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USGS2021

Assessing the biological reactivity of organic compounds on volcanic ash: Implications for human health hazard

Exposure to volcanic ash is a long-standing health concern for people living near active volcanoes and in distal urban areas. During transport and deposition, ash is subjected to various physicochemical processes that may change its surface composition and, consequently, bioreactivity. One such process is the interaction with anthropogenic pollutants; however, the potential for adsorbed, deleterious organic compounds to directly impact human health is unknown. We use an in vitro bioanalytical approach to screen for the presence of organic compounds of toxicological concern on ash surfaces and assess their biological potency. These compounds include polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo- p -dioxins and dibenzofurans (PCDD/Fs) and dioxin-like polychlorinated biphenyls (dlPCBs). Analysis of ash collected in or near urbanised areas at five active volcanoes across the world (Etna, Italy; Fuego, Guatemala; Kelud, Indonesia; Sakurajima, Japan; Tungurahua, Ecuador) using the bioassay inferred the presence of such compounds on all samples. A relatively low response to PCDD/Fs and the absence of a dlPCBs response in the bioassay suggest that the measured activity is dominated by PAHs and PAH-like compounds. This study is the first to demonstrate a biological potency of organic pollutants associated with volcanic ash particles. According to our estimations, they are present in quantities below recommended exposure limits and likely pose a low direct concern for human health.

Bulletin of Volcanology↗

USGS2002

Effect of dissolved organic carbon quality on microbial decomposition and nitrification rates in stream sediments

1. Microbial decomposition of dissolved organic carbon (DOC) contributes to overall stream metabolism and can influence many processes in the nitrogen cycle, including nitrification. Little is known, however, about the relative decomposition rates of different DOC sources and their subsequent effect on nitrification. 2. In this study, labile fraction and overall microbial decomposition of DOC were measured for leaf leachates from 18 temperate forest tree species. Between 61 and 82% (mean, 75%) of the DOC was metabolized in 24 days. Significant differences among leachates were found for labile fraction rates (P < 0.0001) but not for overall rates (P = 0.088). 3. Nitrification rates in stream sediments were determined after addition of 10 mg C L-1 of each leachate. Nitrification rates ranged from below detection to 0.49 ??g N mL sediment-1 day-1 and were significantly correlated with two independent measures of leachate DOC quality, overall microbial decomposition rate (r = -0.594, P = 0.0093) and specific ultraviolet absorbance (r = 0.469, P = 0.0497). Both correlations suggest that nitrification rates were lower in the presence of higher quality carbon. 4. Nitrification rates in sediments also were measured after additions of four leachates and glucose at three carbon concentrations (10, 30, and 50 mg C L-1). For all carbon sources, nitrification rates decreased as carbon concentration increased. Glucose and white pine leachate most strongly depressed nitrification. Glucose likely increased the metabolism of heterotrophic bacteria, which then out-competed nitrifying bacteria for NH4+. White pine leachate probably increased heterotrophic metabolism and directly inhibited nitrification by allelopathy.

Freshwater Biology↗

USGS2010

Microparasite ecology and health status of common bluestriped snapper Lutjanus kasmira from the Pacific Islands

Common bluestriped snappers Lutjanus kasmira were intentionally introduced into Hawaii from the South Pacific in the 1950s and have become well established throughout the archipelago. We examined health, prevalence and infection intensity of 2 microparasites, coccidia and epitheliocystis-like organisms (ELO), in L. kasmira from their introduced and native range including the islands where translocated fish originated (Tahiti and Marquesas Islands, French Polynesia) and from several other islands (American Samoa, Fiji and New Caledonia). In addition, we did a longitudinal survey of these parasites in the introduced range. Coccidia and ELO were widely distributed and were found on all islands except for New Caledonia. Health indices, as measured by overall organ lesions, body condition and parasite intensity, indicated that fish from Samoa were the least healthy, and fish from Midway (Hawaiian Archipelago) were the healthiest. Microparasite diversity was highest on Midway and Hawaii and lowest on New Caledonia. Infection of coccidia followed an asymptotic size–prevalence curve, whereas that of ELO peaked at larger size classes (27.8 cm). Prevalence and aggregation of both parasites in the host varied dynamically over 8 yr, with prevalence and aggregation of coccidia being consistently higher and lower, respectively, than ELO. We hypothesize that these parasites are enzootic to the Hawaiian Islands and were not introduced with fish from Tahiti or the Marquesas Islands. Host response and aggregation parameters suggest that coccidia exert a negative effect on their host and probably have an indirect life cycle, whereas ELO appears less pathogenic and has a direct life cycle.

