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USGS2003

Modeling radium and radon transport through soil and vegetation

A one-dimensional flow and transport model was developed to describe the movement of two fluid phases, gas and water, within a porous medium and the transport of 226Ra and 222Rn within and between these two phases. Included in this model is the vegetative uptake of water and aqueous 226Ra and 222Rn that can be extracted from the soil via the transpiration stream. The mathematical model is formulated through a set of phase balance equations and a set of species balance equations. Mass exchange, sink terms and the dependence of physical properties upon phase composition couple the two sets of equations. Numerical solution of each set, with iteration between the sets, is carried out leading to a set-iterative compositional model. The Petrov-Galerkin finite element approach is used to allow for upstream weighting if required for a given simulation. Mass lumping improves solution convergence and stability behavior. The resulting numerical model was applied to four problems and was found to produce accurate, mass conservative solutions when compared to published experimental and numerical results and theoretical column experiments. Preliminary results suggest that the model can be used as an investigative tool to determine the feasibility of phytoremediating radium and radon-contaminated soil. ?? 2003 Elsevier Science B.V. All rights reserved.

Journal of Contaminant Hydrology↗

USGS2020

A weight-of-evidence approach for defining thermal sensitivity in a federally endangered species

1. Managing for threatened and endangered species under changing environmental conditions is a challenge faced by resource managers worldwide. Lack of basic knowledge of the biology and habitat requirements of these species can contribute to this difficulty, but is confounded by the limitations of working with rare (i.e. few individuals) species or unrefined methods for evaluating stress. 2. A weight of evidence approach was used to evaluate the thermal biology of the federally endangered dwarf wedgemussel ( Alasmidonta heterodon ), utilizing cumulative results from multiple experimental assessments, co-occurring species, and their host fish to begin defining thermal limits and optimal conditions for the species. 3. Results suggest that dwarf wedgemussel and its host fish are thermally sensitive species compared to other Atlantic-slope mussels, with lower critical thermal maximum and selection of reduced temperatures during choice experiments. 4. Physiological studies resulted in lack of statistical significance primarily due to low power which was a function of sample size, one unavoidable problem when studying rare species. Given these limitations, thermal choice and CTM may be more useful endpoints than physiological processes such as clearance and respiration rates when dealing with sample size limitations. 5. These results suggest that management strategies that avoid exposing dwarf wedgemussel and its thermally sensitive host fish to extreme temperatures could be important for species conservation.

New Jersey, Pennsylvania↗

USGS2013

Chemical and biological consequences of using carbon dioxide versus acid additions in ocean acidification experiments

Use of different approaches for manipulating seawater chemistry during ocean acidification experiments has confounded comparison of results from various experimental studies. Some of these discrepancies have been attributed to whether addition of acid (such as hydrochloric acid, HCl) or carbon dioxide (CO 2 ) gas has been used to adjust carbonate system parameters. Experimental simulations of carbonate system parameter scenarios for the years 1766, 2007, and 2100 were performed using the carbonate speciation program CO2SYS to demonstrate the variation in seawater chemistry that can result from use of these approaches. Results showed that carbonate system parameters were 3 percent and 8 percent lower than target values in closed-system acid additions, and 1 percent and 5 percent higher in closed-system CO 2 additions for the 2007 and 2100 simulations, respectively. Open-system simulations showed that carbonate system parameters can deviate by up to 52 percent to 70 percent from target values in both acid addition and CO 2 addition experiments. Results from simulations for the year 2100 were applied to empirically derived equations that relate biogenic calcification to carbonate system parameters for calcifying marine organisms including coccolithophores, corals, and foraminifera. Calculated calcification rates for coccolithophores, corals, and foraminifera differed from rates at target conditions by 0.5 percent to 2.5 percent in closed-system CO 2 gas additions, from 0.8 percent to 15 percent in the closed-system acid additions, from 4.8 percent to 94 percent in open-system acid additions, and from 7 percent to 142 percent in open-system CO 2 additions.

