U.S. Geological Survey View Institution's Website 10 articles published in JoVE Environment In Situ Soil Moisture Sensors in Undisturbed Soils Todd G. Caldwell1, Michael H. Cosh2, Steven R. Evett3, Nathan Edwards4, Heather Hofman5, Bradley G. Illston6, Tilden Meyers7, Marina Skumanich8, Kent Sutcliffe9 1Nevada Water Science Center, U.S. Geological Survey, 2Agricultural Research Service, Hydrology and Remote Sensing Lab., U.S. Department of Agriculture, 3Agricultural Research Service, Conservation and Production Research Lab., U.S. Department of Agriculture, 4South Dakota State University, 5National Water and Climate Center, U.S. Department of Agriculture, 6University of Oklahoma, 7Air Resources Lab, National Oceanic and Atmospheric Administration, 8National Integrated Drought Information System, National Oceanic and Atmospheric Administration, 9Snow Survey Staff, U.S. Department of Agriculture The determination of soil water content is a critical mission requirement for many state and federal agencies. This protocol synthesizes multi-agency efforts to measure soil water content using buried in situ sensors. Environment Manufacturing Simple and Inexpensive Soil Surface Temperature and Gravimetric Water Content Sensors Armin Howell1, Colin Tucker1, Edmund E. Grote1, Maik Veste2,3, Jayne Belnap1, Gerhard Kast4, Bettina Weber5,6, Sasha C. Reed1 1Southwest Biological Science Center, U.S. Geological Survey, 2Centre for Energy Technology Brandenburg, 3Institute of Environmental Sciences, Brandenburg University of Technology Cottbus-Senftenberg, 4Umweltanalytische Produkte GmbH, 5Institute of Plant Sciences, University of Graz, 6Multiphase Chemistry Department, Max Planck Institute for Chemistry Accurately measuring temperature and water content of the upper 5 mm of the soil surface can improve our understanding of environmental controls on biological, chemical, and physical processes. Here we describe a protocol for manufacturing, calibrating, and conducting measurements with soil surface temperature and moisture sensors. Environment Construction of a Compact Low-Cost Radiation Shield for Air-Temperature Sensors in Ecological Field Studies Adam J. Terando1,2, Sara G. Prado2, Elsa Youngsteadt3 1U.S. Geological Survey, Southeast Climate Adaptation Science Center, 2Department of Applied Ecology, NC State University, 3Department of Entomology and Plant Pathology, NC State University With the advent of small, low-cost environmental sensors, it is now possible to deploy high-density networks of sensors to measure hyper localized temperature variation. Here, we provide a detailed methodology for constructing a compact version of a previously described custom-fabricated radiation shield for use with inexpensive thermochrons. Environment Necropsy-based Wild Fish Health Assessment Vicki S. Blazer1, Heather L. Walsh2, Ryan P. Braham1, Cheyenne Smith2 1National Fish Health Research Laboratory, Leetown Science Center, U.S. Geological Survey, 2School of Natural Resources, West Virginia University The health of wild fishes can be used as an indicator of aquatic ecosystem health. Necropsy-based fish health assessments provide documentation of visible lesions or abnormalities, data used to calculate condition indices as well as the opportunity to collect tissues for microscopic evaluation, gene expression and other more in-depth analyses. Environment Methods of Soil Resampling to Monitor Changes in the Chemical Concentrations of Forest Soils Gregory B. Lawrence1, Ivan J. Fernandez2, Paul W. Hazlett3, Scott W. Bailey4, Donald S. Ross5, Thomas R. Villars6, Angelica Quintana7, Rock Ouimet8, Michael R. McHale1, Chris E. Johnson9, Russell D. Briggs10, Robert A. Colter11, Jason Siemion1, Olivia L. Bartlett12, Olga Vargas13, Michael R. Antidormi1, Mary M. Koppers9 1New York Water Science Center, U.S. Geological Survey, 2School of Forest Resources, University of Maine, 3Natural Resources Canada, Canadian Forest Service, 4Northern Research Station, U.S. Forest Service, 5Department of Plant and Soil Science, University of Vermont, 6Ottauquechee NRCD, USDA Natural Resources Conservation Service, 7Green Mountain National Forest, U.S. Forest Service, 8Direction de la Recherche Forestière, Ministère du Québec, 9Department of Civil and Environmental Engineering, Syracuse University, 10Division of Environmental Science, SUNY College of Environmental Science and Forestry, 11White Mountain National Forest, U.S. Forest Service, 12Natural Resources and Earth System