Aquatic Biology↗

USGS2012

Enhanced surveillance strategies for detecting and monitoring chronic wasting disease in free-ranging cervids

The purpose of this document is to provide wildlife management agencies with the foundation upon which they can build scientifically rigorous and cost-effective surveillance and monitoring programs for chronic wasting disease (CWD) or refine their existing programs. The first chapter provides an overview of potential demographic and spatial risk factors of susceptible wildlife populations that may be exploited for CWD surveillance and monitoring. The information contained in this chapter explores historic as well as recent developments in our understanding of CWD disease dynamics. It also contains many literature references for readers who may desire a more thorough review of the topics or CWD in general. The second chapter examines methods for enhancing efforts to detect CWD on the landscape where it is not presently known to exist and focuses on the efficiency and cost-effectiveness of the surveillance program. Specifically, it describes the means of exploiting current knowledge of demographic and spatial risk factors, as described in the first chapter, through a two-stage surveillance scheme that utilizes traditional design-based sampling approaches and novel statistical methods to incorporate information about the attributes of the landscape, environment, populations and individual animals into CWD surveillance activities. By accounting for these attributes, efficiencies can be gained and cost-savings can be realized. The final chapter is unique in relation to the first two chapters. Its focus is on designing programs to monitor CWD once it is discovered within a jurisdiction. Unlike the prior chapters that are more detailed or prescriptive, this chapter by design is considerably more general because providing comprehensive direction for creating monitoring programs for jurisdictions without consideration of their monitoring goals, sociopolitical constraints, or their biological systems, is not possible. Therefore, the authors draw upon their collective experiences implementing disease-monitoring programs to present the important questions to consider, potential tools, and various strategies for those wildlife management agencies endeavoring to create or maintain a CWD monitoring program. Its intent is to aid readers in creating efficient and cost-effective monitoring programs, while avoiding potential pitfalls. It is hoped that these three chapters will be useful tools for wildlife managers struggling to implement efficient and effective CWD disease management programs.

Open-File Report↗

USGS1984

A workshop model simulating fate and effect of drilling muds and cuttings on benthic communities

