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Reconciling catch differences from multiple fishery independent gill net surveys

Fishery independent gill net surveys provide valuable demographic information for population assessment and resource management, but relative to net construction, the effects of ancillary species, and environmental variables on focal species catch rates are poorly understood. In response, we conducted comparative deployments with three unique, inter-agency, survey gill nets used to assess walleye Sander vitreus in Lake Erie. We used an information-theoretic approach with Akaike’s second-order information criterion (AIC c ) to evaluate linear mixed models of walleye catch as a function of net type (multifilament and two types of monofilament netting), mesh size (categorical), Secchi depth, temperature, water depth, catch of ancillary species, and interactions among selected variables. The model with the greatest weight of evidence showed that walleye catches were positively associated with potential prey and intra-guild predators and negatively associated with water depth and temperature. In addition, the multifilament net had higher average walleye catches than either of the two monofilament nets. Results from this study both help inform decisions about proposed gear changes to stock assessment surveys in Lake Erie, and advance our understanding of how multispecies associations explain variation in gill net catches. Of broader interest to fishery-independent gill net studies, effects of abiotic variables and ancillary species on focal specie’s catch rates were small in comparison with net characteristics of mesh size or twine type.

Lake Erie

Louisiana Barrier Island Comprehensive Monitoring (BICM) Program Summary Report: Data and Analyses 2006 through 2010

The Barrier Island Comprehensive Monitoring (BICM) program was implemented under the Louisiana Coastal Area Science and Technology (LCA S&T) office as a component of the System Wide Assessment and Monitoring (SWAMP) program. The BICM project was developed by the State of Louisiana (Coastal Protection Restoration Authority [CPRA], formerly Department of Natural Resources [DNR]) to complement other Louisiana coastal monitoring programs such as the Coastwide Reference Monitoring System-Wetlands (CRMS-Wetlands) and was a collaborative research effort by CPRA, University of New Orleans (UNO), and the U.S. Geological Survey (USGS). The goal of the BICM program was to provide long-term data on the barrier islands of Louisiana that could be used to plan, design, evaluate, and maintain current and future barrier-island restoration projects. The BICM program used both historical and newly acquired (2006 to 2010) data to assess and monitor changes in the aerial and subaqueous extent of islands, habitat types, sediment texture and geotechnical properties, environmental processes, and vegetation composition. BICM datasets included aerial still and video photography (multiple time series) for shoreline positions, habitat mapping, and land loss; light detection and ranging (lidar) surveys for topographic elevations; single-beam and swath bathymetry; and sediment grab samples. Products produced using BICM data and analyses included (but were not limited to) storm-impact assessments, rate of shoreline and bathymetric change, shoreline-erosion and accretion maps, high-resolution elevation maps, coastal-shoreline and barrier-island habitat-classification maps, and coastal surficial-sediment characterization maps. Discussions in this report summarize the extensive data-collection efforts and present brief interpretive analyses for four coastal Louisiana geographic regions. In addition, several coastal-wide and topical themes were selected that integrate the data and analyses within a broader coastal context: (1) barrier-shoreline evolution driven by rapid relative sea-level rise (RSLR), (2) hurricane impacts to the Chandeleur Islands and likelihood of island recovery, (3) impact of tropical storms on barrier shorelines, (4) Barataria Bay tidal-inlet management, and (5) habitat changes related to RSLR. The final theme addresses potential future goals of the BICM program, including rotational annual to semi-decadal monitoring, proposed new-data collection, how to incorporate technological advances with previous data-collection and monitoring protocols, and standardizing methods and quality-control assessments for continued coastal monitoring and restoration.

Louisiana

Ecological Requirements for Pallid Sturgeon Reproduction and Recruitment in the Lower Missouri River: A Research Synthesis 2005-08

This report provides a synthesis of results obtained between 2005 and 2008 from the Comprehensive Sturgeon Research Program, an interagency collaboration between the U.S. Geological Survey, Nebraska Game and Parks Commission, U.S. Fish and Wildlife Service, and the U.S. Army Corps of Engineers' Missouri River Recovery - Integrated Science Program. The goal of the Comprehensive Sturgeon Research Program is to improve fundamental understanding of reproductive ecology of the pallid sturgeon with the intent that improved understanding will inform river and species management decisions. Specific objectives include: *Determining movement, habitat-use, and reproductive behavior of pallid sturgeon; *Understanding reproductive physiology of pallid sturgeon and relations to environmental conditions; *Determining origin, transport, and fate of drifting pallid sturgeon larvae, and evaluating bottlenecks for recruitment of early life stages; *Quantifying availability and dynamics of aquatic habitats needed by pallid sturgeon for all life stages; and *Managing databases, integrating understanding, and publishing relevant information into the public domain. Management actions to increase reproductive success and survival of pallid sturgeon in the Lower Missouri River have been focused on flow regime, channel morphology, and propagation. Integration of 2005-08 Comprehensive Sturgeon Research Program research provides insight into linkages among flow regime, re-engineered channel morphology, and pallid sturgeon reproduction and survival. The research approach of the Comprehensive Sturgeon Research Program integrates opportunistic field studies, field-based experiments, and controlled laboratory studies. The field study plan is designed to explore the role of flow regime and associated environmental cues using two complementary approaches. An upstream-downstream approach compares sturgeon reproductive behavior between an upstream section of the Lower Missouri River with highly altered flow regime to a downstream section that maintains much of its pre-regulation flow variability. The upstream section also has the potential for an experimental approach to compare reproductive behavior in years with pulsed flow modifications ('spring rises') to years without. The reproductive cycle of the female sturgeon requires several years to progress through gonadal development, oocyte maturation, and spawning. Converging lines of evidence support the hypothesis that maturation and readiness to spawn in female sturgeon is cued many months before spawning. Information on reproductive readiness of shovelnose sturgeon indicates that sturgeon at different locations along the Lower Missouri River between St. Louis and Gavins Point Dam are all responding to the same early cue. Although not a perfect surrogate, the more abundant shovelnose sturgeon is morphologically, physiologically, and genetically similar to pallid sturgeon, and thereby provides a useful comparative model for the rarer species. Day length is the likely candidate to define a temporal spawning window. Within the spawning window, one or more additional, short-term, and specific cues may serve to signal ovulation and release of gametes. Of three potential spawning cues - water temperature, water discharge, and day of year - water temperature is the most likely proximate cue because of the fundamental physiological role temperature plays in sturgeon embryo development and survival, and the sensitivity of many fish hormones to temperature change. It also is possible that neither temperature nor discharge is cueing spawning; instead, reproductive behavior may result from the biological clock advancing an individual fish's readiness to spawn day after day through the spawning period until the right moment, independent of local environmental conditions. Separation of the individual effects of discharge events, water temperature, and other possible factors, such as proximity to male

