction and inference when observations of model variables are made. We demonstrate our approach with data from the Cache Creek watershed (a subbasin of the Sacramento River watershed). The empirical models used to generate the needed probability distributions are based on the same empirical models currently being used by the Central Valley Regional Water Quality Control Cache Creek Hg TMDL working group. The significant difference is that input uncertainty and error are explicitly included in the model and propagated throughout its algorithms. This work demonstrates how to integrate uncertainty into the complex and highly uncertain Hg TMDL decisionmaking process. The various sources of uncertainty are propagated as decision risk that allows decisionmakers to simultaneously consider uncertainties in remediation/implementation costs while attempting to meet environmental/ecologic targets. We must note that this research is on going. As more data are collected, the HgT and cost-mitigation submodels are updated and the uncertainties may be reduced. Subsequently, the value of using a probabilistic framework for estimating and explicitly stating these uncertainties within a decisionmaking process can be estimated when new data are collected. Future work includes the design and implementation of a Bayesian network decision support system (BN-DSS) to produce mitigation scenarios for offset-project evaluation in the Cache Creek watershed. The decisionmaker, a wastewater-treatment plant, is expected to evaluate potential Hg-offset programs in terms of changes in HgT load changes, MeHg-production potential, project cost, and other suitability criteria. Subsequently, scenarios can be analyzed by performing sensitivity analyses and ranking environmental and economic uncertainties in terms of the decisionmaker’s preferences and risk choices. Such an analysis allows decisionmakers and stakeholders to explore various scenarios and predict the consequences of different stated preferences over outcomes.

Open-File Report↗

USGS2006

Evaluation of some software measuring displacements using GPS in real-time

For the past decade, the USGS has been monitoring deformation at various locations in the western United States using continuous GPS. The main focus of these measurements are estimates of displacement averaged over one day. Essentially, these consist of recording at 30 seconds intervals the carrier-frequency phase-data (equivalent to travel-time) between a GPS receiver and the GPS satellite network. In turn, these observations, which are converted to pseudo—ranges, are processed using one of the “research grade” programs (GIPSY, Zumberge et al., or GAMIT, wwwgpsg.mit.edu/~simon/gtgk) to estimate the position of the GPS receiver averaged over 24 hours. However, it is possible and desirable to estimate the position of the receiver (actually the antenna) more frequently and to do this within a few seconds of the time actual measurement (known as real-time). A recent example, the 2004 Magnitude 6, Parkfield, California earthquake, demonstrated that having GPS estimates of position more frequently than simply a daily average is required if one requires discrimination between co-seismic and post-seismic deformation (Langbein et al., 2006). The high-rate estimates of position obtained at Parkfield show that post-seismic deformation started less than one-hour after the mainshock and that this deformation was roughly the same magnitude as the co-seismic deformation. The high-rate solutions for Parkfield were done by others including Yehuda Bock at UCSD and Kristine Larson at U. of Colorado, but not the USGS. The Parkfield experience points out the need for an in-house capability by the USGS to be able to accurately measure co-seismic displacements and other rapid, deformation signals using GPS. This applies to both the Earthquake and Volcano Hazard programs. Although at many locations where we monitor deformation, we have strainmeters and tiltmeters in addition to GPS which, in principle, are far more sensitive to rapid deformation over periods of less than a day (Langbein and Bock, 2004). But, not all locales include strain and tiltmeters. Thus, having the capability to extract signals with periods of less than a day is desirable since the distribution of GPS is more extensive than strain and tilt. At both Parkfield and Long Valley, the USGS has been using other software packages to process the GPS data at sub-daily intervals and in real-time. The underlying goal of these types of measurements is to detect any deformation event as it evolves; the 24 hour processing might not provide timely results if such a deformation event is precursory to a geologic hazard (an earthquake for Parkfield and either a volcanic event or an earthquake for Long Valley). In Long Valley, We use the software package called 3DTracker (http://www.3dtracker.com, http://www.condorearth.com) to estimate the changes of in position of a remote site relative to a “fixed” site. The 3DTracker software uses double difference GPS code measurements and receiversatellite-time triple differences from one epoch to the next of the GPS phase data (a proxy for travel-time measurements) and employs a Kalman filter to obtain stability in the estimate of position. That is, the estimate of the current position depends upon the estimate of the prior position. Hence, a time series of position looks fairly smooth depending upon the coefficient selected for the Kalman filter. With triple differences, the sometimes troublesome initial integer cycle ambiguity terms cancel (number of wavelengths between the receiver and each satellite), but only the incremental change in position is calculated. This triple difference Kalman filter solution is slow to converge and less accurate than a double difference (e.g., RTD, Track) solution, but it is robust and computationally efficient (Remondi and Brown, 2000). 3D-Tracker allows use of various single-frequency and dual-frequency GPS phase and code observables including the ionospheric-free combinations (known as LC or L3 and P(L3)) formed from an linear combination of the L1 and L2 carrier phase and code data. The lowest noise observable is the L1 carrier, but it is biased by ionospheric refraction that has amplitudes of about 1 to 10 ppm. This results in a systematic scale error in the relative positions. The L3 phase noise is about 3 times greater than the L1 phase noise, but it is generally used to solve for all but the shortest baselines (< 5 km). In addition, the software does output the position changes is a standard format that can be used for other analysis. At Parkfield, we use the software package called RTD (http://www.geodetics.com). The RTD software has been described in the literature (Bock et al., 2000) but basically, it estimates the position without the constraint of a Kalman filter. It uses double differences (in our studies the LC or ionospheric free observable is used) and the integer ambiguities are resolved independently for each 1-second measurement; Most GPS software that use double-differences require several epochs of measurements to resolve the integer ambiguities. The data files use a proprietary format and can not be read by me or others; rather, Yehuda Bock at UCSD (and author of RTD) translates these files into a standard format that can be read by me. Recently, Tom Herring of MIT has modified the GAMIT software to process kinematically GPS data (www-gpsg.mit.edu/~simon/gtgk/tutorial/Lecture_13.pdf). At this time, the software, known as TRACK, does not process the observations in real-time. Consequently, the latency between the time of the observation and the time when a position estimate is available depends upon the frequency that the data are downloaded and the speed of actually processing the observations; there could be a delay of an hour or two before the a position estimates are available. Unlike RTD and 3DTracker, TRACK comes with GAMIT (which is distributed freely) and is currently operating in a test mode at the USGS office in Pasadena. The LC or ionosphere free observable is used in our TRACK solutions. JPL has a version of their GIPSY software called “Real-time GIPSY (RTG)” (gipsy.jpl.nasa.gov/orms/rtg), which, like TRACK, can process the pseudo-range data “off—line”. However, this software is not freely distributed. Instead, at least one company, NAVCOM, has teamed with JPL to integrate RTG with GPS receivers and telemetry that yields positions in realtime. Kristine Larson of University of Colorado has modified the original GIPSY to estimate positions kinematically. Again, like TRACK, the positions are estimated off—line. Much of her research is described in Larson et al. (2003), and Choi et al. (2004). For Long Valley, out of the 17 GPS sites, we monitor 5 baselines within the caldera at 5 second intervals relative to the Bald Mountain site at the edge of the caldera using 3DTracker. The baseline measurement using 3DTracker consists of determination of the 3 dimensional positions of the 5 remote points (GPS receivers) relative to a GPS site at Bald. A second, independent system collects and downloads once a day the 30-second data used for the 24-hour solutions for the 12 sites not monitored with 3DTracker. For the sites monitored with 3DTracker, the pseudo—range data are decimated to 30 seconds and converted to a form used for the 24-hour solutions. Both sets of telemetry employ 900 MHz spread spectrum radios which require line of site between all of the links. The telemetry for the 3DTracker sites require a dedicated radios at each end and intermediate repeaters as needed, while the telemetry required for the other sites use a single master radio, repeaters as needed, and a radio at each remote site. (The 5 sites being monitored with 3DTracker require 13 radios.) At Parkfield, RTD is used to measure the position changes all 12 baselines at 1 second intervals relative to a site, Pomm, adjacent to the San Andreas Fault. The complete RTD package (hardware and software) collects all of the data and determines the position of each site relative to Pomm. In addition, the system stores both the 1-second and 30-second pseudo-range data for later downloading which are ultimately used in the 24-hour solutions. To do this, each site has a 2.4 GHz radio and a telemetry buffer. The telemetry buffer holds 24-hours of data (in the event that the telemetry link is broken) and converts the RS232 data stream from the GPS receiver into a form compatible with an IP (Internet protocol) network connection. In contrast with the Long Valley system, the telemetry link for GPS at Parkfield consists of a single radio at each remote sites and a single radio at the central site. Although position estimates are produced within 1-second of the observations, these results are not immediately available because there is no high speed Internet connection to Parkfield. Instead, the data are stored on a removable disk and sent to UCSD once per month. Below, I describe the results of a simple experiment to examine the response of some of these systems to simulated deformation that could be an analogue of a tectonic or volcanic event. In many engineering applications, the system response is tested by inputting a step to the system and measuring the output of the system. Essentially, this is what I've done. The experiment described below moves the GPS antenna from its original position to a new position within 1 second; the software tracks the translation. These measurements were conducted in August 2004 with the RTD software at Parkfield, and twice in Long Valley. The first Long Valley test was conducted in September 2004 using 3DTracker on a single baseline. The test was repeated in September 2005 using 3DTracker on two baselines and, importantly, saving the RINEX files of the data so that the data could be replayed through 3DTracker using other options in the program and, using other software packages including TRACK. In addition, we observed a short-term event at the Three Sisters volcano in Oregon. This event was snow melt at a remote GPS site which gave an apparent 15 cm displacement in vertical in less than one-day. 3DTracker is used to monitor this site, and the event was captured with this software. In addition, with the assistance of others, I got additional estimates of position using other software packages; those results are presented. Finally, the precision of both 3DTracker and RTD are compared using a power spectrum. Those results would suggest that 3DTracker using appropriate Kalman filter coefficients would have better precision than RTD; instead, the lower noise level from 3DTracker is a result of smoothing from the Kalman filter. Given the results described in this report, high-rate GPS is certainly capable of accurately measuring displacements of 1 centimeter with a high degree of statistical confidence. Plotting these results show that the time of the displacement can be visually determined to that of the sampling interval of the data. However, especially with small amplitude signals, any of the software packages can yield erroneous deformation “signals” that are either due excess travel-time of the GPS carrier frequency from multipath or a limitation in the software. Thus, the time series of displacements must be viewed with caution and knowledge of external circumstances that might cause a change in position. The casual reader should continue with the next section describing the methods then jump to the last two sections for the discussion and conclusions. I have made some recommendations there.