Scientific Investigations Report↗

USGS2019

On the shoulders of giants: Continuing the legacy of large-scale ecosystem manipulation experiments in Puerto Rico

There is a long history of experimental research in the Luquillo Experimental Forest in Puerto Rico. These experiments have addressed questions about biotic thresholds, assessed why communities vary along natural gradients, and have explored forest responses to a range of both anthropogenic and non-anthropogenic disturbances. Combined, these studies cover many of the major disturbances that affect tropical forests around the world and span a wide range of topics, including the effects of forest thinning, ionizing radiation, hurricane disturbance, nitrogen deposition, drought, and global warming. These invaluable studies have greatly enhanced our understanding of tropical forest function under different disturbance regimes and informed the development of management strategies. Here we summarize the major field experiments that have occurred within the Luquillo Experimental Forest. Taken together, results from the major experiments conducted in the Luquillo Experimental Forest demonstrate a high resilience of Puerto Rico’s tropical forests to a variety of stressors.

Luquillo Experimental Forest↗

USGS1983

Use of digital land-cover data from the Landsat satellite in estimating streamflow characteristics in the Cumberland Plateau of Tennessee

Characteristics of Streamflow at ungaged sites in coal-mining areas of the Cumberland Plateau may be estimated with regression equations that relate streamflow characteristics to the physiographic and climatic characteristics of the corresponding drainage basins. An experiment was performed to compare the accuracy of equations using basin characteristics derived from maps and climatological records (control group equations) with the accuracy of equations using basin characteristics derived from digital processing of Landsat spectral data as well as maps and climatological records (experimental group equations). Results of this experiment show that (with the exception of low flows and four of six annual peak logarithms) drainage area can explain more than 90 percent of the variance in all streamflow characteristics in both groups of equations. Seventeen of 39 experimental group equations that have two basin characteristics each are different from the corresponding control group equations. Five of the 17 differing experimental group equations have no counterpart in the control group because of lack of significance in control group basin characteristics, seven are slightly more accurate, and five are not measurably different in accuracy. When the equations in both groups are arranged into six flow categories, there is no substantial difference in accuracy between equations using basin characteristics derived from maps and climatological records (control group) and equations using basin characteristics derived from Landsat tapes as well as maps and climatological records (experimental group) for this particular study area, the Cumberland Plateau of Tennessee.

Tennessee↗

USGS2017

Carrying capacity in a heterogeneous environment with habitat connectivity

A large body of theory predicts that populations diffusing in heterogeneous environments reach higher total size than if non-diffusing, and, paradoxically, higher size than in a corresponding homogeneous environment. However, this theory and its assumptions have not been rigorously tested. Here, we extended previous theory to include exploitable resources, proving qualitatively novel results, which we tested experimentally using spatially diffusing laboratory populations of yeast. Consistent with previous theory, we predicted and experimentally observed that spatial diffusion increased total equilibrium population abundance in heterogeneous environments, with the effect size depending on the relationship between r and K . Refuting previous theory, however, we discovered that homogeneously distributed resources support higher total carrying capacity than heterogeneously distributed resources, even with species diffusion. Our results provide rigorous experimental tests of new and old theory, demonstrating how the traditional notion of carrying capacity is ambiguous for populations diffusing in spatially heterogeneous environments.

Ecology Letters↗

USGS2009

Constructing constitutive relationships for seismic and aseismic fault slip

For the purpose of modeling natural fault slip, a useful result from an experimental fault mechanics study would be a physically-based constitutive relation that well characterizes all the relevant observations. This report describes an approach for constructing such equations. Where possible the construction intends to identify or, at least, attribute physical processes and contact scale physics to the observations such that the resulting relations can be extrapolated in conditions and scale between the laboratory and the Earth. The approach is developed as an alternative but is based on Ruina (1983) and is illustrated initially by constructing a couple of relations from that study. In addition, two example constitutive relationships are constructed; these describe laboratory observations not well-modeled by Ruina's equations: the unexpected shear-induced weakening of silica-rich rocks at high slip speed (Goldsby and Tullis, 2002) and fault strength in the brittle ductile transition zone (Shimamoto, 1986). The examples, provided as illustration, may also be useful for quantitative modeling.

