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UAV lidar and hyperspectral fusion for forest monitoring in the southwestern USA

Forest vegetation classification and structure measurements are fundamental steps for planning, monitoring, and evaluating large-scale forest changes including restoration treatments. High spatial and spectral resolution remote sensing data are critically needed to classify vegetation and measure their 3-dimensional (3D) canopy structure at the level of individual species. Here we test high-resolution lidar, hyperspectral, and multispectral data collected from unmanned aerial vehicles (UAV) and demonstrate a lidar-hyperspectral image fusion method in treated and control forests with varying tree density and canopy cover as well as in an ecotone environment to represent a gradient of vegetation and topography in northern Arizona, U.S.A. The fusion performs better (88% overall accuracy) than either data type alone, particularly for species with similar spectral signatures, but different canopy sizes. The lidar data provides estimates of individual tree height ( R 2 = 0.90; RMSE = 2.3 m) and crown diameter ( R 2 = 0.72; RMSE = 0.71 m) as well as total tree canopy cover ( R 2 = 0.87; RMSE = 9.5%) and tree density ( R 2 = 0.77; RMSE = 0.69 trees/cell) in 10 m cells across thin only, burn only, thin-and-burn, and control treatments, where tree cover and density ranged between 22 and 50% and 1–3.5 trees/cell, respectively. The lidar data also produces highly accurate digital elevation model (DEM) ( R 2 = 0.92; RMSE = 0.75 m). In comparison, 3D data derived from the multispectral data via structure-from-motion produced lower correlations with field-measured variables, especially in dense and structurally complex forests. The lidar, hyperspectral, and multispectral sensors, and the methods demonstrated here can be widely applied across a gradient of vegetation and topography for monitoring landscapes undergoing large-scale changes such as the forests in the southwestern U.S.A.

Arizona↗

Spectral mixture analysis for surveillance of harmful algal blooms (SMASH): A field-, laboratory-, and satellite-based approach to identifying cyanobacteria genera from remotely sensed data

Algal blooms around the world are increasing in frequency and severity, often with the possibility of adverse effects on human and ecosystem health. The health and economic impacts associated with harmful algal blooms, or HABs, provide compelling rationale for developing new methods for monitoring these events via remote sensing. Although concentrations of chlorophyll- a and key pigments like phycocyanin are routinely estimated from satellite images and used to infer algal or cyanobacterial cell counts, current methods are unable to provide information on the taxonomic composition of a bloom. This study introduced a new approach capable of differentiating among genera based on their reflectance characteristics: Spectral Mixture Analysis for Surveillance of HABs, or SMASH. The foundation of SMASH is a multiple endmember spectral mixture analysis (MESMA) algorithm that takes a library of cyanobacteria endmembers and a hyperspectral image as input and estimates the fractional abundance of each genus, plus water, on a per-pixel basis. Importantly, we assume that the water column consists of only pure water and cyanobacteria, implying that our linear spectral unmixing models do not account for other optically active constituents such as suspended sediment and colored dissolved organic matter (CDOM). We used reflectance spectra for 12 genera measured under a microscope to populate an algal spectral library and applied the SMASH workflow to satellite images from four waterbodies across the United States. Normalized spectral separability scores indicated that the 12 genera were distinct from one another and the MESMA algorithm reproduced known input fractions for simulated mixtures that included all pairwise combinations of genera and water. We used Upper Klamath Lake as an example to illustrate data products generated via SMASH: maps of the normalized difference chlorophyll index and cyanobacterial index, a MESMA-based classification of algal genera, fraction images for each endmember, and a root mean square error (RMSE) image that summarizes uncertainty. For Upper Klamath Lake, these outputs highlighted a complex algal bloom featuring several genera, primarily Aphanizomenon , and intricate spatial patterns associated with gyres. The maximum RMSE constraint imposed on the MESMA algorithm provided a means of avoiding false positive detection of genera not present in a waterbody but must not be set so low as to leave much of an image unclassified in cases where genera included in the library are present. Comparison of endmember fractions with relative biovolumes calculated from field samples indicated that taxonomic information from SMASH was consistent with field observations. For example, the algorithm successfully identified Microcystis in Owasco Lake but avoided misclassifying Asterionella , a genus not yet included in our library, in Detroit Lake. This proof-of-concept investigation demonstrates the potential of SMASH to enhance our understanding of algal blooms, particularly with respect to their spatial and temporal dynamics.