Oil and gas exploration and production at marine sites has generated concern over potential environmental impacts resulting from the discharge of spent drilling muds and cuttings. This concern has led to a broad array of publicly and privately sponsored research. This report described a cooperative modeling effort designed to focus information resulting from this research through construction of explicit equations that simulate the potential impacts of discharge drilling fluids (muds) and cuttings on marine communities. The model is the result of collaboration among more than 30 scientists. The principal cooperating organizations were the E.S. Environmental Protection Agency, the U.S. Minerals Management Service, the Offshore Operators Committee, and the Alaska Oil and Gas Association. The overall simulation model can be conceptualized as three connected submodels: Discharge and Plume Fate, Sediment Redistribution, and Benthic Community Effects. On each day of simulation, these submodels are executed in sequence, with flows of information between submodels. The Benthic Community Effects submodel can be further divided into sections that calculate mortality due to burial, mortality due to toxicity, mortality due to resuspension disturbance, and growth of the community. The model represents a series of seven discrete 1-m 2 plots at specified distances along a transect in one direction away from a discharge point. It consists of coupled difference equations for which parameter values can easily be set to evaluate different conditions or to examine the sensitivity of output to various assumptions. Sets of parameter values were developed to represent four general cases or scenarios: (1) a shallow (5 m), cold environment with ice cover during a substantial fraction of the year, such as might be encountered in the Beaufort Sea, Alaska; (2) a shallow (20 m), temperate environment, such as might be encountered in the Gulf of Mexico; (3) a deeper (80 m), temperate environment, such as might be encountered in the Gulf of Mexico; and (4) a very deep (1,000 m) environment, such as might be encountered on the Atlantic slope. The focus of the modeling effort was on the connection of a reasonable representation of physical fate to the biological responses of populations, rather than on highly detailed representations of individual processes. For example, the calculations of physical fate are not as detailed as those in the recently published model of Brandsma et al. (1983). The value of the model described herein is in the broad scope of processes that are explicitly represented and linked together. The model cannot be considered to produce reliable predictions of the quantitative impacts of discharged drilling fluids and cuttings on biological populations at a particular site. Limitations of the model in predicting integrated fate and effects can be traced to three general areas: level of refinement of the algorithms used in the model; lack of understanding of the processes determining fate and effects; and parameter and data values. Despite the limitations, several qualitative conclusions concerning both potential impacts and the importance of various remaining data gaps can be drawn from the modeling effort. These include: (1) Simple, unequivocal conclusions about fate and effects across geographical regions and drilling operations are difficult, if not misleading, due to the large amount of variability in characteristics of discharged materials (e.g., oil content and toxicity), discharge conditions (e.g., duration of drilling operations), physical environments (e.g., water depth, current direction, and sediment disturbance regimes), and biological communities (e.g., intrinsic growth rates). Different combinations of these characteristics can result in substantial differences in simulated environmental fate and biological effects. For examples, simulated recovery in some high-energy environments occurs within months after the cessation of discharge operations, even at heavily impacted sites, whereas simulated recover in some low-energy environments takes years at heavily impacted sites. <2) Considerable difficulties remain in the reliable extrapolation of results from laboratory toxicity experiments to predictions of population effects in the field. (3) The volume of material discharged and duration of operations in the production drilling operations simulated by the model are sufficient to produce substantial simulated biological impacts at some plots, both in terms of differences from a control plot during the period of discharge operations, and in terms of the recovery period following the perturbations. Evaluation of the significance of potential effects involves the following factors: • Definition of a specific spatial and temporal reference frame (e.g., What is the natural variation? Is 1 year to be considered a "long" or "short" time? Is 50 m to be considered a "large" or "trivial" distance? • Consideration of rare or unique resources and particularly sensitive biotic assemblages. • Consideration of the potential for long term, cumulative effects. Some of these aspects are clearly beyond the scope of this modeling efforts (e.g., the model does not simulate the long term fate of resuspended material). The model does, however, contain an internal "reference frame" by comparison to simulated behavior at a control plot. The model, in general, simulates substantial "natural" variation at the reference or control plots, both over time, due to sediment disturbance events in medium to high energy environments, and over space, due to geographically varying conditions, such as water depth and current regime.

Report↗

USGS1991

Role of exposure mode in the bioavailability of triphenyl phosphate to aquatic organisms

A laboratory study was conducted to investigate the role of the route of triphenyl phosphate (TPP) entry on its aquatic bioavailability and acute biological effects. Three TPP treatments were used for exposures of fish and invertebrates. These consisted of TPP dosed directly into water with and without clean sediment and TPP spiked onto sediment prior to aqueous exposures. Results of static acute toxicity tests (no sediment) were 0.78 mg/L (96-h LC50) for bluegill, 0.36 mg/L (48-h EC50) for midge, and 0.25 mg/L (96-h EC50) for scud. At 24 h, the sediment (1.1% organic carbon)/water partition coefficient (Kp) for TPP was 112. Use of this partition coefficient model to predict the sediment-mediated reduction of TPP concentration in water during toxicity tests resulted in a value that was only 10% less than the nominal value. However, the required nominal concentration of TPP to cause acute toxicity responses in test organisms was significantly higher than the predicted value by the model for both clay and soil-derived sediment. Direct spiking of TPP to soil minimized TPP bioavailability. Data from parallel experiments designed to track TPP residues in water through time suggest that sorption kinetics control residue bioavailability in the initial 24 h of exposure and may account for observed differences in LC50 and EC50 values from the sediment treatments.