Open-File Report↗

USGS2009

Stakeholder Evaluation for Canaan Valley National Wildlife Refuge: Completion Report

The National Wildlife Refuge System, managed by the U.S. Fish and Wildlife Service (FWS), is the largest system of public lands in the world dedicated to wildlife conservation. There are over 545 national wildlife refuges nationwide, encompassing 95 million acres. As part of the National Wildlife Refuge System Improvement Act of 1997, each refuge is developing 15-year comprehensive conservation plans (CCPs). Each CCP describes a vision and desired future condition for the refuge and outlines goals, objectives, and management strategies for each refuge's habitat and visitor service programs. The CCP process for Canaan Valley National Wildlife Refuge (Refuge) in Davis, West Virginia was initiated in 2006. This planning process provides a unique opportunity for public input and involvement. Public involvement is an important part of the CCP process. Participation by parties with a stake in the resource (stakeholders) has the potential to increase understanding and support and reduce conflicts. Additionally, meaningful public participation in a decision process may increase trust and provide satisfaction in terms of both process and outcome for management and the public. Public meetings are a common way to obtain input from community members, visitors, and potential visitors. An 'Issues Workbook' is another tool the FWS uses to obtain public input and participation early in the planning process. Sometimes, however, these traditional methods do not capture the full range of perspectives that exist. A stakeholder evaluation is a way to more fully understand community preferences and opinions related to key topics in refuge planning. It can also help refuge staff understand how changes in management affect individuals in terms of their preference for services and experiences. Secondarily, a process such as this can address 'social goals' such as fostering trust in regulating agencies and reducing conflict among stakeholders. As part of the CCP planning effort at Canaan Valley National Wildlife Refuge, the FWS sponsored a stakeholder evaluation conducted by the Policy Analysis and Science Assistance Branch of U.S. Geological Survey, Fort Collins Science Center the winter of 2006-2007. The stakeholder evaluation was intended to answer the following questions: 1)Which Refuge management issues are most important, and to whom?, 2)How do opinions about what is most important to stakeholders overlap or conflict?, 3)Why do stakeholders emphasize specific issues, and what values are driving this?, and 4)What potential solutions do stakeholders have for addressing important issues? This information will be used by the Refuge to help guide development of their CCP as they strive to balance stakeholder desires with their charge to manage the unique wetlands and uplands of the Canaan Valley for wildlife conservation.

