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USGS2010

Hydrogeomorphic segments and hydraulic microhabitats of the Niobrara River, Nebraska— With special emphasis on the Niobrara National Scenic River

The Niobrara River is an ecologically and economically important resource in Nebraska. The Nebraska Department of Natural Resources’ recent designation of the hydraulically connected surface- and groundwater resources of the Niobrara River Basin as “fully appropriated” has emphasized the importance of understanding linkages between the physical and ecological dynamics of the Niobrara River so it can be sustainably managed. In cooperation with the Nebraska Game and Parks Commission, the U.S. Geological Survey investigated the hydrogeomorphic and hydraulic attributes of the Niobrara River in northern Nebraska. This report presents the results of an analysis of hydrogeomorphic segments and hydraulic microhabitats of the Niobrara River and its valley for the approximately 330-mile reach from Dunlap Diversion Dam to its confluence with the Missouri River. Two spatial scales were used to examine and quantify the hydrogeomorphic segments and hydraulic microhabitats of the Niobrara River: a basin scale and a reach scale. At the basin scale, digital spatial data and hydrologic data were analyzed to (1) test for differences between 36 previously determined longitudinal hydrogeomorphic segments; (2) quantitatively describe the hydrogeomorphic characteristics of the river and its valley; and (3) evaluate differences in hydraulic microhabitat over a range of flow regimes among three fluvial geomorphic provinces. The statistical analysis of hydrogeomorphic segments resulted in reclassification rates of 3 to 28 percent of the segments for the four descriptive geomorphic elements. The reassignment of classes by discriminant analysis resulted in a reduction from 36 to 25 total hydrogeomorphic segments because several adjoining segments shared the same ultimate class assignments. Virtually all of the segment mergers were in the Canyons and Restricted Bottoms (CRB) fluvial geomorphic province. The most frequent classes among hydrogeomorphic segments, and the dominant classes per unit length of river, are: a width-restricted valley confinement condition, sinuous-planview pattern, irregular channel width, and an alternate bar configuration. The Niobrara River in the study area flows through a diversity of fluvial geomorphic settings in its traverse across northern Nebraska. In the Meandering Bottoms (MB) fluvial geomorphic province, river discharge magnitudes are low, and the valley exerts little control on the channel-planview pattern. Within the CRB province, the river flows over a diversity of geologic formations, and the valley and river narrow and expand in approximate synchronicity. In the Braided Bottoms (BB) fluvial geomorphic province, the river primarily flows over Cretaceous Pierre Shale, the valley and channel are persistently wide, and the channel slope is generally uniform. The existence of vegetated islands and consequent multithread channel environments, indicated by a higher braided index, mostly coincided with reaches having gentler slopes and less unit stream power. Longitudinal hydrology curves indicate that the flow of the Niobrara River likely is dominated by groundwater as far downstream as Norden. Unit stream power values in the study area vary between 0 and almost 2 pounds per foot per second. Within the MB province, unit stream power steadily increases as the Niobrara gains discharge from groundwater inflow, and the channel slope steepens. The combination of steep slopes, a constrained channel width, and persistent flow within the CRB province results in unit stream power values that are between three and five times greater than those in less confined segments with comparable or greater discharges. With the exception of hydrogeomorphic segment 3, which is affected by Spencer Dam, unit stream power values in the BB province are generally uniform. Channel sinuosity values in the study area varied generally between 1 and 2.5, but with locally higher values measured in the MB province and at the entrenched bedrock meanders of hydrogeomorphic segment 18 in the CRB province. The differences in channel morphology and hydraulic geometries between fluvial geomorphic provinces are evident in the types, relative abundance, and response of hydraulic microhabitats to changing discharges. The four gaging stations chosen for hydraulic microhabitat analysis are distributed among three different fluvial geomorphic provinces. In the MB province, the smaller channel and lower discharges resulted in the dominance of shallow and intermediate-depth hydraulic environments with the vast majority of hydraulic microhabitat restricted to shallow categories even during upper-decile discharges. In the CRB province, intermediate depth hydraulic conditions, particularly intermediate-swift, dominate over all ranges of discharge. Hydraulic microhabitat conditions were most diverse in the BB province, with most hydraulic microhabitat categories present over the entire range of discharges analyzed. The calculated differences in hydraulic microhabitat distributions, abundance, and adjustments between streamflow-gaging stations were the result of differences in physical structure of the channel and subsequent channel hydraulic geometry. At the reach scale, field measurements made in water years 2008 and 2009 in four study reaches within the Scenic Reach were used to (1) characterize the elevation and geomorphic processes associated with fluvial landforms, (2) build hydraulic geometry relations, (3) examine flow hydraulics over a range of discharges, and (4) examine the types and responses of hydraulic microhabitats to a range of flow magnitudes. Four landform groups were identified and named in order of increasing elevation: low flood plains, intermediate flood plains, low terraces, and high terraces. The terraces were poorly characterized because the surveys did not extend across the full width of the alluvial valley bottom. The two lowest fluvial landforms are likely active in the modern hydroclimatic regime. Sediment samples obtained in the study reaches indicate that the primary bed material in the active channel ranged in size from coarse silt to coarse sand. Grain-size distributions from samples also indicate that the bed of the Niobrara River among the study reaches coarsens and has increasing grainsize variability in the downstream direction. Values of at-a-station hydraulic geometry exponents indicate that the Niobrara River in the study reaches adjusts its geometry to changing discharges primarily through increases in flow depth and velocity. Relations at one cross section indicated that, at least locally, changes in width were also an important channel adjustment mechanism. Hydraulic behavior over the range of flows measured was not consistent among all study reaches, but two general modes of hydraulic behavior were observed in the reaches with substantial coverage of the bed by fine sediment. At the Sunny Brook and Muleshoe study reaches, average boundary-shear stress remained approximately constant, and hydraulic resistance decreased, for discharges below 900 cubic feet per second (ft 3 /s). Above 900 ft 3 /s, average boundary shear stress and hydraulic resistance both increased. The Rock Barn study reach did not exhibit the same two-mode hydraulic behavior observed at the Sunny Brook and Muleshoe reaches. The coincident increase in boundary shear stress above 900 ft 3 /s observed at the Sunny Brook and Muleshoe study reaches represents a potential hydraulic threshold above which bedload transport rates were likely to increase markedly. No consistent bed-adjustment pattern (scour or fill) was identified in the study reaches over the range of flows or over the measurement season. Analysis of hydraulic microhabitats over the range of discharges measured at the study reaches indicates that some percentage of most habitat niche categories was available for at least one discharge condition, but the majority of hydraulic habitat available was within the intermediate-swift and deepswift habitat niche categories. Deep-swift conditions dominated nearly all study reaches under all measured discharge conditions. Slight differences in habitat distributions were observed between the study reaches with substantial coverage of the bed by fine sediment—Sunny Brook, Muleshoe, and Rock Barn—and the bedrock-dominated reach, Crooked Creek. Although the four study reaches occupy three different hydrogeomorphic segments, the types, relative abundance, and response of hydraulic microhabitat niche distributions to changing discharge conditions generally were similar among all reaches.

