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USGS2025

Hydraulic connectivity and hydrochemistry influence microbial community structure in agriculturally-affected alluvial aquifers in the Midwestern United States

Alluvial aquifers can provide ecosystem services and drinking water, but much remains unknown about human effects on aquifer microbiomes. Therefore, we used amplicon sequencing and hydrochemical characterization to pair microbial communities with environmental conditions across 37 alluvial aquifer wells. The study region spanned eastern Iowa and southern Minnesota (USA) and contained a combination of drinking water and monitoring wells. In terms of microbial ecology, dominant phyla across the wells included Proteobacteria, Bacteroidota, Patescibacteria, Planctomycetota, and Nitrospirota. Tritium, an indicator of infiltration and surface water influence, was the highest correlated variable with the Shannon index (α-diversity) by the Spearman rank sum (ρ = 0.60) and one of only four significant environmental variables in the constrained correspondence analysis. We built random forest regression models to predict tritium concentrations from microbial family relative abundance (held-out testing coefficient of determination ( R 2 ) = 0.77 and mean absolute percentage error = 7%) and interpreted the models with Shapley additive explanation values. The most important families for predicting tritium concentrations were Nitrosopumilaceae and Methylomirabilaceae . Upwelling methane could contribute to the unusual coupling of ammonia oxidation by Nitrosopumilaceae with simultaneous nitrite-dependent methane oxidation by Methylomirabilaceae . Taken together, we illuminate the relationship among hydrochemistry, hydraulic connectivity, and alluvial aquifer microbiomes.

Iowa, Minnesota↗
USGS2019

Dissolved organic carbon turnover in permafrost-influenced watersheds of interior Alaska: Molecular insights and the priming effect

Increased permafrost thaw due to climate change in northern high-latitudes has prompted concern over impacts on soil and stream biogeochemistry that affect the fate of dissolved organic carbon (DOC). Few studies to-date have examined the link between molecular composition and biolability of dissolved organic matter (DOM) mobilized from different soil horizons despite its importance in understanding carbon turnover in aquatic systems. Additionally, the effect of mixed DOM sources on microbial metabolism (e.g., priming) is not well understood. No studies to-date have addressed potential priming effects in northern high-latitude or permafrost-influenced aquatic ecosystems, yet these ecosystems may be hot spots of priming where biolabile, ancient permafrost DOC mixes with relatively stable, modern stream DOC. To assess biodegradability and priming of DOC in permafrost-influenced streams, we conducted 28 day bioincubation experiments utilizing a suite of stream samples and leachates of fresh vegetation and different soil horizons, including permafrost, from Interior Alaska. The molecular composition of unamended DOM samples at initial and final time points was determined by ultrahigh resolution mass spectrometry. Initial molecular composition was correlated to DOC biodegradability, particularly the contribution of energy-rich aliphatic compounds, and stream microbial communities utilized 50–56% of aliphatics in permafrost-derived DOM within 28 days. Biodegradability of DOC followed a continuum from relatively stable stream DOC to relatively biolabile DOC derived from permafrost, active layer organic soil, and vegetation leachates. Microbial utilization of DOC was ∼3–11% for stream bioincubations and ranged from 9% (active layer mineral soil-derived) to 66% (vegetation-derived) for leachate bioincubations. To investigate the presence or absence of a priming effect, bioincubation experiments included treatments amended with 1% relative carbon concentrations of simple, biolabile organic carbon substrates (i.e., primers). The amount of DOC consumed in primed treatments was not significantly different from the control in any of the bioincubation experiments after 28 days, making it apparent that the addition of biolabile permafrost-derived DOC to aquatic ecosystems will likely not enhance the biodegradation of relatively modern, stable DOC sources. Thus, future projections of carbon turnover in northern high-latitude region streams may not have to account for a priming effect.