Scientific Investigations Report

The potential influence of changing climate on the persistence of salmonids of the inland west

The Earth's climate warmed steadily during the 20th century, and mean annual air temperatures are estimated to have increased by 0.6°C (Intergovernmental Panel on Climate Change, 2007). Although many cycles of warming and cooling have occurred in the past, the most recent warming period is unique in its rate and magnitude of change (Siegenthaler and others, 2005) and in its association with anthropogenic emissions of greenhouse gases (Intergovernmental Panel on Climate Change , 2007). The climate in the western United States warmed in concert with the global trend but at an accelerated rate (+0.8°C during the 20th century; Saunders and others, 2008). The region could also prove especially sensitive to future changes because the relatively small human population is growing rapidly, as are demands on limited water supplies. Regional hydrological patterns are dominated by seasonal snow accumulation at upper elevations. Most of the region is relatively dry, and both terrestrial and aquatic ecosystems are strongly constrained b y water availability (Barnett and others, 2008; Brown and others, 2008). Stream environments are dynamic and climatically extreme, and salmonid fishes are the dominant elements of the native biodiversity (McPhail and Lindsey, 1986; Waples and others, 2008). Salmonids have broad economic and ecologic importance, but a century of intensive water resource development, nonnative fish stocking, and land use has significantly reduced many populations and several taxa are now protected under the Endangered Species Act (Thurow and others, 1997; Trotter, 2008). Because salmonids require relatively pristine, cold water environments and are often isolated in headwater habitats, members of this group may be especially vulnerable to the effects of a warming climate (Keleher and Rahel, 1996; Rieman and others, 2007; Williams and others, 2009). Warming during the 20th century drove a series of environmental trends that have profound implications for many aspects of salmonid habitat, including disturbance regimes such as wildfire, and unfavorable changes to thermal and hydrologic properties of aquatic systems. Warmer air temperatures have been associated with decreased winter snow accumulations, have accelerated snowmelt, and have advanced the timing of peak runoff by several days to weeks across most of western North America (Stewart and others, 2005; Barnett and others, 2008). Less snow and earlier runoff decrease aquifer recharge, make less water available for groundwater inputs to streams, and are contributing to widespread decreases in summer low flows (Stewart and others, 2005; Rood and others, 2008; Luce and Holden 2009). Interannual variability in stream flow is increasing, as is the persistence of multi-year extreme conditions (McCabe and others, 2004; Pagano and Garen 2005). In many areas of western North America, flood risks have increased in association with warmer temperatures during the 20th century (Hamlet and Lettenmaier, 2005). Streams where midwinter temperatures are near freezing have proven especially sensitive to increased flooding because of associated transitional hydrological patterns (mixtures of rainfall and snowmelt) and propensity for occasional rain-on-snow events to rapidly melt winter snowpack and generate large floods (Hamlet and Lettenmaier, 2005). Stream temperatures in many areas are increasing (Peterson and Kitchell, 2001; Morrison and others, 2002; Bartholow, 2005; Kaushal and others, 2010), due to both air temperature increases and reduced summer flows that make streams more sensitive to warmer air temperatures (Isaak and others, 2010). In recent decades, wildfires have become more common across much of the western United States during periods of more frequent droughts (Westerling and others, 2006; Hoerling and Eischeid, 2007), and local stream temperature can increase in postfire environments (Gresswell, 1999; Dunham and others, 2007). Fire-related temperature increase within streams is commonly a transient phenomenon, lasting only until riparian vegetation has recovered (Gresswell, 1999); however, ongoing climate change could preclude recovery to higher stature, prefire vegetation types in some areas (McKenzie and others, 2004; van Mantgem and Stephenson, 2007), resulting in a loss of critical riparian shading. Additionally, when wildfires occur in steep mountain topographies, the vegetation that stabilize s soils on hillslopes is often killed and landslides become more prevalent (Gresswell, 1999). Landslides int o stream channels form debris flows composed of sediment slurries and dead trees that can scour channels to bedrock and further exacerbate stream heating, delay recovery of riparian areas, or extirpate fish populations (Gresswell, 1999; May and Gresswell, 2003; Dunham and others, 2007). Changes in stream environments will shift habitat distributions, sometimes unpredictably, in both time and space for many salmonid fishes. Water temperature fundamentally influences aquatic ecosystem health because distribution, reproduction, fitness, and survival of ectothermic organisms are inextricably linked to the thermal regime of the environment. Historically, research has focused on defining lethal thermal limits of salmonids (Eaton and others, 1995; Selong and others, 2001; Todd and others, 2008); however, water temperature is known to be important in biological processes at a variety of spatial scales and levels of biological organization (Rahel and Olden, 2008; McCullough and others, 2009). For instance, trout are affected directly by water temperature through feeding, metabolism, and growth rates, and indirectly by factors such as prey availability and species interactions (Wehrly and others, 2007; Rahel and Olden, 2008). Where cold water temperatures currently limit habitat suitability and distributions of some species (for example, at the highest and most northerly distributional extents; Nakano and others, 1996; Coleman and Fausch, 2007), a warming climate may gradually increase the quality and extent of suitable habitat. Over time, previously constrained populations are expected to expand into these new habitats and increase in number. Some evidence suggests this may already be happening in Alaska, where streams in recently deglaciated areas are being colonized by emigrants from nearby salmon and char populations (Milner and others, 2000). Unfortunately, many of the sensitive salmonid species that are often the focus of western managers are unlikely to benefit from future water temperature increases. Warmer stream temperatures will facilitate invasion by nonnative species that are broadly established in downstream areas into upstream areas where they will compete with native species (Rieman and others, 2006; Rahel and Olden, 2008; Fausch and others, 2009). In other cases, warmer stream temperatures will render thermally suitable habitats unsuitable in downstream areas and effect net losses of habitat because upstream distributions are often constrained by streams that are too small or steep (Hari and others, 2006; Isaak and others, 2010). Both scenarios are realistic for fish species like bull trout ( Salvelinus confluentus ) (Rieman and others, 2006; Rieman and others, 2007), the various subspecies of cutthroat trout ( Oncorhynchus clarkii ) (Williams and others, 2009), Gila trout ( Oncorhynchus gilae gilae ) (Kennedy and others, 2008), and Apache trout ( Oncorhynchus gilae apache ) (Rinne and Minckley, 1985; Carmichael and others, 1993). As native species are increasingly confined to smaller and more isolated habitats by a gradually warming climate, the effects of wildfires (whether related to lethal changes in water quality during a fire, channel debris flows, or chronic postfire warming ) could have greater proportional effects on remaining habitats (for example, Brown and others, 2001; Rieman and others, 2007). If these changes were accompanied by additional hydrologic alterations associated with changes to the magnitude, frequency, duration, timing, and rate of change of discharge patterns (Jager and others, 1999; Henderson and others, 2000), populations may begin to lose some of their historic resilience and become ever more susceptible to local extirpations. As dramatic and extensive as climatic and environmental trends are for salmonid habitats, global climate models (GCMs) project that many of these trends will continue and even accelerate until at least the middle of the 21st century (Intergovernmental Panel on Climate Change, 2007). Current projections suggest mean annual air temperatures will increase by an additional 1–3°C, and early indications are that climate trajectory is at the higher end of this range (Pittock, 2006; Raupach and others, 2007). Although predicted changes vary considerably, even the most conservative estimates suggest a warming rate that will be twice that observed during the 20th century. Projections for the midcentury are most certainly due to the effects of greenhouse gases already emitted or predicted in the short term, uncertainties of the effects of longer-term greenhouse gas emissions, short-term climate cycles, and process errors associated with climate models (Cox and Stephenson, 2007). Projections of changes in total precipitation are less certain than those for air temperatures, but most GCMs project relatively small changes in the Northwest, with the exception of slightly drier summer periods (Mote and others, 2008; Karl and others, 2009). In the Southwest, however, significant decreases (such as 15–30 percent ) are projected during most periods of the year, and this area is one of the few for which Intergovernmental Panel on Climate Change (2007) precipitation projections have a high level of certainty (Hoerling and Eischeid, 2007; Karl and others, 2009). Clearly, managers of native salmonids in the wester n United States should consider adjusting management strategies to accommodate a warmer and possibly drier future (Williams and others, 2009). Tools are needed to forecast where important changes may occur and how conservation efforts should be prioritized. In this Open-File Report, we document our initial efforts in this regard for 10 species and subspecies of inland trout and Montana Arctic grayling ( Thymallus arcticus ) across the western United States.