Nebraska↗

USGS2012

Spatial and seasonal variability of base flow in the Verde Valley, central Arizona, 2007 and 2011

Synoptic base-flow surveys were conducted on streams in the Verde Valley, central Arizona, in June 2007 and February 2011 by the U.S. Geological Survey (USGS), in cooperation with the Verde River Basin Partnership, the Town of Clarkdale, and Yavapai County. These surveys, also known as seepage runs, measured streamflow under base-flow conditions at many locations over a short period of time. Surveys were conducted on a segment of the Verde River that flows through the Verde Valley, between USGS streamflow-gaging stations 09504000 and 09506000, a distance of 51 river miles. Data from the surveys were used to investigate the dominant controls on Verde River base flow, spatial variability in gaining and losing reaches, and the effects that human alterations have on base flow in the surface-water system. The most prominent human alterations in the Verde Valley are dozens of surface-water diversions from streams, including gravity-fed ditch diversions along the Verde River.Base flow that entered the Verde River from the tributary streams of Oak Creek, Beaver Creek, and West Clear Creek was found to be a major source of base flow in the Verde River. Groundwater discharge directly into the Verde River near these three confluences also was an important contributor of base flow to the Verde River, particularly near the confluence with Beaver Creek. An examination of individual reaches of the Verde River in the Verde Valley found three reaches (largely unaffected by ditch diversions) exhibiting a similar pattern: a small net groundwater discharge in February 2011 (12 cubic feet per second or less) and a small net streamflow loss in June 2007 (11 cubic feet per second or less). Two reaches heavily affected by ditch diversions were difficult to interpret because of the large number of confounding human factors. Possible lower and upper bounds of net groundwater flux were calculated for all reaches, including those heavily affected by ditches.

Arizona↗

USGS2014

Low-flow characteristics of streams in the Lahaina District, West Maui, Hawai'i

The purpose of this study was to characterize streamflow availability under natural low-flow conditions for streams in the Lahaina District, west Maui, Hawaiʻi. The study-area streams included Honolua Stream and tributary Pāpua Gulch, Honokahua Stream and tributary Mokupeʻa Gulch, Kahana Stream, Honokōwai Stream and tributaries Amalu and Kapāloa Streams, Wahikuli Gulch and tributary Hāhākea Gulch, Kahoma Stream and tributary Kanahā Stream, Kauaʻula Stream, Launiupoko Stream, Olowalu Stream, and Ukumehame Gulch. The results of this study can be used to assist in the determination of technically defensible instream-flow standards for the study-area streams. Low-flow characteristics for natural (unregulated) streamflow conditions were represented by flow-duration discharges that are equaled or exceeded between 50 and 95 percent of the time. Partial-record sites were established on 10 main streams and 5 tributary streams, mainly upstream from existing surface-water diversions. Flow characteristics were determined using historical and current streamflow data from continuous-record streamflow-gaging stations and miscellaneous sites, and additional data collected as part of this study. Based on strategically scheduled observations, six of the study-area streams were ephemeral streams that were observed to remain dry at least 50 percent of the time: Pāpua Gulch, Honokahua Stream and its tributary Mokupeʻa Gulch, Kahana Stream, and Wahikuli Gulch and its tributary Hāhākea Gulch. For the remaining streams with measurable flow, Honolua, Honokōwai, Kahoma, Kanahā, Kauaʻula, Launiupoko, and Olowalu Streams, and Ukumehame Gulch, flow-duration discharges were computed for the 30-year base period (water years 1984–2013), using two record-augmentation techniques. The 95-percent flow-duration discharges ranged from 0 to 4.8 cubic feet per second (ft 3 /s). The 50-percent flow-duration discharges ranged from 0.47 to 9.5 ft 3 /s. This study also estimated the streamflow gains and losses downstream of surface-water diversions using seepage-run measurements. A majority of the streams lost flow downstream from diversions. Measured seepage-loss rates ranged between 0.045 and 1.6 ft3/s per mile of stream reach. Seepage gains mostly occurred upstream from diversions and the measured seepage-gain rates generally ranged between 0.75 and 5.1 ft3/s per mile of stream reach. Under natural-flow conditions, Honolua Stream is estimated to flow to the ocean less than 80 percent of the time and Honokōwai Stream is estimated to flow to the ocean less than 50 percent of the time. Kahoma Stream, Kauaʻula Stream, Olowalu Stream, and Ukumehame Gulch are estimated to flow to the ocean at least 95 percent of the time.