Open-File Report↗

USGS2009

Estimation of Unsaturated Zone Traveltimes for Rainier Mesa and Shoshone Mountain, Nevada Test Site, Nevada, Using a Source-Responsive Preferential-Flow Model

Traveltimes for contaminant transport by water from a point in the unsaturated zone to the saturated zone are a concern at Rainier Mesa and Shoshone Mountain in the Nevada Test Site, Nevada. Where nuclear tests were conducted in the unsaturated zone, contaminants must traverse hundreds of meters of variably saturated rock before they enter the saturated zone in the carbonate rock, where the regional groundwater system has the potential to carry them substantial distances to a location of concern. The unsaturated-zone portion of the contaminant transport path may cause a significant delay, in addition to the time required to travel within the saturated zone, and thus may be important in the overall evaluation of the potential hazard from contamination. Downward contaminant transport through the unsaturated zone occurs through various processes and pathways; this can lead to a broad distribution of contaminant traveltimes, including exceedingly slow and unexpectedly fast extremes. Though the bulk of mobile contaminant arrives between the time-scale end members, the fastest contaminant transport speed, in other words the speed determined by the combination of possible processes and pathways that would bring a measureable quantity of contaminant to the aquifer in the shortest time, carries particular regulatory significance because of its relevance in formulating the most conservative hazard-prevention scenarios. Unsaturated-zone flow is usually modeled as a diffusive process responding to gravity and pressure gradients as mediated by the unsaturated hydraulic properties of the materials traversed. The mathematical formulation of the diffuse-flow concept is known as Richards' equation, which when coupled to a solute transport equation, such as the advection-dispersion equation, provides a framework to simulate contaminant migration in the unsaturated zone. In recent decades awareness has increased that much fluid flow and contaminant transport within the unsaturated zone takes place as preferential flow, faster than would be predicted by the coupled Richards' and advection-dispersion equations with hydraulic properties estimated by traditional means. At present the hydrologic community has not achieved consensus as to whether a modification of Richards' equation, or a fundamentally different formulation, would best quantify preferential flow. Where the fastest contaminant transport speed is what needs to be estimated, there is the possibility of simplification of the evaluation process. One way of doing so is by a two-step process in which the first step is to evaluate whether significant preferential flow and solute transport is possible for the media and conditions of concern. The second step is to carry out (a) a basic Richards' and advection-dispersion equation analysis if it is concluded that preferential flow is not possible or (b) an analysis that considers only the fastest possible preferential-flow processes, if preferential flow is possible. For the preferential-flow situation, a recently published model describable as a Source-Responsive Preferential-Flow (SRPF) model is an easily applied option. This report documents the application of this two-step process to flow through the thick unsaturated zones of Rainier Mesa and Shoshone Mountain in the Nevada Test Site. Application of the SRPF model involves distinguishing between continuous and intermittent water supply to preferential flow paths. At Rainier Mesa and Shoshone Mountain this issue is complicated by the fact that contaminant travel begins at a location deep in the subsurface, where there may be perched water that may or may not act like a continuous supply, depending on such features as the connectedness of fractures and the nature of impeding layers. We have treated this situation by hypothesizing both continuous and intermittent scenarios for contaminant transport to the carbonate aquifer and reporting estimation of the fastest speed for both of th

Open-File Report↗

USGS2024

Reservoir evolution, downstream sediment transport, downstream channel change, and synthesis of geomorphic responses of Fall Creek and Middle Fork Willamette River to water years 2012–18 streambed drawdowns at Fall Creek Lake, Oregon