Pure and Applied Geophysics↗

USGS2006

Comparative evaluation of short-term leach tests for heavy metal release from mineral processing waste

Evaluation of metal leaching using a single leach test such as the Toxicity Characteristic Leaching Procedure (TCLP) is often questionable. The pH, redox potential (Eh), particle size and contact time are critical variables in controlling metal stability, not accounted for in the TCLP. This paper compares the leaching behavior of metals in mineral processing waste via short-term extraction tests such as TCLP, Field Leach Test (FLT) used by USGS and deionized water extraction tests. Variation in the extracted amounts was attributed to the use of different particle sizes, extraction fluid and contact time. In the controlled pH experiments, maximum metal extraction was obtained at acidic pH for cationic heavy metals such as Cu, Pb and Zn, while desorption of Se from the waste resulted in high extract concentrations in the alkaline region. Precipitation of iron, caused by a pH increase, probably resulted in co-precipitation and immobilization of Cu, Pb and Zn in the alkaline pH region. A sequential extraction procedure was performed on the original waste and the solid residue from the Eh-pH experiments to determine the chemical speciation and distribution of the heavy metals. In the as-received waste, Cu existed predominantly in water soluble or sulfidic phases, with no binding to carbonates or iron oxides. Similar characteristics were observed for Pb and Zn, while Se existed mostly associated with iron oxides or sulfides. Adsorption/co-precipitation of Cu, Se and Pb on precipitated iron hydroxides was observed in the experimental solid residues, resulting in metal immobilization above pH 7.

Science of the Total Environment↗

USGS2000

Relation of waterfowl poisoning to sediment lead concentrations in the Coeur d'Alene River Basin

For many years, waterfowl have been poisoned by lead after ingesting contaminated sediment in the Coeur d'Alene River Basin, in Idaho. Results of studies on waterfowl experimentally fed this sediment were combined with results from field studies conducted in the Basin to relate sediment lead concentration to injury to waterfowl. The first step in the model estimated exposure as the relation of sediment lead concentration to blood lead concentration in mute swans ( Cygnus olor ), ingesting 22% sediment in a rice diet. That rate corresponded to the 90th percentile of sediment ingestion estimated from analyses of feces of tundra swans ( Olor columbianus ) in the Basin. Then, with additional laboratory studies on Canada geese ( Branta canadensis ) and mallards ( Anas platyrhynchos ) fed the sediment, we developed the general relation of blood lead to injury in waterfowl. Injury was quantified by blood lead concentrations, ALAD (δ-aminolevulinic acid dehydratase) activity, protoporphyrin concentrations, hemoglobin concentrations, hepatic lead concentrations, and the prevalence of renal nuclear inclusion bodies. Putting the exposure and injury relations together provided a powerful tool for assessing hazards to wildlife in the Basin. The no effect concentration of sediment lead was estimated as 24 mg/kg and the lowest effect level as 530 mg/kg. By combining our exposure equation with data on blood lead concentrations measured in moribund tundra swans in the Basin, we estimated that some mortality would occur at a sediment lead concentration as low as 1800 mg/kg.

Idaho↗

USGS2016

Larval aquatic insect responses to cadmium and zinc in experimental streams

To evaluate the risks of metal mixture effects to natural stream communities under ecologically relevant conditions, the authors conducted 30-d tests with benthic macroinvertebrates exposed to cadmium (Cd) and zinc (Zn) in experimental streams. The simultaneous exposures were with Cd and Zn singly and with Cd+Zn mixtures at environmentally relevant ratios. The tests produced concentration–response patterns that for individual taxa were interpreted in the same manner as classic single-species toxicity tests and for community metrics such as taxa richness and mayfly (Ephemeroptera) abundance were interpreted in the same manner as with stream survey data. Effect concentrations from the experimental stream exposures were usually 2 to 3 orders of magnitude lower than those from classic single-species tests. Relative to a response addition model, which assumes that the joint toxicity of the mixtures can be predicted from the product of their responses to individual toxicants, the Cd+Zn mixtures generally showed slightly less than additive toxicity. The authors applied a modeling approach called Tox to explore the mixture toxicity results and to relate the experimental stream results to field data. The approach predicts the accumulation of toxicants (hydrogen, Cd, and Zn) on organisms using a 2-p K a bidentate model that defines interactions between dissolved cations and biological receptors (biotic ligands) and relates that accumulation through a logistic equation to biological response. The Tox modeling was able to predict Cd+Zn mixture responses from the single-metal exposures as well as responses from field data. The similarity of response patterns between the 30-d experimental stream tests and field data supports the environmental relevance of testing aquatic insects in experimental streams.