Arizona, California, Colorado, Idaho, Montana, Nev

Using constructed analogs to improve the skill of National Multi-Model Ensemble March–April–May precipitation forecasts in equatorial East Africa

In this study we implement and evaluate a simple 'hybrid' forecast approach that uses constructed analogs (CA) to improve the National Multi-Model Ensemble's (NMME) March–April–May (MAM) precipitation forecasts over equatorial eastern Africa (hereafter referred to as EA, 2°S to 8°N and 36°E to 46°E). Due to recent declines in MAM rainfall, increases in population, land degradation, and limited technological advances, this region has become a recent epicenter of food insecurity. Timely and skillful precipitation forecasts for EA could help decision makers better manage their limited resources, mitigate socio-economic losses, and potentially save human lives. The 'hybrid approach' described in this study uses the CA method to translate dynamical precipitation and sea surface temperature (SST) forecasts over the Indian and Pacific Oceans (specifically 30°S to 30°N and 30°E to 270°E) into terrestrial MAM precipitation forecasts over the EA region. In doing so, this approach benefits from the post-1999 teleconnection that exists between precipitation and SSTs over the Indian and tropical Pacific Oceans (Indo-Pacific) and EA MAM rainfall. The coupled atmosphere-ocean dynamical forecasts used in this study were drawn from the NMME. We demonstrate that while the MAM precipitation forecasts (initialized in February) skill of the NMME models over the EA region itself is negligible, the ranked probability skill score of hybrid CA forecasts based on Indo-Pacific NMME precipitation and SST forecasts reach up to 0.45.

