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USGS2015

Quantitative attribution of major driving forces on soil organic carbon dynamics

Soil organic carbon (SOC) storage plays a major role in the global carbon cycle and is affected by many factors including land use/management changes (e.g., biofuel production-oriented changes). However, the contributions of various factors to SOC changes are not well understood and quantified. This study was designed to investigate the impacts of changing farming practices, initial SOC levels, and biological enhancement of grain production on SOC dynamics and to attribute the relative contributions of major driving forces (CO 2 enrichment and farming practices) using a fractional factorial modeling design. The case study at a crop site in Iowa in the United States demonstrated that the traditional corn-soybean (CS) rotation could still accumulate SOC over this century (from 4.2 to 6.8 kg C/m 2 ) under the current condition; whereas the continuous-corn (CC) system might have a higher SOC sequestration potential than CS. In either case, however, residue removal could reduce the sink potential substantially. Long-term simulation results also suggested that the equilibrium SOC level may vary greatly (∼5.7 to ∼11 kg C/m 2 ) depending on cropping systems and management practices, and projected growth enhancement could make the magnitudes higher (∼7.8 to ∼13 kg C/m 2 ). Importantly, the factorial design analysis indicated that residue management had the most significant impact (contributing 49.4%) on SOC changes, followed by CO 2 Enrichment (37%), Tillage (6.2%), the combination of CO 2 Enrichment-Residue removal (5.8%), and Fertilization (1.6%). In brief, this study is valuable for understanding the major forces driving SOC dynamics of agroecosystems and informative for decision-makers when seeking the enhancement of SOC sequestration potential and sustainability of biofuel production, especially in the Corn Belt region of the United States.

Journal of Advances in Modeling Earth Systems↗

USGS2011

Ant-nest ichnofossils in honeycomb calcretes, Neogene Ogallala Formation, High Plains region of western Kansas, U.S.A.

Two new ant-nest trace fossils are described from calcic sandy paleosols of the Neogene Ogallala Formation in western Kansas. The ichnofossils are preserved within and below calcrete beds weathering in positive relief as carbonate-filled casts or as cavities in negative relief. Daimoniobarax ichnogenus nov. is established for burrow systems composed of vertically tiered, horizontally oriented pancake-shaped chambers connected by predominantly vertical and cylindrical shafts ~ 0.8 cm in diameter. Ichnospecies of Daimoniobarax are differentiated based on differences in the plan view outline of chambers, shaft orientation, and junctions between chambers and shafts. Daimoniobarax nephroides ichnospecies nov. is composed of an ~ 24–76 cm long vertical sequence of distinctly lobed chambers (~ 2–20 cm wide and ~ 1 cm high) arranged along sinuous to helical shafts. Chamber shape in plan view ranges from small teardrops to larger kidney- and U-shaped forms. Shafts intersect at chamber edges such that chambers appear to bud from the central shafts. Daimoniobarax nephroides is most similar to the nests of extant seed-harvester ants of the New World genus Pogonomyrmex . Such ants are specialized granivores and prefer sandy soils in arid to semi-arid grassland and desert regions. Daimoniobarax tschinkeli ichnospecies nov. is ~ 30–80 cm in vertical extent. Chambers (~ 2–30 cm wide and ~ 1 cm high) are circular to elongate or pseudopodial in plan view. Vertical shafts are straight to slightly sinuous and intersect most often toward the center of the chambers. The generalized architecture of D. tschinkeli is similar to that of the nests or nest portions of several extant ant genera, though it does not closely resemble any known modern nest. Ant ichnofossils provide valuable information on hidden biodiversity, paleohydrologic regimes, paleopedogenic processes, and paleoclimate during the time of nest occupation. Depth-related changes in chamber size and vertical spacing may also help interpret paleosurfaces and paleodepths, and serve as geopetal features.

Kansas↗

USGS2014

Water movement through the unsaturated zone of the High Plains Aquifer in the Central Platte Natural Resources District, Nebraska, 2008-12

