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USGS2002

Nitrogen in rock: Occurrences and biogeochemical implications

There is a growing interest in the role of bedrock in global nitrogen cycling and potential for increased ecosystem sensitivity to human impacts in terrains with elevated background nitrogen concentrations. Nitrogen-bearing rocks are globally distributed and comprise a potentially large pool of nitrogen in nutrient cycling that is frequently neglected because of a lack of routine analytical methods for quantification. Nitrogen in rock originates as organically bound nitrogen associated with sediment, or in thermal waters representing a mixture of sedimentary, mantle, and meteoric sources of nitrogen. Rock nitrogen concentrations range from trace levels ( <200 mg N kg −1 ) in granites to ecologically significant concentrations exceeding 1000 mg N kg -1 in some sedimentary and metasedimentary rocks. Nitrate deposits accumulated in arid and semi-arid regions are also a large potential pool. Nitrogen in rock has a potentially significant impact on localized nitrogen cycles. Elevated nitrogen concentrations in water and soil have been attributed to weathering of bedrock nitrogen. In some environments, nitrogen released from bedrock may contribute to nitrogen saturation of terrestrial ecosystems (more nitrogen available than required by biota). Nitrogen saturation results in leaching of nitrate to surface and groundwaters, and, where soils are formed from ammonium-rich bedrock, the oxidation of ammonium to nitrate may result in soil acidification, inhibiting revegetation in certain ecosystems. Collectively, studies presented in this article reveal that geologic nitrogen may be a large and reactive pool with potential for amplification of human impacts on nitrogen cycling in terrestrial and aquatic ecosystems.

Global Biogeochemical Cycles↗

USGS2021

Using heat to trace vertical water fluxes in sediment experiencing concurrent tidal pumping and groundwater discharge

Heat has been widely applied to trace groundwater‐surface water exchanges in inland environments, but it is infrequently applied in coastal sediment where head oscillations induce periodicity in water flux magnitude/direction and heat advection. This complicates interpretation of temperatures to estimate water fluxes. We investigate the convolution of thermal and hydraulic signals to assess the viability of using heat as a tracer in environments with tidal head oscillations superimposed on submarine groundwater discharge. We first generate sediment temperature and head time series for conditions ranging from no tide to mega‐tidal using a numerical model (SUTRA) forced with periodic temperature and tidal head signals. We then analyze these synthetic temperature time series using heat tracing software (VFLUX2 and 1DTempPro) to evaluate if conventional terrestrial approaches to infer fluxes from temperatures are applicable for coastal settings. We consider high‐frequency water flux variability within a tidal signal and averaged over tidal signals. Results show that VFLUX2 analytical methods reasonably estimated the mean discharge fluxes in most cases but could not reproduce the flux variability within tidal cycles. The model results further reveal that high‐frequency time series of water fluxes varying in magnitude and direction can be accurately estimated if paired temperature and hydraulic head are analyzed using numerical models (e.g. 1DTempPro) that consider both dynamic hydraulic gradients and thermal signals. These results point to the opportunity to incorporate pressure sensors within heat tracing instrumentation to better assess sub‐daily flux oscillations and associated reactive processes.

Water Resources Research↗

USGS2021

The finicky nature of earthquake shaking-triggered submarine sediment slope failures and sediment gravity flows