Archives of Environmental Contamination and Toxico↗

USGS2020

Post-fire management-scale trials of bacterial soil amendment MB906 show inconsistent control of invasive annual grasses

Rangeland managers need tools to control invasive annual grasses, particularly following wildfire. We assessed responses of native and invasive/exotic grasses to the MB906 soil amendment containing live cultures of a purportedly weed-suppressive strain of the bacterium Pseudomonas fluorescens (“WSB”). MB906 was applied alone and in combination with the pre-emergent herbicide imazapic on >3000 ha across three sagebrush-steppe landscapes burned several months prior. Replicate plots of each treatment type were established and plant cover was measured in the following three years. Cover of invasive-annual grasses (“IAG”) was not responsive to MB906 when all IAG species were considered (“IAG-All”). However, MB906 led to a 54% reduction in the IAG's that were previously reported to be controlled by WSB (“IAG-Target”) in the second year following application (IAG-Target = cheatgrass, Bromus tectorum and medusahead, Taeniatherum caput-medusae; IAG-All also includes Vulpia myuros and Bromus arvensis ). MB906 reduced the effectiveness of co-applied imazapic: Imazapic alone reduced IAG-All by 83% and 68% in years 1 and 2, respectively, while imazapic+MB906 reduced IAG-All by 48% and 38% in years 1 and 2, respectively, across all landscapes, and a similar response pattern was observed for IAG-Target. Perennial grass cover was unaffected by the treatments except where it increased 4-fold in response to imazapic applied at a high rate (0.140 kg a.i. ha −1 ) in one of the landscapes. Tank mixing MB906 and herbicide may have lessened the biological activity of the herbicide by altering the pH or mineral content of the spray solution or by direct metabolism of the herbicide by the bacteria. These results do not provide strong support for MB906 as a tool for annual grass control, though they suggest further investigation may be warranted.

Rangeland Ecology and Management↗

USGS2007

Potential effects of climate change on surface-water quality in North America

Data from long-term ecosystem monitoring and research stations in North America and results of simulations made with interpretive models indicate that changes in climate (precipitation and temperature) can have a significant effect on the quality of surface waters. Changes in water quality during storms, snowmelt, and periods of elevated air temperature or drought can cause conditions that exceed thresholds of ecosystem tolerance and, thus, lead to water-quality degradation. If warming and changes in available moisture occur, water-quality changes will likely first occur during episodes of climate-induced stress, and in ecosystems where the factors controlling water quality are sensitive to climate variability. Continued climate stress would increase the frequency with which ecosystem thresholds are exceeded and thus lead to chronic water-quality changes. Management strategies in a warmer climate will therefore be needed that are based on local ecological thresholds rather than annual median condition. Changes in land use alter biological, physical, and chemical processes in watersheds and thus significantly alter the quality of adjacent surface waters; these direct human-caused changes complicate the interpretation of water-quality changes resulting from changes in climate, and can be both mitigated and exacerbated by climate change. A rigorous strategy for integrated, long-term monitoring of the ecological and human factors that control water quality is necessary to differentiate between actual and perceived climate effects, and to track the effectiveness of our environmental policies.