Uncertainty about the effects of land use and climate on water movement in the unsaturated zone and on groundwater recharge rates can lead to uncertainty in water budgets used for groundwater-flow models. To better understand these effects, a cooperative study between the U.S. Geological Survey and the Central Platte Natural Resources District was initiated in 2007 to determine field-based estimates of recharge rates in selected land-use areas of the Central Platte Natural Resources District in Nebraska. Measured total water potential and unsaturated-zone profiles of tritium, chloride, nitrate as nitrogen, and bromide, along with groundwater-age dates, were used to evaluate water movement in the unsaturated zone and groundwater recharge rates in the central Platte River study area. Eight study sites represented an east-west precipitation contrast across the study area—four beneath groundwater-irrigated cropland (sites 2, 5, and 6 were irrigated corn and site 7 was irrigated alfalfa/corn rotation), three beneath rangeland (sites 1, 4, and 8), and one beneath nonirrigated cropland, or dryland (site 3). Measurements of transient vertical gradients in total water potential indicated that periodic wetting fronts reached greater mean maximum depths beneath the irrigated sites than beneath the rangeland sites, in part, because of the presence of greater and constant antecedent moisture. Beneath the rangeland sites, greater temporal variation in antecedent moisture and total water potential existed and was, in part, likely a result of local precipitation and evapotranspiration. Moreover, greater variability was noticed in the total water potential profiles beneath the western sites than the corresponding eastern sites, which was attributed to less mean annual precipitation in the west. The depth of the peak post-bomb tritium concentration or the interface between the pre-bomb/post-bomb tritium, along with a tritium mass balance, within sampled soil profiles were used to estimate water fluxes in the unsaturated zone at three of the eight study sites: site 2 (irrigated), site 3 (dryland), and site 8 (rangeland). Estimates for recharge were about 68 millimeters per year [(mm/yr), post-bomb peak], 133 to 159 mm/yr (tritium interface), and 137 mm/yr (mass balance) at site 2 (irrigated); about 63 mm/yr (tritium interface) and 12 mm/yr (mass balance) at site 3 (dryland); and about 53 mm/yr (tritium interface) and 10 mm/yr (mass balance) at site 8 (rangeland). Recharge values from the mass balance at site 2 were more than an order of magnitude greater than recharge values at site 3, suggesting irrigation is an important control on water movement through the unsaturated zone. For the remaining five sites, the post-bomb tritium had flushed through the system and recharge was considered modern (within 10 years of sampling). The chloride mass-balance method was used to determine water fluxes below the root zone (less than 2 meters below land surface) at the rangeland sites: sites 1, 4, and 8. At these rangeland sites, water fluxes ranged from 1.8 to 96 mm/yr at site 1, 1.1 to 9.6 mm/yr at site 4, and 1.1 to 68 mm/yr at site 8, with mean rates of 21, 4.3, and 13 mm/yr, respectively. Site 1 had a greater mean water flux, which was consistent with the greater precipitation in the east than at site 8 in the west. Chloride mass balance was not calculated at the irrigated and dryland sites because of uncertainty about additional sources of chloride. Concentrations of nitrate as nitrogen in pore water in the unsaturated zone were larger beneath the irrigated and dryland (agricultural) sites compared with the rangeland sites. The larger concentrations at the agricultural sites are consistent with the application of nitrogen fertilizer at the agricultural sites and no substantial accumulation at the rangeland sites. The shape of the nitrate as nitrogen and chloride concentration profiles at site 1 (rangeland) indicate a reasonably larger and more consistent water flux in the UZ than beneath the other two rangeland sites (sites 4 or 8). Excluding site 7, the general shape of the nitrate as nitrogen profiles was similar beneath the agricultural sites and supports the estimates of water movement and recharge rates determined from the tritium and chloride methods. Movement of bromide through the unsaturated zone indicated greater water fluxes are found beneath irrigated lands than beneath rangeland. Bromide profiles in the unsaturated zone, determined from center of mass and peak displacement methods, document water fluxes ranged from 58 to 394 mm/yr beneath irrigated sites and 9 to 201 mm/yr beneath rangeland sites. Water-flux estimates from the potassium bromide tests at most sites did not represent overall recharge rates because the bromide remained primarily in the root zone. Apparent groundwater age was used to determine the groundwater residence time at the eight sites and to estimate recharge rates. Groundwater ages in the study area ranged from old water (defined here as groundwater that was recharged more than 50 years ago) to modern (defined here as groundwater that has recharged within the past 10 years). Groundwater ages indicated that the shallow monitoring wells generally had younger residence times, whereas the deeper monitoring wells generally had the older residence times. Groundwater dates from the shallowest monitoring wells were used to determine recharge rates at the water table. These rates generally were similar to recharge rates determined from tritium and chloride mass-balance methods. Groundwater recharge rates generally increased with well depth, and the deeper monitoring wells likely do not represent local recharge conditions but recharge from a regional flow system that receives recharge from distant sources. Overall, these data generally indicate that water movement within the unsaturated zone primarily is affected by spatial contrasts in mean annual precipitation and by the land use or land cover. The eight unsaturated-zone sites each generated unique, valuable datasets that likely will improve the understanding of water movement and recharge rates in the central Platte River valley.

Nebraska↗

USGS2005

Seed dispersal into wetlands: Techniques and results for a restored tidal freshwater marsh

Although seed dispersal is assumed to be a major factor determining plant community development in restored wetlands, little research exists on density and species richness of seed available through dispersal in these systems. We measured composition and seed dispersal rates at a restored tidal freshwater marsh in Washington, DC, USA by collecting seed dispersing through water and wind. Seed dispersal by water was measured using two methods of seed collection: (1) stationary traps composed of coconut fiber mat along an elevation gradient bracketing the tidal range and (2) a floating surface trawl net attached to a boat. To estimate wind dispersal rates, we collected seed from stationary traps composed of coconut fiber mat positioned above marsh vegetation. We also collected a small number of samples of debris deposited along high tide lines (drift lines) and feces of Canada Goose to explore their seed content. We used the seedling emergence method to determine seed density in all samples, which involved placing the fiber mats or sample material on top of potting soil in a greenhouse misting room and enumerating emerging seedlings. Seedlings from a total of 125 plant species emerged, during this study (including 82 in river trawls, 89 in stationary water traps, 21 in drift lines, 39 in wind traps, and 10 in goose feces). The most abundant taxa included Bidens frondosa, Boehmeria cylindrica, Cyperus spp., Eclipta prostrata , and Ludwigia palustris . Total seedling density was significantly greater for the stationary water traps (212±30.6 seeds/m 2 /month) than the equal-sized stationary wind traps (18±6.0 seeds/m 2 /month). Lower-bound estimates of total species richness based on the non-parametric Chao 2 asymptotic estimators were greater for seeds in water (106±1.4 for stationary water traps and 104±5.5 for trawl samples) than for wind (54±6.4). Our results indicate that water is the primary source of seeds dispersing to the site and that a species-rich pool of dispersing propagules is present, an interesting result given the urbanized nature of the surrounding landscape. However, species composition of dispersing seeds differed from vegetation of restored and natural tidal freshwater marshes, indicating that planting is necessary for certain species. At other restoration sites, information on densities of dispersing seeds can support decisions on which species to plant.

Washington D.C.↗

USGS2012

Watershed modeling applications in south Texas

Watershed models can be used to simulate natural and human-altered processes including the flow of water and associated transport of sediment, chemicals, nutrients, and microbial organisms within a watershed. Simulation of these processes is useful for addressing a wide range of water-resource challenges, such as quantifying changes in water availability over time, understanding the effects of development and land-use changes on water resources, quantifying changes in constituent loads and yields over time, and quantifying aquifer recharge temporally and spatially throughout a watershed. The U.S. Geological Survey (USGS), in cooperation with State and Federal agency partners, developed simulation models for several watersheds in south Texas. These models provide the capability to simulate scenarios of possible future conditions and management alternatives to help water-resource professionals with planning decisions. The program used for creating these Texas watershed models is the Hydrological Simulation Program - FORTRAN (HSPF). HSPF is one of the most comprehensive watershed modeling programs because it can simulate a variety of stream and watershed conditions with reasonable accuracy and enables flexibility in adjusting the model to simulate alternative conditions or scenarios. The HSPF model provides time-series data simulating water movement (runoff from land surfaces, infiltration of water through soil layers, flow in stream channels) and water-quality parameter values and constituent concentrations associated with the water movement at any selected location in the watershed. Time-series outputs from an HSPF simulation are continuous (for example, hourly or daily). Continuous models provide the advantage of simulating watershed processes for a full range of streamflow conditions. Continuous models can illustrate how processes that appreciably affect water-quality conditions during low flows might have relatively minor effects on water-quality conditions during high flows. This fact sheet presents an overview of six selected watershed modeling studies by the USGS and partners that address a variety of water-resource issues in south Texas. These studies provide examples of modeling applications and demonstrate the usefulness and versatility of watershed models in aiding the understanding of hydrologic systems.