Since 2011, seafloor temperatures, pressures, and seismic ground motions have been measured by the seafloor cabled Dense Oceanfloor Network system for Earthquakes and Tsunamis (DONET) on the Nankai margin. These measurements, high-resolution bathymetry, and abundant contextual information make the DONET region seem ideally suited to provide constraints on seismic shaking-triggered sediment slope failures and gravity flows, particularly since numerous published studies have linked paleo- to modern earthquakes to failures and flows within the DONET. The occurrences of the local 2016 M6.0 Mie-ken and regional M7.0 Kumamoto earthquakes within and at regional distances, respectively, from the DONET data set provided an opportunity to explore this potential. We used DONET seismic recordings of the posited triggering shaking and to search for submarine slide signals and continuous temperature and pressure data to detect pulses of warm and densified water indicative of passing flows. We developed and applied a variety of analytical methods to eliminate signals generated by water column processes, while leaving slope failures and sediment gravity flow anomalies as residuals. Our explorations yielded no evidence that earthquake shaking initiated either phenomenon, which we suggest reflects the finicky nature both of the detection of and the physical processes that contribute to slope failures and flows (i.e., both require satisfying precise suites of conditions). Nonetheless, this negative result, our analyses, and the estimates of physical properties we derived for them, provide useful lessons and inputs for future studies.

Journal of Geophysical Research↗

USGS2012

Recent advances in understanding the interaction of groundwater and surface water

The most common image of the interaction of groundwater and surface water is that of the interaction of streams with a contiguous alluvial aquifer. This type of system has been the focus of study for more than 100 years, from the work of Boussinesq (1877) to the present, and stream-aquifer interaction continues to be the most common topic of papers discussing the interaction of groundwater and surface water. However, groundwater and surface water interact in a wide variety of landscapes from alpine to coastal. Within these landscapes, ground-water systems range in scale from local to regional, and the types of surface water include streams, lakes, wetlands, and oceans. Given the broad spectrum of the topic of groundwater and surface water interaction, an overview of studies of this topic could be organized according to surface water type, landscape type, scale of hydrologic systems, or field and analytical methods. All these factors are discussed, but this paper is organized according to landscape type because of the great increase in studies of the interaction of groundwater and surface water in landscapes other than riverine systems in the last 15 years. Furthermore, discussing studies by landscape type facilitates comparison of methods and results from different geologic and climatic settings. The general landscapes discussed are mountain terrane, riverine systems, coastal terrane, hummocky terrane, and karst terrane.

Reviews of Geophysics↗

USGS1998

Data from selected U.S. Geological Survey National Stream Water Quality Monitoring Networks

A nationally consistent and well-documented collection of water quality and quantity data compiled during the past 30 years for streams and rivers in the United States is now available on CD-ROM and accessible over the World Wide Web. The data include measurements from two U.S. Geological Survey (USGS) national networks for 122 physical, chemical, and biological properties of water collected at 680 monitoring stations from 1962 to 1995, quality assurance information that describes the sample collection agencies, laboratories, analytical methods, and estimates of laboratory measurement error (bias and variance), and information on selected cultural and natural characteristics of the station watersheds. The data are easily accessed via user-supplied software including Web browser, spreadsheet, and word processor, or may be queried and printed according to user-specified criteria using the supplied retrieval software on CD-ROM. The water quality data serve a variety of scientific uses including research and educational applications related to trend detection, flux estimation, investigations of the effects of the natural environment and cultural sources on water quality, and the development of statistical methods for designing efficient monitoring networks and interpreting water resources data.

Water Resources Research↗

USGS2010

Theoretical analysis of the transient pressure response from a constant flow rate hydraulic conductivity test

Incorporating a flow pump into a conventional triaxial laboratory system allows fluid to be supplied to or withdrawn from the base of a sediment sample at small and constant rates. An initial transient record of hydraulic head versus time is observed which eventually stabilizes to a constant steady state gradient across the sample; values of hydraulic conductivity can subsequently be determined from Darcy's law. In this paper, analytical methods are presented for determining values of specific storage and hydraulic conductivity from the initial transient phase of such a constant flow rate test. These methods are based on a diffusion equation involving pore pressure and are analogous to those used to describe the soil consolidation process and also to interpret aquifer properties from pumping tests. Examination of the effective stress distributions within the test specimen induced during this type of measurement shows that values of specific storage corresponding to both compression and rebound conditions can be deduced and differentiated simply by reversing the direction of fluid flow. Applicability and limitations of the methods are illustrated with analyses of recently reported flow pump test measurements conducted on a silty-clay specimen.