Executive Summary Chapter A. Introduction Fall Creek Dam impounds Fall Creek Lake, a 10-kilometer-long reservoir in western Oregon and is operated by the U.S. Army Corps of Engineers (USACE) primarily for flood-risk management (or flood control) in late autumn through early spring months, as well as for water quality, irrigation, recreation, and habitat in late spring through early autumn. Since 2011 (water year [WY] 2012), Fall Creek Lake has been temporarily drawn down each year to facilitate downstream passage of juvenile spring Chinook salmon ( Oncorhynchus tshawytscha ) through the 55-meter (m) high dam. This annual dam operation is temporary, typically lasting about 1–2 weeks from WY 2012 through 2020 (drawdown operations in WY 2022–24 have increased to more than 6 weeks). Drawdown of the reservoir results in lake levels being lowered to the elevation near the historical, pre-dam streambed. The annual streambed drawdowns of WY 2012–18 have improved fish passage and led the USACE to formally adopt streambed drawdowns as part of annual operations at Fall Creek Dam. However, temporarily lowering the lake to streambed creates free-flowing conditions in the reservoir that result in the erosion and episodic export of predominantly sand and finer-grained sediments (less than 2 millimeters [mm]) to the lower gravel-bed reaches of Fall Creek and the Middle Fork Willamette River. The introduction of large volumes of sand and finer-grain sediment into the dam-regulated reaches downstream from Fall Creek Dam prompted questions about the geomorphic responses to annual streambed drawdowns within Fall Creek Lake and downstream reaches along Fall Creek and the Middle Fork Willamette River. The U.S. Geological Survey (USGS) in partnership with USACE initiated a comprehensive geomorphic and sediment transport investigation to assess the coupled processes of reservoir erosion, sediment evacuation from Fall Creek Lake, and patterns of sediment transport and deposition in reaches downstream from the Fall Creek Dam that have resulted from annual streambed drawdowns. The purpose of this report is to systematically describe the processes of sediment erosion, transport, and deposition at Fall Creek Lake and geomorphic interactions between reaches upstream and downstream from Fall Creek Dam that relate to dam operations. Specifically, this report focuses on evaluating geomorphic responses to streambed drawdowns from WY 2012 through 2018 and placing drawdown-induced geomorphic responses within the broader context of physiographic and historical conditions and dam operations of Fall Creek and Middle Fork Willamette Rivers. Key objectives for this study were to characterize changes in reservoir morphology and substrate at Fall Creek Lake, describe the character and temporal pattern of sediment transport downstream from Fall Creek Dam, characterize geomorphic changes in channel reaches downstream from the Fall Creek Dam, and relate these data to the annual streambed drawdowns of WY 2012–18. This study uses multiple independent monitoring and measurement approaches to assess site, reach, and river-scale geomorphic responses to drawdowns to inform dam and reservoir management. Patterns and processes of reservoir evolution were assessed with geomorphic mapping and volumetric analyses of topography through comparison of multiple digital surface models (DSMs). Just downstream from Fall Creek Dam, analyses of sediment export from the reservoir focused on suspended sediment but also incorporated bedload analyses to assess sediment sizes. Geomorphic assessments downstream from the dam used reach-scale and site-scale approaches to document changes in channel morphology and substrate, including site measurements of sand and finer-grained sediment deposition and in-channel bed-material, volumetric change analyses from comparison of digital elevation models (DEMs), and repeat geomorphic mapping. Findings from this study inform river management and dam operations by providing an understanding of (1) coupled upstream-downstream geomorphic responses to the Fall Creek Lake streambed drawdowns, (2) geomorphic responses of Fall Creek Lake streambed drawdowns in comparison to drawdowns at other large dams, (3) controls on reservoir erosion and downstream geomorphic responses, and (4) implications for future hydrogeomorphic changes that may result from continued drawdowns and monitoring activities to assess those changes. Chapter B. Reservoir Morphology and Evolution Related to Dam Operations at Fall Creek Lake To understand the volume and distribution of sediment accumulation in Fall Creek Lake since dam closure in 1965, decadal-scale sedimentation patterns (spanning approximately 1965–2016) are evaluated using a combination of storage curve analyses and geomorphic mapping. Short-term (drawdown event-scale) patterns of erosion, sedimentation, and sediment export downstream are evaluated using a combination of geomorphic mapping and change detection analyses that quantify the distribution and total volume of sediment erosion and deposition within Fall Creek Lake. Geomorphic mapping of reservoir topography and analyses of historical datasets reveals four categories of landforms and sediment processes within Fall Creek Lake related to lake level operations: lacustrine sedimentation expressed in the reservoir floor, fluvial erosion and deposition within historical stream channels during streambed drawdowns, channel-like features created by erosion within the reservoir floor during streambed drawdowns, and erosion on reservoir hillslopes. Where the reservoir floor is mapped for this study as pelagic (deep water), deposition up to 3 meters (m) thick by lacustrine processes and burial of pre-dam topography with deposits thinning toward the edges of the valley floor and upstream areas of reservoir are observed. Despite over 50 years of sediment accumulation since dam construction, the main stream channels of Fall and Winberry Creeks (or reservoir thalwegs) through the reservoir are well defined, though their distinct morphology is likely influenced by a long history of recurring historical drawdowns to or near streambed since dam construction. Unregulated streamflow and sediment transport through the reservoir primarily are confined to these channels during the streambed drawdown periods. Erosional channel-like features created by drawdowns are carved through underlying, unconsolidated reservoir floor sediments and are most prominent in the lower reservoir below minimum conservation pool (the low pool elevation during winter flood season); sediment generated from the formation of these drawdown channels is more likely to be transported through and out of the reservoir than sediment deposits along the reservoir hillslopes at the valley margins that are separated from main channels by areas of low-gradient reservoir floor. Morphologic changes in the lower reservoir topography between January 2012 and November 2016 indicate overall net erosion of about 129,500 cubic meters (m 3 ). The most prominent geomorphic changes occurred along the main channels of Fall and Winberry Creeks near the Fall Creek Dam where incision, lateral migration, and slumping banks resulted in vertical and lateral adjustments to channel position, whereas most changes fell below the detectable limit on higher-elevation reservoir floor surfaces except where erosion occurred along features mapped as drawdown channels. Chapter C. Sediment Delivery from Fall Creek Lake and Transport through Downstream Reaches USGS implemented a sediment monitoring program in WY 2013–18 to evaluate the quantity and character of reservoir sediment exported from Fall Creek Lake during streambed drawdowns. Turbidity and suspended sediments were monitored annually autumn through spring to span the WY 2013–18 streambed drawdowns; however, unequal monitoring timeframes each year reduced the ability to compare results and factors affecting sediment export from the reservoir difficult between years. These data were originally measured to develop regressions and compute suspended-sediment loads (SSL). Bedload sediment monitoring from a cableway at the Fall Creek streamgage was completed in the autumn-winter of WY 2013 and 2017. The limited number of samples and presumed variability in sediment supply from the reservoir precluded construction of streamflow and bedload discharge relations to compute more than instantaneous bedload. Sand and finer-grained silts and clays were transported from the reservoir in suspension, though some coarser grains (up to 32 mm) were also mobilized and transported downstream from the dam as bedload. Observations of increased sediment transport downstream from Fall Creek Dam coincided with lake levels approaching about 3 m (10 feet [ft] or elevation 690 ft) above the streambed regulating outlets. Suspended-sediment loads computed for the full monitoring periods WY 2013–18 at the Fall Creek streamgage, located 1.4 kilometers (km) downstream from Fall Creek Dam, range from 54,700 metric tons (t) in WY 2013 to 13,900 t in WY 2018. Although the total annual SSL varied from year to year, the overall seasonal patterns of suspended sediment transport throughout each year were similar during monitoring in WY 2013-18. Suspended-sediment loads were low prior to the drawdown, then increased rapidly as lake levels lowered and approached the streambed. In the weeks following the drawdown period, as pool levels were increased, SSL remained slightly elevated above pre-drawdown levels but generally declined through the following winter and spring except during streamflow-driven pulses of suspended-sediment transport. WY 2013 had the greatest total computed SSL for each streambed drawdown and partial-year monitoring period. SSL computed for the partial-year period have generally decreased since WY 2013 and have varied by about 6,800 t with the exception of WY 2014. WY 2014 SSL reflects anomalously low sediment export due to low streamflows and freezing conditions that stabilized reservoir floor deposits. Bedload measurements in the short 1.4-km reach between Fall Creek Dam and the Fall Creek streamgage showed an inverse correlation between bedload transport rates and discharge, which probably reflects diminishing supply of coarse-sized sediment. Sand was more abundant (60–100 percent) than gravel in bedload samples confirming sand and finer-grained sediment dominated sediment evacuated from the reservoir during streambed drawdowns at Fall Creek Lake. Chapter D. Geomorphic Responses to Fall Creek Lake Streambed Drawdowns Downstream from Fall Creek Dam In the days, weeks, and months following streambed drawdown operations at Fall Creek Dam through WY 2018, sites downstream from the dam displayed a variety of geomorphic responses to reservoir sediment delivery within the main channel and overbank areas. Evaluation of streambed elevations at two streamgages located 1.4 km downstream from the dam on Fall Creek and 16.3 km downstream from the dam on the Middle Fork Willamette River indicated the effects of drawdown sediment on bed elevations were modest and transient. Repeat particle size measurements (October 2015 and September 2016) at five sites along Fall Creek and the Middle Fork Willamette River showed similar grain-sized distributions that do not reveal substantial deposition of fine-grained sediment related to the WY 2016 streambed drawdown. Altogether, these findings indicate that transport capacity in the main, low-flow channels of Fall Creek and Middle Fork Willamette River during WY 2012–18 was sufficient to mobilize and evacuate reservoir sediments from streambed drawdowns or other bank material and tributary