New York, Oregon, Texas↗

Stable isotopes used to infer trophic position of green turtles (Chelonia mydas) from Dry Tortugas National Park, Gulf of Mexico, United States

Evaluating resource use patterns for imperiled species is critical for understanding what supports their populations. Here we established stable isotope ( δ 13 "> δ13 C, δ 15 "> δ15 N) values for the endangered green sea turtle ( Chelonia mydas ) population found within the boundaries of Dry Tortugas National Park (DRTO), south Florida, USA. There is little gene flow between turtles sampled at DRTO and in other rookeries in Florida, underscoring the need to study this distinct population. Between 2008 and 2015 we collected multiple sample types (skin [homogenized epidermis/dermis], whole blood, red blood cells, plasma, carapace) from 151 unique green turtles, including 43 nesting females and 108 in-water captures; some individuals were resampled multiple times across years to evaluate consistency of isotope signatures. Isotopic ratios ranged from -27.3 to -5.4 for δ 13 "> δ 13 C and 3.7 to 10.6 for δ 15 "> δ 15 N. Using linear mixed models, we evaluated covariates (sample type, turtle size and year) that best explained the isotope patterns observed in turtle tissues. Predictions from the top model for δ 13 "> δ 13 C indicated a slight decrease over time and for δ 15 "> δ 15 N a slight increase in the middle sampling years (2010–2012); results indicated that turtle size appeared to be the driver behind the range in δ 13 "> δ 13 C and δ 15 "> δ 15 N observed in turtle skin. We found a pattern in stable carbon isotope values that are indicative of an ontogenetic change from an omnivorous diet in smaller turtles to a seagrass-based diet in larger turtles. When we compared the stable carbon and nitrogen isotope values of the samples collected from turtles with that of seagrasses found in DRTO, we found that turtles > 65 cm SCL had similar stable carbon isotope values to the seagrass species present. Results of this study suggest stable isotope analysis coupled with data for available resources can be useful for tracking and detecting future changes in green turtle resource shifts in DRTO.

Florida↗

Environmental contaminants and biomarker responses in fish from the Rio Grande and its U.S. tributaries: Spatial and temporal trends

We collected, examined, and analyzed 368 fish of seven species from 10 sites on rivers of the Rio Grande Basin (RGB) during late 1997 and early 1998 to document temporal and geographic trends in the concentrations of accumulative contaminants and to assess contaminant effects on the fish. Sites were located on the mainstem of the Rio Grande and on the Arroyo Colorado and Pecos River in Texas (TX), New Mexico (NM), and Colorado. Common carp (Cyprinus carpio) and largemouth bass (Micropterus salmoides) were the targeted species. Fish were examined in the field for internal and external visible gross lesions, selected organs were weighed to compute ponderal and organosomatic indices, and samples of tissues and fluids were obtained and preserved for analysis of fish health and reproductive biomarkers. Whole fish from each station were composited by species and gender and analyzed for organochlorine chemical residues and elemental contaminants using instrumental methods, and for 2,3,7,8-tetrachloro dibenzo-p-dioxin-like activity (TCDD-EQ) using the H4IIE rat hepatoma cell bioassay. Overall, fish from lower RGB stations contained greater concentrations of organochlorine pesticide residues and appeared to be less healthy than those from sites in the central and upper parts of the basin, as indicated by a general gradient of residue concentrations and biomarker responses. A minimal number of altered biomarkers and few or no elevated contaminant concentrations were noted in fish from the upper RGB. The exception was elevated concentrations [up to 0.46 ??g/g wet-weight (ww)] of total mercury (Hg) in predatory species from the Rio Grande at Elephant Butte Reservoir, NM, a condition documented in previous studies. Arsenic (As) and selenium (Se) concentrations were greatest in fish from sites in the central RGB; Se concentrations in fish from the Pecos River at Red Bluff Lake, TX and from the Rio Grande at Langtry, TX and Amistad International Reservoir, TX exceeded published fish and wildlife toxicity thresholds. In the lower RGB, residues of p,p???-DDT metabolites (???1.69 ??g/g ww), chlordane-related compounds (???0.21 ??g/g ww), dieldrin (???0.0.05 ??g/g ww), and toxaphene (???2.4 ??g/g ww) were detected in fish from most sites; maximum concentrations were in channel catfish (Ictalurus punctatus) from the Arroyo Colorado at Harlingen, TX. Concentrations of one or more residues exceeded toxicity thresholds for fish and wildlife in fish from this site and from the Rio Grande at Mission, TX and Brownsville, TX; however, concentrations were lower than those reported by previous studies. In addition, the proportional concentrations of p,p???-DDT at all sites were low, indicating weathered DDT rather than the influx of new material. Concentrations of total PCBs (<0.05 ??g/g ww) and TCDD-EQ (???6 pg/g ww) were comparatively low in all samples. Hepatic ethoxyresorufin O-deethylase (EROD) activity in some fish was elevated relative to reference rates at most sites, but was generally lower than previously reported activity in fish from heavily contaminated locations. The comparatively low PCB and TCDD-EQ concentrations together with elevated EROD activity may reflect exposure to polycyclic aromatic hydrocarbons. Reproductive biomarkers were consistent with chronic contaminant exposure at lower RGB sites; comparatively large percentages of intersex male largemouth bass, relatively low gonadosomatic indices, and elevated plasma vitellogenin concentrations in male fish were noted at three of the four stations. Large percentages of atretic eggs were also observed in the ovaries of female common carp from the Rio Grande at Brownsville, TX. Although many of the conditions noted may have other causes in addition to contaminant exposure, the biomarker results for the lower RGB sites are consistent with subtle responses of fish to contaminants, an interpretation supported by the chemical data of this and other investigations.