Environmental Toxicology and Chemistry↗

USGS2015

Amphibole reaction rims as a record of pre-eruptive magmatic heating: An experimental approach

Magmatic minerals record the pre-eruptive timescales of magma ascent and mixing in crustal reservoirs and conduits. Investigations of the mineral records of magmatic processes are fundamental to our understanding of what controls eruption style, as ascent rates and magma mixing processes are well known to control and/or trigger potentially hazardous explosive eruptions. Thus, amphibole reaction rims are often used to infer pre-eruptive magma dynamics, and in particular to estimate magma ascent rates. However, while several experimental studies have investigated amphibole destabilization during decompression, only two investigated thermal destabilization relevant to magma mixing processes. This study examines amphibole decomposition experimentally through isobaric heating of magnesio-hornblende phenocrysts within a natural high-silica andesite glass. The experiments first equilibrated for 24 h at 870 °C and 140 MPa at H 2 O-saturated conditions and ƒO 2 ∼ Re–ReO prior to rapid heating to 880, 900, or 920 °C and hold times of 3–48 h. At 920 °C, rim thicknesses increased from 17 μm after 3 h, to 55 μm after 12 h, and became pseudomorphs after longer durations. At 900 °C, rim thicknesses increased from 7 μm after 3 h, to 80 μm after 24 h, to pseudomorphs after longer durations. At 880 °C, rim thicknesses increased from 7 μm after 3 h, to 18 μm after 36 h, to pseudomorphs after 48 h. Reaction rim microlites vary from 5–16 μm in size, with no systematic relationship between crystal size and the duration or magnitude of heating. Time-averaged rim microlite growth rates decrease steadily with increasing experimental duration (from to 3.1 to ). Time-averaged microlite nucleation rates also decrease with increasing experimental duration (from to 5.3 mm −3 s −1 ). There is no systematic relationship between time-averaged growth or nucleation rates and the magnitude of the heating step. Ortho- and clinopyroxene together constitute 57–90 modal % mineralogy in each reaction rim. At constant temperature, clinopyroxene abundances decrease with increasing experimental duration, from 72 modal % (3 h at 900 °C) to 0% (48 h at 880 °C, and 36 h at 900 and 920 °C). Fe–Ti oxides increase from 6–12 modal % (after 3–6 h) to 26–34 modal % (after 36–48 h). Plagioclase occurs in relatively minor amounts (<1–11 modal %), with anorthite contents that increase from An56 to An88 from 3 to 36 h of heating. Distal glass compositions (>500 μm from reacted amphibole) are consistent with inter-microlite rim glasses (71.3–77.7 wt.% SiO 2 ) within a given experiment and there is a weakly positive correlation between increasing run duration and inter-microlite melt SiO 2 (68.9–78.5 wt.%). Our results indicate that experimental heating-induced amphibole reaction rims have thicknesses, textures, and mineralogies consistent with many of the natural reaction rims seen at arc-andesite volcanoes. They are also texturally consistent with experimental decompression reaction rims. On this basis it may be challenging to distinguish between decompression and heating mechanisms in nature.

Earth and Planetary Science Letters↗

USGS2015

Compound-specific sulfur isotope analysis of thiadiamondoids of oils from the Smackover Formation, USA