Journal of the American Water Resources Associatio↗

USGS2020

Global status of trout and char: Conservation challenges in the twenty-first century

Freshwater ecosystems are among the most threatened ecosystems in the world (Richter et al. 1997; Strayer and Dudgeon 2010), and freshwater fishes may now be the most threatened group of vertebrates (Ricciardi and Rasmussen 1999; Vorosmarty et al. 2010; Darwall and Freyhof 2016). Of the 7,300 freshwater fish species globally assessed by the International Union for Conservation of Nature (IUCN, www.iucnredlist.org) in 2013, nearly one of every three species was threatened with extinction (Darwall and Freyhof 2016). Growing pressures from a multitude of direct and indirect human stressors (e.g., habitat loss and degradation, pollution, invasive species, overexploitation, diversion or alteration of biological flows, climate change, and others) threaten the persistence of many freshwater fish species and entire aquatic communities around the globe (Limburg et al. 2011). This pattern is particularly true for salmonid fishes (family Salmonidae, subfamily Salmoninae, belonging to the genera Oncorhynchus, Salvelinus, Salmo, Hucho, Parahucho, Brachymystax, and Salvethymus). Salmonids are globally-distributed, coldwater taxa with life-cycles restricted entirely to freshwater ecosystems (typically referred to as trout and char), but also Atlantic and Pacific salmon with more complex anadromous life-histories.

Book chapter↗

USGS2023

A review of grass carp and related species literature on diet, behavior, toxicology, and physiology focused on informing development of controls for invasive grass carp populations in North America

Grass carp ( Ctenopharyngodon idella ) are globally important in aquaculture and aquatic vegetation control. However, escaped grass carp have established invasive populations. A targeted keyword search was performed on a carp (order: Cypriniformes) literature database maintained by the U.S. Geological Survey to identify literature relevant to grass carp. Additional sources cited in reviewed documents and provided by numerous reviewers were also included. There were three focus areas designed to provide support for invasive grass carp management: (1) diet and behavior; (2) physiological constraints, toxicity, and biology; and (3) gut physiology. Each focus area provides information to guide development of potential pathways for invasive grass carp control. Information from other carp species was used to fill in gaps where grass carp information was lacking and provide additional, potential research directions. Diet-related information included food selection and aquacultural diet formulations. Behavioral information included stimuli and non-physical barriers to attract, repel, or stop movement. Physiological constraints, toxicology, reproductive control, and biological control provide a research review for control options. Gut physiology and related control pathways provide knowledge to improve toxin or pathogen delivery. This review provides a basis for developing approaches and research for controlling invasive grass carp populations, aquaculture, and native population management.

Fishes↗

USGS2017

Hydrologic metrics for status-and-trends monitoring in urban and urbanizing watersheds

Local governmental agencies are increasingly undertaking potentially costly “status-and-trends” monitoring to evaluate the effectiveness of stormwater control measures and land-use planning strategies, or to satisfy regulatory requirements. Little guidance is presently available for such efforts, and so we have explored the application, interpretation, and temporal limitations of well-established hydrologic metrics of runoff changes from urbanization, making use of an unusually long-duration, high-quality data set from the Pacific Northwest (USA) with direct applicability to urban and urbanizing watersheds. Three metrics previously identified for their utility in identifying hydrologic conditions with biological importance that respond to watershed urbanization—T Qmean (the fraction of time that flows exceed the mean annual discharge), the Richards-Baker Index (characterizing flashiness relative to the mean discharge), and the annual tally of wet-season day-to-day flow reversals (the total number of days that reverse the prior days’ increasing or decreasing trend)—are all successful in stratifying watersheds across a range of urbanization, as measured by total contributing area of urban development. All metrics respond with statistical significance to multi-decadal trends in urbanization, but none detect trends in watershed-scale urbanization over the course of a single decade. This suggests a minimum period over which dependable trends in hydrologic alteration (or improvement) can be detected with confidence. The metrics also prove less well suited to urbanizing watersheds in a semi-arid climate, with only flow reversals showing a response consistent with prior findings from more humid regions. We also explore the use of stage as a surrogate for discharge in calculating these metrics, recognizing potentially significant agency cost savings in data collection with minimal loss of information. This approach is feasible but cannot be implemented under current data-reporting practices, requiring measurement of water-depth values and preservation of the full precision of the original recorded data. With these caveats, however, hydrologic metrics based on stage should prove as or more useful, at least in the context of status-and-trends monitoring, as those based on subsequent calculations of discharge.