sources. However, other monitoring for this study indicate low-velocity zones in off-channel areas are prime locations for sand and finer-grain sediment deposition. Patterns of overbank sediment accumulation indicate that the magnitude and timing of overbank deposition on bars and low-elevation floodplain varies with proximity to the dam, geomorphic setting, streamflows, and other factors. Sand and finer-grained reservoir sediments carried as suspended-sediment load in the reaches downstream from Fall Creek Dam were deposited in overbank areas as observed with clay-horizon markers during WY 2016–17. Overbank deposition quantified with Geomorphic Change Detection (GCD) software evaluated landform-scale patterns of erosion and deposition using repeat light detection and ranging (lidar) surveys at two sites in the Upper Fall Creek reach and one site in the Jasper reach for 3 years (2012–15) and one site in the Clearwater reach for 6 years (2009–15). Deposition thickness and spatial patterns from the GCD analysis were variable; some sites had dispersed but measurable deposition while at others, deposition was highly localized and exceeded 1 m in depth. Patterns of overbank deposition illustrate interactions among bar morphology, local hydraulics, and suspended-sediment transport dynamics that can create patches of highly localized deposition. The measured deposition at the two Fall Creek GCD sites likely resulted from reservoir sediments released from Fall Creek Lake during streambed drawdowns in WY 2016 and 2017 because the limited sediment inputs from bank material (geomorphically laterally stable reach) or tributaries (no significant tributaries) provided few other sediment sources. On the Middle Fork Willamette River, observed patterns of overbank deposition could reflect sediment sourced from upstream tributaries, bank erosion, or Fall Creek Lake streambed drawdown operations. Despite the introduction of several thousand tons of reservoir sediment delivered from the Fall Creek Lake streambed drawdowns to below-dam river corridors, reach-scale mapping of channel features downstream from Fall Creek Dam shows minimal evidence of changes in channel planform or landforms that can be attributed to a drawdowns in WY 2012–16. On Upper Fall Creek reach, widespread increases in gravel bars or other in-channel sediment did not result from the five streambed drawdowns. The main changes attributable to sediment releases from Fall Creek Lake were localized increases in vegetated bar area, particularly on channel margin areas where sand and finer-grain sediment was deposited and rapidly colonized by vegetation. The area of mapped secondary water features decreased between 2005 and 2016, but that may be due to lower discharges depicted in the 2016 aerial photographs and less mapped area of inundation. Primary changes along the Lower Fall Creek reach include a 6.4 percent decrease in area of secondary water features between 2011 and 2016, and a nearly twofold increase in the area of unvegetated bars. Immediately downstream from the Fall Creek confluence, there were negligible changes in the location and areas of vegetated bars and the main wetted channel between 2005 and 2016, and local increases in bar area cannot be attributed solely to deposition of reservoir sediments from Fall Creek Lake because (1) areas along the Middle Fork Willamette River just upstream from the Fall Creek confluence display similar type and magnitude of changes and (2) some of the increases at the confluence area pre-date the drawdowns. The cumulative effect of sediment releases from Fall Creek Lake streambed drawdowns from WY 2012 to 2016 on downstream channel planform and landforms are modest compared to the river-scale transformations and planform changes that occurred in the decades following dam construction. Chapter E. Discussion of Geomorphic Responses of Fall Creek and Middle Fork Willamette River to Streambed Drawdowns at Fall Creek Lake Multiple aspects of Fall Creek Dam infrastructure and operations exert first-order controls on the magnitudes of reservoir erosion that occur during the streambed drawdowns and ultimately determine the sediment delivery to downstream reaches. Key aspects of the dam and its operations that are most relevant to assessing geomorphic responses to streambed drawdowns include the (1) dam infrastructure, including configuration and size of regulating outlets and their proximity to the streambed which dictates the capacity and competence of the river to deliver sediment to downstream reaches and mode of sediment transport as suspended-sediment load or bedload; (2) frequency of historical drawdowns and long-term, year-round dam operations and lake level management, which partly dictate reservoir morphology and locations and magnitudes of readily erodible materials; (3) dam operations and hydroclimatic conditions during the streambed drawdown (including length of the drawdown and streamflows entering the reservoir), which directly control the timing, duration and magnitude of reservoir erosion and sediment evacuation; and (4) dam operations following the streambed drawdown operation that regulate streamflows (and thereby sediment transport conditions) downstream of Fall Creek Dam which primarily reflect interactions between hydroclimatic conditions and flood control operations. Patterns of sediment erosion and evacuation observed in this study at Fall Creek Lake from WY 2012–18 suggest that reservoir erosion during annual streambed drawdowns may remain similar or decrease in future years assuming (1) annual streambed drawdown operations are implemented in similar manner as the WY 2012–18 drawdowns (in terms of duration, late autumn or early winter implementation, rate of pool-level lowering to reach streambed, and other factors), (2) streambed drawdowns coincide with similar conditions as were observed WY 2012–18 (similar sediment yield into reservoir, low reservoir inflows, limited precipitation, moderate air temperature), and (3) no major geomorphic changes in the main reservoir channels of Fall and Winberry Creeks occur (for example, channel avulsion). Under such conditions, it is hypothesized that the stream channel within the reservoir would achieve a quasi-equilibrium state with respect to annual influx and export of sediment and aided by the substantial amount of in-channel bedrock, will remain laterally stable without erosion across reservoir deposits. Patterns of sediment transport measured at the Fall Creek streamgage downstream from Fall Creek Dam provide insight into the potential effects of future streambed drawdowns at Fall Creek Lake. Analyses of suspended sediment measured in WY 2013–18 show a major reduction in suspended-sediment loads between WY 2013 and later years, indicating streamflows transporting sediment through the reservoir to downstream reaches during streambed drawdowns have become supply limited. The 6-year suspended-sediment monitoring and sampling program is insufficient to make predictions about future sediment transport conditions because of uneven monitoring periods and varying controls on reservoir sediment erosion. It is likely that future suspended-sediment loads will be variable but similar to those observed in WY 2015–18 if operational, climatic, and geomorphological factors remain similar to those monitored WY 2015–18. Suspended-sediment loads downstream from Fall Creek Lake will likely remain highest when regulating outlets are fully open and Fall Creek is free flowing with the reservoir fully drained with little to no residual pool. Over time, it is possible that the suspended-sediment loads would reflect mobilization of reservoir sediment deposited in the previous year rather than erosion of sediment deposited years or decades earlier. Bedload is likely to remain a small fraction of the total sediment load evacuated from the reservoir and is relatively modest compared with pre-dam bedload transport rates because most coarse sediment remains trapped by the dam. If sediment releases from Fall Creek Lake and ensuing streamflow conditions follow a similar pattern in the future as was assessed in this study spanning WY 2012–18, near-term geomorphic adjustments downstream of the dam are expected to be modest. Barring major operational, climatic, and geomorphological changes, local site-scale deposition on bars, overbank areas, or off-channel features that persists several months after the streambed drawdown will likely continue to be highly variable, ranging from negligible to several centimeters of deposition. At the landform-scale, low velocity areas nearest to Fall Creek Dam will likely continue to undergo rapid deposition immediately during and after a streambed drawdown event, similar to patterns observed for WY 2012–18. Some of the sediment entering these off-channel features and margin areas may be temporarily stored, then later remobilized and dispersed farther downstream. But if newly deposited sediment persists through the following spring, there is a greater likelihood that local vegetation will establish, reinforce deposited material, and trap sediment during later drawdowns. The reach-scale geomorphic changes may become more apparent if (1) streambed drawdowns continued for several decades, and geomorphic changes were measured at decadal scales or (2) the amount of sediment introduced to downstream reaches substantially increased and (or) sediment transport capacity decreased. The continued streamflow regulation of Fall Creek Dam after sediment releases provides an opportunity to strategically manage streamflows during and after the streambed drawdowns to minimize downstream sediment impacts and ensure other operational thresholds are satisfied. This study provides a comprehensive foundation of datasets and geomorphic analyses to inform dam operations at Fall Creek Lake, monitor sediment transport downstream, and consider operational schemes for future drawdowns. The datasets from this study also provide baselines of sediment transport and geomorphic conditions to assess future changes in reservoir and downstream environments. Future monitoring could be tailored to address specific questions regarding the long-term geomorphic effects of streambed drawdowns on fluvial habitats, flood hazards, cultural resources, or downstream water quality. Future monitoring activities could focus on the relevant geomorphic processes and spatial domains within the three categories used for this study: (1) reservoir erosion and net sediment evacuation, (2) sediment delivery to downstream reaches, including magnitude and temporal pattern of sediment transport, and (3) geomorphic responses of downstream reaches to sediment delivery. Specifically, high priority future monitoring activities could include: Repeat topographic or photographic surveys in the reservoir to characterize changes occurring within individual drawdowns, to quantify sediment export, to determine temporal changes in reservoir storage, and to identify locations of erosion and deposition. Continuous, year-round turbidity monitoring supplemented with suspended-sediment measurements at a streamflow-gaging station immediately downstream from the dam to quantify sediment export. Repeat geomorphic monitoring, mapping, or modeling in downstream reaches to track changes in channel and over bank features using a combination of site- and reach-scale monitoring approaches. This could support assessments of sediment deposition and ensuing vegetation encroachment on flood hazards and habitats and examine how sediment transport and depositional processes may be affected by different sediment supply, streamflow, or dam management scenarios.

