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From agricultural geology to hydropedology: Forging links within the twenty-first-century geoscience community

Despite historical linkages, the fields of geology and soil science have developed along largely divergent paths in the United States during much of the mid- to late-twentieth century. The shift in recent decades within both disciplines, towards greater emphasis on environmental-quality issues and a systems approach, has created new opportunities for collaboration and cross-training. Because of the importance of the soil as a dynamic interface between the hydrosphere, biosphere, atmosphere and lithosphere, introductory and advanced soil-science classes are now taught in a number of Earth and environmental science departments. The National Research Council's recent report, Basic Research Opportunities in Earth Science, highlights the soil zone as part of the land surface to groundwater 'critical zone' requiring additional investigation. To better prepare geology undergraduates to deal with complex environmental problems, their training should include a fundamental understanding of the nature and properties of soils. Those undergraduate geology students with an interest in this area should be encouraged to view soil science as a viable Earth-science specialty area for graduate study. ?? The Geological Society of London 2006.

Geological Society Special Publication↗

Description of the L1C signal

Detailed design of the modernized LI civil signal (L1C) signal has been completed, and the resulting draft Interface Specification IS-GPS-800 was released in Spring 2006. The novel characteristics of the optimized L1C signal design provide advanced capabilities while offering to receiver designers considerable flexibility in how to use these capabilities. L1C provides a number of advanced features, including: 75% of power in a pilot component for enhanced signal tracking, advanced Weilbased spreading codes, an overlay code on the pilot that provides data message synchronization, support for improved reading of clock and ephemeris by combining message symbols across messages, advanced forward error control coding, and data symbol interleaving to combat fading. The resulting design offers receiver designers the opportunity to obtain unmatched performance in many ways. This paper describes the design of L1C. A summary of LIC's background and history is provided. The signal description then proceeds with the overall signal structure consisting of a pilot component and a carrier component. The new L1C spreading code family is described, along with the logic used for generating these spreading codes. Overlay codes on the pilot channel are also described, as is the logic used for generating the overlay codes. Spreading modulation characteristics are summarized. The data message structure is also presented, showing the format for providing time, ephemeris, and system data to users, along with features that enable receivers to perform code combining. Encoding of rapidly changing time bits is described, as are the Low Density Parity Check codes used for forward error control of slowly changing time bits, clock, ephemeris, and system data. The structure of the interleaver is also presented. A summary of L 1C's unique features and their benefits is provided, along with a discussion of the plan for L1C implementation.

Conference Paper↗

Applications of GIS and database technologies to manage a Karst Feature Database

This paper describes the management of a Karst Feature Database (KFD) in Minnesota. Two sets of applications in both GIS and Database Management System (DBMS) have been developed for the KFD of Minnesota. These applications were used to manage and to enhance the usability of the KFD. Structured Query Language (SQL) was used to manipulate transactions of the database and to facilitate the functionality of the user interfaces. The Database Administrator (DBA) authorized users with different access permissions to enhance the security of the database. Database consistency and recovery are accomplished by creating data logs and maintaining backups on a regular basis. The working database provides guidelines and management tools for future studies of karst features in Minnesota. The methodology of designing this DBMS is applicable to develop GIS-based databases to analyze and manage geomorphic and hydrologic datasets at both regional and local scales. The short-term goal of this research is to develop a regional KFD for the Upper Mississippi Valley Karst and the long-term goal is to expand this database to manage and study karst features at national and global scales.

Journal of Cave and Karst Studies↗

Effect of tidal fluctuations on contaminant transfer to the ocean

Variable-density groundwater flow was simulated to examine the effects that tide has on the coastward migration of a contaminant through a freshwater/saltwater interface and toward a coastal ocean boundary. Simulated ocean tides did not significantly affect the total contaminant mass input to the ocean; however, the difference in tidal and non-tidal simulated concentrations could be as much as 15%. It may be possible to numerically approximate the tidal-driven hydraulic transients in transport models that do not explicitly include tides by locally increasing dispersivity. Copyright ?? 2007 IAHS Press.