Thiadiamondoids (TDs) are diamond-like compounds with a sulfide bond located within the cage structure. These compounds were suggested as a molecular proxy for the occurrence and extent of thermochemical sulfate reduction (TSR). Compound-specific sulfur-isotope analysis of TDs may create a multi-parameter system, based on molecular and δ34S values that may be sensitive over a wider range of TSR and thermal maturation stages. In this study, we analyzed a suite of 12 Upper Jurassic oil and condensate samples generated from source rocks in the Smackover Formation to perform a systematic study of the sulfur isotope distribution in thiadiamondoids (one and two cages). For comparison we measured the δ34S composition of benzothiophenes (BTs) and dibenzothiophenes (DBTs). We also conducted pyrolysis experiments with petroleum and model compounds to have an insight into the formation mechanisms of TDs. The δ34S of the TDs varied significantly (ca 30&permil;) between the different oils depending on the degree of TSR alteration. The results showed that within the same oil, the one-cage TDs were relatively uniform, with 34S enriched values similar to those of the coexisting BTs. The two-cage TDs had more variable δ34S values that range from the δ34S values of BTs to those of the DBTs, but with general 34S depletion relative to one cage TDs. Hydrous pyrolysis experiments (360 °C, 40 h) with either CaSO4 or elemental S (equivalent S molar concentrations) and adamantane as a model compound demonstrate the formation of one cage TDs in relatively low yields (<0.2%). Higher concentrations of TDs were observed in the elemental sulfur experiments, most likely because of the higher rates of reaction with adamantane under these experimental conditions. These results show that the formation of TDs is not exclusive to TSR reactions, and that they can also form by reaction with reduced S species apart from sulfate reduction, though at low yields. Oxygenated compounds, most notably 2-thiaadamantanone and phenol, were also formed during these pyrolysis experiments. This may represent the first stage in the formation of sulfurized compounds and the oxidation of organic matter under TSR conditions. Pyrolysis experiments with elemental S and a TD-enriched oil showed that the δ34S values of the TDs did not change, whereas the BTs did change significantly. It is therefore concluded that TDs do not exchange S atoms with coexisting inorganic reduced sulfur species. They can only change their δ34S values via addition of newly generated TDs that form predominantly during TSR. We therefore suggest that TDs will preserve their δ34S values even under high-temperature reservoir conditions and will reflect the original sulfates δ34S value. The combination of TDs, BTs, and DBTs δ34S values and concentrations allowed for a more reliable detection of the occurrence and extent of TSR than either proxy alone. It showed that except for two oils, all of the oils that were measured in this study were affected by TSR or TSR-sourced H2S, to some degree. It is still not known if some of the oils with the lower concentrations of TDs and enriched δ34S values (close to sulfate minerals) were affected by TSR or by a secondary charge of 34S-enriched H2S.

Geochimica et Cosmochimica Acta↗

USGS2010

Ground-water flow in low permeability environments

Certain geologic media are known to have small permeability; subsurface environments composed of these media and lacking well developed secondary permeability have groundwater flow sytems with many distinctive characteristics. Moreover, groundwater flow in these environments appears to influence the evolution of certain hydrologic, geologic, and geochemical systems, may affect the accumulation of pertroleum and ores, and probably has a role in the structural evolution of parts of the crust. Such environments are also important in the context of waste disposal. This review attempts to synthesize the diverse contributions of various disciplines to the problem of flow in low-permeability environments. Problems hindering analysis are enumerated together with suggested approaches to overcoming them. A common thread running through the discussion is the significance of size- and time-scale limitations of the ability to directly observe flow behavior and make measurements of parameters. These limitations have resulted in rather distinct small- and large-scale approaches to the problem. The first part of the review considers experimental investigations of low-permeability flow, including in situ testing; these are generally conducted on temporal and spatial scales which are relatively small compared with those of interest. Results from this work have provided increasingly detailed information about many aspects of the flow but leave certain questions unanswered. Recent advances in laboratory and in situ testing techniques have permitted measurements of permeability and storage properties in progressively “tighter” media and investigation of transient flow under these conditions. However, very large hydraulic gradients are still required for the tests; an observational gap exists for typical in situ gradients. The applicability of Darcy's law in this range is therefore untested, although claims of observed non-Darcian behavior appear flawed. Two important nonhydraulic flow phenomena, osmosis and ultrafiltration, are experimentally well established in prepared clays but have been incompletely investigated, particularly in undisturbed geologic media. Small-scale experimental results form much of the basis for analyses of flow in low-permeability environments which occurs on scales of time and size too large to permit direct observation. Such large-scale flow behavior is the focus of the second part of the review. Extrapolation of small-scale experimental experience becomes an important and sometimes controversial problem in this context. In large flow systems under steady state conditions the regional permeability can sometimes be determined, but systems with transient flow are more difficult to analyze. The complexity of the problem is enhanced by the sensitivity of large-scale flow to the effects of slow geologic processes. One-dimensional studies have begun to elucidate how simple burial or exhumation can generate transient flow conditions by changing the state of stress and temperature and by burial metamorphism. Investigation of the more complex problem of the interaction of geologic processes and flow in two and three dimensions is just beginning. Because these transient flow analyses have largely been based on flow in experimental scale systems or in relatively permeable systems, deformation in response to effective stress changes is generally treated as linearly elastic; however, this treatment creates difficulties for the long periods of interest because viscoelastic deformation is probably significant. Also, large-scale flow simulations in argillaceous environments generally have neglected osmosis and ultrafiltration, in part because extrapolation of laboratory experience with coupled flow to large scales under in situ conditions is controversial. Nevertheless, the effects are potentially quite important because the coupled flow might cause ultra long lived transient conditions. The difficulties associated with analysis are matched by those of characterizing hydrologic conditions in tight environments; measurements of hydraulic head and sampling of pore fluids have been done only rarely because of the practical difficulties involved. These problems are also discussed in the second part of this paper.