Water Resources Research↗

USGS2025

STREAMS guidelines: Standards for technical reporting in environmental and host-associated microbiome studies

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.

Nature Microbiology↗

USGS2017

Water quality measurements in San Francisco Bay by the U.S. Geological Survey, 1969–2015

The U.S. Geological Survey (USGS) maintains a place-based research program in San Francisco Bay (USA) that began in 1969 and continues, providing one of the longest records of water-quality measurements in a North American estuary. Constituents include salinity, temperature, light extinction coefficient, and concentrations of chlorophyll- a , dissolved oxygen, suspended particulate matter, nitrate, nitrite, ammonium, silicate, and phosphate. We describe the sampling program, analytical methods, structure of the data record, and how to access all measurements made from 1969 through 2015. We provide a summary of how these data have been used by USGS and other researchers to deepen understanding of how estuaries are structured and function differently from the river and ocean ecosystems they bridge.

California↗

USGS2021

Geochemistry and mineralogy of metallurgical slag

Slag is a waste product from the pyrometallurgical processing of natural ores or the recycling of man-made materials. This chapter provides an overview of the geochemical and mineralogical characteristics of different types of slag. A review of the analytical methods used to determine these characteristics is also provided. Ferrous slags include blast furnace, steelmaking, and ferroalloy slags; the compositions of these slags are generally dominated by Ca and Si, some with significant Al, Fe, and/or Mg. Whereas, the composition of non-ferrous slags, mostly from base-metal production, are generally dominated by Fe and Si with significant but lesser amounts of Al and Ca. As for primary mineralogical phases, olivine-group phases, spinels, and glass are common among all types of slag. Other silicates such as melilite, pyroxene, feldspars, and oxides also occur. Sulfides are more common in non-ferrous slags and metals and intermetallic compounds can be found in both base-metal and ferrous slags. Carbonates are generally exclusive of ferrous slags. The chemical composition of slag depends on the furnace feed, fluxes, fuel source, and furnace conditions and efficiency of metal extraction. The chemistry and texture of mineralogical phases found in slag reflect melt composition and cooling rates. Overall, the mineralogy and chemistry of slags will determine its fate as an environmental liability or a valuable resource.

Book chapter↗

USGS2008

Relations between and among contaminant concentrations and biomarkers in black bass (Micropterus spp.) and common carp (Cyprinus carpio) from large U.S. rivers, 1995-2004

Environmental contaminant and biomarker monitoring data from major U.S. river basins were summarized for black bass (Micropterus spp.) and common carp (Cyprinus carpio) sampled over a nine year period. Cumulative frequency distributions revealed taxon differences for many organochlorine residue concentrations, elemental contaminant concentrations, and biomarkers, but few gender differences were evident for chemical concentrations. Concentrations of dacthal, pentachloroanisole, p,p???-DDE, endosulfan sulfate, barium, cadmium, copper, manganese, lead, selenium, vanadium, and zinc were greater in carp than bass, but concentrations of mercury and magnesium were greater in bass. Gender differences were evident in bass for mercury and in carp for zinc, but the differences were small compared to taxon differences. Greater vitellogenin concentrations, 17??-estradiol concentrations, 17??-estradiol/11-ketotestosterone ratios, and percent oocyte atresia in female carp compared to female bass may be related to the sequential spawning of carp. Regression analyses indicated that as much as 78% of biomarker variation was explained by chemical contaminant concentrations. Sites grouped consistently by river basin in the chemical contaminant principal components analysis (PCA) models and were driven by mercury, magnesium, barium, mirex, and oxychlordane. PCA models for the biomarkers did not group the sites by basin for either bass or carp. Statistical analyses and data interpretation were limited by the study design. The implications of these limitations are discussed. Recommendations to be considered during the planning of future monitoring studies include the exclusion of gender- and species-specific sampling for certain chemical contaminants considering analytical methods with appropriate sensitivities; and allowing for the addition of new chemical and biological variables as methods and information needs evolve. ?? The Royal Society of Chemistry.