Conference Paper↗

Anurans in a Subarctic Tundra Landscape Near Cape Churchill, Manitoba

Distribution, abundance, and habitat relationships of anurans inhabiting subarctic regions are poorly understood, and anuran monitoring protocols developed for temperate regions may not be applicable across large roadless areas of northern landscapes. In addition, arctic and subarctic regions of North America are predicted to experience changes in climate and, in some areas, are experiencing habitat alteration due to high rates of herbivory by breeding and migrating waterfowl. To better understand subarctic anuran abundance, distribution, and habitat associations, we conducted anuran calling surveys in the Cape Churchill region of Wapusk National Park, Manitoba, Canada, in 2004 and 2005. We conducted surveys along ~l-km transects distributed across three landscape types (coastal tundra, interior sedge meadow-tundra, and boreal forest-tundra interface) to estimate densities and probabilities of detection of Boreal Chorus Frogs (Pseudacris maculata) and Wood Frogs (Lithobates sylvaticus). We detected a Wood Frog or Boreal Chorus Frog on 22 (87%) of 26 transects surveyed, but probability of detection varied between years and species and among landscape types. Estimated densities of both species increased from the coastal zone inland toward the boreal forest edge. Our results suggest anurans occur across all three landscape types in our study area, but that species-specific spatial patterns exist in their abundances. Considerations for both spatial and temporal variation in abundance and detection probability need to be incorporated into surveys and monitoring programs for subarctic anurans.

Canadian Field-Naturalist↗

Response to critique by lucas et al. (2009) of paper by Fassett (2009) documenting Paleocene dinosaurs in the San Juan Basin

In this issue of Palaeontologia Electronica Lucas, et al. (2009) question the validity f the Fassett (2009) paper that presented evidence for Paleocene dinosaurs in the San Juan Basin of New Mexico and Colorado. Their challenges focus primarily on the lithostratigraphy, palynology, and paleomagnetism of the dinosaur-bearing Ojo Alamo Sandstone, shown by Fassett to be of Paleocene age. The lithostratigraphy of the Ojo Alamo is addressed by Lucas et al. (2009) based on detailed studies of outcrops of this formation in two relatively small areas in the southern San Juan Basin where Ojo Alamo dinosaur fossils have been found. When viewed over its 13,000 km2 extent, the Ojo Alamo is seen to be a much more complex formation than these authors recognize, thus their perception and description of the lithostratigraphy of this rock unit is limited and provincial. Fassett (2009) presented a detailed discussion of the palynology of the rocks adjacent to the Cretaceous-Tertiary (K-T) interface in the San Juan Basin, including a 67-page appendix and 25 tables listing the 244 palynomorph species identified from these strata. The Ojo Alamo Sandstone produced 103 palynomorphs from five principal localities including one especially prolific sample set from drill core through K-T strata. Without exception, all samples collected from the Ojo Alamo Sandstone for palynologic analysis were found to contain Paleocene palynomorph assemblages. Lucas et al. challenge only one Ojo Alamo palynomorph assemblage from one of the five areas studied, stating that they were unable to find palynomorph-productive samples at that locality. They submit no new palynologic data that refutes the Paleocene palynologic age of the Ojo Alamo Sandstone. In addressing the paleomagnetism of the Ojo Alamo, these authors dismiss the presence of a critical normal-polarity magnetochron discovered in the lower part of the Ojo Alamo - magnetochron C29n.2n of Fassett (2009) with no evidence to justify this dismissal. This magnetochron has been identified at five localities in the basin, thus its existence seems unquestionable. At the Mesa Portales locality, this normal chron was found in Ojo Alamo strata containing Paleocene palynomorph assemblages verifying its identification as chron C29n. Other minor arguments of Lucas et al. (2009) are also addressed in this paper. In sum, Lucas et al. (2009) present no new data to contradict the data presented in Fassett (2009).