Alaska↗
USGS2009

An Atlas of ShakeMaps and population exposure catalog for earthquake loss modeling

We present an Atlas of ShakeMaps and a catalog of human population exposures to moderate-to-strong ground shaking (EXPO-CAT) for recent historical earthquakes (1973-2007). The common purpose of the Atlas and exposure catalog is to calibrate earthquake loss models to be used in the US Geological Survey's Prompt Assessment of Global Earthquakes for Response (PAGER). The full ShakeMap Atlas currently comprises over 5,600 earthquakes from January 1973 through December 2007, with almost 500 of these maps constrained-to varying degrees-by instrumental ground motions, macroseismic intensity data, community internet intensity observations, and published earthquake rupture models. The catalog of human exposures is derived using current PAGER methodologies. Exposure to discrete levels of shaking intensity is obtained by correlating Atlas ShakeMaps with a global population database. Combining this population exposure dataset with historical earthquake loss data, such as PAGER-CAT, provides a useful resource for calibrating loss methodologies against a systematically-derived set of ShakeMap hazard outputs. We illustrate two example uses for EXPO-CAT; (1) simple objective ranking of country vulnerability to earthquakes, and; (2) the influence of time-of-day on earthquake mortality. In general, we observe that countries in similar geographic regions with similar construction practices tend to cluster spatially in terms of relative vulnerability. We also find little quantitative evidence to suggest that time-of-day is a significant factor in earthquake mortality. Moreover, earthquake mortality appears to be more systematically linked to the population exposed to severe ground shaking (Modified Mercalli Intensity VIII+). Finally, equipped with the full Atlas of ShakeMaps, we merge each of these maps and find the maximum estimated peak ground acceleration at any grid point in the world for the past 35 years. We subsequently compare this "composite ShakeMap" with existing global hazard models, calculating the spatial area of the existing hazard maps exceeded by the combined ShakeMap ground motions. In general, these analyses suggest that existing global, and regional, hazard maps tend to overestimate hazard. Both the Atlas of ShakeMaps and EXPO-CAT have many potential uses for examining earthquake risk and epidemiology. All of the datasets discussed herein are available for download on the PAGER Web page ( http://earthquake.usgs.gov/ eqcenter/pager/prodandref/ ). ?? 2009 Springer Science+Business Media B.V.

Bulletin of Earthquake Engineering↗
USGS2009

Sources of land-derived runoff to a coral reef-fringed embayment identified using geochemical tracers in nearshore sediment traps

Geochemical tracers, including Ba, Co, Th, 7 Be, 137 Cs and 210 Pb, and magnetic properties were used to characterize terrestrial runoff collected in nearshore time-series sediment traps in Hanalei Bay, Kauai, during flood and dry conditions in summer 2006, and to fingerprint possible runoff sources in the lower watershed. In combination, the tracers indicate that runoff during a flood in August could have come from cultivated taro fields bordering the lower reach of the river. Land-based runoff associated with summer floods may have a greater impact on coral reef communities in Hanalei Bay than in winter because sediment persists for several months. During dry periods, sediment carried by the Hanalei River appears to have been mobilized primarily by undercutting of low 7 Be, low 137 Cs riverbanks composed of soil weathered from tholeiitic basalt with low Ba and Co concentrations. Following a moderate rainfall event in September, high 7 Be sediment carried by the Hanalei River was probably mobilized by overland flow in the upper watershed. Ba-desorption in low-salinity coastal water limited its use to a qualitative runoff tracer in nearshore sediment. 210 Pb had limited usefulness as a terrestrial tracer in the nearshore due to a large dissolved oceanic source and scavenging onto resuspended bottom sediment. 210 Pb-scavenging does, however, illustrate the role resuspension could play in the accumulation of particle-reactive contaminants in nearshore sediment. Co and 137 Cs were not affected by desorption or geochemical scavenging and showed the greatest potential as quantitative sediment provenance indicators in material collected in nearshore sediment traps.

Estuarine, Coastal and Shelf Science↗
USGS2026

Small cumulative survival costs of enzootic disease could suppress long-term population size

Fungal pathogens can cause epizootics that result in widespread mortality and rapid population declines in some species. However, even in the absence of high disease-induced mortality, enzootic mycoses could have large-scale impacts on host population dynamics. Here, we examined the effects of ophidiomycosis, an enzootic fungal disease, on a Louisiana snake community over a 3-year period using a multi-state Jolly–Seber model with disease-state misclassification. We did not detect a difference between the average weekly apparent survival probability of uninfected and infected hosts for either Nerodia species or Thamnophis proximus . We also found a strong positive association between snout-to-vent length and weekly apparent survival probability across all species. We found that recruitment of infected hosts was slightly higher than recruitment of uninfected hosts for two of the three species. Population projections suggested divergent trajectories between disease-present and disease-absent scenarios, where disease-absent populations had higher abundance than disease-present populations. Our results highlight that small differences in survival can accumulate over time, as well as the challenges of quantifying population-level impacts of enzootic diseases when survival differences are not readily detected, underscoring the importance of continued long-term monitoring to assess whether ophidiomycosis affects snake population dynamics.