Oregon↗

USGS2011

User's manual for the National Water-Quality Assessment Program Invertebrate Data Analysis System (IDAS) software, version 5

The Invertebrate Data Analysis System (IDAS) software was developed to provide an accurate, consistent, and efficient mechanism for analyzing invertebrate data collected as part of the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program. The IDAS software is a stand-alone program for personal computers that run Microsoft Windows(Registered). It allows users to read data downloaded from the NAWQA Program Biological Transactional Database (Bio-TDB) or to import data from other sources either as Microsoft Excel(Registered) or Microsoft Access(Registered) files. The program consists of five modules: Edit Data, Data Preparation, Calculate Community Metrics, Calculate Diversities and Similarities, and Data Export. The Edit Data module allows the user to subset data on the basis of taxonomy or sample type, extract a random subsample of data, combine or delete data, summarize distributions, resolve ambiguous taxa (see glossary) and conditional/provisional taxa, import non-NAWQA data, and maintain and create files of invertebrate attributes that are used in the calculation of invertebrate metrics. The Data Preparation module allows the user to select the type(s) of sample(s) to process, calculate densities, delete taxa on the basis of laboratory processing notes, delete pupae or terrestrial adults, combine lifestages or keep them separate, select a lowest taxonomic level for analysis, delete rare taxa on the basis of the number of sites where a taxon occurs and (or) the abundance of a taxon in a sample, and resolve taxonomic ambiguities by one of four methods. The Calculate Community Metrics module allows the user to calculate 184 community metrics, including metrics based on organism tolerances, functional feeding groups, and behavior. The Calculate Diversities and Similarities module allows the user to calculate nine diversity and eight similarity indices. The Data Export module allows the user to export data to other software packages (CANOCO, Primer, PC-ORD, MVSP) and produce tables of community data that can be imported into spreadsheet, database, graphics, statistics, and word-processing programs. The IDAS program facilitates the documentation of analyses by keeping a log of the data that are processed, the files that are generated, and the program settings used to process the data. Though the IDAS program was developed to process NAWQA Program invertebrate data downloaded from Bio-TDB, the Edit Data module includes tools that can be used to convert non-NAWQA data into Bio-TDB format. Consequently, the data manipulation, analysis, and export procedures provided by the IDAS program can be used to process data generated outside of the NAWQA Program.

Techniques and Methods↗

USGS2002

Standard errors of annual discharge and change in reservoir content data from selected stations in the lower Colorado River streamflow-gaging station network, 1995-99

The Bureau of Reclamation is currently (1995–2001) testing the Lower Colorado River Accounting System as a method to estimate the consumptive use of Colorado River water by diverters from Hoover Dam to Mexico. Consumptive use is estimated in the Lower Colorado River Accounting System method, in part, on the basis of the annual discharge or annual change in reservoir contents, as well as the variance of estimate of the annual discharge or the annual change in reservoir contents at several surface-water gaging stations in the lower Colorado River stream-gaging network. The standard error and the variance of estimate were determined for the annual discharge at 14 streamflow-gaging stations and for the annual change in content at 2 reservoir-content gaging stations used in the Lower Colorado River Accounting System for calendar years 1995–99. The standard error of the annual discharge was determined by using modifications to an existing method that assumes that the uncertainty in the discharge-rating shift is the main source of uncertainty in computed discharges and that the discharge-rating shift behaves as a first-order Markovian process. The method uses Kalman filtering of a first-order Markovian process as a statistical analogy to computing streamflow with a shifted discharge rating. Temporally unbiased residuals from a discharge rating are used as a surrogate for the actual shifts used to compute discharge. The standard error of the annual discharge is determined by using Kalman-filter theory and estimates of four parameters: (1) the measurement variance of the discharge measurements used to determine the discharge-rating shift, (2) the process variance of the discharge-rating residuals, (3) the serial correlation of the discharge-rating residuals, and (4) the frequency of the discharge measurements. The existing methodology was improved by estimating the measurement variance from a semivariogram of the discharge-rating residuals, rather than on the basis of empirically derived error estimates for discharge measurements. The process variance and serial correlation of the discharge-rating residuals are estimated from the semivariogram, rather than a variogram, of the discharge-rating residuals. The empirically derived estimates are based on characteristics of the discharge measurements such as number of depth and velocity observation sections, type of current meter, and bed material composition and stability. Measurement variance determined from the semivariograms was site specific and is therefore considered a better estimate than measurement variance determined from the empirically-derived estimates. The method of estimating the standard error of the annual discharge requires the assumption of unbiased discharge-rating residuals, and for this reason, the standard errors presented in this report only represent the random error in the annual discharge data. Estimates of the standard error of the annual change in reservoir content were determined on the basis of the reservoir-surface area and the standard error of reservoir-stage readings. The standard error of the annual discharge, as a percentage, ranged from 0.11 percent for the All- American Canal near Imperial Dam in 1998 to 12.3 percent for the Colorado River below Imperial Dam in 1996. The standard error of the annual discharge was less than 2 percent for all 5 years for 11 of the 14 streamflow-gaging stations. In terms of flow volume, the standard error of the annual discharge ranged from 97 acre-feet for the Mittry Lake Diversions in 1995 to 77,000 acre-feet for the Colorado River at the northerly international boundary with Mexico in 1998. In general, the standard error of the annual discharge, as a percentage, was smallest at streamflow-gaging stations on the main stem of the Colorado River; however, the standard error of the annual discharge in acre-feet was largest at these stations because of the large annual discharge on the main stem. The standard error of the annual change in content for the two reservoirs ranged from 1,590 acre-feet for Lake Havasu in 1996 to 2,790 acre-feet for Lake Mohave in 1995. The variance of estimate of the annual discharge for a streamflow-gaging station can be reduced by making additional discharge measurements; either by increasing the number of discharge measurements made per site visit, or by increasing the frequency of site visits. Measurement error can be reduced by using the average shift for two or more discharge measurements made during a site visit. For a streamflow-gaging station where measurement error is much greater than process error and the serial correlation of the discharge-rating residuals is high, an improved gaging strategy would involve making multiple discharge measurements per site visit. In contrast, for a streamflow-gaging station where process error is much greater than measurement error and the serial correlation of discharge-rating residuals is low, the gaging strategy would consist of several single discharge-measurement site visits. For a given operating cost or for a given variance of estimate of the annual discharge at a streamflow-gaging station, the optimal site-visit and discharge-measurement strategy can be determined, providing that the travel costs as well as the measurement variance, process variance, and serial correlation of discharge-rating residuals are known.