Hawai'i↗

USGS2017

An evaluation of the zooplankton community at the Sheboygan River Area of Concern and non-Area of Concern comparison sites in western Lake Michigan rivers and harbors in 2016

The Great Lakes Areas of Concern (AOCs) are considered to be the most severely degraded areas within the Great Lakes basin, as defined in the Great Lakes Water Quality Agreement and amendments. Among the 43 designated AOCs are four Lake Michigan AOCs in the State of Wisconsin. The smallest of these AOCs is the Sheboygan River AOC, which was designated as an AOC because of sediment contamination from polychlorinated biphenyl compounds (PCBs), polycyclic aromatic hydrocarbons (PAHs), volatile organic compounds (VOCs), and heavy metals. The Sheboygan River AOC has 9 of 14 possible Beneficial Use Impairments (BUIs), which must be addressed to improve overall water-quality, and to ultimately delist the AOC. One of the BUIs associated with this AOC is the “degradation of phytoplankton and zooplankton populations,” which can be removed from the list of impairments when it has been determined that zooplankton community composition and structure at the AOC do not differ significantly from communities at non-AOC comparison sites. In 2012 and 2014, the U.S. Geological Survey collected plankton (phytoplankton and zooplankton) community samples at the Sheboygan River AOC and selected non-AOC sites as part of a larger Great Lakes Restoration Initiative study evaluating both the benthos and plankton communities in all four of Wisconsin’s Lake Michigan AOCs. Although neither richness nor diversity of phytoplankton or zooplankton in the Sheboygan River AOC were found to differ significantly from the non-AOC sites in 2012, results from the 2014 data indicated that zooplankton diversity was significantly lower, and so rated as degraded, when compared to the Manitowoc and Kewaunee Rivers, two non-AOC sites of similar size, land use, and close geographic proximity. As a follow-up to the 2014 results, zooplankton samples were collected at the same locations in the AOC and non-AOC sites during three sampling trips in spring, summer, and fall 2016. An analysis of similarity indicated no significant difference between the zooplankton community composition and structure in the AOC and non-AOC sites. Zooplankton taxa richness in the AOC was rated as “not degraded” in 2016 because of significantly higher taxa richness values in samples collected from the Sheboygan River AOC, compared with the non-AOC sites as a group (that is, data pooled from both non-AOC sites). Zooplankton diversity in 2016, however, was characterized as “degraded” in the AOC on the basis of significantly lower (p<0.05) values in samples collected from the AOC compared with those collected from the non-AOC sites as a group. Annual variation in zooplankton community composition and structure at the Sheboygan River AOC was significantly different among all 3 years sampled, as indicated by an analysis of similarity test. Zooplankton richness was significantly higher in 2014 than in both 2012 and 2016, and diversity was significantly higher in 2012 than in both 2014 and 2016. Postremediation recovery can often be complicated by non-AOC-related stressors such as nutrients, invasive species, and extremes in flow, which could affect the recovery of zooplankton communities in the Sheboygan River AOC. The effect of the stressors on postremediation recovery underscores the importance of sampling multiple years when assessing the effectiveness of remediation activities. The results from this study will be used by the Wisconsin Department of Natural Resources and the U.S. Environmental Protection Agency to determine if restoration efforts have been effective in removing the plankton BUI and to monitor future conditions in the AOC.

Wisconsin↗

USGS2018

Postglacial eruptive history and geochemistry of Semisopochnoi volcano, western Aleutian Islands, Alaska

Semisopochnoi Island, located in the Rat Islands group of the western Aleutian Islands and Aleutian volcanic arc, is a roughly circular island composed of scattered volcanic vents, the prominent caldera of Semisopochnoi volcano, and older, ancestral volcanic rocks. The oldest rocks on the island are gently radially dipping lavas that are the remnants of a shield volcano and of Ragged Top, which is an eroded stratocone southeast of the current caldera. None of these oldest rocks have been dated, but they all are likely Pleistocene in age. Anvil Peak, to the caldera’s north, has the morphology of a young stratocone and is latest Pleistocene to early Holocene in age. The oldest recognized Holocene deposits are those of the caldera-forming eruption, which produced the 7- by 6-km caldera in the center of the island, left nonwelded ignimbrite in valleys below the edifice, and left welded ignimbrite high on its flanks. The caldera-forming eruption produced rocks showing a range of intermediate whole-rock compositions throughout the eruption sequence, although a majority of clasts analyzed form a fairly tight cluster on SiO 2 -variation diagrams at 62.9 to 63.4 weight percent SiO 2 . This clustering of compositions at about 63 weight percent SiO 2 includes black, dense, obsidian-like clasts, as well as tan, variably oxidized, highly inflated pumice clasts. The best estimate for the timing of the eruption is from a soil dated at 6,920±60 14 C years before present underlying a thin facies of the ignimbrite deposit on the island’s north coast. Shortly after the caldera-forming eruption, two scoria cones on the northwest flank of the volcano outside the caldera, Ringworm crater and Threequarter Cone, simultaneously erupted small volumes of andesite. The oldest intracaldera lavas, on the floor of the caldera, are andesitic to dacitic, but are mostly covered by younger lavas and tephras. These intracaldera lavas include the basaltic andesites of small Windy cone, as well as the more voluminous basaltic andesites of three-peaked Mount Cerberus, which takes up most of the west half of the caldera and has erupted lavas that flowed to the sea on the southwestern coast of the island. Apparently active at the same time as Mount Cerberus, extracaldera Sugarloaf Peak at the southern point of the island has exclusively erupted basalts. Its young satellite peak, Sugarloaf Head, has erupted morphologically young lavas and cinder cones and may be the source of the last historical eruption in 1987. Several tephra sections on the east half of the island record as many as 50 tephras, mostly from Mount Cerberus, Sugarloaf Peak, and Sugarloaf Head, over the past several thousand years. Eruptive products of Semisopochnoi Island show an overall compositional range of basalt to dacite, though basaltic andesite and andesite constitute the largest proportions of rock types. They are tholeiitic, low to medium K, and have geochemical characteristics typical of magmatic arcs. The earliest Pleistocene lavas are mostly basalts that show the greatest geochemical diversity, as illustrated by, for example, La N /Yb N ratios of 1.9 to 3.5, suggesting fluctuations in the magma source region over the hundreds of thousands of years recorded by these older lavas. The Holocene rocks, in contrast, follow arrays in compositional space that suggest crystallization differentiation from discrete, subtly different batches of magma under varying pressure and temperature conditions. Increasingly negative Eu anomalies and an only modestly increasing alumina saturation index value with differentiation suggest that plagioclase and mafic silicates (amphibole and pyroxene) were involved to varying degrees in fractional crystallization to produce Semisopochnoi’s magmatic diversity. The crystal-poor, andesitic magmas that erupted during caldera formation likely separated from a plagioclase-, amphibole-, and clinopyroxene-dominated crystal residue in the upper crust at less than 900 °C, possibly following a period of decreased magmatic flux. During the Holocene, basaltic Sugarloaf Peak appears to bypass any upper crustal magmatic storage region and erupt crystal-rich basalts. Recent seismic swarms and long-lived warm springs attest to ongoing magmatic activity. The Holocene eruptive record at Semisopochnoi volcano is one of diverse eruptive styles as well as frequent eruptions from multiple vents located within and outside the caldera. The number and diversity of postcaldera vents means that the sites of future eruptions cannot be predicted with certainty. Future eruptions of ash similar in magnitude to the VEI 3 or less eruptions recorded in the documented tephra deposits would pose a hazard to aircraft in the region.