Water Resources Research↗

USGS2023

Effects of temperature on viral load, inclusion body formation, and host response in Pacific Herring with viral erythrocytic necrosis (VEN)

Objective The primary objective of this study was to determine the effects of temperature on viral erythrocytic necrosis (VEN) progression under controlled conditions. Secondarily, this study was intended to evaluate the combined effects of temperature and VEN on the Pacific Herring Clupea palasii transcriptome. Methods The effects of temperature on VEN progression were assessed by waterborne exposure of laboratory-reared, specific-pathogen-free Pacific Herring to tissues homogenates containing erythrocytic necrosis virus (ENV) at 6.9, 9.0, or 13.5°C. Result Exposure of Pacific Herring to ENV resulted in the establishment of infections characterized by high infection prevalence (89%; 40/45) and mean viral loads (5.5 log 10 [gene copies/μg genomic DNA]) in kidney tissues at 44 days postexposure. Mean viral loads were significantly higher in fish from the ambient (mean = 9.0°C) and warm (mean = 13.5°C) treatments (6.1–6.2 log 10 [gene copies/total genomic DNA]) than in fish from the cool (mean = 6.9°C) treatment (4.3 log 10 [gene copies/μg genomic DNA]). Similarly, the peak proportion of diseased fish was directly related to temperature, with cytoplasmic inclusion bodies detected in 21% of fish from the cool treatment, 52% of fish from the ambient treatment, and 60% of fish from the warm treatment. The mean VEN load in each fish (enumerated as the percentage of erythrocytes with cytoplasmic inclusions) at 44 days postexposure increased with temperature from 15% in the cool treatment to 36% in the ambient treatment and 32% in the warm treatment. Transcriptional analysis indicated that the number of differentially expressed genes among ENV-exposed Pacific Herring increased with temperature, time postexposure, and viral load. Correlation network analysis of transcriptomic data showed robust activation of interferon and viral immune responses in the hepatic tissue of infected individuals independent of other experimental variables. Conclusion Results from this controlled laboratory study, combined with previous observations of natural epizootics in wild populations, support the conclusion that temperature is an important disease cofactor for VEN in Pacific Herring.

Journal of Aquatic Animal Health↗

USGS1998

Experimental investigations regarding the use of sand as an inhibitor of air convection in deep seismic boreholes