Palaeontologia Electronica↗

An adaptive approach to invasive plant management on U.S. Fish and Wildlife Service-owned native prairies in the Prairie Pothole Region: decision support under uncertainity

Much of the native prairie managed by the U.S. Fish and Wildlife Service (Service) in the Prairie Pothole Region (PPR) is extensively invaded by the introduced cool-season grasses smooth brome (Bromus inermis) and Kentucky bluegrass (Poa pratensis). The central challenge to managers is selecting appropriate management actions in the face of biological and environmental uncertainties. We describe the technical components of a USGS management project, and explain how the components integrate and inform each other, how data feedback from individual cooperators serves to reduce uncertainty across the whole region, and how a successful adaptive management project is coordinated and maintained on a large scale. In partnership with the Service, the U.S. Geological Survey is developing an adaptive decision support framework to assist managers in selecting management actions under uncertainty and maximizing learning from management outcomes. The framework is built around practical constraints faced by refuge managers and includes identification of the management objective and strategies, analysis of uncertainty and construction of competing decision models, monitoring, and mechanisms for model feedback and decision selection. Nineteen Service field stations, spanning four states of the PPR, are participating in the project. They share a common management objective, available management strategies, and biological uncertainties. While the scope is broad, the project interfaces with individual land managers who provide refuge-specific information and receive updated decision guidance that incorporates understanding gained from the collective experience of all cooperators.

Prairie Pothole Region↗

Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile

Nearly half the earth's surface is occupied by dryland ecosystems, regions susceptible to reduced states of biological productivity caused by climate fluctuations. Of these regions, arid zones located at the interface between vegetated semiarid regions and biologically unproductive hyperarid zones are considered most vulnerable. The objective of this study was to conduct a deep diversity analysis of bacterial communities in unvegetated arid soils of the Atacama Desert, to characterize community structure and infer the functional potential of these communities based on observed phylogenetic associations. A 454-pyrotag analysis was conducted of three unvegetated arid sites located at the hyperarid-arid margin. The analysis revealed communities with unique bacterial diversity marked by high abundances of novel Actinobacteria and Chloroflexi and low levels of Acidobacteria and Proteobacteria , phyla that are dominant in many biomes. A 16S rRNA gene library of one site revealed the presence of clones with phylogenetic associations to chemoautotrophic taxa able to obtain energy through oxidation of nitrite, carbon monoxide, iron, or sulfur. Thus, soils at the hyperarid margin were found to harbor a wealth of novel bacteria and to support potentially viable communities with phylogenetic associations to non-phototrophic primary producers and bacteria capable of biogeochemical cycling.

Atacama Desert↗

The Colorado Plateau: cultural, biological, and physical research

Stretching from the four corners of Arizona, New Mexico, Colorado, and Utah, the Colorado Plateau is a natural laboratory for a wide range of studies. This volume presents 23 original articles drawn from more than 100 research projects presented at the Sixth Biennial Conference of Research on the Colorado Plateau. This scientific gathering revolved around research, inventory, and monitoring of lands in the region. The book's contents cover management techniques for cultural, biological, and physical resources, representing collaborative efforts among federal, university, and private sector scientists and land managers. Chapters on cultural concerns cover benchmarks of modern southwestern anthropological knowledge, models of past human activity and impact of modern visitation at newly established national monuments, challenges in implementing the 1964 Wilderness Act, and opportunities for increased federal research on Native American lands. The section on biological resources comprises sixteen chapters, with coverage that ranges from mammalian biogeography to responses of elk at the urban-wildland interface. Additional biological studies include the effects of fire and grazing on vegetation; research on bald eagles at Grand Canyon and tracking wild turkeys using radio collars; and management of palentological resources. Two final chapters on physical resources consider a proposed rerouting of the Rio de Flag River in urban Flagstaff, Arizona, and an examination of past climate patterns over the Plateau, using stream flow records and tree ring data. In light of similarities in habitat and climate across the Colorado Plateau, techniques useful to particular management units have been found to be applicable in many locations. This volume highlights an abundance of research that will prove useful for all of those working in the region, as well as for others seeking comparative studies that integrate research into land management actions.