Alaska↗

USGS2018

Characterizing variability in vertical profiles of streamwise velocity and implications for streamgaging practices in the Chicago Sanitary and Ship Canal near Lemont, Illinois, January 2014 to July 2017

A critical component of the Lake Michigan Diversion Accounting program, which oversees the diversion of Great Lakes water by the State of Illinois, is the U.S. Geological Survey streamgage on the Chicago Sanitary and Ship Canal near Lemont, Illinois. The long-term application of an up-looking acoustic Doppler current profiler at this streamgage allows the flows at this study site to be examined from a new perspective: one that is not possible with the horizontally oriented instruments typically used at the site. This report presents results from more than 3.5 years of continuous monitoring data from the up-looking acoustic Doppler current profiler deployed at the study site, which allowed variability in the vertical profile of streamwise velocity to be characterized over a wide range of highly unsteady flows. These data revealed seasonal, density-driven underflows correlated with a combination of environmental variables. Two new methods for computing discharge were developed using this instrument and were determined to be of sufficient quality for Lake Michigan Diversion Accounting purposes. Finally, the up-looking acoustic Doppler current profiler and a barge-detection camera allowed the effect of commercial tows on streamgaging at the site to be evaluated. The addition of the up-looking acoustic Doppler current profiler to the U.S. Geological Survey streamgage on the Chicago Sanitary and Ship Canal near Lemont, Illinois, has ensured the best current engineering practices and scientific knowledge are implemented in the Lake Michigan Diversion Accounting program in accordance with the U.S. Supreme Court decree of 1967, as amended in 1980.

Illinois↗

USGS2003

Anaerobic degradation of 1,1,2,2-tetrachloroethane and association with microbial communities in a freshwater tidal wetland, Aberdeen Proving Ground, Maryland: Laboratory experiments and comparisons to field data