Science of the Total Environment↗

Environmental contaminants and biomarker responses in fish from the Columbia River and its tributaries: spatial and temporal trends

Fish were collected from 16 sites on rivers in the Columbia River Basin (CRB) from September 1997 to April 1998 to document temporal and spatial trends in the concentrations of accumulative contaminants and to assess contaminant effects on the fish. Sites were located on the mainstem of the Columbia River and on the Snake, Willamette, Yakima, Salmon, and Flathead Rivers. Common carp (Cyprinus carpio), black bass (Micropterus sp.), and largescale sucker (Catostomus macrocheilus) were the targeted species. Fish were field-examined for external and internal lesions, selected organs were weighed to compute somatic indices, and tissue and fluid samples were preserved for fish health and reproductive biomarker analyses. Composite samples of whole fish, grouped by species and gender, from each site were analyzed for organochlorine and elemental contaminants using instrumental methods and for 2,3,7,8-tetrachloro dibenzo-p-dioxin-like activity (TCDD-EQ) using the H4IIE rat hepatoma cell bioassay. Overall, pesticide concentrations were greatest in fish from lower CRB sites and elemental concentrations were greatest in fish from upper CRB sites. These patterns reflected land uses. Lead (Pb) concentrations in fish from the Columbia River at Northport and Grand Coulee, Washington (WA) exceeded fish and wildlife toxicity thresholds (> 0.4 ??g/g). Selenium (Se) concentrations in fish from the Salmon River at Riggins, Idaho (ID), the Columbia River at Vernita Bridge, WA, and the Yakima River at Granger, WA exceeded toxicity thresholds for piscivorous wildlife (> 0.6 ??g/g). Mercury (Hg) concentrations in fish were elevated throughout the basin but were greatest (> 0.4 ??g/g) in predatory fish from the Salmon River at Riggins, ID, the Yakima River at Granger, WA, and the Columbia River at Warrendale, Oregon (OR). Residues of p,p???-DDE were greatest (> 0.8 ??g/g) in fish from agricultural areas of the Snake, Yakima, and Columbia River basins but were not detected in upper CRB fish. Other organochlorine pesticides did not exceed toxicity thresholds in fish or were detected infrequently. Total polychlorinated biphenyls (PCBs; > 0.11 ??g/g) and TCDD-EQs (> 5 pg/g) exceeded wildlife guidelines in fish from the middle and lower CRB, and ethoxyresorufin O-deethylase (EROD) activity was also elevated at many of the same sites. Temporal trend analysis indicated decreasing or stable concentrations of Pb, Se, Hg, p,p???-DDE, and PCBs at most sites where historical data were available. Altered biomarkers were noted in fish throughout the CRB. Fish from some stations had responded to chronic contaminant exposure as indicated by fish health and reproductive biomarker results. Although most fish from some sites had grossly visible external or internal lesions, histopathological analysis determined these to be inflammatory responses associated with helminth or myxosporidian parasites. Many largescale sucker from the Columbia River at Northport and Grand Coulee, WA had external lesions and enlarged spleens, which were likely associated with infections. Intersex male smallmouth bass (Micropterus dolomieu) were found in the Snake River at Lewiston, ID and the Columbia River at Warrendale, OR. Male bass, carp, and largescale sucker containing low concentrations of vitellogenin were common in the CRB, and comparatively high concentrations (> 0.3 mg/mL) were measured in male fish from the Flathead River at Creston, Montana, the Snake River at Ice Harbor Dam, WA, and the Columbia River at Vernita Bridge, WA and Warrendale, OR. Results from our study and other investigations indicate that continued monitoring in the CRB is warranted to identify consistently degraded sites and those with emerging problems. ?? 2005 Elsevier B.V. All rights reserved.