Louisiana↗
USGS2019

Discovery of an extensive deep-sea fossil serpulid reef associated with a cold seep, Santa Monica Basin, California

Multi-beam mapping of the Santa Monica Basin in the eastern Pacific has revealed the existence of a number of elevated bathymetric features, or mounds, harboring cold seep communities. During 2013-2014, mounds at ~600 m water depth were observed for the first time and sampled by Monterey Bay Aquarium Research Institute’s ROV Doc Ricketts. Active cold seeps were found, but surprisingly one of these mounds was characterized by massive deposits composed of fossil serpulid worm tubes (Annelida: Serpulidae) exhibiting various states of mineralization by authigenic carbonate. No living serpulids with equivalent tube morphologies were found at the site; hence the mound was termed ‘Fossil Hill’. In the present study, the identity of the fossil serpulids and associated fossil community, the ages of fossils and authigenic carbonates, the formation of the fossil serpulid aggregation, and the geological structure of the mound are explored. Results indicate that the tubes were most likely made by a deep-sea serpulid lineage, with radiocarbon dating suggesting that they have a very recent origin during the Late Pleistocene, specifically to the Last Glacial Maximum ~20,000 years ago. Additional U-Th analyses of authigenic carbonates mostly corroborate the radiocarbon dates, and also indicate that seepage was occurring while the tubes were being formed. We also document similar, older deposits along the approximate trajectory of the San Pedro Basin Fault. We suggest that the serpulid tube facies formed in situ, and that the vast aggregation of these tubes at Fossil Hill is likely due to a combination of optimal physical environmental conditions and chemosynthetic production, which may have been particularly intense as a result of sea-level lowstand during the Last Glacial Maximum.

California↗
USGS2015

Topography and climate are more important drivers of long-term, post-fire vegetation assembly than time-since-fire in the Sonoran Desert, US

Questions Do abiotic environmental filters or time-since-fire (TSF) explain more variability in post-fire vegetation assembly? Do these influences vary between vegetation structure and composition, and across spatial scales? Location Sonoran Desert of southwestern Arizona, US. Methods We measured perennial vegetation in a chronosequence of 13 fires (8-33 yr TSF) spanning a broad regional gradient. The relative influence of environmental filters (topography and climate) and TSF were compared as predictors of long-term, post-fire vegetation assembly. Analyses considered different measures of vegetation structure (cover, height and density) and scales of community organization (species composition, structure and landscape). Results Species and growth form composition did not exhibit directional responses with increasing TSF, but sorted along abiotic gradients. Differences in vegetation cover and height between burned and unburned control areas were attributed primarily to gradients of topography and climate. In contrast, vegetation density initially increased in burned areas but declined to pre-burn levels with increasing TSF. The strongest predictors of landscape-scale recovery of vegetation cover, height and density were elevation, post-fire precipitation and average annual precipitation, respectively. Recovery of vegetation height was positively correlated with precipitation in the first year following fire, suggesting that abiotic conditions of the immediate post-fire environment may drive long-term variability in vegetation structure. Conclusions We find substantial evidence that environmental filters, rather than TSF, drive the majority of variability in long-term, post-fire vegetation assembly within the Sonoran Desert. Careful consideration of spatial variability in abiotic conditions may benefit post-fire vegetation modelling, as well as fire management and restoration strategies.