Environmental Research Letters

Limitations and potential of satellite imagery to monitor environmental response to coastal flooding

Storm-surge flooding and marsh response throughout the coastal wetlands of Louisiana were mapped using several types of remote sensing data collected before and after Hurricanes Gustav and Ike in 2008. These included synthetic aperture radar (SAR) data obtained from the (1) C-band advance SAR (ASAR) aboard the Environmental Satellite, (2) phased-array type L-band SAR (PALSAR) aboard the Advanced Land Observing Satellite, and (3) optical data obtained from Thematic Mapper (TM) sensor aboard the Land Satellite (Landsat). In estuarine marshes, L-band SAR and C-band ASAR provided accurate flood extent information when depths averaged at least 80 cm, but only L-band SAR provided consistent subcanopy detection when depths averaged 50 cm or less. Low performance of inundation mapping based on C-band ASAR was attributed to an apparent inundation detection limit (>30 cm deep) in tall Spartina alterniflora marshes, a possible canopy collapse of shoreline fresh marsh exposed to repeated storm-surge inundations, wind-roughened water surfaces where water levels reached marsh canopy heights, and relatively high backscatter in the near-range portion of the SAR imagery. A TM-based vegetation index of live biomass indicated that the severity of marsh dieback was linked to differences in dominant species. The severest impacts were not necessarily caused by longer inundation but rather could be caused by repeated exposure of the palustrine marsh to elevated salinity floodwaters. Differential impacts occurred in estuarine marshes. The more brackish marshes on average suffered higher impacts than the more saline marshes, particularly the nearshore coastal marshes occupied by S. alterniflora.

Journal of Coastal Research

Geospatial Technology Applications and Infrastructure in the Biological Resources Division

Executive Summary -- Automated spatial processing technology such as geographic information systems (GIS), telemetry, and satellite-based remote sensing are some of the more recent developments in the long history of geographic inquiry. For millennia, humankind has endeavored to map the Earth's surface and identify spatial relationships. But the precision with which we can locate geographic features has increased exponentially with satellite positioning systems. Remote sensing, GIS, thematic mapping, telemetry, and satellite positioning systems such as the Global Positioning System (GPS) are tools that greatly enhance the quality and rapidity of analysis of biological resources. These technologies allow researchers, planners, and managers to more quickly and accurately determine appropriate strategies and actions. Researchers and managers can view information from new and varying perspectives using GIS and remote sensing, and GPS receivers allow the researcher or manager to identify the exact location of interest. These geospatial technologies support the mission of the U.S. Geological Survey (USGS) Biological Resources Division (BRD) and the Strategic Science Plan (BRD 1996) by providing a cost-effective and efficient method for collection, analysis, and display of information. The BRD mission is 'to work with others to provide the scientific understanding and technologies needed to support the sound management and conservation of our Nation's biological resources.' A major responsibility of the BRD is to develop and employ advanced technologies needed to synthesize, analyze, and disseminate biological and ecological information. As the Strategic Science Plan (BRD 1996) states, 'fulfilling this mission depends on effectively balancing the immediate need for information to guide management of biological resources with the need for technical assistance and long-range, strategic information to understand and predict emerging patterns and trends in ecological systems.' Information sharing plays a key role in nearly everything BRD does. The Strategic Science Plan discusses the need to (1) develop tools and standards for information transfer, (2) disseminate information, and (3) facilitate effective use of information. This effort centers around the National Biological Information Infrastructure (NBII) and the National Spatial Data Infrastructure (NSDI), components of the National Information Infrastructure. The NBII and NSDI are distributed electronic networks of biological and geographical data and information, as well as tools to help users around the world easily find and retrieve the biological and geographical data and information they need. The BRD is responsible for developing scientifically and statistically reliable methods and protocols to assess the status and trends of the Nation's biological resources. Scientists also conduct important inventory and monitoring studies to maintain baseline information on these same resources. Research on those species for which the Department of the Interior (DOI) has trust responsibilities (including endangered species and migratory species) involves laboratory and field studies of individual animals and the environments in which they live. Researchboth tactical and strategicis conducted at the BRD's 17 science centers and 81 field stations, 54 Cooperative Fish and Wildlife Research Units in 40 states, and at 11 former Cooperative Park Study Units. Studies encompass fish, birds, mammals, and plants, as well as their ecosystems and the surrounding landscape. Biological Resources Division researchers use a variety of scientific tools in their endeavors to understand the causes of biological and ecological trends. Research results are used by managers to predict environmental changes and to help them take appropriate measures to manage resources effectively. The BRD Geospatial Technology Program facilitates the collection, analysis, and dissemination of data and informat

Information and Technology Report

Evolving environmental and geometric controls on Columbia Glacier’s continued retreat

Geometry strongly controls the dynamic behavior of marine‐terminating (tidewater) glaciers, significantly influencing advance and retreat cycles independent of climate. Yet the recent, nearly ubiquitous retreat of tidewater glaciers suggests that changes in atmospheric and oceanic forcing may also drive dynamic change. To isolate the influence of geometry on tidewater glacier dynamics, we analyzed detailed observational time series from 2012 to 2016 for two tidewater glaciers with shared dynamic histories and environmental forcing: Columbia Glacier and its former tributary (Post Glacier) in southcentral Alaska. We find that although terminus retreat has driven decadal‐scale changes in dynamics of the Columbia‐Post system, environmental factors contribute to short‐term (i.e., seasonal) dynamic variability. In particular, analysis of force balance time series indicates that observed variations in speed result from seasonal changes to the subglacial hydrologic system and associated changes in basal drag. Variations in terminus position only drive noticeable speed change when the terminus retreats from regions of relatively high basal drag. In agreement with long‐term analyses of Columbia Glacier, we find that terminus geometry can perturb the timing of seasonal ice flow patterns. Specifically, our data support the idea that retreat of a glacier terminus into deeper water is accompanied by a shift in the primary control on frontal ablation. Although our analysis focuses on two Alaskan glaciers, our data suggest that changes in the relative importance of surface meltwater and buoyancy effects on submarine melting and/or calving may manifest as a shift in terminus change seasonality and offer a mechanism to identify frontal ablation controls.

Alaska

An investigation of the bactericidal activity of selected essential oils to Aeromonas spp.