Columbia River Basin↗

Linking non-culturable (qPCR) and culturable enterococci densities with hydrometeorological conditions

Quantitative polymerase chain reaction (qPCR) measurement of enterococci has been proposed as a rapid technique for assessment of beach water quality, but the response of qPCR results to environmental conditions has not been fully explored. Culture-based E. coli and enterococci have been used in empirical predictive models to characterize their responses to environmental conditions and to increase monitoring frequency and efficiency. This approach has been attempted with qPCR results only in few studies. During the summer of 2006, water samples were collected from two southern Lake Michigan beaches and the nearby river outfall (Burns Ditch) and were analyzed for enterococci by culture-based and non-culture-based (i.e., qPCR) methods, as well as culture-based E. coli . Culturable enterococci densities (log CFU/100 ml) for the beaches were significantly correlated with enterococci qPCR cell equivalents (CE) ( R = 0.650, P < 0.0001, N = 32). Enterococci CE and CFU densities were highest in Burns Ditch relative to the beach sites; however, only CFUs were significantly higher ( P < 0.0001). Culturable enterococci densities at Burns Ditch and the beaches were significantly correlated ( R = 0.565, P < 0.0001, N = 32). Culturable E. coli and enterococci densities were significantly correlated ( R = 0.682, P < 0.0001, N = 32). Regression analyses suggested that enterococci CFU could be predicted by lake turbidity, Burns Ditch discharge, and wind direction (adjusted R 2 = 0.608); enterococci CE was best predicted by Burns Ditch discharge and log-transformed lake turbidity × wave height (adjusted R 2 = 0.40). In summary, our results show that analytically, the qPCR method compares well to the non-culture-based method for measuring enterococci densities in beach water and that both these approaches can be predicted by hydrometeorological conditions. Selected predictors and model results highlight the differences between the environmental responses of the two method endpoints and the potentially high variance in qPCR results

Lake Michigan↗

Incorporation of inorganic mercury (Hg2+) in pelagic food webs of ultraoligotrophic and oligotrophic lakes: the role of different plankton size fractions and species assemblages

In lake food webs, pelagic basal organisms such as bacteria and phytoplankton incorporate mercury (Hg 2+ ) from the dissolved phase and pass the adsorbed and internalized Hg to higher trophic levels. This experimental investigation addresses the incorporation of dissolved Hg 2+ by four plankton fractions (picoplankton: 0.2–2.7 μm; pico + nanoplankton: 0.2–20 μm; microplankton: 20–50 μm; and mesoplankton: 50–200 μm) obtained from four Andean Patagonian lakes, using the radioisotope 197 Hg 2+ . Species composition and abundance were determined in each plankton fraction. In addition, morphometric parameters such as surface and biovolume were calculated using standard geometric models. The incorporation of Hg 2+ in each plankton fraction was analyzed through three concentration factors: BCF (bioconcentration factor) as a function of cell or individual abundance, SCF (surface concentration factor) and VCF (volume concentration factor) as functions of individual exposed surface and biovolume, respectively. Overall, this investigation showed that through adsorption and internalization, pico + nanoplankton play a central role leading the incorporation of Hg 2+ in pelagic food webs of Andean lakes. Larger planktonic organisms included in the micro- and mesoplankton fractions incorporate Hg 2+ by surface adsorption, although at a lesser extent. Mixotrophic bacterivorous organisms dominate the different plankton fractions of the lakes connecting trophic levels through microbial loops (e.g., bacteria–nanoflagellates–crustaceans; bacteria–ciliates–crustaceans; endosymbiotic algae–ciliates). These bacterivorous organisms, which incorporate Hg from the dissolved phase and through their prey, appear to explain the high incorporation of Hg 2+ observed in all the plankton fractions.

Patagonia↗

Prevalence of toxin-producing Clostridium botulinum associated with the macroalga Cladophora in three Great Lakes: Growth and management

The reemergence of avian botulism caused by Clostridium botulinum type E has been observed across the Great Lakes in recent years. Evidence suggests an association between the nuisance algae, Cladophora spp., and C. botulinum in nearshore areas of the Great Lakes. However, the nature of the association between Cladophora and C. botulinum is not fully understood due, in part, to the complex food web interactions in this disease etiology. In this study, we extensively evaluated their association by quantitatively examining population size and serotypes of C. botulinum in algal mats collected from wide geographic areas in lakes Michigan, Ontario, and Erie in 2011&ndash;2012 and comparing them with frequencies in other matrices such as sand and water. A high prevalence (96%) of C. botulinum type E was observed in Cladophora mats collected from shorelines of the Great Lakes in 2012. Among the algae samples containing detectable C. botulinum , the population size of C. Botulinum type E was 10 0 &ndash;10 4 MPN/g dried algae, which was much greater (up to 10 3 fold) than that found in sand or the water column, indicating that Cladophora mats are sources of this pathogen. Mouse toxinantitoxin bioassays confirmed that the putative C. botulinum belonged to the type E serotype. Steam treatment was effective in reducing or eliminating C. botulinum type E viable cells in Cladophora mats, thereby breaking the potential transmission route of toxin up to the food chain. Consequently, our data suggest that steam treatment incorporated with a beach cleaning machine may be an effective treatment of Cladophora -borne C. botulinum and may reduce bird mortality and human health risks.