Journal of Vegetation Science↗
USGS2016

Predictive mapping of seabirds, pinnipeds and cetaceans off the Pacific Coast of Washington

About this report This report supports Washington-led marine spatial planning and responsible stewardship of natural and cultural resources by the Olympic Coast National Marine Sanctuary. Washington state agencies and the sanctuary continually seek the best available science to improve management of marine uses and stewardship of resources (Etheridge et al., 2010; Washington Department of Fish and Wildlife, 2015a). This report and associated data provide new, state- and sanctuary-requested information on seabird, pinniped, and cetacean distributions. Through spatial planning, information on species distributions can help to identify high-value conservation areas, minimize adverse effects of ocean uses and mitigate impacts of coastal hazards. Correspondingly, the Washington Department of Fish and Wildlife has already begun to use the maps of predicted relative density presented in this report to identify ecologically important areas off the Pacific Coast of Washington and apply this information to plan for offshore renewable energy development. This is the culmination of three years of work to compile information on seabirds, pinnipeds, and cetaceans, and advance a modeling framework that can integrate data sets and develop accurate predictions of relative density for important species off the Pacific Coast of Washington. Previous reports, which evaluated existing datasets of at-sea observations (Menza et al., 2014; Kracker and Menza, 2015) and presented superseded versions of seabird models (Menza et al., 2015), provided base information for this report. In addition to the maps in this published report, all new seabird, pinniped and cetacean predictions will be made publicly available as digital geospatial data through the National Centers for Environmental Information. This research supports the National Oceanic and Atmospheric Administration (NOAA) Coastal Zone Management Program, a voluntary partnership between the federal government and U.S. coastal and Great Lakes states and territories authorized by the Coastal Zone Management Act (CZMA) of 1972 to address national coastal issues. The act provides the basis for protecting, restoring, and responsibly developing our nation’s diverse coastal communities and resources. To meet the goals of the CZMA, the national program takes a comprehensive approach to coastal resource management – balancing the often competing and occasionally conflicting demands of coastal resource use, economic development, and conservation. A wide range of issues are addressed through the program, including coastal development, water quality, public access, habitat protection, energy facility siting, ocean governance and planning, coastal hazards, and climate change. Accurate maps of seabird and marine mammal distributions are an important tool for making informed management decisions that affect all of these issues.

Washington↗
USGS2014

Acute survivorship of the deep-sea coral Lophelia pertusa from the Gulf of Mexico under acidification, warming, and deoxygenation

Changing global climate due to anthropogenic emissions of CO2 are driving rapid changes in the physical and chemical environment of the oceans via warming, deoxygenation, and acidification. These changes may threaten the persistence of species and populations across a range of latitudes and depths, including species that support diverse biological communities that in turn provide ecological stability and support commercial interests. Worldwide, but particularly in the North Atlantic and deep Gulf of Mexico, Lophelia pertusa forms expansive reefs that support biological communities whose diversity rivals that of tropical coral reefs. In this study, L. pertusa colonies were collected from the Viosca Knoll region in the Gulf of Mexico (390 to 450 m depth), genotyped using microsatellite markers, and exposed to a series of treatments testing survivorship responses to acidification, warming, and deoxygenation. All coral nubbins survived the acidification scenarios tested, between pH of 7.67 and 7.90 and aragonite saturation states of 0.92 and 1.47. However, net calcification generally declined with respect to pH, though a disparate response was evident where select individuals net calcified and others exhibited net dissolution near a saturation state of 1. Warming and deoxygenation both had negative effects on survivorship, with up to 100% mortality observed at temperatures above 14°C and oxygen concentrations of approximately 1.5 ml· l−1. These results suggest that, over the short-term, climate change and OA may negatively impact L. pertusa in the Gulf of Mexico, though the potential for acclimation and the effects of genetic background should be considered in future research.

Gulf of Mexico↗
USGS1995

Effect of lake-wide planktivory by the pelagic prey fish community in Lakes Michigan and Ontario

We compared predatory demand by pelagic planktivorous prey fish with invertebrate production in Lake Michigan during 1987 and in Lake Ontario during 1990. Predation by the planktivores in Lake Ontario was nearly fourfold higher than in Lake Michigan (approx. 87 g wet weight∙m −2 ∙year −1 ). Predation rates on Mysis were comparable in Lakes Michigan and Ontario (approx. 21 g∙m −2 ∙year −1 ), while predation on Diporeia was markedly higher in Lake Michigan than in Lake Ontario (21.3 vs. 8.5 g wet weight∙m −2 ∙year −1 ). In Lake Ontario, predatory demand on zooplankton exceeded our best estimate of production by a factor of 1.7. Similarly, predation estimates on Mysis in Lake Ontario were 1.2–2.0 times the estimated rate of production, depending on the production model used. Lake Michigan planktivores consumed approximately 55% of available zooplankton production in 1987, indicating that competition for prey resources, if operating, was not as intense as that in Lake Ontario in 1990. It is unclear how to resolve the paradox that predation could markedly exceed available prey production in some cases. There could be sources of error in the estimates of both the supply and demand sides of these trophic relationships.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2005