Texas↗

USGS2011

Hydrogeology, chemical characteristics, and water sources and pathways in the zone of contribution of a public-supply well in San Antonio, Texas

In 2001, the National Water-Quality Assessment (NAWQA) Program of the U.S. Geological Survey initiated a series of studies on the transport of anthropogenic and natural contaminants (TANC) to public-supply wells (PSWs). The main goal of the TANC project was to better understand the source, transport, and receptor factors that control contaminant movement to PSWs in representative aquifers of the United States. Regional- and local-scale study areas were selected from within existing NAWQA study units, including the south-central Texas Edwards aquifer. The local-scale TANC study area, nested within the regional-scale NAWQA study area, is representative of the regional Edwards aquifer. The PSW selected for study is within a well field of six production wells. Although a single PSW was initially selected, because of constraints of well-field operation, samples were collected from different wells within the well field for different components of the study. Data collected from all of the well-field wells were considered comparable because of similar well construction, hydrogeology, and geochemistry. An additional 38 PSWs (mostly completed in the confined part of the aquifer) were sampled throughout the regional aquifer to characterize water quality. Two monitoring well clusters, with wells completed at different depths, were installed to the east and west of the well field (the Zarzamora and Timberhill monitoring well clusters, respectively). One of the monitoring wells was completed in the overburden to evaluate potential hydrologic connectivity with the Edwards aquifer. Geophysical and flowmeter logs were collected from one of the well-field PSWs to determine zones of contribution to the wellbore. These contributing zones, associated with different hydrogeologic units, were used to select monitoring well completion depths and groundwater sample collection depths for depth-dependent sampling. Depth-dependent samples were collected from the PSW from three different depths and under three different pumping conditions. Additionally, selected monitoring wells and one of the well-field PSWs were sampled several times in response to a rainfall and recharge event to assess short-term (event-scale) temporal variations in water quality. For comparison purposes, groundwater samples were categorized as being from regional aquifer PSWs, from the well field (wellhead samples), from the monitoring wells (excluding the overburden well), from the overburden well, from the PSW depth-dependent sampling, and from temporal sampling. Groundwater samples were analyzed for inorganic, organic, isotopic, and age-dating tracers to characterize geochemical conditions in the aquifer and provide understanding of the mechanisms of mobilization and movement of selected constituents from source areas to a PSW. Sources, tracers, and conditions used to assess water quality and processes affecting the PSW and the aquifer system included (1) carbonate host rock composition; (2) physicochemical constituents; (3) major and trace element concentrations; (4) saturation indices with respect to minerals in aquifer rocks; (5) elemental ratios, such as magnesium to calcium ratios, that are indicative of water-rock interaction processes; (6) oxidation-reduction conditions; (7) nutrient concentrations, in particular nitrate concentrations; (8) the isotopic composition of nitrate, which can point to specific nitrate sources; (9) strontium isotopes; (10) stable isotopes of hydrogen and oxygen; (11) organic contaminant concentrations, including pesticides and volatile organic compounds; (12) age tracers, apparent-age distribution, and dissolved gas data used in age interpretations; (13) depth-dependent water chemistry collected from the PSW under different pumping conditions to assess zones of contribution; and (14) temporal variability in groundwater composition from the PSW and selected monitoring wells in response to an aquifer recharge event. Geochemical results indicate that the well-field and monitoring well samples were largely representative of groundwater in the regional confined aquifer. Constituents of concern in the Edwards aquifer for the long-term sustainability of the groundwater resource include the nutrient nitrate and anthropogenic organic contaminants. Nitrate concentrations (as nitrogen) for regional aquifer PSWs had a median value of 1.9 milligrams per liter, which is similar to previously reported values for the regional aquifer. Nitrate-isotope compositions for groundwater samples collected from the well-field PSWs and monitoring wells had a narrow range, with values indicative of natural soil organic values. A comparison with historical nitrate-isotope values, however, suggests that a component of nitrate in groundwater from biogenic sources might have increased over the last 30 years. Several organic contaminants (the pesticide atrazine, its degradate deethylatrazine, trichloromethane (chloroform; a drinking-water disinfection byproduct), and the solvent tetrachloroethene (PCE)) were widely distributed throughout the regional aquifer and in the local-scale TANC study area at low concentrations (less than 1 microgram per liter). Higher concentrations of PCE were detected in samples from the well-field PSWs and Zarzamora monitoring wells relative to the regional aquifer PSWs. The urban environment is a likely source of contaminants to the aquifer, and these results indicate that one or more local urban sources might be supplying PCE to the Zarzamora monitoring wells and the well-field wells. Samples from the well field also had high concentrations of chloroform relative to the monitoring wells and regional aquifer PSWs. For samples from the regional aquifer PSWs, the most frequently detected organic contaminants generally decreased in concentration with increasing well depth. Deeper wells might intercept longer regional flow paths with higher fractions of older water or water recharged in rural recharge areas in the western part of the aquifer that have been less affected by anthropogenic contaminants. A scenario of hypothetical contaminant loading was evaluated by using results from groundwater-flow-model particle tracking to assess the response of the aquifer to potential contamination. Results indicate that the aquifer responds quickly (less than 1 year to several years) to contaminant loading; however, it takes a relatively long time (decades) for concentrations to reach peak values. The aquifer also responds quickly (less than 1 year to several years) to the removal of contaminant loading; however, it also takes a relatively long time (decades) to reach near background concentrations. Interpretation of geochemical age tracers in this well-mixed karst system was complicated by contamination of a majority of measured tracers and complexities of extensive mixing. Age-tracer results generally indicated that groundwater samples were composed of young, recently recharged water with piston-flow model ages ranging from less than 1 to 41 years, with a median of 17 years. Although a piston-flow model is typically not valid for karst aquifers, the model ages provide a basis for comparing relative ages of different samples and a reference point for more complex hydrogeologic models for apparent-age interpretations. Young groundwater ages are consistent with particle-tracking results from hydrogeologic modeling for the local-scale TANC study area. Age-tracer results compared poorly with other geochemical indicators of groundwater residence time and anthropogenic effects on water quality, indicating that hydrogeologic conceptual models used in groundwater age interpretations might not adequately account for mixing in this karst system. Groundwater samples collected from the well field under a variety of pumping conditions were relatively homogeneous and well mixed for numerous geochemical constituents (with the notable exception of age tracers). Groundwater contributions to the PSW were dominated by well-mixed, relatively homogeneous groundwater, typical of the regional confined aquifer. Zones of preferential flow were determined for the PSW, but groundwater samples from different stratigraphic units were not geochemically distinct. Variations in chemical constituents in response to a rainfall and aquifer recharge event occurred but were relatively minor in the PSW and monitoring wells. This observation is consistent with the hypothesis that the response to individual recharge events in the confined aquifer, unless intersecting conduit flow paths, might be attenuated by mixing processes along regional flow paths. Results of this study are consistent with the existing conceptual understanding of aquifer processes in this karst system and are useful for water-resource development and management practices.