Defining biodegradation rates and processes is a critical part of assessing the feasibility of monitored natural attenuation as a remediation method for ground water containing organic contaminants. During 1998–2001, the U.S. Geological Survey conducted a microbial study at a freshwater tidal wetland along the West Branch Canal Creek, Aberdeen Proving Ground, Maryland, as part of an investigation of natural attenuation of chlorinated volatile organic compounds (VOCs) in the wetland sediments. Geochemical analyses and molecular biology techniques were used to investigate factors controlling anaerobic degradation of 1,1,2,2-tetrachloroethane (TeCA), and to characterize the microbial communities that potentially are important in its degradation. Rapid TeCA and daughter product degradation observed in laboratory experiments and estimated with field data confirm that natural attenuation is a feasible remediation method at this site. The diverse microbial community that seems to be involved in TeCA degradation in the wetland sediments varies with changing spatial and seasonal conditions, allowing continued effective natural attenuation throughout the year. Rates of TeCA degradation in anaerobic microcosm experiments conducted with wetland sediment collected from two different sites (WB23 and WB30) and during three different seasons (March–April 1999, July–August 1999, and October–November 2000) showed little spatial variability but high seasonal variability. Initial first-order degradation rate constants for TeCA ranged from 0.10±0.01 to 0.16±0.05 per day (halflives of 4.3 to 6.9 days) for March–April 1999 and October–November 2000 microcosms incubated at 19 degrees Celsius, whereas lower rate constants of 0±0.03 and 0.06±0.03 per day were obtained in July–August 1999 microcosms incubated at 19 degrees Celsius. Microbial community profiles showed that low microbial biomass and microbial diversity in the summer, possibly due to competition for nutrients by the wetland vegetation, could account for these unexpectedly low degradation rates. In microcosms incubated at 5 degrees Celsius, about 50 percent of the initial TeCA in solution was converted to daughter products within a 35-day incubation period, indicating that biodegradation in the wetland sediments can continue during cold winter temperatures. Initial pathways of TeCA degradation were the same in the wetland sediment microcosms regardless of the season or sediment collection site, the reduction-oxidation conditions, and the previous exposure of the sediment to contamination. Immediate and simultaneous dichloroelimination and hydrogenolysis, producing 1,2-dichloroethene (12DCE) and 1,1,2-trichloroethane (112TCA), respectively, were the initial TeCA degradation pathways in all live microcosm experiments. The production and degradation of vinyl chloride (VC), which is the most toxic of the TeCA daughter compounds, was affected by spatial and seasonal variability, reduction-oxidation condition, and pre-exposure of the wetland sediment. TeCA-amended microcosms constructed with WB30 sediment showed approximately twice as much VC production as those constructed with WB23 sediment. Results of 112TCA-amended microcosms indicated that the greater production of VC in the WB30 sediment resulted from a greater predominance of the 112TCA dichloro elimination pathway in these sediments. VC degradation also was substantially higher in microcosms constructed with WB30 sediment than those constructed with WB23 sediment, resulting in lower VC concentrations at the end of WB30 microcosms. Enrichment experiments in which microcosm slurry was amended with high initial VC concentrations showed that the spatial difference in VC degradation was negligible after prolonged incubation under methanogenic conditions. Inhibition of methanogenic activity in microcosms by addition of sulfate or of 2-bromoethanesulfonic acid inhibited production and degradation of VC. Inhibition of methanogenesis by addition of ferric iron or of 2-bromoethanesulfonic acid also completely inhibited VC degradation in VC-amended enrichment experiments. Pre-exposure to VC substantially increased degradation in VC-amended enrichment experiments. A microbial consortium, rather than one microbial species or group, likely is involved in the degradation of TeCA, as indicated by the occurrence of multiple degradation pathways and the variability in VC production and degradation. A bacterial peak at 90 base pair (bp) fragment length in terminal- restriction fragment length polymorphism (TRFLP) profiles was associated with TeCA hydrogenolysis to 112TCA, and bacterial species represented by 198 and 170 bp fragment lengths were associated with TeCA dichloroelimination to 12DCE. Dichloroelimination of 112TCA to VC was associated with increasing dominance of the 198 bp bacterial peak in March–April 1999 and October–November 2000 microcosms, whereas an 86 bp or the 170 bp bacterial peak was associated with 112TCA dichloroelimination in the summer experiment. Hydrogenolysis of 12DCE to VC was associated with a carbon dioxide-utilizing methanogen at 307 bp in the March–April 1999 and October–November 2000 microcosm experiments, whereas production of VC occurred despite low methanogen biomass and methane production in the July–August 1999 experiments. Production of VC in the absence of methane production also occurred in 12DCE-amended enrichment cultures. The exponential production of VC in the 12DCE-amended enrichment cultures after an initial lag indicated growth of a microbial species or group, possibly one of the known dehalorespiring bacteria. Molecular analyses using specific primers targeting dehalorespiring bacteria of the Dehalococcoides group (Dehalococcoides ethenogenes and Dehalococcoides sp. strain FL2) and of the acetate-oxidizing Desulfuromonas group (Desulfuromonas sp. strain BB1 and Desulfuromonas chloroethenica) showed the presence of these bacteria in microcosm slurry from site WB30 but not from site WB23. Addition of hydrogen, which is the favored substrate of Dehalococcoides, tripled VC production in 12DCE-amended enrichment cultures. VC degradation showed a marked association with an increase in the relative proportion of Methanosarcinaceae, a family of methanogens that includes all those capable of utilizing acetate as a substrate, in the total methanogen community. Half-lives for TeCA and TCE estimated from field data were in the range of 60 to 100 days, which agrees well with laboratory estimates of degradation rates considering the inherent differences in the laboratory and field systems. Both laboratory microcosm experiments and field data showed that 12DCE and VC are the predominant, persistent daughter compounds from TeCA degradation. In addition, porewater chemistry showed higher accumulation of VC in the wetland sediment at site WB30 than at site WB23, as was observed in the microcosm experiments. Molecular analyses of grab samples of surficial wetland sediment showed that all the microbial species or groups linked to TeCA degradation in the microcosm experiments were present in all sediment samples. Microbial biomass and diversity were lowest in an area of the wetland (transect C-C') where porewater VOC concentrations are highest, indicating that the higher VOC concentrations could result from lower degradation rates. The lower microbial biomass and diversity in this area could be caused by toxic effects of the contaminants, or possibly from differences in frequency and duration of tidal inundation.

Maryland↗

USGS1984

Water quality in the New River from Calexico to the Salton Sea, Imperial County, California

The New River enters the United States at Calexico, Calif., after it crosses the international boundary. Water-quality data from routine collection indicated that the New River was degraded by high organic and bacterial content. Intensive sampling for chemical and physical constituents and properties of the river was done May 9-13, 1977, to quantify the chemical composition of the water and to identify water-quality problems. Concentrations of total organic carbon in the New River at Calexico ranged from 80 to 161 milligrams per liter and dissolved organic carbon ranged from 34 to 42 milligrams per liter; the maximum chemical oxygen demand was 510 milligrams per liter. Intensive sampling for chemical and biological characteristics was done in the New River from May 1977 to June 1978 to determine the occurrence of the organic material and its effects on downstream water quality. Dissolved-oxygen concentration was measured along longitudinal profiles of the river from Calexico to the Salton Sea. A dissolved-oxygen sag downstream from the Calexico gage varied seasonally. The sag extended farther downstream and had lower concentrations of dissolved oxygen during the summer months than during the winter months. The sag of zero dissolved-oxygen concentration extended 26 miles in July 1977. In December 1976, the sag extended 20 miles but the minimum dissolved-oxygen concentration was 2.5 milligrams per liter. The greatest diel (24-hour) variation in dissolved-oxygen concentration occurred in the reach from the Calexico gage to Lyons Crossing, 8.8 miles downstream. High concentrations of organic material were detected as far as Highway 80, 19.5 miles downstream from the international boundary. Biological samples analyzed for benthic invertebrates showed that water at the Calexico and Lyons Crossing sites, nearest the international boundary, was of such poor quality that very few bottom-dwelling organisms could survive. Although the water was of poor quality at Keystone Road, 36 miles downstream, it was able to support a benthic community. The April sample had more than 9,150 organisms on a multiplate sampler, 8,770 of which were of one species. Farther downstream at the Westmorland gage, the water quality, as indicated by the number and diversity of organisms, had improved over that at the Keystone site. The Alamo River at its outlet to the Salton Sea--the control site--had the greatest diversity of all the study sites. This diversity, when compared with the diversity at the Westmorland gage, indicated that the effects of the degraded water quality observed at the New River at Calexico are detected as far as 62 miles downstream. Standard bacteria indicator tests indicate that fecal contamination exists in the New River. Counts of fecal coliform bacteria ranged from 180,000 to 2,800,000 colonies per 100 milliliters for the 20-mile reach from Calexico to Highway 80, and fecal streptococcal bacteria ranged from 5,000 to 240,000 colonies per 100 milliliters.