Arizona;California↗

USGS2002

Water quality and environmental isotopic analyses of ground-water samples collected from the Wasatch and Fort Union Formations in areas of coalbed methane development — Implications to recharge and ground-water flow, eastern Powder River Basin, Wyoming

Chemical analyses of ground-water samples were evaluated as part of an investigation of lower Tertiary aquifers in the eastern Powder River Basin where coalbed methane is being developed. Ground-water samples were collected from two springs discharging from clinker, eight monitoring wells completed in the Wasatch aquifer, and 13 monitoring or coalbed methane production wells completed in coalbed aquifers. The ground-water samples were analyzed for major ions and environmental isotopes (tritium and stable isotopes of hydrogen and oxygen) to characterize the composition of waters in these aquifers, to relate these characteristics to geochemical processes, and to evaluate recharge and ground-water flow within and between these aquifers. This investigation was conducted in cooperation with the Wyoming State Engineer's Office and the Bureau of Land Management. Water quality in the different aquifers was characterized by major-ion composition. Samples collected from the two springs were classified as calcium-sulfate-type and calcium-bicarbonate-type waters. All ground-water samples from the coalbed aquifers were sodium-bicarbonate-type waters as were five of eight samples collected from the overlying Wasatch aquifer. Potential areal patterns in ionic composition were examined. Ground-water samples collected during this and another investigation suggest that dissolved-solids concentrations in the coalbed aquifers may be lower south of the Belle Fourche River (generally less than 600 milligrams per liter). As ground water in coalbed aquifers flows to the north and northwest away from an inferred source of recharge (clinker in the study area), dissolved-solids concentrations appear to increase. Variation in ionic composition in the vertical dimension was examined qualitatively and statistically within and between aquifers. A relationship between ionic composition and well depth was noted and corroborates similar observations by earlier investigators in the Powder River Basin in both Wyoming and Montana. This relationship results in two different water-quality zones with different characteristics - a shallow zone, comprising the upper part of the Wasatch aquifer, characterized by mixed cation composition and either sulfate or bicarbonate as the dominant anion; and a deeper zone, comprising the lower (deeper) part of the Wasatch aquifer and the underlying coalbed aquifers, characterized by sodium-bicarbonate-type waters. The zonation appears to be related to geochemical processes described by earlier investigators such as dissolution and precipitation of minerals, ion exchange, sulfate reduction, and mixing of waters. Qualitative and statistically significant differences were observed in sulfate concentrations between the coalbed aquifers and the overlying Wasatch aquifer. Ionic composition suggests that bacterially mediated redox processes such as sulfate reduction were probably the dominant geochemical processes in the anaerobic coalbed aquifers. Tritium was used to qualitatively estimate the time of ground-water recharge. Tritium concentrations in both springs suggests that both were recharged after 1952 and contain modern water. Tritium was not detected at concentrations suggestive of modern water in any ground-water samples collected from the coalbed aquifers or in six of eight ground-water samples collected from the overlying Wasatch aquifer. Tritium concentrations in the remaining two wells from the Wasatch aquifer suggest a mixture between submodern (recharged before 1952) and modern water, although the low concentrations suggest that ground water in these two wells have very little modern water. The relative absence of modern water in all aquifers in the study area suggests that recharge processes to these aquifers are probably very slow. Paired d 2 H (deuterium/hydrogen isotopic ratio) and d 18 O (oxygen-18/oxygen-16 isotopic ratio) values for samples collected from the springs and all aquifers are close to the Global Meteoric Water Line, a meteoric water line for North American continental precipitation, and an estimated local meteoric water line, suggesting the water in the aquifers is of meteoric origin. The d 2 H and d 18 O values suggest that the waters were recharged in a colder climate or temperature, mid-latitudes, and mid-continent. In general, the samples do not form separate groups based on aquifer origin; this suggests either intermixing of the waters in the aquifers or that the different aquifers are subject to similar recharge and/or evolutional paths for the water. However, examination of the differences in the values of d 2 H and d 18 O, in combination with major-ion chemistry at three monitoring-well clusters, suggest that changes in the values with depth may represent different timing or sources of recharge to the different aquifers. The areal distribution of d 2 H was examined and an apparent break in the d 2 H along a northwest to southeast trend was observed. In the coalbed aquifers, all but one ground-water sample (collected from the Big George coal bed), show a pattern where the d 2 H values become more negative towards the center of the Powder River Basin and values greater (less negative) than an arbitrary reference value of -140 ‰ (per mil or parts per thousand) were observed near the outcrop area of the Wyodak-Anderson coal zone. In the overlying Wasatch aquifer, the d 2 H values became less negative towards the center of the basin. The values more negative than -140 ‰ are near the outcrop area and the values that are less negative than -140 ‰ are closer to the basin center. It is unclear if this pattern is a result of sample size, different recharge mechanisms, geochemical processes, or if the processes producing these differences are independent or unrecognized. Results of water-quality sampling were compared with selected regulatory and non-regulatory standards as well as commonly-used guidelines for proposed water uses. Dissolved solids was the measure that most frequently exceeded U.S. Environmental Protection Agency public water-supply standards and State of Wyoming domestic-use standards in ground-water samples collected from the Wasatch aquifer and coalbed aquifers. The State of Wyoming agricultural standards (irrigation) for sulfate and dissolved solids were exceeded in some samples collected from the Wasatch aquifer and coalbed aquifers. The State of Wyoming livestock standard for pH was exceeded in some samples collected from the Wasatch aquifer. Water from the Wasatch aquifer ranged from soft to very hard, and water from the coalbed aquifers ranged from moderately hard to very hard. Samples collected from wells completed in both the Wasatch aquifer and coalbed aquifers plotted in a wide range of both sodium- and salinity-hazard classes, but most samples clustered in or near the combined medium-sodium-hazard—high-salinity-hazard classes.