Utah;Colorado;Arizona;New Mexico↗

The Colorado Plateau IV: shaping conservation through science and management

Roughly centered on the Four Corners region of the southwestern United States, the Colorado Plateau covers some 130,000 square miles of sparsely vegetated plateaus, mesas, canyons, arches, and cliffs in Arizona, Utah, Colorado, and New Mexico. With elevations ranging from 3,000 to 14,000 feet, the natural systems found within the plateau are dramatically varied, from desert to alpine conditions. This book focuses on the integration of science and resource management issues in this unique and highly varied environment. Broken into three subsections, this volume addresses conservation biology, biophysical resources, and inventory and monitoring concerns. The chapters range in content, addressing conservation issues–past, present, and future–on the Colorado Plateau, measurement of human impacts on resources, grazing and wildland-urban interfaces, and tools and methods for monitoring habitats and species. An informative read for people interested in the conservation and natural history of the region, the book will also serve as a valuable reference for those people engaged in the management of cultural and biological resources of the Colorado Plateau, as well as scientists interested in methods and tools for land and resource management throughout the West.

Utah;Colorado;Arizona;New Mexico↗

Overpressure and hydrocarbon accumulations in Tertiary strata, Gulf Coast of Louisiana

Many oil and gas reservoirs in Tertiary strata of southern Louisiana are located close to the interface between a sand-rich, normally pressured sequence and an underlying sand-poor, overpressured sequence. This association, recognized for many years by Gulf Coast explorationists, is revisited here because of its relevance to an assessment of undiscovered oil and gas potential in the Gulf Coast of Louisiana. The transition from normally pressured to highly overpressured sediments is documented by converting mud weights to pressure, plotting all pressure data from an individual field as a function of depth, and selecting a top and base of the pressure transition zone. Vertical extents of pressure transition zones in 34 fields across southern onshore Louisiana range from 300 to 9000 ft and are greatest in younger strata and in the larger fields. Display of pressure transition zones on geologic cross sections illustrates the relative independence of the depth of the pressure transition zone and geologic age. Comparison of the depth distribution of pressure transition zones with production intervals confirms previous findings that production intervals generally overlap the pressure transition zone in depth and that the median production depth lies above the base of the pressure transition zone in most fields. However, in 11 of 55 fields with deep drilling, substantial amounts of oil and gas have been produced from depths deeper than 2000 ft below the base of the pressure transition zone. Mud-weight data in 7 fields show that "local" pressure gradients range from 0.91 to 1.26 psi/ft below the base of the pressure transition zone. Pressure gradients are higher and computed effective stress gradients are negative in younger strata in coastal areas, indicating that a greater potential for fluid and sediment movement exists there than in older Tertiary strata.