Texas↗

USGS2022

Causality guided machine learning model on wetland CH4 emissions across global wetlands

Wetland CH 4 emissions are among the most uncertain components of the global CH 4 budget. The complex nature of wetland CH 4 processes makes it challenging to identify causal relationships for improving our understanding and predictability of CH 4 emissions. In this study, we used the flux measurements of CH 4 from eddy covariance towers (30 sites from 4 wetlands types: bog, fen, marsh, and wet tundra) to construct a causality-constrained machine learning (ML) framework to explain the regulative factors and to capture CH 4 emissions at sub-seasonal scale. We found that soil temperature is the dominant factor for CH 4 emissions in all studied wetland types. Ecosystem respiration (CO 2 ) and gross primary productivity exert controls at bog, fen, and marsh sites with lagged responses of days to weeks. Integrating these asynchronous environmental and biological causal relationships in predictive models significantly improved model performance. More importantly, modeled CH 4 emissions differed by up to a factor of 4 under a +1°C warming scenario when causality constraints were considered. These results highlight the significant role of causality in modeling wetland CH 4 emissions especially under future warming conditions, while traditional data-driven ML models may reproduce observations for the wrong reasons. Our proposed causality-guided model could benefit predictive modeling, large-scale upscaling, data gap-filling, and surrogate modeling of wetland CH 4 emissions within earth system land models.

Agricultural and Forest Meteorology↗

USGS2019

Remote sensing of dryland ecosystem structure and function: Progress, challenges, and opportunities

Drylands make up roughly 40% of the Earth's land surface, and billions of people depend on services provided by these critically important ecosystems. Despite their relatively sparse vegetation, dryland ecosystems are structurally and functionally diverse, and emerging evidence suggests that these ecosystems play a dominant role in the trend and variability of the terrestrial carbon sink. More, drylands are highly sensitive to climate and are likely to have large, non-linear responses to hydroclimatic change. Monitoring the spatiotemporal dynamics of dryland ecosystem structure (e.g., leaf area index) and function (e.g., primary production and evapotranspiration) is therefore a high research priority. Yet, dryland remote sensing is defined by unique challenges not typically encountered in mesic or humid regions. Major challenges include low vegetation signal-to-noise ratios, high soil background reflectance, presence of photosynthetic soils (i.e., biological soil crusts), high spatial heterogeneity from plot to regional scales, and irregular growing seasons due to unpredictable seasonal rainfall and frequent periods of drought. Additionally, there is a relative paucity of continuous, long-term measurements in drylands, which impedes robust calibration and evaluation of remotely-sensed dryland data products. Due to these issues, remote sensing techniques developed in other ecosystems or for global application often result in inaccurate, poorly constrained estimates of dryland ecosystem structural and functional dynamics. Here, we review past achievements and current progress in remote sensing of dryland ecosystems, including a detailed discussion of the major challenges associated with remote sensing of key dryland structural and functional dynamics. We then identify strategies aimed at leveraging new and emerging opportunities in remote sensing to overcome previous challenges and more accurately contextualize drylands within the broader Earth system. Specifically, we recommend: 1) Exploring novel combinations of sensors and techniques (e.g., solar-induced fluorescence, thermal, microwave, hyperspectral, and LiDAR) across a range of spatiotemporal scales to gain new insights into dryland structural and functional dynamics; 2) utilizing near-continuous observations from new-and-improved geostationary satellites to capture the rapid responses of dryland ecosystems to diurnal variation in water stress; 3) expanding ground observational networks to better represent the heterogeneity of dryland systems and enable robust calibration and evaluation; 4) developing algorithms that are specifically tuned to dryland ecosystems by utilizing expanded ground observational network data; and 5) coupling remote sensing observations with process-based models using data assimilation to improve mechanistic understanding of dryland ecosystem dynamics and to better constrain ecological forecasts and long-term projections.