Hydrological Processes↗

USGS2017

Evidence for early life in Earth’s oldest hydrothermal vent precipitates

Although it is not known when or where life on Earth began, some of the earliest habitable environments may have been submarine-hydrothermal vents. Here we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Quebec, Canada. These structures occur as micrometre-scale haematite tubes and filaments with morphologies and mineral assemblages similar to those of filamentous microorganisms from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes and magnetite–haematite granules, and is associated with carbonate in direct contact with the putative microfossils. Collectively, these observations are consistent with an oxidized biomass and provide evidence for biological activity in submarine-hydrothermal environments more than 3,770 million years ago.

Quebec↗

USGS2018

Modelling sound attenuation in heterogeneous environments for improved bioacoustic sampling of wildlife populations

Acoustic sampling methods are becoming increasingly important in biological monitoring. Sound attenuation is one of the most important dynamics affecting the utility of acoustic data as it directly affects the probability of detection of individuals by acoustic sensor arrays and especially the localization of acoustic signals necessary in telemetry studies. Therefore, models of sound attenuation are necessary to make efficient use of acoustic data in ecological monitoring and assessment applications. Models of attenuation in widespread use are based on Euclidean distance between source and sensor, which is justified under spherical attenuation of sound waves in homogeneous environments. In this paper, I develop a model of sound attenuation based on a non‐Euclidean cost‐weighted distance metric which contains attenuation coefficients that characterize the attenuation of sound due to environmental heterogeneity in the vicinity of an acoustic sensor array. I show that parameters of the proposed attenuation model can be estimated by maximum likelihood using experimental data from an array of fixed sources, thus allowing investigators who use bioacoustic methods to devise explicit models of sound attenuation in situ and apply them to localization of sources and density estimation. In addition, drawing on analogy with spatial capture–recapture models, I argue that parameters of the non‐Euclidean model of attenuation can be estimated when source locations are unknown . Thus, the models can be applied to real field studies which require estimation of attenuation parameters or localization of signals. Models of heterogeneous sound attenuation allow more accurate descriptions of acoustic monitoring data, and therefore should produce more accurate estimates of ecological parameters of interest, including source locations, density, and movement trajectories. Moreover, the ability to test specific hypotheses about the effects of habitat and landscape structure on sound attenuation can improve the design of acoustic monitoring arrays and lead to more efficient deployment of acoustic sensing technology.

Methods in Ecology and Evolution↗

USGS2025

Using plant invasions to compare occurrence- and abundance-based calculations of biotic homogenisation: Are results complementary or contradictory?

Aim Beta diversity quantifies the similarity of ecological assemblages. Its increase, known as biotic homogenisation, can be a consequence of biological invasions. However, species occurrence (presence/absence) and abundance-based analyses can produce contradictory assessments of the magnitude and direction of changes in beta diversity. Previous work indicates these contradictions should be less frequent in nature than in theory, but a growing number of empirical studies report discrepancies between occurrence- and abundance-based approaches. Understanding if these discrepancies represent a few isolated cases or are systematic across a diversity of ecosystems would allow us to better understand the general patterns, mechanisms and impacts of biotic homogenisation. Location United States. Time Period 1963–2020. Major Taxa Studied Vascular plants. Methods We used a dataset of more than 70,000 vegetation survey plots to assess differences in biotic homogenisation with and without invasion using both occurrence- and abundance-based metrics of beta diversity. We estimated taxonomic biotic homogenisation by comparing beta diversity of invaded and uninvaded plots with both classes of metrics and investigated the characteristics of the non-native species pool that influenced the likelihood that these metrics disagree. Results In 78% of plot comparisons, occurrence- and abundance-based calculations agreed in direction, and the two metrics were generally well correlated. Our empirical results are consistent with previous theory. Discrepancies between the metrics were more likely when the same non-native species was at high cover at both plots compared for beta diversity, and when these plots were spatially distant. Main Conclusions In about 20% of cases, our calculations revealed differences in direction (homogenisation vs. differentiation) when comparing occurrence- and abundance-based metrics, indicating that the metrics are not interchangeable, especially when distances between plots are high and invader diversity is low. When data permit, combining the two approaches can offer insights into the role of invasions and extirpations in driving biotic homogenisation/differentiation.