Louisiana↗

2009 Observer Survey Report

The USA‐National Phenology Network (USA‐NPN) seeks to engage volunteer observers in collecting phenological observations of plants and animals using consistent standards and to contribute their observations to a national data repository. In March 2009, the National Coordinating Office staff implemented an online monitoring program for 213 plant species. In this pilot year of the program, 547 observers reported phenology observations on one or more plants via the online interface. To learn more about our participants and to improve our program and our participants’ experience, we undertook a survey of individuals registered in the USA‐NPN phenology observation program. This report summarizes the results of the 2009 observer surveys. Two populations were targeted via separate surveys: Individuals who registered with the USA‐NPN plant phenology monitoring program via MyNPN but did not submit any data in 2009 (hereafter termed “non‐reporting participants”), and Individuals who submitted phenology observations via MyNPN in 2009 (hereafter termed “reporting participants”). In general, all participants in the 2009 USA‐NPN plant phenology observation program seemed to have a generally good experience. When asked why they would or would not recommend the program to friends, the majority of comments were of a positive nature, and included explanations such as, “It is an interesting and fairly light duty activity”, “It’s a cool program!”, and “A way to contribute to science”. The most commonly indicated reason for not submitting observations among non‐reporters was getting lost in the registration process (14% of respondents). Another 14% of respondents indicated that they had collected observations but did not submit them online, indicating that more people may be engaged in understanding phenology than our estimates based on data submitted suggest. Survey participants’ suggestions for improving the program fell into several categories, including the need for a more expansive list of plants from which to pick, the ability to monitor animals, and more information on the plants, including photographs of the various phenophases to aid in identification. Participants also requested increased contact from the USA‐NPN, in the form of weekly or monthly emails or newsletters and reminders to collect and submit observations. Many of these suggestions are either already being addressed in changes being made to the monitoring system and online entry system or are planned for the future.

USA-NPN Technical Series↗

Status of Shortnose Sturgeon in the Potomac River. Part 1: Field Studies

Field studies during more than 3 years (March 2004–July 2007) collected data on life history of Potomac River shortnose sturgeon Acipenser brevirostrum to understand their biological status in the river. We sampled intensively for adults using gill nets, but captured only one adult in 2005. Another adult was captured in 2006 by a commercial fisher. Both fish were females with excellent body and fin condition, both had mature eggs, and both were telemetrytagged to track their movements. The lack of capturing adults, even when intensive netting was guided by movements of tracked fish, indicated abundance of the species was less than in any river known with a sustaining population of the species. Telemetry tracking of the two females (one during September 2005–July 2007, one during March 2006–February 2007) found they remained in the river for all the year, not for just a few months like sturgeons on a coastal migration. Further, one fish used the same freshwater reach during three summers. The two sturgeons used different reaches during some seasons, with one fish using saline water more than the other. The adults homed to small reaches in the same month each year, like shortnose sturgeon in their natal river. The total reach used by tracked sturgeons was 124 km (rkm 63–187), of which the lowermost 78 km, which was used for summering and wintering, contained the freshwater: saltwater interface. The most upstream reach used (rkm 185–187) contained potential spawning habitat. This reach was visited by one female on a pre-spawning migration in April 2006, but spawning was likely unsuccessful. Water quality (dissolved oxygen and temperature) in the summering–wintering reach was adequate all the year, although during the summer it was minimally acceptable. We periodically recaptured the same tagged female and found she healed well after tagging, appeared healthy in body and fins, grew well, and rapidly matured a new clutch of eggs. All surveys indicated adults had sufficient habitat and water quality needed to complete their life history. While we studied only two adults, all data strongly suggests shortnose sturgeons are a permanent resident of the Potomac River diadromous fish community. Life-history movements of the Potomac River adults were similar to adults in northcentral rivers, like the Delaware River, not to adults in southern rivers. We did not identify a unique life history behavior that separated Potomac River adults from other populations. Life history data indicates Potomac River shortnose sturgeons are most likely remnants of the natal population or colonizers from a north-central river, like the Delaware River.

Report↗

Search without Boundaries Using Simple APIs

The U.S. Geological Survey (USGS) Library, where the author serves as the digital services librarian, is increasingly challenged to make it easier for users to find information from many heterogeneous information sources. Information is scattered throughout different software applications (i.e., library catalog, federated search engine, link resolver, and vendor websites), and each specializes in one thing. How could the library integrate the functionalities of one application with another and provide a single point of entry for users to search across? To improve the user experience, the library launched an effort to integrate the federated search engine into the library's intranet website. The result is a simple search box that leverages the federated search engine's built-in application programming interfaces (APIs). In this article, the author describes how this project demonstrated the power of APIs and their potential to be used by other enterprise search portals inside or outside of the library.