Remote Sensing of Environment↗

USGS2001

Green fluorescent protein is lighting up fungal biology

Prasher ( 42 ) cloned a cDNA for the green fluorescent protein (GFP) gene from the jellyfish Aequorea victoria in 1992. Shortly thereafter, to the amazement of many investigators, this gene or derivatives thereof were successfully expressed and conferred fluorescence to bacteria and Caenorhabditis elegans cells in culture ( 10 , 31 ), followed by yeast ( 24 , 39 ), mammals ( 40 ), Drosophila ( 66 ), Dictyostelium ( 23 , 30 ), plants ( 28 , 49 ), and filamentous fungi ( 54 ). The tremendous success of GFP as a reporter can be attributed to unique qualities of this 238-amino-acid, 27-kDa protein which absorbs light at maxima of 395 and 475 nm and emits light at a maximum of 508 nm. The fluorescence of GFP requires only UV or blue light and oxygen, and therefore, unlike the case with other reporters (β-glucuronidase, β-galacturonidase, chloramphenicol acetyltransferase, and firefly luciferase) that rely on cofactors or substrates for activity, in vivo observation of gfp expression is possible with individual cells, with cell populations, or in whole organisms interacting with symbionts or environments in real time. Complications caused by destructive sampling, cell permeablization for substrates, or leakage of products do not occur. Furthermore, the GFP protein is extremely stable in vivo and has been fused to the C or N terminus of many cellular and extracellular proteins without a loss of activity, thereby permitting the tagging of proteins for gene regulation analysis, protein localization, or specific organelle labeling. The mature protein resists many proteases and is stable up to 65°C and at pH 5 to 11, in 1% sodium dodecyl sulfate or 6 M guanidinium chloride (reviewed in references 17 and 67 ), and in tissue fixed with formaldehyde, methanol, or glutaraldehyde. However, GFP loses fluorescence in methanol-acetic acid (3:1) and can be masked by autofluorescent aldehyde groups in tissue fixed with glutaraldehyde. Fluorescence is optimal at pH 7.2 to 8.0 ( 67 ). Limitations on GFP as a reporter for some applications are its low turnover rate, 2-h lag time for autoactivation of its chromophore, improper folding at high temperatures (37°C), which results in nonfluorescent and insoluble forms of the protein, and requirement for oxygen, which is not present in equal concentrations in all subcellular locations or cell types (reviewed in references 17 and 67 ). These characteristics of GFP, however, have not posed a problem for many applications, and mutant forms of GFP that have an ability to fold properly at high temperatures, increased solubility and fluorescence, reduced photobleaching ( 16 , 17 , 51 ), and reduced half-lives ( 1 ) have been developed. Coupled with fluorescence-activated cell sorting, confocal microscopy or quantitative image analysis techniques, GFP technology can be used to isolate transformed cells or specific cell types from populations of cells ( 14 ), to quantify gene expression of individual cells within whole organisms ( 8 ), or to assess the dispersal and biomass of organisms in complex environments, such as in animal or plant hosts ( 38 , 59 ), in biofilms ( 55 ), in fermentors ( 41 ), on leaf surfaces ( 53 , 61 ), or in soils ( 2 ). The vast majority of studies utilizing GFP expression in fungi have been with yeast (reviewed in reference 13 ). Ustilago maydis was the first filamentous fungus for which successful expression of gfp was reported ( 54 ), followed closely by Aspergillus nidulans ( 22 , 57 ) and Aureobasidium pullulans ( 61 ). Presently, gfp expression has been reported for 16 species comprising 12 genera of filamentous fungi, including Colletotrichum ( 21 , 44 ), Mycosphaerella ( 52 ), Magnaporthe ( 32 , 35 ), Cochliobolus ( 38 ), Trichoderma ( 2 , 70 ), Podospora ( 5 ), Sclerotinia ( 63 ), Schizophyllum ( 37 ), Aspergillus ( 20 , 47 , 50 ) and Phytophthora ( 7 , 62 ). In this review we draw on published reports, with the goal of providing an overview of GFP technology as it applies to the biology of filamentous fungi. These reports are not exhaustive of potential applications of GFP technology, as examples of genomic approaches to utilizing GFP in bacterial and yeast systems attest ( 4 , 46 , 60 , 65 ). Expression of gfp in filamentous fungi requires a gfp variant that is efficiently translated in fungi, a transformation system, and a fungal promoter that satisfies the requirements of a given experimental objective. Transformation of fungi has recently been reviewed by Gold et al. ( 26 ). Robinson and Sharon ( 44 ) suggest that GFP can actually be used to optimize transformation protocols. In addition to reporting the construction of a new fungal transformation vector that expresses SGFP under the control of the ToxA gene promoter from Pyrenophora tritici-repentis ( 12 ) and demonstrating its use in plant pathogens belonging to eight different genera of filamentous fungi ( Fusarium, Botrytis, Pyrenophora, Alternaria, Cochliobolus, Sclerotinia, Colletotrichum , and Verticillium ), in this review we also enumerate and describe a comprehensive list of vectors for expressing GFP in fungi.

Applied and Environmental Microbiology↗

USGS2007

Major Turbidity Events in the North Santiam River Basin, Oregon, Water Years 1999-2004

Multiple high-turbidity events with values greater than 250 Formazin Nephelometric Units occurred in streams of the North Santiam River basin during water years 1999-2004. By using a combination of field reconnaissance, aerial photography, and geographic information systems, eight of these high-turbidity events were investigated and linked to at least one likely source area and became known as 'major turbidity events.' Sediment source type and location, the amount of material transported, and the results of any follow-up investigation of the source area were recorded for each event. Significant findings from this study include: * Although heavy precipitation caused basinwide erosion that increased turbidity in streams, a major turbidity event often required at least one landslide or similar type of contributing source to introduce enough sediment to raise the turbidity value to greater than 250 Formazin Nephelometric Units. * Different processes drove sediment loading at different times. In general, precipitation eroded sediment from source areas or induced landslides. However, in two cases, warm temperatures caused rapid snowmelt, which supplied the water necessary to erode unconsolidated glacial soils or other sediment material and increase turbidity. * Some source areas, such as existing earthflows, repeatedly supplied a large volume of sediment to streams, whereas other sources, such as landslides or debris flows, were unpredictable and sporadically supplied large volumes of sediment to streams. * Major turbidity events were well distributed throughout the North Santiam River basin; discrete events were observed in each of the five subbasins along unregulated streams. * Suspended-sediment loads and clay-water (persistently turbid water) volume estimates were event-specific and varied greatly between major turbidity events, even though, in some cases, the source area was the same; however, high yields generally were observed for events in the Blowout Creek, Breitenbush River, and Little North Santiam River subbasins. * Suspended-sediment loads for each 3-day precipitation-driven major turbidity event supplied greater than 36 percent of the annual load, and snowmelt-driven events supplied greater than 27 percent of the annual load in a single day. * Clay-water yields for event periods generally were highest in the Little North Santiam River subbasin. In addition, average annual percentage of clay-water volume during the period of record was highest in the Little North Santiam River. The second highest average was in Blowout Creek.