Journal of Environmental Monitoring↗

USGS2008

New Orleans and Hurricane Katrina. IV: Orleans East Bank (Metro) protected basin

This paper addresses damage caused by Hurricane Katrina to the main Orleans East Bank protected basin. This basin represented the heart of New Orleans, and contained the main downtown area, the historic French Quarter, the Garden District, and the sprawling Lakefront and Canal Districts. Nearly half of the loss of life during this hurricane, and a similar fraction of the overall damages, occurred in this heavily populated basin. There are a number of important geotechnical lessons, as well as geo-forensic lessons, associated with the flooding of this basin. These include the difficulties associated with the creation and operation of regional-scale flood protection systems requiring federal and local cooperation and funding over prolonged periods of time. There are also a number of engineering and policy lessons regarding (1) the accuracy and reliability of current analytical methods; (2) the shortcomings and potential dangers involved in decisions that reduced short-term capital outlays in exchange for increased risk of potential system failures; (3) the difficulties associated with integrating local issues with a flood risk reduction project; and (4) the need to design and maintain levees as systems; with each of the many individual project elements being required to mesh seamlessly. These lessons are of interest and importance for similar flood protection systems throughout numerous other regions of the United States and the world. ?? 2008 ACSE.

Journal of Geotechnical and Geoenvironmental Engin↗

USGS2022

Regional-scale liquefaction analyses

Regional-scale liquefaction hazard analyses are necessary for resilience planning and prioritization of seismic upgrades for critical distributed infrastructure such as levees, pipelines, roadways, and electrical transmission facilities. Two approaches are often considered for liquefaction hazard analysis of distributed infrastructure: (1) conventional, site-specific probe or borehole-based analyses, which do not quantify the uncertainty between investigation locations; or (2) surface geology-based analyses, which often neglect localized geotechnical properties and include a great amount of uncertainty. We describe an analytical method to unify the disparate site-specific and deposit-scale approaches using Gaussian processes. We use borehole data to produce spatial fields of random variables for liquefaction triggering analyses, such as groundwater elevation, soil texture classification, penetration resistance, and cyclic resistance ratio that converge to the site-specific uncertainty at sampling locations but also quantify the uncertainty in-between sampling locations. We demonstrate the effectiveness of Gaussian process models for regional-scale liquefaction hazard analyses in two example studies in Washington state and California, US.

Conference Paper↗

USGS2004

Tigers and their prey: Predicting carnivore densities from prey abundance

The goal of ecology is to understand interactions that determine the distribution and abundance of organisms. In principle, ecologists should be able to identify a small number of limiting resources for a species of interest, estimate densities of these resources at different locations across the landscape, and then use these estimates to predict the density of the focal species at these locations. In practice, however, development of functional relationships between abundances of species and their resources has proven extremely difficult, and examples of such predictive ability are very rare. Ecological studies of prey requirements of tigers Panthera tigris led us to develop a simple mechanistic model for predicting tiger density as a function of prey density. We tested our model using data from a landscape-scale long-term (1995-2003) field study that estimated tiger and prey densities in 11 ecologically diverse sites across India. We used field techniques and analytical methods that specifically addressed sampling and detectability, two issues that frequently present problems in macroecological studies of animal populations. Estimated densities of ungulate prey ranged between 5.3 and 63.8 animals per km 2 . Estimated tiger densities (3.2-16.8 tigers per 100 km 2 ) were reasonably consistent with model predictions. The results provide evidence of a functional relationship between abundances of large carnivores and their prey under a wide range of ecological conditions. In addition to generating important insights into carnivore ecology and conservation, the study provides a potentially useful model for the rigorous conduct of macroecological science.