Computers in Libraries↗

USGS Nonindigenous Aquatic Species database with a focus on the introduced fishes of the lower Tennessee and Cumberland drainages

The Nonindigenous Aquatic Species (NAS) database (http://nas.er.usgs.gov) functions as a national repository and clearinghouse for occurrence data for introduced species within the United States. Included is locality information on over 1,100 species of vertebrates, invertebrates, and vascular plants introduced as early as 1850. Taxa include foreign (exotic) species and species native to North America that have been transported outside of their natural range. Locality data are obtained from published and unpublished literature, state, federal and local monitoring programs, museum accessions, on-line databases, websites, professional communications and on-line reporting forms. The NAS web site provides immediate access to new occurrence records through a real-time interface with the NAS database. Visitors to the web site are presented with a set of pre-defined queries that generate lists of species according to state or hydrologic basin of interest. Fact sheets, distribution maps, and information on new occurrences are updated as new records and information become available. The NAS database allows resource managers to learn of new introductions reported in their region or nearby regions, improving response time. Conversely, managers are encouraged to report their observations of new occurrences to the NAS database so information can be disseminated to other managers, researchers, and the public. In May 2004, the NAS database incorporated an Alert System to notify registered users of new introductions as part of a national early detection/rapid response system. Users can register to receive alerts based on geographic or taxonomic criteria. The NAS database was used to identify 23 fish species introduced into the lower Tennessee and Cumberland drainages. Most of these are sport fish stocked to support fisheries, but the list also includes accidental and illegal introductions such as Asian Carps, clupeids, various species popular in the aquarium trade, and Atlantic Needlefish ( Strongylura marina ) that was introduced via the newly-constructed Tennessee-Tombigbee Canal.

Cumberland River;Tennessee River↗

Water resources in the Everglades

Aerial photography is playing an important role in the evaluation of the water resources of the almost-inaccessible 1,400 square miles of Everglades in southern Florida. Color, infrared, and panchromatic photographs show salient features that permit evaluation of the overall water resources picture. The fresh water-salt water interface, drainage patterns, ecologic changes resulting from flood and drought, quantities of flow, and other hydrologic features are easily observed or measured from the photographs. Such data permit areal extension of very limited point observations of water resources data, and will assist in providing the necessary guidelines for decisions in water management in the Everglades.

Florida↗

SToRM: A Model for Unsteady Surface Hydraulics Over Complex Terrain

A two-dimensional (depth-averaged) finite volume Godunov-type shallow water model developed for flow over complex topography is presented. The model is based on an unstructured cellcentered finite volume formulation and a nonlinear strong stability preserving Runge-Kutta time stepping scheme. The numerical discretization is founded on the classical and well established shallow water equations in hyperbolic conservative form, but the convective fluxes are calculated using auto-switching Riemann and diffusive numerical fluxes. The model’s implementation within a graphical user interface is discussed. Field application of the model is illustrated by utilizing it to estimate peak flow discharges in a flooding event of historic significance in Colorado, U.S.A., in 2013.

Conference Paper↗

User Manual for SAHM package for VisTrails

The Software for Assisted Habitat I\•1odeling (SAHM) has been created to both expedite habitat modeling and help maintain a record of the various input data, pre-and post-processing steps and modeling options incorporated in the construction of a species distribution model. The four main advantages to using the combined VisTrail: SAHM package for species distribution modeling are: 1. formalization and tractable recording of the entire modeling process 2. easier collaboration through a common modeling framework 3. a user-friendly graphical interface to manage file input, model runs, and output 4. extensibility to incorporate future and additional modeling routines and tools. This user manual provides detailed information on each module within the SAHM package, their input, output, common connections, optional arguments, and default settings. This information can also be accessed for individual modules by right clicking on the documentation button for any module in VisTrail or by right clicking on any input or output for a module and selecting view documentation. This user manual is intended to accompany the user guide which provides detailed instructions on how to install the SAHM package within VisTrails and then presents information on the use of the package.

Report↗