Scientific Investigations Report↗

USGS1988

An isotopic study of a fluvial-lacustrine sequence: The Plio-Pleistocene koobi fora sequence, East Africa

Stable isotopic analyses of Plio-Pleistocene and modern sediments in the fluvial-lacustrine system occupying the Turkana Basin, East Africa provide constraints on the paleoenvironmental and diagenetic histories of the Pliocene through the Recent sediments in the basin. The δ 13 C values for carbonates in lacustrine sediments range from −15 to +22‰ relative to PDB, depending on the varying proportions of CO 2 from the atmospheric reservoir and from various metabolic sources. The δ 18 O values of carbonates in lacustrine sediments indicate that the isotopic composition of paleolake water varied by over 10‰ from the Pliocene to the present. The δ 13 C values for pedogenic carbonates record paleoccologic variations and suggest that C 4 plants did not become well established in the preserved depositional parts of the basin until about 1.8 myr ago. The δ 18 O values pedogenic carbonates suggest a range of over 10‰ for the isotopic composition of soil water during this interval. They also suggest a period of major climatic instability from about 3.4 to 3.1 myr and at about 1.8 myr. Together, the δ 13 C and δ 18 O values of pedogenic carbonates indicate that the present conditions are as arid and hot as any that had prevailed during deposition of these Plio-Pleistocene sediments.

Lake Turkana Basin↗

USGS2013

Shallow groundwater in the Matanuska-Susitna Valley, Alaska—Conceptualization and simulation of flow

The Matanuska-Susitna Valley is in the Upper Cook Inlet Basin and is currently undergoing rapid population growth outside of municipal water and sewer service areas. In response to concerns about the effects of increasing water use on future groundwater availability, a study was initiated between the Alaska Department of Natural Resources and the U.S. Geological Survey. The goals of the study were (1) to compile existing data and collect new data to support hydrogeologic conceptualization of the study area, and (2) to develop a groundwater flow model to simulate flow dynamics important at the regional scale. The purpose of the groundwater flow model is to provide a scientific framework for analysis of regional-scale groundwater availability. To address the first study goal, subsurface lithologic data were compiled into a database and were used to construct a regional hydrogeologic framework model describing the extent and thickness of hydrogeologic units in the Matanuska-Susitna Valley. The hydrogeologic framework model synthesizes existing maps of surficial geology and conceptual geochronologies developed in the study area with the distribution of lithologies encountered in hundreds of boreholes. The geologic modeling package Geological Surveying and Investigation in Three Dimensions (GSI3D) was used to construct the hydrogeologic framework model. In addition to characterizing the hydrogeologic framework, major groundwater-budget components were quantified using several different techniques. A land-surface model known as the Deep Percolation Model was used to estimate in-place groundwater recharge across the study area. This model incorporates data on topography, soils, vegetation, and climate. Model-simulated surface runoff was consistent with observed streamflow at U.S. Geological Survey streamgages. Groundwater withdrawals were estimated on the basis of records from major water suppliers during 2004-2010. Fluxes between groundwater and surface water were estimated during field investigations on several small streams. Regional groundwater flow patterns were characterized by synthesizing previous water-table maps with a synoptic water-level measurement conducted during 2009. Time-series water-level data were collected at groundwater and lake monitoring stations over the study period (2009–present). Comparison of historical groundwater-level records with time-series groundwater-level data collected during this study showed similar patterns in groundwater-level fluctuation in response to precipitation. Groundwater-age data collected during previous studies show that water moves quickly through the groundwater system, suggesting that the system responds quickly to changes in climate forcing. Similarly, the groundwater system quickly returns to long-term average conditions following variability due to seasonal or interannual changes in precipitation. These analyses indicate that the groundwater system is in a state of dynamic equilibrium, characterized by water-level fluctuation about a constant average state, with no long-term trends in aquifer-system storage. To address the second study goal, a steady-state groundwater flow model was developed to simulate regional groundwater flow patterns. The groundwater flow model was bounded by physically meaningful hydrologic features, and appropriate internal model boundaries were specified on the basis of conceptualization of the groundwater system resulting in a three-layer model. Calibration data included 173 water‑level measurements and 18 measurements of streamflow gains and losses along small streams. Comparison of simulated and observed heads and flows showed that the model accurately simulates important regional characteristics of the groundwater flow system. This model is therefore appropriate for studying regional-scale groundwater availability. Mismatch between model-simulated and observed hydrologic quantities is likely because of the coarse grid size of the model and seasonal transient effects. Next steps towards model refinement include the development of a transient groundwater flow model that is suitable for analysis of seasonal variability in hydraulic heads and flows. In addition, several important groundwater budget components remain poorly quantified—including groundwater outflow to the Matanuska River, Little Susitna River, and Knik Arm.

Alaska↗

USGS2013

Importance of biogeomorphic and spatial properties in assessing a tidal salt marsh vulnerability to sea-level rise

We evaluated the biogeomorphic processes of a large (309 ha) tidal salt marsh and examined factors that influence its ability to keep pace with relative sea-level rise (SLR). Detailed elevation data from 1995 and 2008 were compared with digital elevation models (DEMs) to assess marsh surface elevation change during this time. Overall, 37 % (113 ha) of the marsh increased in elevation at a rate that exceeded SLR, whereas 63 % (196 ha) of the area did not keep pace with SLR. Of the total area, 55 % (169 ha) subsided during the study period, but subsidence varied spatially across the marsh surface. To determine which biogeomorphic and spatial factors contributed to measured elevation change, we collected soil cores and determined percent and origin of organic matter (OM), particle size, bulk density (BD), and distance to nearest bay edge, levee, and channel. We then used Akaike Information Criterion (AICc) model selection to assess those variables most important to determine measured elevation change. Soil stable isotope compositions were evaluated to assess the source of the OM. The samples had limited percent OM by weight (<5.5 %), with mean bulk densities of 0.58 g cm -3 , indicating that the soils had high mineral content with a relatively low proportion of pore space. The most parsimonious model with the highest AICc weight (0.53) included distance from bay's edge (i.e., lower intertidal) and distance from levee (i.e., upper intertidal). Close proximity to sediment source was the greatest factor in determining whether an area increased in elevation, whereas areas near landward levees experienced subsidence. Our study indicated that the ability of a marsh to keep pace with SLR varied across the surface, and assessing changes in elevation over time provides an alternative method to long-term accretion monitoring. SLR models that do not consider spatial variability of biogeomorphic and accretion processes may not correctly forecast marsh drowning rates, which may be especially true in modified and urbanized estuaries. In light of SLR, improving our understanding of elevation change in these dynamic marsh systems will play a crucial role in forecasting potential impacts to their sustainability and the survival of these ecosystems.