Host population persistence in the face of introduced vector-borne diseases: Hawaii amakihi and avian malaria

The past quarter century has seen an unprecedented increase in the number of new and emerging infectious diseases throughout the world, with serious implications for human and wildlife populations. We examined host persistence in the face of introduced vector-borne diseases in Hawaii, where introduced avian malaria and introduced vectors have had a negative impact on most populations of Hawaiian forest birds for nearly a century. We studied birds, parasites, and vectors in nine study areas from 0 to 1,800 m on Mauna Loa Volcano, Hawaii from January to October, 2002. Contrary to predictions of prior work, we found that Hawaii amakihi (Hemignathus virens), a native species susceptible to malaria, comprised from 24.5% to 51.9% of the avian community at three low-elevation forests (55-270 m). Amakihi were more abundant at low elevations than at disease-free high elevations, and were resident and breeding there. Infection rates were 24-40% by microscopy and 55-83% by serology, with most infected individuals experiencing low-intensity, chronic infections. Mosquito trapping and diagnostics provided strong evidence for year-round local transmission. Moreover, we present evidence that Hawaii amakihi have increased in low elevation habitats on south-eastern Hawaii Island over the past decade. The recent emergent phenomenon of recovering amakihi populations at low elevations, despite extremely high prevalence of avian malaria, suggests that ecological or evolutionary processes acting on hosts or parasites have allowed this species to recolonize low-elevation habitats. A better understanding of the mechanisms allowing coexistence of hosts and parasites may ultimately lead to tools for mitigating disease impacts on wildlife and human populations.

Proceedings of the National Academy of Sciences of↗
USGS1989

IRIS/USGS plans for upgrading the Global Seismograph Network

This report has been prepared to provide information to organizations that may be asked to participate in a program to upgrade the global seismographic network. In most cases, the organizations that will be offered new instrumentation by the U.S. Geological Survey currently operate stations in the World-Wide Standardized Seismograph Network (WWSSN) or the Global Digital Seismograph Network (GDSN). The deployment of the WWSSN in the 1960's and the subsequent equipping of some WWSSN stations with digital equipment and borehole seismometers during the 1970's has been a remarkably successful program that generated the high- quality data needed to fuel an unprecedented period of progress in earthquake and tectonic research. The success of the WWSSN can be attributed to the importance of the data, to the strong commitment by participating organizations to international scientific cooperation, to the dedication and skill of the station operators, and to the resourcefulness of the staff supporting the network. Benefits have been widespread. The community of scientists world-wide has benefited from unrestricted access to a standardized base of calibrated data, and the participating stations have benefited from the donation of modern observatory instruments that have been useful for local earthquake studies and for the training of scientists and engineers. Now, an exciting opportunity has arisen to deploy a new generation of seismograph systems to replace the outdated equipment at many of the WWSSN and GDSN stations. The U.S. Geological Survey (USGS) is cooperating with the Incorporated Research Institutions for Seismology (IRIS) in a program to upgrade the global seismograph network. The equipment development phase is nearly complete with a prototype of the new broadband seismograph system currently undergoing final testing at the USGS Albuquerque Seismological Laboratory. Deployment of the new equipment is expected to begin in early 1990. As this report will demonstrate, the IRIS broadband seismograph system combines the very latest data acquisition and computer technology to produce seismic data with unprecedented bandwidth and dynamic range. Moreover, the system has been designed so that the high-quality digital data are accessible for local display and analysis. The functional design of the new system, which uses off-the-shelf modules and a standard computer bus, will make it much easier than it has been in the past to modify and upgrade the data acquisition system as improvements in technology become available. With adequate support for the program, the new IRIS seismograph system need never become obsolete. We want you to be aware of our plans and the possibility that you may be asked to participate in this ,program. The schedule for upgrading WWSSN and GDSN stations depends on the level of funding earmarked for the program by our National Science Foundation. We hope to deploy at least ten new GSN data systems each year. If you have any questions concerning this program, please contact the Albuquerque Seismological Laboratory, U.S. Geological Survey, Albuquerque, New Mexico 87115-5000. This report was revised in February 1992 in order to update information concerning the current program and instrumentation. The amp in Figure 1 was revised in June 1993, April 1994, December 1994, and September 1996 to reflect updated siting information. In September 1996 a composite photo of standard and optional components of the IRIS-2 GSN system hardware was added as a separate page between Figures 9 and 10.