Diseases of fishes caused by Aeromonas spp. are common, have broad host ranges and may cause high mortality. Treatments of captive-reared populations using antimicrobials are limited with concerns for bacterial resistance development and environmental dissemination. This study was done to determine whether selected plant-derived essential oils were bactericidal to Aeromonas spp. Initially, twelve essential oils were evaluated using a disk diffusion assay to an isolate of A . salmonicida subsp. salmonicida , cause of fish furunculosis. The greatest zones of inhibition were obtained with oils of cinnamon Cinnamomum cassia , oregano Origanum vulgare , lemongrass Cymbopogon citratus and thyme Thymus vulgaris . Minimum bactericidal concentrations (MBC’s) were determined for these four oils, Allimed® (garlic extract, Allium sativum ) and colloidal silver to sixty-nine isolates representing nine Aeromonas spp. The lowest mean MBCs (0.02–0.04%) were obtained with three different sources of cinnamon oil. MBCs for three sources of oregano and lemongrass oils ranged from 0.14% to 0.30% and 0.10% to 0.65%, respectively, and for two thyme oils were 2.11% and 2.22%. The highest concentration (5%) of Allimed® tested resulted in MBCs to twelve isolates. A concentration of silver greater than 15 mg/L would be required to determine MBCs for all but one isolate.

Journal of Advanced Research

Southern Salish Sea Habitat Map Series: Admiralty Inlet

In 2010 the Environmental Protection Agency, Region 10 initiated the Puget Sound Scientific Studies and Technical Investigations Assistance Program, designed to support research in support of implementing the Puget Sound Action Agenda. The Action Agenda was created in response to Puget Sound having been designated as one of 28 estuaries of national significance under section 320 of the U.S. Clean Water Act, and its overall goal is to restore the Puget Sound Estuary's environment by 2020. The Southern Salish Sea Mapping Project was funded by the Assistance Program request for proposals process, which also supports a large number of coastal-zone- and ocean-management issues. The issues include the recommendations of the Marine Protected Areas Work Group to the Washington State Legislature (Van Cleve and others, 2009), which endorses a Puget Sound and coast-wide marine conservation needs assessment, gap analysis of existing Marine Protected Areas (MPA) and recommendations for action. This publication is the first of four U.S. Geological Survey Scientific Investigation Maps that make up the Southern Salish Sea Mapping Project. The remaining three map blocks to be published in the future, located south of Admiralty Inlet, are shown in figure 1. Puget Sound is a deep, fjord-type estuary covering an area of 2,330 km 2 in the Pacific Northwest region of the United States (fig. 1). It is connected to the ocean by the Strait of Juan de Fuca, a turbulent passage approximately 160 km in length and 22 km wide at its west end, expanding to over 40 km wide at its east end (Thomson, 1994). During the Pleistocene, the area was occupied several times by lobes of continental ice, resulting in a complex basin-fill of glacial and interglacial deposits that are locally as thick as 1100 m (Johnson and others, 2001). The last glaciation, called the Fraser glaciation, began after 28,800±740 14 C yr B.P. when ice started a slow expansion (Clague, 1981). At peak advance the westward Juan de Fuca lobe reached the edge of the continental shelf through the Juan de Fuca Strait shortly before 14,460±200 14 C yr B.P. (Herzer and Bornhold, 1982). The southward Puget lobe advanced to its terminal position in Puget Sound by around 14,150 14 C yr B.P. (Porter and Swanson, 1998). Ice retreated from its maximum to northern Whidbey Island by 13,650±350 14 C yr B.P. (Dethier and others, 1995). Retreating glaciers resulted in a thick sequence of ice-contact, glacial-marine sediment, and early post-glacial sediments (Linden and Schurrer, 1988). These deposits have experienced the effects of a marine transgression followed by regression, resulting in a sea-level several tens of meters lower than the present day (Linden and Schurrer, 1988). A second transgression brought sea level to about the present level by around 5,470±120 14 C yr B.P. (Clague and others, 1982) establishing the present oceanographic and geologic environment Puget Sound is separated into four interconnected basins; Whidbey, Central (Main), Hood Canal, and South (Thomson, 1994). The Whidbey, Central, and Hood Canal basins are the three main branches of the Puget Sound estuary and are separated from the Strait of Juan de Fuca by a double sill at Admiralty Inlet. The Admiralty Inlet map area includes the Inlet and a portion of the Whidbey Basin (fig. 1). The shallower South Basin is separated by a sill at Tacoma Narrows and is highly branched with numerous finger inlets. Flow within Puget Sound is dominated by tidal currents of as much as 1 m/s at Admiralty Inlet, reducing to approximately 0.5 m/s in the Central Basin (Lavelle and others, 1988). The lack of silt and clay-sized sediments in the Admiralty Inlet map area is likely a result of the strong currents (see Ground-Truth Studies for the Admiralty Inlet Map Area, sheet 3). The subtidal component of flow reaches approximately 0.1 m/s and is driven by density gradients arising from the contrast in salty ocean water at the entrance and freshwater inputs from stream flow (Lavelle and others, 1988). The total freshwater input to Puget Sound is approximately 3.4 x 10 6 m 3 /day, primarily from the Skagit River (Cannon, 1983). The subtidal circulation mostly consists of a two-layered flow in the basins with fresher water exiting at the surface and saltier water entering at depth (Ebbesmeyer and Cannon, 2001). In general, surface waters flow north and deeper waters flow south; variations arise from wind effects that can drive a surface current in the same direction as the wind, and a baroclinic response in the lower layer to about 100-m depth (Matsuura and Cannon, 1997). Oceanographic properties are influenced by temporal forcing parameters such as reduced stream flow during the 2000-01 drought that increased surface salinity and decreased differences between surface and bottom waters (Newton and others, 2003). On offshore seismic-reflection profiles, Pleistocene strata (excluding latest Pleistocene glacial and post-glacial deposits) form a distinct seismic unit, bounded below by pre-Tertiary or Tertiary basement and above by typically flat-lying latest Pleistocene to Holocene deposits that fill in erosional or depositional relief (Johnson and others, 2001). Cores from central Puget Sound have accumulation rates that range from 85 to 1200 mg/cm 2 /yr, or 0.12 to 2.4 cm/yr; the highest accumulation rates are near the southern end of central Puget Sound (Carpenter and others, 1985). Carpenter and others (1985) un-weighted arithmetic mean of accumulation rates for central Puget Sound deeper stations is 480±340 (± one standard deviation) mg/cm 2 /yr. Lavelle and others (1985) also found rates as high as 1200 mg/cm 2 /yr over the past approximately 70 years in cores in the Central Basin off of and north and south of Elliott Bay. Puget Sound basin rates are comparable to rates in midshelf silt deposits on the Washington coast north of the Columbia River (Nittrouer and others, 1979). The deep subtidal (in other words, below SCUBA depths) habitats of Puget Sound are relatively poorly known. A few subtidal surveys exist for several habitat types from the 1960s and 1970s (reviewed in Dethier, 1990), using grab and box core data. The Dethier (1990) review divides habitat up into Coast and Marine Ecological Classification Standard (CMECS) substrate, water column energy, and depth zones but does not attempt to map these habitats, rather it is an inventory of habitats found in the area and the flora and fauna associated with each habitat. The approach of the Southern Salish Sea Mapping project is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data (the undersea equivalent of satellite remote-sensing data in terrestrial mapping), acoustic backscatter, seafloor video, seafloor photography, and bottom-sediment sampling data. This approach is based in part on methods presented and data collection and product needs identified at the Washington State Seafloor Mapping Workshop (Washington State Seafloor Mapping Workshop Steering Committee, 2008), attended by coastal and marine managers and scientists. The map products display seafloor geomorphology and substrate, and identify potential marine benthic habitats. It is emphasized that the more interpretive habitat and geology maps rely on the integration of multiple, new high-resolution datasets and that mapping at small scales would not be possible without such data. Oceanographic current and wave data is not included in this analysis, however, the accompanying geographic information system (GIS) data set is designed and intended to be combined with oceanographic and biologic data sets assembled by others in the future and some of the GIS data has already been incorporated in the unpublished Nature Conservancy Benthic Habitats of Puget Sound database. This publication includes four map sheets, explanatory text, and a descriptive pamphlet. Each map sheet is published as a portable document format (PDF) file. ESRI ArcGIS compatible geotiffs (for example, bathymetry) and shapefiles (for example video observation points) will be available for download in the data catalog associated with this publication (Cochrane, 2015). An ArcGIS Project File with the symbology used to generate the map sheets is also provided. For those who do not own the full suite of ESRI GIS and mapping software, the data can be read using ESRI ArcReader, a free viewer that is available at http://www.esri.com/software/arcgis/arcreader/index.html .