Estuaries and Coasts↗

USGS1998

Faulting apparently related to the 1994 Northridge, California, earthquake and possible co-seismic origin of surface cracks in Potrero Canyon, Los Angeles County, California

Apparent southward-dipping, reverse-fault zones are imaged to depths of about 1.5 km beneath Potrero Canyon, Los Angeles County, California. Based on their orientation and projection to the surface, we suggest that the imaged fault zones are extensions of the Oak Ridge fault. Geologic mapping by others and correlations with seismicity studies suggest that the Oak Ridge fault is the causative fault of the 17 January 1994 Northridge earthquake (Northridge fault). Our seismically imaged faults may be among several faults that collectively comprise the Northridge thrust fault system. Unusually strong shaking in Potrero Canyon during the Northridge earthquake may have resulted from focusing of seismic energy or co-seismic movement along existing, related shallow-depth faults. The strong shaking produced ground-surface cracks and sand blows distributed along the length of the canyon. Seismic reflection and refraction images show that shallow-depth faults may underlie some of the observed surface cracks. The relationship between observed surface cracks and imaged faults indicates that some of the surface cracks may have developed from nontectonic alluvial movement, but others may be fault related. Immediately beneath the surface cracks, P-wave velocities are unusually low (<400 m/sec), and there are velocity anomalies consistent with a seismic reflection image of shallow faulting to depths of at least 100 m. On the basis of velocity data, we suggest that unconsolidated soils (<800 m/sec) extend to depths of about 15 to 20 m beneath our datum (<25 m below ground surface). The underlying rocks range in velocity from about 1000 to 5000 m/sec in the upper 100 m. This study illustrates the utility of high-resolution seismic imaging in assessing local and regional seismic hazards.

California↗

USGS2004

Occurrence and distribution of trace elements in snow, streams, and streambed sediments, Cape Krusenstern National Monument, Alaska, 2002-2003

Cape Krusenstern National Monument is located in Northwest Alaska. In 1985, an exchange of lands and interests in lands between the Northwest Alaska Native Association and the United States resulted in a 100-year transportation system easement for 19,747 acres in the monument. A road was then constructed along the easement from the Red Dog Mine, a large zinc concentrate producer and located northeast of the monument, through the monument to the coast and a port facility. Each year approximately 1.3 million tonnes of zinc and lead concentrate are transported from the Red Dog Mine via this access road. Concern about the possible deposition of cadmium, lead, zinc and other trace elements in the monument was the basis of a cooperative project with the National Park Service. Concentrations of dissolved cadmium, dissolved lead, and dissolved zinc from 28 snow samples from a 28 mile by 16 mile grid were below drinking water standards. In the particulate phase, approximately 25 percent of the samples analyzed for these trace elements were higher than the typical range found in Alaska soils. Boxplots of concentrations of these trace elements, both in the dissolved and particulate phase, indicate higher concentrations north of the access road, most likely due to the prevailing southeast wind. The waters of four streams sampled in Cape Krusenstern National Monument are classified as calcium bicarbonate. Trace-element concentrations from these streams were below drinking water standards. Median concentrations of 39 trace elements from streambed sediments collected from 29 sites are similar to the median concentrations of trace elements from the U.S. Geological Survey?s National Water-Quality Assessment database. Statistical differences were noted between trace-element concentrations of cadmium, lead, and zinc at sites along the access road and sites north and south of the access road; concentrations along the access road being higher than north or south of the road. When normalized to 1 percent organic carbon, the concentrations of these trace elements are not expected to be toxic to aquatic life when compared to criteria established by the Canadian government and other recent research.

Scientific Investigations Report↗

USGS2020

Comparison of storm runoff models for a small watershed in an urban metropolitan area, Albuquerque, New Mexico

In order to comply with a current U.S. Environmental Protection Agency watershed-based National Pollutant Discharge Elimination System permit, the City of Albuquerque required a better understanding of the rainfall-runoff processes in its small urban watersheds. That requirement prompted the initiation of the assessment of three existing watershed models that were developed to simulate those processes. Three existing rainfall-runoff modeling software packages—Hydrologic Engineering Center Hydrologic Modeling System (HEC-HMS) (using two sets of methods), Program for Predicting Polluting Particle Passage Through Pits, Puddles, and Ponds (P8), and Arid-Lands Hydrologic Model (AHYMO)—were compared to determine which provided the best balance of accuracy and usability for simulating storm runoff in small watersheds in the urbanized area of Albuquerque, New Mexico. Additionally, results of this study could help inform model users who have interest in simulating storm runoff in similar urban areas throughout the United States. Each model was used to simulate storm runoff in the Hahn Arroyo watershed, an urbanized watershed with concrete-lined arroyo channels in the northeastern quadrant of Albuquerque that exhibits flashy, monsoonal-driven storm runoff. Model results were compared to observed discharge data, according to literature-recommended performance measures and performance evaluation criteria. The HEC-HMS model using the Soil Conservation Service (SCS) curve number (CN) and SCS unit hydrograph methods ranked the highest when averaging the individual performance measures (Nash-Sutcliffe Efficiency, percent bias, and coefficient of determination) rankings together across the hourly calibration and validation periods, followed by P8, which was tied with the HEC-HMS initial and constant approach. For daily rankings using the same rank-averaging approach, the HEC-HMS CN-based model and P8 were tied for the highest ranking, followed by the HEC-HMS initial and constant approach. Alternatively, rating performance using validation period results as an indication of the expected confidence in forecasted results for future conditions, the P8 model performed best for both hourly and daily time-steps, followed by the HEC-HMS CN-based model and the HEC-HMS initial and constant-based model. However, based on the literature performance evaluation criteria, the HEC-HMS and P8 models overall had marginally satisfactory performance only for operation at the daily time-step. Direct comparison of the HEC-HMS and P8 models to the AHYMO is difficult, given the different performance assessment criteria used to assess these models separately in this study, as recommended by the literature. The AHYMO results generally lacked precision, given the wide range in the performance assessment values across events in percent error in peak discharge, difference in timing of peak discharge, percent error in total runoff volume, and difference in duration of event relative to observed data. For some events, however, the AHYMO results were fairly accurate, and AHYMO was likely a good predictor of the timing of storm runoff and the shape of the hydrograph. This study did not assess the results for all potential applications of the models in the Albuquerque urbanized area. Further study may be required to assess the model performance capabilities in other modeling applications.