Open-File Report↗
USGS2021

Assessing the uncertainties in climatic estimates based on vegetation assemblages: Examples from modern vegetation assemblages in the American Southwest

Assemblages of fossil plant remains have been widely used to reconstruct past climatic conditions, usually through the application of methods that involve either finding vegetation analogues on the modern landscape (and using the modern associated climatic values as the basis for an estimate) or using the modern climatic ranges of individual taxa in an assemblage to determine the range of a given climate variable that would allow these plant taxa to live together. Although these approaches are relatively straightforward, it is difficult to assess the uncertainties associated with each approach, particularly in regard to their application to plant macrofossil assemblages. To explore the uncertainty that may arise from inaccuracy and imprecision in climate reconstructions and from ecological considerations we used variants of both approaches to estimate climate from two data sets of modern vegetation assemblages from the southwestern United States: (1) 1752 gridded “virtual plant assemblages” based on plant range maps that provide uniform spatial coverage of the presence or absence of major woody plant taxa across the study area; and (2) 43 modern packrat ( Neotoma spp.) midden presence-absence assemblages that are similar to fossil midden assemblages. By comparing observed and estimated climate values, we evaluated the quality of the climate estimates, identified sources of uncertainty, and characterized the nature and magnitude of the effects of these uncertainties on the climate estimates. Uncertainties in estimating climate from vegetation assemblages arise because any given plant taxon (or assemblage) must have the resiliency to survive a range of climatic variability, and because of the strong intercorrelations among climatic variables in the modern climate data. Additional sources of uncertainty in climate estimates from plant assemblages include: (1) the modern climate and plant distribution data that are selected as the basis for estimation; (2) the particular quantitative approach that is used to estimate climate; (3) the sufficiency of the number of taxa in the analysis for providing an unbiased representation of the vegetation community as it existed for each time period in the analysis; and, (4) the location of the assemblage on the climatic and environmental gradients in the calibration data set for each climate variable under consideration. We conclude that vegetation assemblages can provide valid and reproducible estimates of climatic variables and that the primary trends and mapped patterns in the observed climate data can be reconstructed from such estimates. However, many factors may affect the quality of an estimate from a given plant assemblage, including aspects of data selection, data adequacy, methodologies, and the location of the assemblage site relative to gradients in the base climate data. It is particularly difficult to accurately estimate extreme values in the observed climate data, because estimated values from either end of an observed climate gradient necessarily “move toward the middle” of the gradient. In addition, the interval chosen to represent modern climate (here we used 1961 to 1990) may have a large impact on the size of the estimated difference between modern and past climate at a given site.

Arizona, California, Colorado, Nevada, New Mexico,↗
USGS2019

Cryptosporidium incidence and surface water influence of groundwater supplying public water systems in Minnesota, USA

Regulations for public water systems (PWS) in the U.S. consider Cryptosporidium a microbial contaminant of surface water supplies. Ground- water is assumed free of Cryptosporidium unless surface water is entering supply wells. We determined the incidence of Cryptosporidium in PWS wells varying in surface water influence. Community and noncommunity PWS wells (n = 145) were sampled (n = 964) and analyzed for Cryptosporidium by qPCR and immunofluorescence assay (IFA). Surface water influence was assessed by stable isotopes and the expert judgment of hydrogeologists using site-specific data. Fifty-eight wells (40%) and 107 samples (11%) were Cryptosporidium- positive by qPCR, and of these samples 67 were positive by IFA. Cryptosporidium concentrations measured by qPCR and IFA were significantly correlated (p < 0.001). Cryptosporidium incidence was not associated with surface water influence as assessed by stable isotopes or expert judgment. We successfully sequenced 45 of the 107 positive samples to identify species, including C. parvum (41), C. andersoni (2), and C. hominis (2), and the predominant subtype was C. parvum IIa A17G2R1. Assuming USA regulations for surface water-supplied PWS were applicable to the study wells, wells positive for Cryptosporidium by IFA would likely be required to add treatment. Cryptosporidium is not uncommon in groundwater, even when surface water influence is absent.