Wyoming↗

USGS1997

Interim results of quality-control sampling of surface water for the Upper Colorado River National Water-Quality Assessment Study Unit, water years 1995-96

Quality-control samples provide part of the information needed to estimate the bias and variability that result from sample collection, processing, and analysis. Quality-control samples of surface water collected for the Upper Colorado River National Water-Quality Assessment study unit for water years 1995?96 are presented and analyzed in this report. The types of quality-control samples collected include pre-processing split replicates, concurrent replicates, sequential replicates, post-processing split replicates, and field blanks. Analysis of the pre-processing split replicates, concurrent replicates, sequential replicates, and post-processing split replicates is based on differences between analytical results of the environmental samples and analytical results of the quality-control samples. Results of these comparisons indicate that variability introduced by sample collection, processing, and handling is low and will not affect interpretation of the environmental data. The differences for most water-quality constituents is on the order of plus or minus 1 or 2 lowest rounding units. A lowest rounding unit is equivalent to the magnitude of the least significant figure reported for analytical results. The use of lowest rounding units avoids some of the difficulty in comparing differences between pairs of samples when concentrations span orders of magnitude and provides a measure of the practical significance of the effect of variability. Analysis of field-blank quality-control samples indicates that with the exception of chloride and silica, no systematic contamination of samples is apparent. Chloride contamination probably was the result of incomplete rinsing of the dilute cleaning solution from the outlet ports of the decaport sample splitter. Silica contamination seems to have been introduced by the blank water. Sampling and processing procedures for water year 1997 have been modified as a result of these analyses.

Colorado↗

USGS2024

Observing glacier elevation changes from spaceborne optical and radar sensors – an inter-comparison experiment using ASTER and TanDEM-X data

Observations of glacier mass changes are key to understanding the response of glaciers to climate change and related impacts, such as regional runoff, ecosystem changes, and global sea level rise. Spaceborne optical and radar sensors make it possible to quantify glacier elevation changes, and thus multi-annual mass changes, on a regional and global scale. However, estimates from a growing number of studies show a wide range of results with differences often beyond uncertainty bounds. Here, we present the outcome of a community-based inter-comparison experiment using spaceborne optical stereo (ASTER) and synthetic aperture radar interferometry (TanDEM-X) data to estimate elevation changes for defined glaciers and target periods that pose different assessment challenges. Using provided or self-processed digital elevation models (DEMs) for five test sites, 12 research groups provided a total of 97 spaceborne elevation-change datasets using various processing approaches. Validation with airborne data showed that using an ensemble estimate is promising to reduce random errors from different instruments and processing methods but still requires a more comprehensive investigation and correction of systematic errors. We found that scene selection, DEM processing, and co-registration have the biggest impact on the results. Other processing steps, such as treating spatial data voids, differences in survey periods, or radar penetration, can still be important for individual cases. Future research should focus on testing different implementations of individual processing steps (e.g. co-registration) and addressing issues related to temporal corrections, radar penetration, glacier area changes, and density conversion. Finally, there is a clear need for our community to develop best practices, use open, reproducible software, and assess overall uncertainty to enhance inter-comparison and empower physical process insights across glacier elevation-change studies.

The Cryosphere↗

USGS2025

Comparing the efficacy of two immobilization drug combinations for the chemical restraint of bobcats (Lynx rufus)

Chemical immobilization agents that provide rapid induction time, short duration of action, wide margin of safety, and postreversal recovery are important attributes to the handling process of immobilized animals. We evaluated differences in induction, recovery, and physiologic parameters in 23 (13 female, nine adults and four yearlings; 10 male, nine adults and one yearling) free-ranging bobcats ( Lynx rufus ) chemically immobilized with an intramuscular combination of ketamine (10 mg/kg) and xylazine (KX; 1.5 mg/kg; n =11) or a combination of butorphanol (0.8 mg/ kg), azaperone (0.27 mg/kg), and medetomidine (BAM; 0.32 mg/kg; n =12). Induction parameters, time to first effect, hemoglobin oxygen saturation, and anesthesia between bobcats administered KX and BAM were similar. Pulse rate was significantly higher for KX than for BAM. Time to standing and full recovery after reversal were faster for bobcats administered BAM than KX. Six of 11 (55%) bobcats given KX were effectively immobilized with a single injection, and five required additional drugs to allow adequate time for processing. Of 12 bobcats given BAM, six (50%) were effectively immobilized with a single injection, three (25%) individuals were not completely immobilized and required additional doses to allow adequate time for processing, and three (25%) required additional doses after complete arousal during processing. We found that BAM provided reduced sedation and processing times (<30 min), whereas KX provided extended sedation and processing times beyond 30 min. We suggest that researchers increase initial BAM drug volumes for yearling and adult bobcats at time of processing and consider taking appropriate safety precautions when handling free-ranging bobcats.

Journal of Wildlife Diseases↗

USGS2000

Analytical group decision making in natural resources: Methodology and application

Group decision making is becoming increasingly important in natural resource management and associated scientific applications, because multiple values are treated coincidentally in time and space, multiple resource specialists are needed, and multiple stakeholders must be included in the decision process. Decades of social science research on decision making in groups have provided insights into the impediments to effective group processes and on techniques that can be applied in a group context. Nevertheless, little integration and few applications of these results have occurred in resource management decision processes, where formal groups are integral, either directly or indirectly. A group decision-making methodology is introduced as an effective approach for temporary, formal groups (e.g., workshops). It combines the following three components: (1) brainstorming to generate ideas; (2) the analytic hierarchy process to produce judgments, manage conflict, enable consensus, and plan for implementation; and (3) a discussion template (straw document). Resulting numerical assessments of alternative decision priorities can be analyzed statistically to indicate where group member agreement occurs and where priority values are significantly different. An application of this group process to fire research program development in a workshop setting indicates that the process helps focus group deliberations; mitigates groupthink, nondecision, and social loafing pitfalls; encourages individual interaction; identifies irrational judgments; and provides a large amount of useful quantitative information about group preferences. This approach can help facilitate scientific assessments and other decision-making processes in resource management.

Forest Science↗