Lake Erie, Lake Michigan, Lake Ontario↗

Comparison of in vitro estrogenic activity and estrogen concentrations insource and treated waters from 25 U.S. drinking water treatment plants

In vitro bioassays have been successfully used to screen for estrogenic activity in wastewater and surface water, however, few have been applied to treated drinking water. Here, extracts of source and treated water samples were assayed for estrogenic activity using T47D-KBluc cells and analyzed by liquid chromatography-Fourier transform mass spectrometry (LC-FTMS) for natural and synthetic estrogens (including estrone, 17β-estradiol, estriol, and ethinyl estradiol). None of the estrogenswere detected above the LC-FTMS quantification limits in treated samples and only 5 source waters had quantifiable concentrations of estrone, whereas 3 treated samples and 16 source samples displayed in vitro estrogenicity. Estrone accounted for themajority of estrogenic activity in respective samples, however the remaining samples that displayed estrogenic activity had no quantitative detections of known estrogenic compounds by chemical analyses. Source water estrogenicity (max, 0.47 ng 17β-estradiol equivalents (E2Eq) L−1) was below levels that have been linked to adverse effects in fish and other aquatic organisms. Treated water estrogenicity (max, 0.078 ng E2Eq L−1) was considerably below levels that are expected to be biologically relevant to human consumers. Overall, the advantage of using in vitro techniques in addition to analytical chemical determinations was displayed by the sensitivity of the T47D-KBluc bioassay, coupled with the ability tomeasure cumulative effects of mixtures, specifically when unknown chemicals may be present.

Science of the Total Environment↗

Mercury risk to avian piscivores across western United States and Canada

The widespread distribution of mercury (Hg) threatens wildlife health, particularly piscivorous birds. Western North America is a diverse region that provides critical habitat to many piscivorous bird species, and also has a well-documented history of mercury contamination from legacy mining and atmospheric deposition. The diversity of landscapes in the west limits the distribution of avian piscivore species, complicating broad comparisons across the region. Mercury risk to avian piscivores was evaluated across the western United States and Canada using a suite of avian piscivore species representing a variety of foraging strategies that together occur broadly across the region. Prey fish Hg concentrations were size-adjusted to the preferred size class of the diet for each avian piscivore (Bald Eagle = 36 cm, Osprey = 30 cm, Common and Yellow-billed Loon = 15 cm, Western and Clark's Grebe = 6 cm, and Belted Kingfisher = 5 cm) across each species breeding range. Using a combination of field and lab-based studies on Hg effect in a variety of species, wet weight blood estimates were grouped into five relative risk categories including: background (< 0.5 &mu;g/g), low (0.5&ndash;1 &mu;g/g), moderate (1&ndash;2 &mu;g/g), high (2&ndash;3 &mu;g/g), and extra high (> 3 &mu;g/g). These risk categories were used to estimate potential mercury risk to avian piscivores across the west at a 1 degree-by-1 degree grid cell resolution. Avian piscivores foraging on larger-sized fish generally were at a higher relative risk to Hg. Habitats with a relatively high risk included wetland complexes (e.g., prairie pothole in Saskatchewan), river deltas (e.g., San Francisco Bay, Puget Sound, Columbia River), and arid lands (Great Basin and central Arizona). These results indicate that more intensive avian piscivore sampling is needed across Western North America to generate a more robust assessment of exposure risk.

Science of the Total Environment↗

The precipitation of indium at elevated pH in a stream influenced by acid mine drainage

Indium is an increasingly important metal in semiconductors and electronics and has uses in important energy technologies such as photovoltaic cells and light-emitting diodes (LEDs). One significant flux of indium to the environment is from lead, zinc, copper, and tin mining and smelting, but little is known about its aqueous behavior after it is mobilized. In this study, we use Mineral Creek, a headwater stream in southwestern Colorado severely affected by heavy metal contamination as a result of acid mine drainage, as a natural laboratory to study the aqueous behavior of indium. At the existing pH of ~ 3, indium concentrations are 6–29 μg/L (10,000 × those found in natural rivers), and are completely filterable through a 0.45 μm filter. During a pH modification experiment, the pH of the system was raised to > 8, and > 99% of the indium became associated with the suspended solid phase (i.e. does not pass through a 0.45 μm filter). To determine the mechanism of removal of indium from the filterable and likely primarily dissolved phase, we conducted laboratory experiments to determine an upper bound for a sorption constant to iron oxides, and used this, along with other published thermodynamic constants, to model the partitioning of indium in Mineral Creek. Modeling results suggest that the removal of indium from the filterable phase is consistent with precipitation of indium hydroxide from a dissolved phase. This work demonstrates that nonferrous mining processes can be a significant source of indium to the environment, and provides critical information about the aqueous behavior of indium.