Minnesota↗
USGS2019

Survival outcome patterns revealed by deploying advanced tags in quantity: Pacific halibut (Hippoglossus stenolepis) survivals after release from trawl catches through expedited sorting

Bycatch of Pacific halibut ( Hippoglossus stenolepis ) limits many trawl fisheries in Alaska and greatly concerns stakeholders from local communities and fisheries that rely on Pacific halibut. To reduce Pacific halibut mortality, trawlers in the Bering Sea that target flatfish have been developing expedited release procedures to sort Pacific halibut from catches earlier than current regulations allow, while continuing accurate bycatch accounting. We studied survival rates of released Pacific halibut from three trawlers by deploying accelerometer-equipped pop-up satellite archival tags (PSATs) on 160 fish handled under expedited procedures. PSATs recorded and transmitted two metrics indicating swimming activity every 2 h while attached to the fish (for up to 60 days). Analysis of the resulting survival outcomes largely validated current survival-estimation methods, based on structured viability assessments, and found that longer fish length, shorter duration of air exposure, and shorter duration of trawl tow improved predicted Pacific halibut survival. Differences in these results were detected among vessel trips and species targeted by trawling. PSATs provided detailed data from nearly all tagged fish, while exposing fish to conditions experienced by normal releases.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2013

2010 Joint United States-Canadian Program to explore the limits of the Extended Continental Shelf aboard U.S. Coast Guard Cutter Healy--Cruise HLY1002

In August and September 2010, the U.S. Geological Survey, in cooperation with Natural Resources Canada, Geological Survey of Canada, conducted bathymetric and geophysical surveys in the Beaufort Sea and eastern Arctic Ocean aboard the U.S. Coast Guard Cutter Healy. The principal objective of this mission to the high Arctic was to acquire data in support of a delineation of the outer limits of the U.S. and Canadian Extended Continental Shelf in the Arctic Ocean, in accordance with the provisions of Article 76 of the United Nations Convention on the Law of the Sea. The Healy was accompanied by the Canadian Coast Guard icebreaker Louis S. St-Laurent. The scientific parties on board the two vessels consisted principally of staff from the U.S. Geological Survey (Healy), and the Geological Survey of Canada and the Canadian Hydrographic Service (Louis). The crew also included marine-mammal observers, Native-community observers, ice observers, and biologists conducting research of opportunity in the Arctic Ocean. Despite interruptions necessitated by three medical emergencies, the joint survey proved largely successful. The Healy collected 7,201 trackline-kilometers of swath (multibeam) bathymetry (47,663 square kilometers) and CHIRP subbottom data, with accompanying marine gravity measurements, and expendable bathythermograph data. The Louis acquired 3,673 trackline-kilometers of multichannel seismic (airgun) deep-penetration reflection data along 25 continuous profiles, as well as 34 sonobuoy refraction stations and 9,500 trackline-kilometers of single-beam bathymetry. The coordinated efforts of the two vessels resulted in seismic-reflection-profile data that were of much higher quality and continuity than if the data had been acquired with a single vessel alone. The equipment-failure rate of the seismic equipment aboard the Louis was greatly reduced when the Healy led as the ice breaker. When ice conditions proved too severe to deploy the seismic system, the Louis led the Healy, resulting in much improved quality of the swath bathymetric and CHIRP subbottom data in comparison with data collected either by the Healy in the lead or the Healy working alone. During periods when the Healy was operating alone (principally when the Louis was diverted for emergency medical evacuations or ship repairs), the Healy was able to deploy a piston-core-sampler (10 meters maximum potential recovery depending on configuration). The coring operations resulted in recovery of cores at five locations ranging from 2.4 to 5.7 meters in length from water depths ranging from 1,157 to 3,700 meters. One of these cores sited on the Alaskan margin recovered the first reported occurrence of methane hydrate from the Arctic Ocean. Ancillary science objectives, including ice observations and deployment of ice-monitoring buoys and water-column sampling to measure acidification of Arctic waters were successfully conducted. The water-column sampling included using 10 full-ocean-depth, water-sampling casts with accompanying conductivity-temperature-depth measurements. Except for the data deemed proprietary, data from the cruise have been archived and are available for download at the National Geophysical Data Center and at cooperating organizations. Outreach staff and guest teachers aboard the two vessels provided near-real-time connection between the research activities and the public through online blogs, web pages, and other media.