New Mexico↗

USGS2009

Impact of wildfire on levels of mercury in forested watershed systems: Voyageurs National Park, Minnesota

Atmospheric deposition of mercury to remote lakes in mid-continental and eastern North America has increased approximately threefold since the mid-1800s (Swain and others, 1992; Fitzgerald and others, 1998; Engstrom and others, 2007). As a result, concerns for human and wildlife health related to mercury contamination have become widespread. Despite an apparent recent decline in atmospheric deposition of mercury in many areas of the Upper Midwest (Engstrom and Swain, 1997; Engstrom and others, 2007), lakes in which fish contain levels of mercury deemed unacceptable for human consumption and possibly unacceptable for fish-consuming wildlife are being detected with increasing frequency. In northern Minnesota, Voyageurs National Park (VNP) (fig. 1) protects a series of southern boreal lakes and wetlands situated on bedrock of the Precambrian Canadian Shield. Mercury contamination has become a significant resource issue within VNP as high concentrations of mercury in loons, bald eagle eaglets, grebes, northern pike, and other species of wildlife and fish have been found. The two most mercury-contaminated lakes in Minnesota, measured as methylmercury in northern pike ( Esox lucius ), are in VNP. Recent multidisciplinary U.S. Geological Survey (USGS) research demonstrated that the bulk of the mercury in lake waters, soils, and fish in VNP results from atmospheric deposition (Wiener and others, 2006). The study by Wiener and others (2006) showed that the spatial distribution of mercury in watershed soils, lake waters, and age-1 yellow perch ( Perca flavescens ) within the Park was highly variable. The majority of factors correlated for this earlier study suggested that mercury concentrations in lake waters and age-1 yellow perch reflected the influence of ecosystem processes that affected within-lake microbial production and abundance of methylmercury (Wiener and others, 2006), while the distribution of mercury in watershed soils seemed to be partially dependent on forest disturbance, especially the historic forest fire pattern (Woodruff and Cannon, 2002). Forest fire has an essential role in the forest ecosystems of VNP (Heinselman, 1996). Because resource and land managers need to integrate both natural wildfire and prescribed fire in management plans, the potential influence of fire on an element as sensitive to the environment as mercury becomes a critical part of their decisionmaking. A number of recent studies have shown that while fire does have a significant impact on mercury at the landscape level, the observed effects of fire on aquatic environments are highly variable and unpredictable (Caldwell and others, 2000; Garcia and Carrigan, 2000; Kelly and others, 2006; Nelson and others, 2007). Caldwell and others (2000) described an increase in methylmercury in reservoir sediments resulting from mobilization and transport of charred vegetative matter following a fire in New Mexico. Krabbenhoft and Fink (2000) attributed increases in total mercury concentrations in young-of-the-year fish in the Florida Everglades to release of mercury resulting from peat oxidation following fires. A fivefold increase in whole-body mercury accumulation by rainbow trout ( Oncorhynchus mykiss ) following a fire in Alberta, Canada, apparently resulted from increased nutrient concentrations that enhanced productivity and restructured the food web of a lake within the fire’s burn footprint (Kelly and others, 2006). For this study, we determined the short-term effects of forest fire on mercury concentrations in terrestrial and aquatic environments in VNP by comparing and contrasting mercury concentrations in forest soils, lake waters, and age-1 yellow perch for a burned watershed and an adjacent lake, with similar samples from watersheds and lakes with no fire activity (control watersheds and lakes). The concentration of total mercury in whole, 1-year-old yellow perch serves as a good biological indicator for monitoring trends in methylmercury concentrations in food webs of lakes in North America (Wiener and others, 2007). With a limited gape, age-1 yellow perch that hatched the previous year and resided in a lake for 1 year feed largely on zooplankton and small benthic invertebrates. Thus, age-1 yellow perch provide a baseline for methylmercury concentrations for individual lakes that can be compared across spatial areas. The nine appendixes that accompany this report contain the complete datasets for soils, lake waters, and age-1 yellow perch collected for this study. This report uses data from these three media to provide a framework for evaluating short-term effects of fire on mercury in forested soils and possible effects of the mobilization of mercury from soils on lake water quality and aquatic health.

Minnesota↗

USGS2012

Organic carbon burial rates in mangrove sediments: strengthening the global budget

Mangrove wetlands exist in the transition zone between terrestrial and marine environments and as such were historically overlooked in discussions of terrestrial and marine carbon cycling. In recent decades, mangroves have increasingly been credited with producing and burying large quantities of organic carbon (OC). The amount of available data regarding OC burial in mangrove soils has more than doubled since the last primary literature review (2003). This includes data from some of the largest, most developed mangrove forests in the world, providing an opportunity to strengthen the global estimate. First-time representation is now included for mangroves in Brazil, Colombia, Malaysia, Indonesia, China, Japan, Vietnam, and Thailand, along with additional data from Mexico and the United States. Our objective is to recalculate the centennial-scale burial rate of OC at both the local and global scales. Quantification of this rate enables better understanding of the current carbon sink capacity of mangroves as well as helps to quantify and/or validate the other aspects of the mangrove carbon budget such as import, export, and remineralization. Statistical analysis of the data supports use of the geometric mean as the most reliable central tendency measurement. Our estimate is that mangrove systems bury 163 (+40; -31) g OC m -2 yr -1 (95% C.I.). Globally, the 95% confidence interval for the annual burial rate is 26.1 (+6.3; -5.1) Tg OC. This equates to a burial fraction that is 42% larger than that of the most recent mangrove carbon budget (2008), and represents 10–15% of estimated annual mangrove production. This global rate supports previous conclusions that, on a centennial time scale, 8–15% of all OC burial in marine settings occurs in mangrove systems.

Global Biogeochemical Cycles↗