Colorado↗

Quantifying anthropogenic contributions to century-scale groundwater salinity changes, San Joaquin Valley, California, USA

Total dissolved solids (TDS) concentrations in groundwater tapped for beneficial uses (drinking water, irrigation, freshwater industrial) have increased on average by about 100 mg/L over the last 100 years in the San Joaquin Valley, California (SJV). During this period land use in the SJV changed from natural vegetation and dryland agriculture to dominantly irrigated agriculture with growing urban areas. Century-scale salinity trends were evaluated by comparing TDS concentrations and major ion compositions of groundwater from wells sampled in 1910 (Historic) to data from wells sampled in 1993-2015 (Modern). TDS concentrations in subregions of the SJV, the southern (SSJV), western (WSJV), northeastern (NESJV), and southeastern (SESJV) were calculated using a cell-declustering method. TDS concentrations increased in all regions, with the greatest increases found in the SSJV and SESJV. Evaluation of the Modern data from the NESJV and SESJV found higher TDS concentrations in recently recharged (post-1950) groundwater from shallow (< 50 m) wells surrounded predominantly by agricultural land uses, while premodern (pre-1950) groundwater from deeper wells, and recently recharged groundwater from wells surrounded by mainly urban, natural, and mixed land uses had lower TDS concentrations, approaching the TDS concentrations in the Historic groundwater. For the NESJV and SESJV, inverse geochemical modeling with PHREEQC indicated that weathering of primary silicate minerals accounted for the majority of the increase in TDS concentrations, contributing more than nitrate from fertilizers and sulfate from soil amendments combined. Bicarbonate showed the greatest increase among major ions, resulting from enhanced silicate weathering due to recharge of irrigation water enriched in CO2 during the growing season. The results of this study demonstrate that large anthropogenic changes to the hydrologic regime, like massive development of irrigated agriculture in semi-arid areas like the SJV, can cause large changes in groundwater quality on a regional scale.

California↗

Relation of fish intersex to contaminants in riverine sport fishes

Endocrine active compounds (EACs) are pollutants that have been recognized as an emerging and widespread threat to aquatic ecosystems globally. Intersex, the presence of female germ cells within a predominantly male gonad, is considered a biomarker of endocrine disruption caused by EACs. We measured a suite of EACs and assessed their associated impacts on fish intersex occurrence and severity in a large, regulated river system in North Carolina and South Carolina, USA. Our specific objective was to determine the relationship of contaminants in water, sediment, and fish tissue with the occurrence and severity of the intersex condition in wild, adult black bass ( Micropterus ), sunfish ( Lepomis ), and catfish (Ictaluridae) species at 11 sites located on the Yadkin-Pee Dee River. Polycyclic aromatic hydrocarbons (PAHs), ethinylestradiol (EE2), and heavy metals were the most prevalent contaminants that exceeded effect levels for the protection of aquatic organisms. Fish intersex condition was most frequently observed and most severe in black basses and was less frequently detected and less severe in sunfishes and catfishes. The occurrence of the intersex condition in fish showed site-related effects, rather than increasing longitudinal trends from upstream to downstream. Mean black bass and catfish tissue contaminant concentrations were higher than that of sunfish, likely because of the latter's lower trophic position in the food web. Principal component analysis identified waterborne PAHs as the most correlated environmental contaminant with intersex occurrence and severity in black bass and sunfish. As indicated by the intersex condition, EACs have adverse but often variable effects on the health of wild sport fishes in this river, likely due to fluctuations in EAC inputs and the dynamic nature of the riverine system. These findings enhance the understanding of the relationship between contaminants and fish health and provide information to guide ecologically comprehensive conservation and management decisions.