Open-File Report↗
USGS2008

Effect of rhizosphere on soil microbial community and in-situ pyrene biodegradation

To access the influence of a vegetation on soil microorganisms toward organic pollutant biogegration, this study examined the rhizospheric effects of four plant species (sudan grass, white clover, alfalfa, and fescue) on the soil microbial community and in-situ pyrene (PYR) biodegradation. The results indicated that the spiked PYR levels in soils decreased substantially compared to the control soil without planting. With equal planted densities, the efficiencies of PYR degradation in rhizosphere with sudan grass, white clover, alfalfa and fescue were 34.0%, 28.4%, 27.7%, and 9.9%, respectively. However, on the basis of equal root biomass the efficiencies were in order of white clover >> alfalfa > sudan > fescue. The increased PYR biodegradation was attributed to the enhanced bacterial population and activity induced by plant roots in the rhizosphere. Soil microbial species and biomasses were elucidated in terms of microbial phospholipid ester-linked fatty acid (PLFA) biomarkers. The principal component analysis (PCA) revealed significant changes in PLFA pattern in planted and non-planted soils spiked with PYR. Total PLFAs in planted soils were all higher than those in non-planted soils. PLFA assemblages indicated that bacteria were the primary PYR degrading microorganisms, and that Gram-positive bacteria exhibited higher tolerance to PYR than Gram-negative bacteria did. ?? 2008 Higher Education Press and Springer-Verlag GmbH.

Frontiers of Environmental Science and Engineering↗
USGS2022

Crowd-sourced SfM: Best practices for high resolution monitoring of coastal cliffs and bluffs

Structure from motion (SfM) photogrammetry is an increasingly common technique for measuring landscape change over time by deriving 3D point clouds and surface models from overlapping photographs. Traditional change detection approaches require photos that are geotagged with a differential GPS (DGPS) location, which requires expensive equipment that can limit the ability of communities and researchers to perform frequent ( i.e. daily, weekly, and/or monthly) surveys. Crowd-sourced photos can lower the barrier to entry and substantially increase the frequency of surveys, although such photos often lack accurate location information and can vary in quality. This paper presents a SfM approach for monitoring environmental change in high relief coastal environments that does not require all photos have DGPS location information and does not require field survey data. A 1.5 km section of coastal bluffs near the Elwha River Delta (Washington state) is used to demonstrate the efficacy of this approach. Photos of the bluff were collected with a digital SLR camera or phone camera while either on foot along the beach or from a boat as part of monitoring following removal of two large dams along the Elwha River during 2011–2013. Only 33% of photos had DGPS location information, whereas most photos had no location information or locations that were accurate to a couple of meters. All photos were processed using 3D, 4D, and fixed-floating (FF) SfM alignment methods and the resulting dense point clouds are used to compare the different alignment approaches with crowd-sourced photo sets. Results demonstrate that 4D and FF approaches are more likely to reconstruct and are more accurate than the 3D approach. While the 4D and FF have comparable accuracies, the FF approach is several orders of magnitude more efficient, as this method can leverage camera location information from relatively few photos to improve the accuracy of all aligned and derived products. Effectively utilizing crowd-sourced photos in SfM change detection can improve the frequency of surveying a landscape in a more cost-effective approach that also has potential for citizen-science engagement and communication. This is especially important for data-poor environments such as high-relief coastal cliffs and bluffs, where near-nadir imagery and LIDAR may fail to accurately capture near-vertical cliffs or bluff faces. Based on the analysis of different photo alignment and filtering approaches, we present suggested best practices for engaging citizen scientists in coastal cliff and bluff monitoring efforts through collecting photos amenable for SfM reconstruction.

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