Washington

Tributyltin: Advancing the science on assessing endocrine disruption with an unconventional endocrine-disrupting compound

Tributyltin (TBT) has been recognized as an endocrine disrupting chemical (EDC) for several decades. However, only in the last decade, was its primary endocrine mechanism of action (MeOA) elucidated—interactions with the nuclear retinoid-X receptor (RXR), peroxisome proliferator-activated receptor γ (PPARγ), and their heterodimers. This molecular initiating event (MIE) alters a range of reproductive, developmental, and metabolic pathways at the organism level. It is noteworthy that a variety of MeOAs have been proposed over the years for the observed endocrine-type effects of TBT; however, convincing data for the MIE was provided only recently and now several researchers have confirmed and refined the information on this MeOA. One of the most important lessons learned from years of research on TBT concerns apparent species sensitivity. Several aspects such as the rates of uptake and elimination, chemical potency, and metabolic capacity are all important for identifying the most sensitive species for a given chemical, including EDCs. For TBT, much of this was discovered by trial and error, hence important relationships and important sensitive taxa were not identified until several decades after its introduction to the environment. As recognized for many years, TBT-induced responses are known to occur at very low concentrations for molluscs, a fact that has more recently also been observed in fish species. This review explores the MeOA and effects of TBT in different species (aquatic molluscs and other invertebrates, fish, amphibians, birds, and mammals) according to the OECD Conceptual Framework for Endocrine Disruptor Testing and Assessment (CFEDTA). The information gathered on biological effects that are relevant for populations of aquatic animals was used to construct Species Sensitivity Distributions (SSDs) based on No Observed Effect Concentrations (NOECs) and Lowest Observed Effect Concentrations (LOECs). Fish appear at the lower end of these distributions, showing that they are as sensitive as molluscs, and for some species, even more sensitive. Concentrations in the range of 1 ng/L for water exposure (10 ng/g for whole-body burden) have been shown to elicit endocrine-type responses, whereas mortality occurs at water concentrations ten times higher. Current screening and assessment methodologies as compiled in the OECD CFEDTA are able to identify TBT as a potent endocrine disruptor with a high environmental risk for the original use pattern. If those approaches had been available when TBT was introduced to the market, it is likely that its use would have been regulated sooner, thus avoiding the detrimental effects on marine gastropod populations and communities as documented over several decades.

Book chapter

Advancements in hydrochemistry mapping: methods and application to groundwater arsenic and iron concentrations in Varanasi, Uttar Pradesh, India

The area east of Varanasi is one of numerous places along the watershed of the Ganges River with groundwater concentrations of arsenic surpassing the maximum value of 10 parts per billion (ppb) recommended by the World Health Organization in drinking water. Here we apply geostatistics and compositional data analysis for the mapping of arsenic and iron to help in understanding the conditions leading to the occurrence of elevated level of arsenic in groundwater. The methodology allows for displaying concentrations of arsenic and iron as maps consistent with the limited information from 95 water wells across an area of approximately 210 km 2 ; visualization of the uncertainty associated with the sampling; and summary of the findings in the form of probability maps. For thousands of years, Varanasi has been on the erosional side in a meander of the river that is free of arsenic values above 10 ppb. Maps reveal two anomalies of high arsenic concentrations on the depositional side of the valley, which has started seeing urban development. The methodology using geostatistics combined with compositional data analysis is completely general, so this study could be used as a prototype for hydrochemistry mapping in other areas.