Tilt has been the nemesis of horizontal long period seismology since its inception. Modern horizontal long period seismometers with their long natural periods are incredibly sensitive to tilt. They can sense tilts smaller than 10 -11 radians. To most readers, this is just a very very small number, so we will begin with an example, which should help to illustrate just how small 10 -11 radians is. Suppose we have an absolutely rigid rod which is approximately 4170 kilometers long; this just happens to be the Rand McNally map scaled crow flight distance between Los Angeles and Boston. Tilting this rod 10 -11 radians corresponds to raising one end of the rod 0.0000417 meters. Alas, this is just another very very small number! However, this corresponds to slipping a little less than one third a sheet of ordinary copying paper under one end of this perfectly rigid rod. To clarify, we mean, take a sheet of paper just like the paper this report is printed on and split it a little less than one third in the thickness direction, then put it under the end of the 4170 kilometer long rod! This will tilt the rod 10 -11 radians. Real world seismometers are nowhere near the length of this rod. A KS-54000 is about two meters long. Tilting a rod only two meters long 10~n radians corresponds to moving one end of this rod a mere 0.00000000002 meters or 0.02 millimicrons. As one of the authors old math teachers used to say, "That's PDS" (PDS = Pretty Damn Small). Unfortunately, the long period seismologist does not have the luxury of ignoring PDS numbers when it suits him as the mathematician frequently does. He must live in the real world in which tilts this small create severe contamination of long period seismic data. At periods longer than 20 seconds, tilt noise contaminates the long period data from all instruments installed on or near the earth's surface. Many years of experimentation revealed that installing the sensors at depth in deep mines drastically reduced the level of tilt noise in long period data. However, low levels of tilt noise persisted even at great depth; this noise was caused by air convection in the vault in which the sensors were installed. Over the years, methods were developed to control the air motion with mechanical barriers (boxes) around the sensors and by stratifying (creating a situation in which the air temperature increases with height) the air in the vault near the seismometer. These methods decreased tilt noise in deep mines to very low levels. However, deep mines, that are economically and environmentally suitable and accessible to seismology, are not plentiful and are not evenly distributed over the earth's surface. Therefore, the borehole deployable Teledyne Geotech KS-36000 and later the KS-54000 sensor systems were developed to fulfill the need for instruments that could be installed at depth wherever high quality long period data was desired. Early in the development program, it became evident to the Teledyne Geotech personnel that air convection within the borehole was going to be a significant problem in KS deployments. Experimental and theoretical investigations conducted by Teledyne Geotech (see Douze and Sherwin, 1975, and Sherwin and Cook, 1976) produced a list of recommended installation procedures for reducing the effects of air convection. These procedures consisted of wrapping the sensor in a relatively thin layer of foam insulation, filling the free space volume in the vicinity of the centralizer-bail assembly with foam insulation, and the installation of styrofoam hole plugs immediately above the cable strain relief assembly at the top of the sensor package and at the top of the borehole. This technology has performed quite satisfactorily for over 20 years but evidence of tilt noise in the system output has persisted throughout the KS deployment program (the evidence was that the horizontal components were usually noisier than the vertical components) even in deep boreholes. Some deep borehole sites have been plagued by quite high levels of horizontal noise. Therefore, there has been a definite need for a new technique for controlling low level tilt noise in deep boreholes and the use of sand has been under consideration for several years. Figure 1 contains conceptual illustrations of both the conventional holelock installed KS sensor system and the same sensor installed in sand. This figure demonstrates the major differences between the two installation methods. The curved arrows in the borehole on the left in the figure denote possible air convection cells which are believed to be the source of tilt noise in some of the conventional installations. This air motion is eliminated in a sand installation by filling most of the free air volume surrounding the seismometer with sand as shown in the right hand portion of the figure. The sand actually performs two functions; it prevents air motion and provides a remarkably ridgid clamping of the seismometer in the borehole. This report presents the results of quantitative experimental investigations into the effectiveness of controlling low level air convection in seismic borehole installations with sand. The main body of the experimental effort consisted of installing two KS-540001 sensor systems in closely spaced shallow boreholes, allowing the sensors to reach equilibrium operation, and then pouring sand into both boreholes to observe any changes caused by pouring sand into the holes. The hypothesis of the experiment was that the sand would fill up the entire free air volume between the sensor package and the borehole walls thereby preventing movement of the air in the vicinity of the sensor package. The validity of this hypothesis had been qualitatively proven by earlier experiments at ASL and by the sand installations at the IRIS/ASL stations ANMO in 1995 and COLA in 1996. This experiment documents the degree of improved noise levels to be expected if KS instruments are installed in sand instead of in the conventional manner.