Proceedings of the National Academy of Sciences↗

USGS2020

Liquid chromatographic determination of oxytetracycline in edible fish fillets from six species of fish

The approved use of oxytetracycline (OTC) in U.S. aquaculture is limited to specific diseases in salmonids and channel catfish. OTC may also be effective in controlling diseases in other fish species important to public aquaculture, but before approved use of OTC can be augmented, an analytical method for determining OTC in fillet tissue from multiple species of fish will be required to support residue depletion studies. The objective of this study was to develop and validate a liquid chromatographic (LC) method that is accurate, precise, and sensitive for OTC in edible fillets from multiple species of fish. Homogenized fillet tissues from walleye, Atlantic salmon, striped bass, white sturgeon, rainbow trout, and channel catfish were fortified with OTC at nominal concentrations of 10, 20, 100,1000, and 5000 ng/g. In tissues fortified with OTC at 100,1000, and 5000 ng/g, mean recoveries ranged from 83 to 90%, and relative standard deviations (RSDs) ranged from 0.9 to 5.8%. In all other tissues, mean recoveries ranged from 59 to 98%, and RSDs ranged from 3.3 to 20%. Method quantitation limits ranged from 6 to 22 ng/g for the 6 species. The LC parameters produced easily in teg ratable OTC peaks without coelution of endogenous compounds. The method is accurate, precise, and sensitive for OTC in fillet tissue from 6 species of fish from 5 phylogenetically diverse groups.

Journal of AOAC International↗

USGS2020

Liquid chromatographic determination of para-toluenesulfonamide in edible fillet tissues from three species of fish

Chloramine-T ( N -sodium- N -chloro- p -toluene-sulfonamide) is a candidate therapeutic drug for treating bacterial gill disease, a predominant disease of a variety of fish species. Research has been initiated to obtain the U.S. Food and Drug Administration’s (FDA) approval for the use of chloramine-T on a variety of fish species. An attribute of a therapeutic aquaculture drug that must be characterized before the FDA approves its use is depletion of the drug’s marker residue (the drug’s parent compound or metabolite of highest concentration in an edible tissue). para -Toluenesulfonamide (p-TSA) is the primary degradation product and marker residue for chloramine-T in rainbow trout. To conduct residue depletion studies for chloramine-T in fish, a robust analytical method sensitive and specific for p-TSA residues in edible fillet tissue from a variety of fish was required. Homogenized fillet tissues from rainbow trout ( Oncorhynchus mykiss ), walleye ( Stizostedion vitreum ), and channel cattish ( Ictalurus punctatus ) were fortified at nominal p-TSA concentrations of 17, 67, 200, 333, and 1000 ng/g. Samples were analyzed by isocratic reversed-phase liquid chromatography (LC) with absorbance detection at 226 nm. Mean recoveries of p-TSA ranged from 77 to 93.17%; relative standard deviations ranged from 1.5 to 14%; method quantitation limits ranged from 13 to 18 ng/g; and method detection limits ranged from 3.8 to 5.2 ng/g. The LC parameters produced p-TSA peaks without coelution of endogenous compounds and excluded chromatographic interference from at least 20 chemicals and drugs of potential use in aquaculture.

Journal of AOAC International↗

USGS2019

Determination of 3-trifluoromethyl-4-nitrophenol and 3-trifluoromethyl-4-nitrophenol glucuronide in edible fillet tissue of rainbow trout and channel catfish by solid-phase extraction and liquid chromatography

3-Trifluoromethyl-4-nitrophenol (TFM) is a pesticide used for the selective control of sea lampreys ( Petromyzon marinus ) in stream and river tributaries of the Great Lakes. To determine concentrations of TFM and TFM glucuronide in the edible fillet tissue of fish during sea lamprey control treatments, an analytical method was developed to determine the concentrations of these residues in rainbow trout ( Oncorhynchus mykiss ; RBT) and channel catfish ( Ictalurus punctatis ; CCF). Homogenized fillets were extracted with methanol–water (80 + 20). TFM and TFM glucuronide were isolated from coextractives by C 18 solid-phase extraction. TFM glucuronide was hydrolyzed to TFM by the addition of β-glucuronidase to the TFM glucuronide extract. The extracts were analyzed separately by liquid chromatography with UV–visible detection. Recoveries from TFM-fortified CCF and RBT tissues were 84.1 and 96.1%, respectively. The method detection limits (MDLs) are 2.4 ng/g for TFM-fortified tissues of CCF and 3 ng/g for those of RBT. Recoveries were 78.8 and 77%from TFM glucuronide-fortified CCF and RBT tissues, respectively. The MDLs for TFM glucuronide-fortified tissues are 3.5 and 6.9 ng/g for CCF and RBT, respectively.