Uttar Pradesh

Diverse portfolios: Investing in tributaries for restoration of large river fishes in the Anthropocene

Rehabilitation of large Anthropocene rivers requires engagement of diverse stakeholders across a broad range of sociopolitical boundaries. Competing objectives often constrain options for ecological restoration of large rivers whereas fewer competing objectives may exist in a subset of tributaries. Further, tributaries contribute toward building a “portfolio” of river ecosystem assets through physical and biological processes that may present opportunities to enhance the resilience of large river fishes. Our goal is to review roles of tributaries in enhancing mainstem large river fish populations. We present case histories from two greatly altered and distinct large-river tributary systems that highlight how tributaries contribute four portfolio assets to support large-river fish populations: 1) habitat diversity, 2) connectivity, 3) ecological asynchrony, and 4) density-dependent processes. Finally, we identify future research directions to advance our understanding of tributary roles and inform conservation actions. In the Missouri River United States, we focus on conservation efforts for the state endangered lake sturgeon, which inhabits large rivers and tributaries in the Midwest and Eastern United States. In the Colorado River, Grand Canyon United States, we focus on conservation efforts for recovery of the federally threatened humpback chub. In the Missouri River, habitat diversity focused on physical habitats such as substrate for reproduction, and deep-water habitats for refuge, whereas augmenting habitat diversity for Colorado River fishes focused on managing populations in tributaries with minimally impaired thermal and flow regimes. Connectivity enhancements in the Missouri River focused on increasing habitat accessibility that may require removal of physical structures like low-head dams; whereas in the Colorado River, the lack of connectivity may benefit native fishes as the disconnection provides refuge from non-native fish predation. Hydrologic variability among tributaries was present in both systems, likely underscoring ecological asynchrony. These case studies also described density dependent processes that could influence success of restoration actions. Although actions to restore populations varied by river system, these examples show that these four portfolio assets can help guide restoration activities across a diverse range of mainstem rivers and their tributaries. Using these assets as a guide, we suggest these can be transferable to other large river-tributary systems.

Frontiers in Environmental Science

Bridging groundwater models and decision support with a Bayesian network

Resource managers need to make decisions to plan for future environmental conditions, particularly sea level rise, in the face of substantial uncertainty. Many interacting processes factor in to the decisions they face. Advances in process models and the quantification of uncertainty have made models a valuable tool for this purpose. Long-simulation runtimes and, often, numerical instability make linking process models impractical in many cases. A method for emulating the important connections between model input and forecasts, while propagating uncertainty, has the potential to provide a bridge between complicated numerical process models and the efficiency and stability needed for decision making. We explore this using a Bayesian network (BN) to emulate a groundwater flow model. We expand on previous approaches to validating a BN by calculating forecasting skill using cross validation of a groundwater model of Assateague Island in Virginia and Maryland, USA. This BN emulation was shown to capture the important groundwater-flow characteristics and uncertainty of the groundwater system because of its connection to island morphology and sea level. Forecast power metrics associated with the validation of multiple alternative BN designs guided the selection of an optimal level of BN complexity. Assateague island is an ideal test case for exploring a forecasting tool based on current conditions because the unique hydrogeomorphological variability of the island includes a range of settings indicative of past, current, and future conditions. The resulting BN is a valuable tool for exploring the response of groundwater conditions to sea level rise in decision support.

Water Resources Research

Relationships between reef fish communities and remotely sensed rugosity measurements in Biscayne National Park, Florida, USA

The realization that coral reef ecosystem management must occur across multiple spatial scales and habitat types has led scientists and resource managers to seek variables that are easily measured over large areas and correlate well with reef resources. Here we investigate the utility of new technology in airborne laser surveying (NASA Experimental Advanced Airborne Research Lidar (EAARL)) in assessing topographical complexity (rugosity) to predict reef fish community structure on shallow (<10 m deep) patch reefs. Marine portions of Biscayne National Park, Florida, USA, were surveyed remotely using the EAARL, and reef fish populations were visually surveyed on 10 patch reefs at independent, randomly selected stations ( n = 10–13 per reef). Rugosity at each station was assessed in situ by divers using the traditional chain-transect method (10-m scale), and remotely using the EAARL submarine topography data at multiple spatial scales (2, 5, and 10 m). The rugosity and biological datasets were analyzed together to elucidate the predictive power of EAARL rugosity in describing the variance in reef fish community variables and to assess the correlation between chain-transect and EAARL rugosity. EAARL rugosity was not well correlated with chain-transect rugosity, or with species richness of fishes (although statistically significant, the amount of variance explained by the model was very low). Variance in reef fish community attributes was better explained in reef-by-reef variability than by physical variables. However, once the reef-by-reef variability was taken into account in a two-way analysis of variance, the importance of rugosity could be seen on individual reefs. Fish species richness and abundance were statistically higher at high rugosity stations compared to medium and low rugosity stations, as predicted by prior ecological research. The EAARL shows promise as an important mapping tool for reef resource managers as they strive to inventory and protect coral reef resources.