Sciences, University of New Hampshire, 13Greenwich, NY Field Office, USDA Natural Resources Conservation Service Repeated soil sampling has recently been shown to be an effective way to monitor forest soil change over years and decades. To support its use, a protocol is presented that synthesizes the latest information on soil resampling methods to aid in the design and implementation of successful soil monitoring programs. Environment Integrating Remote Sensing with Species Distribution Models; Mapping Tamarisk Invasions Using the Software for Assisted Habitat Modeling (SAHM) Amanda M. West1, Paul H. Evangelista1, Catherine S. Jarnevich2, Nicholas E. Young1, Thomas J. Stohlgren1, Colin Talbert2, Marian Talbert3, Jeffrey Morisette3, Ryan Anderson1 1Natural Resource Ecology Laboratory, Colorado State University, 2U.S. Geological Survey, Fort Collins Science Center, 3U.S. Geological Survey - U.S. Department of the Interior, North Central Climate Science Center We demonstrate the utility of remotely sensed data and the newly developed Software for Assisted Habitat Modeling (SAHM) in predicting invasive species occurrence on the landscape. An ensemble of predictive models produced highly accurate maps of tamarisk (Tamarix spp.) invasion in Southeastern Colorado, USA when assessed with subsequent field validations. Environment Laboratory Estimation of Net Trophic Transfer Efficiencies of PCB Congeners to Lake Trout (Salvelinus namaycush) from Its Prey Charles P. Madenjian1, Richard R. Rediske2, James P. O'Keefe2, Solomon R. David3 1Great Lakes Science Center, U. S. Geological Survey, 2Annis Water Resources Institute, Grand Valley State University, 3Daniel P. Haerther Center for Conservation and Research, Shedd Aquarium A technique for laboratory estimation of net trophic transfer efficiency of polychlorinated biphenyl (PCB) congeners to piscivorous fish from their prey is presented. To maximize applicability of the laboratory results to the field, the piscivorous fish should be fed prey fish that are typically eaten in the field. Biology A New Clarification Method to Visualize Biliary Degeneration During Liver Metamorphosis in Sea Lamprey (Petromyzon marinus) Yu-Wen Chung-Davidson1, Peter J. Davidson1, Anne M. Scott1, Erin J. Walaszczyk1, Cory O. Brant1, Tyler Buchinger1, Nicholas S. Johnson2, Weiming Li1 1Department of Fisheries & Wildlife, Michigan State University, 2Hammond Bay Biological Station, Great Lakes Science Center, U.S. Geological Survey Sea lamprey lose the gall bladder and bile ducts during metamorphosis, a process similar to human biliary atresia. A new fixation and clarification method (CLARITY) was modified to visualize the entire biliary tree using laser scanning confocal microscopy. This method provides a powerful tool to study biliary degeneration. Immunology and Infection Glass Wool Filters for Concentrating Waterborne Viruses and Agricultural Zoonotic Pathogens Hana T. Millen1, Jordan C. Gonnering1, Ryan K. Berg2, Susan K. Spencer3, William E. Jokela3, John M. Pearce4, Jackson S. Borchardt1, Mark A. Borchardt3 1Wisconsin Water Science Center, United States Geological Survey, 2University of Wisconsin – Madison, 3Agricultural Research Service, United States Department of Agriculture, 4Alaska Science Center, United States Geological Survey Glass wool filters have been used to concentrate waterborne viruses by a number of research groups around the world. Here we show a simple approach for constructing glass wool filters and demonstrate the filters are also effective in concentrating waterborne viral, bacterial and protozoan pathogens. Immunology and Infection Rapid Diagnosis of Avian Influenza Virus in Wild Birds: Use of a Portable rRT-PCR and Freeze-dried Reagents in the Field John Y. Takekawa1, Nichola J. Hill1,2, Annie K. Schultz1, Samuel A. Iverson1, Carol J. Cardona3,4, Walter M. Boyce2, Joseph P. Dudley5 1USGS Western Ecological Research Center, 2Wildlife Health Center, University of California, Davis, 3Department of Population Health and Reproduction, University of California, Davis, 4Department of Veterinary and Biomedical Sciences, University of Minnesota, 5Science Applications International Corporation This study describes diagnosis of avian influenza in wild birds using a portable rRT-PCR system. The method takes advantage of freeze-dried reagents to screen wild birds in a non-laboratory setting, typical of an outbreak scenario. Use of molecular tools provides accurate and sensitive alternatives for rapid diagnosis.