California↗

USGS2025

A practical framework for identifying genetic subpopulations and ESUs: Insights for IUCN assessments and broader management

The International Union for Conservation of Nature (IUCN) sets global conservation standards, including the Red List of Threatened Species and the Green Status of Species. Recent analyses showed that genetic diversity has not been effectively considered by IUCN species assessments, despite being fundamental to species’ fitness and adaptive potential. Incorporation of genetic diversity into IUCN assessments can support its successful long-term conservation. To enhance the preservation of genetic diversity, assessments should include genetically meaningful within-species units. Subpopulations are recognized units by the IUCN for protecting natural connectivity, however infrequently evaluated. Evolutionarily Significant Units (ESUs) are currently not recognized as a formal unit by the IUCN. However, incorporating ESUs into conservation frameworks could significantly enhance our capacity to identify and protect adaptive genetic diversity. To facilitate inclusion of these units in IUCN assessments, we outline a widely applicable framework for their identification that uses non-molecular and molecular data for global accessibility.

EcoEvoRxiv↗

USGS2003

Two distinct phylogenetic clades of infectious hematopoietic necrosis virus overlap within the Columbia River basin

Infectious hematopoietic necrosis virus (IHNV), an aquatic rhabdovirus, causes a highly lethal disease of salmonid fish in North America. To evaluate the genetic diversity of IHNV from throughout the Columbia River basin, excluding the Hagerman Valley, Idaho, the sequences of a 303 nt region of the glycoprotein gene (mid-G) of 120 virus isolates were determined. Sequence comparisons revealed 30 different sequence types, with a maximum nucleotide diversity of 7.3% (22 mismatches) and an intrapopulational nucleotide diversity of 0.018. This indicates that the genetic diversity of IHNV within the Columbia River basin is 3-fold higher than in Alaska, but 2-fold lower than in the Hagerman Valley, Idaho. Phylogenetic analyses separated the Columbia River basin IHNV isolates into 2 major clades, designated U and M. The 2 clades geographically overlapped within the lower Columbia River basin and in the lower Snake River and tributaries, while the upper Columbia River basin had only U clade and the upper Snake River basin had only M clade virus types. These results suggest that there are co-circulating lineages of IHNV present within specific areas of the Columbia River basin. The epidemiological significance of these findings provided insight into viral traffic patterns exhibited by IHNV in the Columbia River basin, with specific relevance to how the Columbia River basin IHNV types were related to those in the Hagerman Valley. These analyses indicate that there have likely been 2 historical events in which Hagerman Valley IHNV types were introduced and became established in the lower Columbia River basin. However, the data also clearly indicates that the Hagerman Valley is not a continuous source of waterborne virus infecting salmonid stocks downstream.

Diseases of Aquatic Organisms↗

USGS2005

Oceanographic conditions structure forage fishes into lipid-rich and lipid-poor communities in lower Cook Inlet, Alaska, USA

Forage fishes were sampled with a mid-water trawl in lower Cook Inlet, Alaska, USA, from late July to early August 1996 to 1999. We sampled 3 oceanographically distinct areas of lower Cook Inlet: waters adjacent to Chisik Island, in Kachemak Bay, and near the Barren Islands. In 163 tows using a mid-water trawl, 229437 fishes with fork length <200 mm were captured. More than 39 species were captured in lower Cook Inlet, but Pacific sand lance Ammodytes hexapterus, juvenile Pacific herring Clupea pallasi, and juvenile walleye pollock Theragra chalcogramma comprised 97.5% of the total individuals. Both species richness and species diversity were highest in warm, low-salinity, weakly stratified waters near Chisik Island. Kachemak Bay, which had thermohaline values between those found near Chisik Island and the Barren Islands, had an intermediate value of species richness. Species richness was lowest at the Barren Islands, an exposed region that regularly receives oceanic, upwelled water from the Gulf of Alaska. Non-metric multidimensional scaling (NMDS) was used to compute axes of species composition based on an ordination of pairwise site dissimilarities. Each axis was strongly rank-correlated with unique groups of species and examined separately as a function of environmental parameters (temperature, salinity, depth), area, and year. Oceanographic parameters accounted for 41 and 12% of the variability among forage fishes indicated by Axis 1 and Axis 2, respectively. Axis 1 also captured the spatial variability in the upwelled area of lower Cook Inlet and essentially contrasted the distribution of species among shallow, nearshore (sand lance, herring) and deep, offshore (walleye pollock) habitats. Axis 2 captured the spatial variability in forage fish communities from the north (Chisik Island) to the south (Barren Islands) of lower Cook Inlet and essentially contrasted a highly diverse community dominated by salmonids and osmerids (warmer, less saline) with a fish community dominated by Pacific sand lance (colder, more saline). Axis 3 reflected the negative spatial association of capelin Mallotus villosus and Pacific cod Gadus macrocephalus. Correlations of year with Axes 1 and 3 indicate that from 1996 to 1999 the forage fish community significantly decreased in lipid-poor gadids (walleye pollock and Pacific cod), and significantly increased in lipid-rich species such as Pacific sand lance, Pacific herring, and capelin.