Open-File Report↗

USGS2022

Spatial models can improve the experimental design of field-based transplant gardens by preventing bias due to neighborhood crowding

Field-based transplant gardens, including common and reciprocal garden experiments, are a powerful tool for studying genetic variation and gene-by-environment interactions. These experiments assume that individuals within the garden represent independent replicates growing in a homogenous environment. Plant neighborhood interactions are pervasive across plant populations and could violate assumptions of transplant garden experiments. We demonstrate how spatially explicit models for plant–plant interactions can provide novel insights on genotypes' performance in field-transplant garden designs. We used individual-based models, based on data from a sagebrush ( Artemisia spp.) common garden, to simulate the impact of spatial plant–plant interactions on between-group differences in plant growth. We found that planting densities within the range of those used in many common gardens can bias experimental outcomes. Our results demonstrate that higher planting densities can lead to inflated group differences and may confound genotypes' competitive ability and genetically underpinned variation. Synthesis. We propose that spatially explicit models can help avoid biased results by informing the design and analysis of field-based transplant garden experiments. Alternately, including neighborhood effects in post hoc analyses of transplant garden experiments is likely to provide novel insights into the roles of biotic factors and density dependence in genetic differentiation.

Ecology and Evolution↗

USGS2022

Smoothed Particle Hydrodynamics simulations of reef surf zone processes driven by plunging irregular waves

As waves interact with the slopes of coral reefs and other steep bathymetry profiles, plunging breaking usually occurs where the free surface overturns and violent water motion is triggered. Resolving these surf zone processes pose significant challenges for conventional mesh-based hydrodynamic models, due to the rapidly-deforming nature of the free surface and associated flows. Yet the accurate prediction of these surf zone hydrodynamics is critical for predicting a wide range of nearshore processes driven by wave breaking (e.g., wave dissipation and energy transfers; mean water levels and currents; and wave runup). In this study we assess the ability of the mesh-free, Lagrangian particle-based numerical modelling approach Smoothed Particle Hydrodynamics (SPH) based on DualSPHysics, to simulate the fine-scale hydrodynamic processes driven by irregular wave transformation over a fringing reef profile, by comparing results against detailed experimental observations from a physical modelling study. To greatly improve the computational efficiency, the SPH model was coupled to the mesh-based multi-layer nonhydrostatic wave-flow model SWASH. With this coupled approach, SWASH was used to efficiently simulate the evolution of non-breaking waves from the wavemaker up to the fore reef slope, with the SPH model then used to simulate the detailed hydrodynamic processes over the reef from just offshore of the breakpoint to the shoreline . The SPH model was able to accurately reproduce the complex free surface deformations during plunging breaking, the spectral evolution of waves across the reef flat (including nonlinear wave shape), the mean water levels and currents, and wave runup at the shoreline. Using the long duration simulations (>400 wave periods), the model was able to reproduce the full range of wave motions over the reef (from sea-swell to infragravity frequencies), including the increasing dominance of low frequency waves towards the shoreline and the large cross-reef standing wave motions excited by the reef geometry.

Ocean Modelling↗

USGS2022

Environmental filtering controls soil biodiversity in wet tropical ecosystems

The environmental factors controlling soil biodiversity along resource gradients remain poorly understood in wet tropical ecosystems. Aboveground biodiversity is expected to be driven by changes in nutrient availability in these ecosystems, however, much less is known about the importance of nutrient availability in driving soil biodiversity. Here, we combined a cross-continental soil survey across tropical regions with a three decades' field experiment adding nitrogen (N) and phosphorus (P) (100 kg N ha −1 y −1 and 100 kg P ha −1 y −1 ) to Hawai'ian tropical forests with contrasting substrate ages (300 and 4,100,000 years) to investigate the influence of nutrient availability to explain the biodiversity of soil bacteria, fungi, protists, invertebrates and key functional genes. We found that soil biodiversity was driven by soil acidification during long-term pedogenesis and across environmental gradients, rather than by nutrient limitations. In fact, our results showed that experimental N additions caused substantial acidification in soils from Hawai'i. These declines in pH were related to large decreases in soil biodiversity from tropical ecosystems in four continents. Moreover, the microbial activity did not change in response to long-term N and P additions. We concluded that environmental filtering drives the biodiversity of multiple soil organisms, and that the acidification effects associated with N additions can further create substantial undesired net negative effects on overall soil biodiversity in naturally tropical acid soils. This knowledge is integral for the understanding and management of soil biodiversity in tropical ecosystems globally.

Hawai'i↗