North Carolina, South Carolina↗

In vitro effects-based method and water quality screening model for use in pre- and post-distribution treated waters

Recent urban public water supply contamination events emphasize the importance of screening treated drinking water quality after distribution. In vitro bioassays, when run concurrently with analytical chemistry methods, are effective tools to evaluating the efficacy of water treatment processes and water quality. We tested 49 water samples representing the Chicago Department of Water Management service areas for estrogen, (anti)androgen, glucocorticoid receptor-activating contaminants and cytotoxicity. We present a tiered screening approach suitable to samples with anticipated low-level activity and initially tested all extracts for statistically identifiable endocrine activity; performing a secondary dilution-response analysis to determine sample EC 50 and biological equivalency values (BioEq). Estrogenic activity was detected in untreated Lake Michigan intake water samples using mammalian (5/49; median: 0.21 ng E2Eq/L) and yeast cell (5/49; 1.78 ng E2Eq/L) bioassays. A highly sensitive (anti)androgenic activity bioassay was applied for the first time to water quality screening and androgenic activity was detected in untreated intake and treated pre-distribution samples (4/49; 0.93 ng DHTEq/L). No activity was identified above method detection limits in the yeast androgenic, mammalian anti-androgenic, and both glucocorticoid bioassays. Known estrogen receptor agonists were detected using HPLC/MS-MS (estrone: 0.72-1.4 ng/L; 17α-estradiol: 1.3-1.5 ng/L; 17β-estradiol: 1.4 ng/L; equol: 8.8 ng/L), however occurrence did not correlate with estrogenic bioassay results. Many studies have applied bioassays to water quality monitoring using only relatively small samples sets often collected from surface and/or wastewater effluent. However, to realistically adapt these tools to treated water quality monitoring, water quality managers must have the capacity to screen potentially hundreds of samples in short timeframes. Therefore, we provided a tiered screening model that increased sample screening speed, without sacrificing statistical stringency, and detected estrogenic and androgenic activity only in pre-distribution Chicago area samples.

Illinois, Indiana↗

Simultaneous stream assessment of antibiotics, bacteria, antibiotic resistant bacteria, and antibiotic resistant genes in an agricultural region of the United States

Antimicrobial resistance is now recognized as a leading global threat to human health. Nevertheless, there currently is a limited understanding of the environment's role in the spread of AMR and antibiotic resistant genes (ARG). In 2019, the U.S. Geological Survey conducted the first statewide assessment of antibiotic resistant bacteria (ARB) and ARGs in surface water and bed sediment collected from 34 stream locations across Iowa. Environmental samples were analyzed for a suite of 29 antibiotics and plated on selective media for 15 types of bacteria growth; DNA was extracted from culture growth and used in downstream polymerase chain reaction (PCR) assays for the detection of 24 ARGs. ARGs encoding resistance to antibiotics of clinical importance to human health and disease prevention were prioritized as their presence in stream systems has the potential for environmental significance. Total coliforms, Escherichia coli ( E. coli ) , and staphylococci were nearly ubiquitous in both stream water and stream bed sediment samples, with enterococci present in 97 % of water samples, and Salmonella spp. growth present in 94 % and 67 % of water and bed sediment samples. Bacteria enumerations indicate that high bacteria loads are common in Iowa's streams, with 23 (68 %) streams exceeding state guidelines for primary contact for E. coli in recreational waters and 6 (18 %) streams exceeding the secondary contact advisory level. Although antibiotic-resistant E. coli growth was detected from 40 % of water samples, vancomycin-resistant enterococci (VRE) and penicillinase-resistant Staphylococcus aureus (MRSA) colony growth was detected from nearly all water samples. A total of 14 different ARGs were detected from viable bacteria cells from 30 Iowa streams (88 %, n = 34). Study results provide the first baseline understanding of the prevalence of ARB and ARGs throughout Iowa's waterways and health risk potential for humans, wildlife, and livestock using these waterways for drinking, irrigating, or recreating.

Iowa↗

Flow cytometric assessments of metabolic activity in bacterial assemblages provide insight into ecosystem condition along the Buffalo National River, Arkansas