Global Ecology and Biogeography↗

USGS2012

Strategies for soil quality assessment using VNIR gyperspectral spectroscopy in a western Kenya Chronosequence

Visible and near-infrared reflectance spectroscopy (VNIRS) is a rapid and nondestructive method that can predict multiple soil properties simultaneously, but its application in multidimensional soil quality (SQ) assessment in the tropics still needs to be further assessed. In this study, VNIRS (350–2500 nm) was employed to analyze 227 air-dried soil samples of Ultisols from a soil chronosequence in western Kenya and assess 16 SQ indicators. Partial least squares regression (PLSR) was validated using the full-site cross-validation method by grouping samples from each farm or forest site. Most suitable models successfully predicted SQ indicators (R 2 ≥ 0.80; ratio of performance to deviation [RPD] ≥ 2.00) including soil organic matter (OM LOI ), active C, Ca, cation exchange capacity (CEC), and clay. Moderately-well predicted indicators (0.50 ≤ R 2 < 0.80; 1.40 ≤ RPD < 2.00) were water stable aggregation (WSA), Cu, silt, Mg, pH, sand, water content at permanent wilting point (Θ pwp ), and field capacity (Θ fc ). Poorly predicted indicators (R 2 < 0.50; RPD < 1.40) were EC, S, P, available water capacity (AWC), K, Zn, and penetration resistance. Combining VNIRS with selected field- and laboratory-measured SQ indicator values increased predictability. Furthermore, VNIRS showed moderate to substantial agreement in predicting interpretive SQ scores and a composite soil quality index (CSQI) especially when combined with directly measured SQ indicator values. In conclusion, VNIRS has good potential for low cost, rapid assessment of physical and biological SQ indicators but conventional soil chemical tests may need to be retained to provide comprehensive SQ assessments.

Western Kenya↗

USGS2015

Literature review of giant gartersnake ( Thamnophis gigas ) biology and conservation

This report reviews the available literature on giant gartersnakes ( Thamnophis gigas ) to compile existing information on this species and identify knowledge gaps that, if addressed, would help to inform conservation efforts for giant gartersnakes. Giant gartersnakes comprise a species of semi-aquatic snake precinctive to wetlands in the Central Valley of California. The diversion of surface water and conversion of wetlands to agricultural and other land uses resulted in the loss of more than 90 percent of natural giant gartersnake habitats. Because of this habitat loss, giant gartersnakes are now listed by the United States and California Endangered Species Acts as Threatened. Most extant populations occur in the rice-growing regions of the Sacramento Valley, which comprises the northern portion of the giant gartersnake’s former range. The huge demand for water in California for agriculture, industry, recreation, and other human consumption, combined with periodic severe drought, places remaining giant gartersnake habitats at increased risk of degradation and loss. This literature review summarizes the available information on giant gartersnake distribution, habitat relations, behavior, demography, and other aspects of its biology relevant to conservation. This information is then compiled into a graphical conceptual model that indicates the importance of different aspects of giant gartersnake biology for maintaining positive population growth, and identifies those areas for which important information relevant for conservation is lacking. Directing research efforts toward these aspects of giant gartersnake ecology will likely result in improvements to conserving this unique species while meeting the high demands for water in California.