Alaska↗

USGS2020

Genetic and environmental indicators of climate change vulnerability for desert bighorn sheep

Assessments of organisms’ vulnerability to potential climatic shifts are increasingly common. Such assessments are often conducted at the species level and focused primarily on the magnitude of anticipated climate change (i.e., climate exposure). However, wildlife management would benefit from population-level assessments that also incorporate measures of local or regional potential for organismal adaptation to change. Estimates of genetic diversity, gene flow, and landscape connectivity can address this need and complement climate exposure estimates to establish management priorities at broad to local scales. We provide an example of this holistic approach for desert bighorn sheep ( Ovis canadensis nelsoni ) within and surrounding lands administered by the U.S. National Park Service. We used genetic and environmental data from 62 populations across the southwestern U.S. to delineate genetic structure, evaluate relationships between genetic diversity and isolation, and estimate relative climate vulnerability for populations as a function of five variables associated with species’ responses to climate change: genetic diversity, genetic isolation, geographic isolation, forward climate velocity within a population’s habitat patch (a measure of geographic movement rate required for an organism to maintain constant climate conditions), and maximum elevation within the habitat patch (a measure of current climate stress, as lower maximum elevation is associated with higher temperature, lower precipitation, and lower population persistence). Genetic structure analyses revealed a high-level division between populations in southeastern Utah and populations in the remainder of the study area, which were further differentiated into four lower-level genetic clusters. Genetic diversity decreased with population isolation, whereas genetic differentiation increased, but these patterns were stronger for native populations than for translocated populations. Populations exhibited large variation in predicted vulnerability across the study area with respect to all variables, but native populations occupying relatively intact landscapes, such as Death Valley and Grand Canyon national parks, had the lowest overall vulnerability. These results provide local and regional context for conservation and management decisions regarding bighorn populations in a changing climate. Our study further demonstrates how assessments combining multiple factors could allow a more integrated response, such as increasing efforts to maintain connectivity and thus potential for adaptation in areas experiencing rapid climate change.

Arizona, California, Nevada, Utah↗

USGS2023

DNA virome composition of two sympatric wild felids, bobcat (Lynx rufus) and puma (Puma concolor) in Sonora, Mexico

With viruses often having devastating effects on wildlife population fitness and wild mammals serving as pathogen reservoirs for potentially zoonotic diseases, determining the viral diversity present in wild mammals is both a conservation and One Health priority. Additionally, transmission from more abundant hosts could increase the extinction risk of threatened sympatric species. We leveraged an existing circular DNA enriched metagenomic dataset generated from bobcat ( Lynx rufus , n = 9) and puma ( Puma concolor , n = 13) scat samples non-invasively collected from Sonora, Mexico, to characterize fecal DNA viromes of each species and determine the extent that viruses are shared between them. Using the metaWRAP pipeline to co-assemble viral genomes for comparative metagenomic analysis, we observed diverse circular DNA viruses in both species, including circoviruses, genomoviruses, and anelloviruses. We found that differences in DNA virome composition were partly attributed to host species, although there was overlap between viruses in bobcats and pumas. Pumas exhibited greater levels of alpha diversity, possibly due to bioaccumulation of pathogens in apex predators. Shared viral taxa may reflect dietary overlap, shared environmental resources, or transmission through host interactions, although we cannot rule out species-specific host-virus coevolution for the taxa detected through co-assembly. However, our detection of integrated feline foamy virus (FFV) suggests Sonoran pumas may interact with domestic cats. Our results contribute to the growing baseline knowledge of wild felid viral diversity. Future research including samples from additional sources (e.g., prey items, tissues) may help to clarify host associations and determine the pathogenicity of detected viruses.

Sonora↗

USGS2024

Benthic macroinvertebrate response to estuarine emergent marsh restoration across a delta-wide environmental gradient

Benthic invertebrates play vital roles in estuarine ecosystems, but like other taxa they have been excluded from former marshlands by diking and land use conversion. Dike removal is one way of restoring marsh, but the response of benthic invertebrates has been little studied. Also understudied is variation in benthic invertebrate communities across entire deltas, particularly in the Pacific Northwest of North America where deltas receive high flows and sediment loads for their size. Our goals were to evaluate invertebrate response to large-scale dike removal on the Nisqually River Delta in Puget Sound, Washington, U.S.A., characterize delta-wide invertebrate community variation, and relate invertebrate response and spatial variation to environmental conditions. We sampled invertebrates annually from one year before to three years after dike removal in restoring marsh, previously restored marsh, undisturbed reference marsh, and adjacent tidal flats. Marine taxa immediately colonized the area recently restored to tidal inundation and population size grew exponentially thereafter for several of them. Community composition and diversity recovered completely, and density and biomass were approaching recovery three years later. Invertebrate communities converged between restoring and pre-existing marsh (previously restored and reference), suggesting an influence of reestablished connectivity. Just offshore from the dike line, invertebrates declined one year after dike removal but then rebounded indicating resilience to short-term disturbance. Dike removal effects were not detected farther offshore. Near the offshore edge of the delta, invertebrate biomass and body size were greater than elsewhere and a diverse assemblage of crustaceans, polychaetes, and bivalves was present. Farther inshore, tidal flats were dominated by a few species of small-bodied polychaetes and had higher density but lower biomass and diversity. Facultative detritivores, which can also filter feed, were the dominant feeding guild everywhere on the tidal flats. Density, biomass, diversity, and community composition on the marsh were more similar to the inner than outer tidal flats. Environmental variables most associated with invertebrate community variation were elevation, salinity, and sediment grain size and organic content. Our results are relevant to assessing performance and setting expectations for future restorations and have broad implications for the role of benthic invertebrates in estuarine ecosystems.

Washington↗

USGS2021

Novel insights into the genetic population connectivity of transient whale sharks (Rhincodon typus) in Pacific Panama provide crucial data for conservation efforts

The whale shark ( Rhincodon typus ) is an endangered and highly migratory species, of which solitary individuals or aggregations are observed in oceans worldwide and for which conservation efforts are hindered by a lack of comprehensive data on genetic population connectivity. Tissue samples were collected from wandering whale sharks in Pacific Panama to determine genetic diversity, phylogeographic origin, and possible global and local connectivity patterns using a 700–800 bp fragment of the mitochondrial control region gene. Genetic diversity among samples was high, with five new haplotypes and nine polymorphic sites identified among the 15 sequences. Haplotype diversity ( H d = 0.83) and nucleotide diversity (π = 0.00516) were similar to those reported in other studies. Our sequences, in particular haplotypes PTY1 and PTY2 , were similar to those previously reported in the Arabian Gulf and the Western Indian Ocean populations (a novel occurrence in the latter case). Haplotypes PTY3 , PTY4 , and PTY5 were similar to populations in Mexico and the Gulf of California. In contrast, the only populations to which our Panamanian sequences were genetically dissimilar were those from the Atlantic Ocean. The absence of reference sequences in GenBank from southern sites in the Eastern Tropical Pacific, such as Galapagos (Ecuador), Gorgona and Malpelo Islands (Colombia), and Coco Island (Costa Rica), reduced our capacity to genetically define regional patterns. Genetic differentiation and connectivity were also assessed using an analysis of molecular variance (AMOVA), which showed a similar population structure (five groups) to the neighbor-joining tree. Other population features based on neutrality tests, such as Tajima’s D and Fu’s Fs statistics, showed positive values for Panama of 0.79 and 1.61, respectively. Positive values of these statistics indicate a lack of evidence for population expansion among the sampled individuals. Our results agree with previous reports suggesting that whale sharks can travel over long distances and that transboundary conservation measures may be effective for species protection.