Journal of AOAC International↗

USGS2019

Case studies in groundwater contaminant fate and transport

A case study of groundwater contamination is a detailed study of a single site contaminated with a chemical or mixture that is known to be a problem at many sites. The goal of case studies is to provide insights into the physical, chemical, and biological processes controlling migration, natural attenuation, or remediation of common groundwater contaminants. Ideally, processes occurring at a case study site are representative of other sites so that knowledge gained from these intensive studies can be applied at thousands of sites where fewer data are available. Several characteristics of case studies contribute to their value. First, they may have tens to hundreds of monitoring wells, compared to fewer than ten wells at some contaminated sites. Second, some case studies continue for many years or even decades, providing insights into temporal progression of slow processes. Third, analytical methods prohibitively expensive for routine use or under development may be tested at case study sites. Finally, the ongoing characterization typical of case study sites builds a foundation of knowledge that facilitates sophisticated experimental design and testing of new methods. This article is divided into sections based on the contaminant type because the chemical and biological processes required for remediation vary for each contaminant. Most importantly, some contaminants can be biodegraded whereas metals and radionuclides cannot be destroyed but can be immobilized or rendered less toxic. The emphasis is on case studies of natural processes that control the fate and transport of contaminants in groundwater rather than on active remediation methods. The principles learned from these studies may form the basis for design of remedial strategies. The organic contaminants are divided into: petroleum hydrocarbons, fuel oxygenates, coal tar and wastes from manufactured gas plants, and chlorinated solvents. The inorganic contaminants covered are metals and radionuclides, arsenic, and nitrate. Case studies of mixed waste plumes from landfills are also described. Experimental sites where contaminants have been introduced into an aquifer as an emplaced source or a controlled release may not meet the above definition of case studies, but some are included because the overall goal is to impart lessons learned from detailed field studies. It is impossible to cover all case studies in this short format. Conversely, focusing on one or two does not convey the breadth of research results in entire range of case studies. Instead, the strategy is to describe the evolution of knowledge for each contaminant class while providing citations of relevant case studies. Much of the progress in understanding of the fate of contaminants in groundwater is based on laboratory studies; thus whenever possible, papers that included both field and laboratory results have been included among the citations. Two topics of growing importance have not been covered. These are the fate of pharmaceuticals in groundwater and discharge of contaminant plumes to surface water. These topics merit coverage in the future as knowledge grows and case studies increase in number.

Environmental Science↗

USGS2019

Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate

The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent lizard radiation and combine a summary-coalescent species tree based on 1225 exons with a probabilistic model that links dispersal capacity to an evolving trait, to investigate whether ecological specialization has influenced the probability of trans-oceanic dispersal. Cryptoblepharus species that occur in coastal habitats have on average dispersed 13 to 14 times more frequently than non-coastal species and coastal specialization has, therefore, led to an extraordinarily widespread distribution that includes multiple continents and distant island archipelagoes. Furthermore, their presence across the Pacific substantially predates the age of human colonization and we can explicitly reject the possibility that these patterns are solely shaped by human-mediated dispersal. Overall, by combining new analytical methods with a comprehensive phylogenomic dataset, we use a quantitative framework to show how coastal specialization can influence dispersal capacity and eventually shape geographical distributions at a macroevolutionary scale.

Proceedings of the Royal Society B: Biological Sci↗