Open-File Report↗

USGS2020

Identifying candidate reference reaches to assess the physical and biological integrity of wadeable streams in different ecoregions and among stream sizes

Efforts to quantify disturbances to aquatic systems often use landscape-level metrics, presumably linked to ecological integrity, but fewer studies have directly linked ecological integrity to instream habitat, and applied these results to unsampled stream reaches throughout a landscape. We developed a flexible, quantitative approach that characterizes stream impairment across a landscape and identifies least-disturbed stream reaches to serve as benchmarks for high quality physical habitat and ecological integrity. Fish and macroinvertebrate community characteristics, reach-level physical habitat and water quality metrics were summarized in 891 wadeable stream reaches across two ecoregions in Missouri, USA. The influence of reach and water-quality characteristics as well as landscape-level variables on 7 fish and 3 macroinvertebrate community biological indicator metrics was then modeled using boosted regression trees (BRTs). On average, reach-level models explained more variance (25 and 27% in the two ecoregions examined) in biotic metrics than landscape-level models (18% and 20%). Abiotic and biotic associations differed among ecoregions and stream sizes, however, reach-level habitat (e.g., bankfull width/depth ratio, channel incision height) and water quality (e.g., dissolved oxygen, total chlorophyll) were consistently top predictors. At the landscape scale, fish richness in the agriculturally dominated ecoregion increased with decreased fragmentation/flow modification, while invertebrate metrics responded to agricultural disturbances. Invertebrate metrics in the forested ecoregion showed community degradation apparent with crop coverage as low as 8-10% of the riparian zone, while urban impairment was best detected using invertebrate indicators of biotic integrity and measures of fish trophic ecology. Relationships among landscape-scale variables and reach characteristics identified as top predictors in BRTs also highlighted potential mechanistic relationships among landscape, habitat, and measures of ecological integrity. Using the results of the landscape-level models, estimates for overall ecological integrity were predicted for over 28,000 stream reaches throughout Missouri, and a total of 1,423 candidate reference reaches were identified. The objective approach to characterizing stream impairment developed in this study offers specific advantages, including a reach and landscape-level evaluation of human disturbance as well as an inductive, multi-metric determination of ecological integrity.

Missouri↗

USGS2014

Modelling non-Euclidean movement and landscape connectivity in highly structured ecological networks

Movement is influenced by landscape structure, configuration and geometry, but measuring distance as perceived by animals poses technical and logistical challenges. Instead, movement is typically measured using Euclidean distance, irrespective of location or landscape structure, or is based on arbitrary cost surfaces. A recently proposed extension of spatial capture-recapture (SCR) models resolves this issue using spatial encounter histories of individuals to calculate least-cost paths (ecological distance: Ecology , 94 , 2013, 287) thereby relaxing the Euclidean assumption. We evaluate the consequences of not accounting for movement heterogeneity when estimating abundance in highly structured landscapes, and demonstrate the value of this approach for estimating biologically realistic space-use patterns and landscape connectivity. We simulated SCR data in a riparian habitat network, using the ecological distance model under a range of scenarios where space-use in and around the landscape was increasingly associated with water (i.e. increasingly less Euclidean). To assess the influence of miscalculating distance on estimates of population size, we compared the results from the ecological and Euclidean distance based models. We then demonstrate that the ecological distance model can be used to estimate home range geometry when space use is not symmetrical. Finally, we provide a method for calculating landscape connectivity based on modelled species-landscape interactions generated from capture-recapture data. Using ecological distance always produced unbiased estimates of abundance. Explicitly modelling the strength of the species-landscape interaction provided a direct measure of landscape connectivity and better characterised true home range geometry. Abundance under the Euclidean distance model was increasingly (negatively) biased as space use was more strongly associated with water and, because home ranges are assumed to be symmetrical, produced poor characterisations of home range geometry and no information about landscape connectivity. The ecological distance SCR model uses spatially indexed capture-recapture data to estimate how activity patterns are influenced by landscape structure. As well as reducing bias in estimates of abundance, this approach provides biologically realistic representations of home range geometry, and direct information about species-landscape interactions. The incorporation of both structural (landscape) and functional (movement) components of connectivity provides a direct measure of species-specific landscape connectivity.

Methods in Ecology and Evolution↗