Gulf of Chiriqu↗

USGS2025

Metal fingerprints of Eocene rhyolite magmas coincident with Carlin-type gold deposition in Nevada USA

Eocene magmatic systems contemporaneous with world-class Carlin-type Au deposits in Nevada (USA) have been proposed by some researchers as a key ingredient for Au mineralization, though evidence conclusively demonstrating their genetic relationship remains tenuous. This study provides the first direct evidence of the pre-eruptive metal budget of volatile- and metal-charged silicic magmas coincident in time (~41 to 34 Ma) and space (within 5 km) with Carlin-type Au deposits. We characterize the pre-eruptive metal fingerprints of these diverse magmatic systems to assess their potential as sources of metals for Carlin-type Au mineralization. Metal abundances from quartz-hosted melt inclusions (Au, Te, Ag, Sb, Tl, Mo, W, Sn, As, Pb, Co, Cu, Ni, and Zn) characterized in situ by SHRIMP-RG and LA-ICP-MS represent our best (and only) estimates for the pre-eruptive metal budget in these systems. Median metal concentrations are generally within one order of magnitude of average upper crust and average continental rhyolite values. But there are two notable exceptions, with median Au contents extending >1 order of magnitude higher than average upper crust and median Cu contents ranging >1 order of magnitude lower than upper crust. Despite this, melts contain lower Au/Cu (<0.1), Au/Ag (<5), and Au/Tl (<0.3) than most ore-grade Carlin-type rock samples and quartz-hosted fluid inclusions, regardless of their age and timing relative to nearby Carlin-type Au mineralization. The metal fingerprints of these magmatic systems, de-fined both by traditional and multivariate compositional data analysis techniques, are distinct from one another. Yet none are particularly specialized, e.g., high Au/Cu, in terms of being ideal ingredients as postulated by magmatic models for Carlin-type Au mineralization. Magmatic Au contents do not appear to be correlated with rhyolite “flavors” in the way that Cu, Sn, and Nb contents are. Fluid/melt partitioning modeling and magma volume estimates support the idea that a diverse array of non-specialized silicic magmas could feasibly contribute some or potentially all of the Au, Ag, and Cu in Carlin-type systems. The compositional diversity among contemporaneous magmatic systems could possibly contribute to some of the diversity observed across Carlin-type Au districts in Nevada.

Nevada↗

USGS2012

Associations of benthic macroinvertebrate assemblages with environmental variables in the upper Clear Creek watershed, California

Benthic macroinvertebrates are integral components of stream ecosystems and are often used to assess the ecological integrity of streams. We sampled streams in the upper Clear Creek drainage in the Klamath—Siskiyou Ecoregion of northwestern California in fall 2004 (17 sites) and 2005 (original 17 plus 4 new sites) with the objectives of documenting the benthic macroinvertebrate assemblages supported by the streams in the area, determining how those assemblages respond to environmental variables, assessing the biological condition of the streams using a benthic index of biotic integrity (IBI), and understanding the assemblages in the context of biodiversity of the ecoregion. We collected both reach-wide (RW) and targeted-riffle (TR) macroinvertebrate samples at each site. The macroinvertebrate assemblages were diverse, with over 150 genera collected for each sampling protocol. The macroinvertebrate assemblages appeared to be most responsive to a general habitat gradient based on stream size, gradient, flow, and dominance of riffles. A second important habitat gradient was based on elevation and dominance of riffles. A gradient in water quality based on concentrations of dissolved ions and metals was also important. Models based on these 3 gradients had Spearman's rank correlations with macroinvertebrate taxonomic composition of 0.60 and 0.50 for the TR and RW samples, respectively. The majority (>50%) of the sites were in good or very good biological condition based on IBI scores. The diversity of macroinvertebrate assemblages is associated with the diversity of habitats available in the Klamath—Siskiyou Ecoregion. Maintaining the aquatic habitats in good condition is important in itself but is also vital to maintaining biodiversity in this diverse and unique ecoregion.

California↗

USGS2017

Conservation genetics of American crocodile, Crocodylus acutus , populations in Pacific Costa Rica

Maintaining genetic diversity is crucial for the survival and management of threatened and endangered species. In this study, we analyzed genetic diversity and population genetic structure at neutral loci in American crocodiles, Crocodylus acutus, from several areas (Parque Nacional Marino Las Baulas, Parque Nacional Santa Rosa, Parque Nacional Palo Verde, Rio Tarcoles, and Osa Conservation Area) in Pacific Costa Rica. We genotyped 184 individuals at nine microsatellite loci to describe the genetic diversity and conservation genetics between and among populations. No population was at Hardy-Weinberg Equilibrium (HWE) over all loci tested and a small to moderate amount of inbreeding was present. Populations along the Pacific coast had an average heterozygosity of 0.572 across all loci. All populations were significantly differentiated from each other with both FST and RST measures of population differentiation with a greater degree of molecular variance (81%) found within populations. Our results suggest C. acutus populations in Pacific Costa Rica were not panmictic with moderate levels of genetic diversity. An effective management plan that maintains the connectivity between clusters is critical to the success of C. acutus in Pacific Costa Rica.

Nature Conservation↗