Florida

Integrated rangeland fire management strategy actionable science plan completion assessment: Restoration topic, 2015–20

Loss and degradation of sagebrush rangelands due to an accelerated invasive annual grass-wildfire cycle and other stressors are substantial management, conservation, and economic issues in the western United States. These sagebrush rangelands comprise a unique biome spanning 11 states, support over 350 wildlife species, and provide important ecosystem services that include stabilizing the economies of western communities. Impacts to sagebrush ecosystem processes over large areas due to the annual grass-wildfire cycle necessitated the development of a coordinated, science-based strategy for improving efforts to achieve long-term protection, conservation, and restoration of sagebrush rangelands, which was framed in 2015 under the Integrated Rangeland Fire Management Strategy (IRFMS). Central to this effort was the development of an Actionable Science Plan (Plan) that identified 37 priority science needs (Needs) for informing the actions proposed under the 5 topics (Fire, Invasives, Restoration, Sagebrush and Sage-Grouse, Climate and Weather) that were part of the collective focus of the IRFMS. Notable keys to this effort were identification of the Needs co-produced by managers and researchers, and a focus on resulting science being “actionable.” Substantial investments aimed at fulfilling the Needs identified in the Plan have been made since its release in 2016. While the state of the science has advanced considerably, the extent to which knowledge gaps remain relative to identified Needs is relatively unknown. Moreover, new Needs have likely emerged since the original strategy as results from actionable science reveal new questions, and possible (yet untested) solutions. A quantifiable assessment of the progress made on the original science Needs can identify unresolved gaps and new information that can help inform prioritization of future research efforts. This report details a systematic literature review that evaluated how well peer-reviewed journal articles and formal technical reports published between January 1, 2015, and December 31, 2020, addressed 10 needs (hereinafter “Needs”) identified under the Restoration topic in the Plan. The topic outlined research Needs for improving restoration success in degraded sagebrush rangelands. We established the level of progress towards addressing each Need following a standardized set of criteria, and developed summaries detailing how research objectives nested within Needs identified in the Plan (“Next Steps”) were either addressed well, partially addressed or remain outstanding (that is, addressed poorly) in the literature through 2020. Our searches resulted in the inclusion of 371 science products that at least partially addressed a Need identified in the Restoration topic. The Needs that were well and partially addressed included: the development of methods to improve seeding success of native plants after fire; evaluation of short- and long-term plant responses relative to biotic and abiotic factors following restoration treatments; assessments of long-term effects on ecosystem processes following conifer removal treatments and development of decision support tools to aid in conifer management; determination of the costs of restoration treatments relative to the benefits to sage-grouse occupancy, survival, and populations; and assessments of the factors which contribute to soil degradation and development of soil enhancement methods that enhance seed germination and seedling survival while resisting nonnative plants. Needs that were not addressed well included: the development of methods for the rapid recovery of sagebrush and native herbaceous plants following wildfire and determination of whether treatments benefit sage-grouse and mitigate impacts from fires; determination of thresholds for successful restoration across a range of environmental conditions and development of decision support tools to assist with restoration effectiveness monitoring; and development and evaluation of the utility of seed transfer zones. The information provided in this assessment will assist updating the Plan along with other science strategies.

western United States

Process-guided deep learning predictions of lake water temperature

The rapid growth of data in water resources has created new opportunities to accelerate knowledge discovery with the use of advanced deep learning tools. Hybrid models that integrate theory with state‐of‐the art empirical techniques have the potential to improve predictions while remaining true to physical laws. This paper evaluates the Process‐Guided Deep Learning (PGDL) hybrid modeling framework with a use‐case of predicting depth‐specific lake water temperatures. The PGDL model has three primary components: a deep learning model with temporal awareness (long short‐term memory recurrence), theory‐based feedback (model penalties for violating conversation of energy), and model pretraining to initialize the network with synthetic data (water temperature predictions from a process‐based model). In situ water temperatures were used to train the PGDL model, a deep learning (DL) model, and a process‐based (PB) model. Model performance was evaluated in various conditions, including when training data were sparse and when predictions were made outside of the range in the training data set. The PGDL model performance (as measured by root‐mean‐square error (RMSE)) was superior to DL and PB for two detailed study lakes, but only when pretraining data included greater variability than the training period. The PGDL model also performed well when extended to 68 lakes, with a median RMSE of 1.65 °C during the test period (DL: 1.78 °C, PB: 2.03 °C; in a small number of lakes PB or DL models were more accurate). This case‐study demonstrates that integrating scientific knowledge into deep learning tools shows promise for improving predictions of many important environmental variables.

Minnesota, Wisconsin

Opportunities and challenges for incorporating lithium-ion batteries into geophysical power systems

Batteries play a critical role at seismic and other geophysical stations in ensuring that the equipment receives uninterrupted power to make continuous observations of the Earth. Often sited in remote environments under a wide range of environmental conditions, these stations have almost ubiquitously used conventional lead‐acid batteries. However, recent advances in rechargeable lithium‐ion battery technology have led to the development of lithium‐iron phosphate (LFP) batteries that can replace lead‐acid batteries in energy storage systems. In the past three years, LFP battery production has grown over an order of magnitude, reducing their cost and increasing their availability. In this article, we examine the benefits and challenges associated with incorporating several types of LFP batteries into the power systems of geophysical stations. We review how fundamental differences in battery chemistry enable LFP batteries to weigh less than half of comparable lead‐acid batteries and may have longer service lives but have the added complexity of being managed by an integrated battery monitoring system (BMS) microcontroller. Through a controlled heat chamber experiment, we demonstrate that LFP batteries can be ideally suited for use in high‐temperature environments by offering longer service lives than lead‐acid batteries. However, for safety reasons, the BMS prevents most LFP batteries from being charged at temperatures <0°C, which complicates their use in colder regions and can lead to equipment damage if the charging system is not appropriately designed for this battery type. Finally, we address some of the unique challenges associated with adopting lithium batteries, including unexpected substantial (≤14 W) power consumption from the BMS, safety concerns, and shipping restrictions. It is our goal to help inform station operators and geophysicists about potential benefits and issues that can arise from using LFP batteries at seismic and geophysical stations in a range of environments.

Seismological Research Letters