The Buffalo National River (BNR), on karst terrain in Arkansas, is considered an extraordinary water resource. Water collected in Spring 2017 along BNR was metagenomically analyzed using 16S rDNA, and for 17 months (5/2017–11/2018), bacterial responses were measured in relation to nutrients sampled along a stretch of BNR near a concentrated animal feed operation (CAFO) on Big Creek. Because cell count and esterase activity can increase proportionally with organic enrichment, they were hypothesized to be elevated near the CAFO. Counts (colony forming units; CFUs) were different among sites for 73 % of the months; Big Creek generated highest CFUs 27 % of the time, with the closest downstream site at 13.3 %. Esterase activity was different among sites 94 % of the time, with Big Creek exhibiting lowest activity 71 % of the time. Over the months, activity was similar across sites at ~70 % active, except at Big Creek (56 %). The α-diversity of BNR microbial consortia near a wastewater treatment plant (WWTP) and the CAFO was related to distance from the WWTP and CAFO. The inverse relationship between high CFUs and low esterase activity at Big Creek ( r = −0.71) actuated in vitro exposures of bacteria to organic wastewater contaminants (OWC) previously identified in the watershed. Exponential-phase Escherichia coli (stock strain), Streptococcus suis (avirulent, from swine), and S. dysgalactiae (virulent, from silver carp, Hypophthalmichthys molitrix ) were incubated with atrazine, pharmaceuticals (17 α-ethynylestradiol and trenbolone), and antimicrobials (tylosin and butylparaben). Bacteria were differentially responsive. Activity varied with exposure time and OWC type, but not concentration; atrazine decreased it most. Taken together - the metagenomic taxonomic similarities along BNR, slightly higher bacterial growth and lower bacterial esterase at the CAFO, and the lab exposures of bacterial strains showing that OWC altered metabolism - the results indicated that bioactive OWC entering the watershed can strongly influence microbial processes in the aquatic ecosystem.

Science of the Total Environment↗

Field test comparison of an autocorrelation technique for determining grain size using a digital 'beachball' camera versus traditional methods

This extensive field test of an autocorrelation technique for determining grain size from digital images was conducted using a digital bed-sediment camera, or 'beachball' camera. Using 205 sediment samples and >1200 images from a variety of beaches on the west coast of the US, grain size ranging from sand to granules was measured from field samples using both the autocorrelation technique developed by Rubin [Rubin, D.M., 2004. A simple autocorrelation algorithm for determining grain size from digital images of sediment. Journal of Sedimentary Research, 74(1): 160-165.] and traditional methods (i.e. settling tube analysis, sieving, and point counts). To test the accuracy of the digital-image grain size algorithm, we compared results with manual point counts of an extensive image data set in the Santa Barbara littoral cell. Grain sizes calculated using the autocorrelation algorithm were highly correlated with the point counts of the same images (r2 = 0.93; n = 79) and had an error of only 1%. Comparisons of calculated grain sizes and grain sizes measured from grab samples demonstrated that the autocorrelation technique works well on high-energy dissipative beaches with well-sorted sediment such as in the Pacific Northwest (r2 ??? 0.92; n = 115). On less dissipative, more poorly sorted beaches such as Ocean Beach in San Francisco, results were not as good (r2 ??? 0.70; n = 67; within 3% accuracy). Because the algorithm works well compared with point counts of the same image, the poorer correlation with grab samples must be a result of actual spatial and vertical variability of sediment in the field; closer agreement between grain size in the images and grain size of grab samples can be achieved by increasing the sampling volume of the images (taking more images, distributed over a volume comparable to that of a grab sample). In all field tests the autocorrelation method was able to predict the mean and median grain size with ???96% accuracy, which is more than adequate for the majority of sedimentological applications, especially considering that the autocorrelation technique is estimated to be at least 100 times faster than traditional methods.

Sedimentary Geology↗

Biological and mineralogical controls over cycling of low molecular weight organic compounds along a soil chronosequence

Low molecular weight organic compounds (LMWOC) represent a small but critical component of soil organic matter (SOM) for microbial growth and metabolism. The fate of these compounds is largely under microbial control, yet outside the cell, intrinsic soil properties can also significantly influence their turnover and retention. Using a chronosequence representing 1200 ka of pedogenic development, we compared physicochemical vs biological controls on the turnover and retention of fast-cycling carbon (C), e.g. glucose (GLU) and p-hydroxybenzoic acid (PHBA). Along the chronosequence, we observed mineralogical gradients whereby amorphous constituents were greatest in intermediate-aged sites, while older sites demonstrated soils with more ordered and less reactive mineralogy. Soil microbial community composition varied along the soil chronosequence and we observed reductions in total biomass and fungal biomass from younger to older sites, but this did not affect the turnover of LMWOC. Microbial utilization of LMWOC was substrate- and soil-dependent; amorphous Fe and Al oxides reduced the respiration of PHBA but respiration from glucose remained less affected. Variation in soil mineralogy did not significantly alter recovery of PHBA within microbial biomass or fungal vs. bacterial biomarkers, suggesting that reduced respiration of the phenolic resulted from direct mineral interaction with ionizable functional groups rather than changes to microbial allocation of PHBA. We conclude patterns of soil carbon storage observed across chronosequences are moderated by mineralogical effects on microbial access to LMWOC, independent of variation in microbial community composition. Keywords: 13C; Glucose; Microbial biomass C; Organo-mineral interactions; p-Hydroxybenzoic acid; Selective dissolution mineralogical analyses

Soil Biology and Biochemistry↗