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At least 1,153 records · Page 64Linked to original sources

USGS2025

Shotgun sequencing of airborne eDNA achieves rapid assessment of whole biomes, population genetics and genomic variation

Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel technology can help to capture and record genetic diversity before it is lost and to measure population shifts and pathogen distributions. Here we report the rapid application of shotgun long-read environmental DNA (eDNA) analysis for non-invasive biodiversity, genetic diversity and pathogen assessments from air. We also compared air eDNA with water and soil eDNA. Coupling long-read sequencing with established cloud-based biodiversity pipelines enabled a 2-day turnaround from airborne sample collection to completed analysis by a single investigator. To determine the full utility of airborne eDNA, we also conducted a local bioinformatic analysis and deep short-read shotgun sequencing. From outdoor air eDNA alone, comprehensive genetic analysis was performed, including population genetics (phylogenetic placement) of a charismatic mammal (bobcat, Lynx rufus ) and a venomous spider (golden silk orb weaver, Trichonephila clavipes ), and haplotyping humans ( Homo sapiens ) from natural complex community settings, such as subtropical forests and temperate locations. The rich datasets also enabled deeper analysis of specific species and genomic regions of interest, including viral variant calling, human variant analysis and antimicrobial resistance gene surveillance from airborne DNA. Our results highlight the speed, versatility and specificity of pan-biodiversity monitoring via non-invasive eDNA sampling using current benchtop/portable and cloud-based approaches. Furthermore, they reveal the future feasibility of scaling down (equipment and temporally) these approaches for near real-time analysis. Together these approaches can enable rapid simultaneous detection of all life and its genetic diversity from air, water and sediment samples for unbiased non-targeted information-rich genomics-empowered (1) biodiversity monitoring, (2) population genetics, (3) pathogen and disease-vector genomic surveillance, (4) allergen and narcotic surveillance, (5) antimicrobial resistance surveillance and (6) bioprospecting.

Nature Ecology & Evolution↗

USGS2021

Opportunities and challenges of macrogenetic studies

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

Nature Reviews Genetics↗

USGS2022

Long-term ice phenology records spanning up to 578 years for 78 lakes around the Northern Hemisphere

In recent decades, lakes have experienced unprecedented ice loss with widespread ramifications for winter ecological processes. The rapid loss of ice, resurgence of winter biology, and proliferation of remote sensing technologies, presents a unique opportunity to integrate disciplines to further understand the broad spatial and temporal patterns in ice loss and its consequences. Here, we summarize ice phenology records for 78 lakes in 12 countries across North America, Europe, and Asia to permit the inclusion and harmonization of in situ ice phenology observations in future interdisciplinary studies. These ice records represent some of the longest climate observations directly collected by people. We highlight the importance of applying the same definition of ice-on and ice-off within a lake across the time-series, regardless of how the ice is observed, to broaden our understanding of ice loss across vast spatial and temporal scales.

Scientific Data↗

USGS2025

Sentinel-2 based estimates of rangeland fractional cover and canopy gap class for the western United States

Rangelands are extensive ecosystems, providing important ecosystem services while undergoing continuous change. As a result, improved monitoring technologies can help better characterize vegetation change. Satellite remote sensing has proven effective in this regard, tracking vegetation dynamics at broad and fine scales. We leveraged the spatial, spectral, and temporal resolution of Sentinel-2 satellites to estimate fractional cover and canopy gap across rangelands of the western United States. We produced annual, 10 m spatial resolution estimates of fractional cover and canopy gap size class for years 2018 to 2024. Fractional cover estimates include that of common plant functional types (annual forb and grass, bareground, littler, perennial forb and grass, shrub, tree) and select genera (including invasive annual grass species, pinyon-juniper species, and sagebrush species); canopy gap size classes include gap sizes 25 to 50, 51 to 100, 101 to 200, and greater than 200 cm. We make these data available as Cloud Optimized GeoTIFFs, organized as 75 × 75 km tiles covering the 17 western states of the United States.

western United States↗

USGS2021

Comparison of sample types from white-tailed deer (Odocoileus virginianus) for DNA extraction and analyses

Collection of biological samples for DNA is necessary in a variety of disciplines including disease epidemiology, landscape genetics, and forensics. Quantity and quality of DNA varies depending on the method of collection or media available for collection (e.g., blood, tissue, fecal). Blood is the most common sample collected in vials or on Whatman Flinders Technology Associates (FTA) cards with short- and long-term storage providing adequate DNA for study objectives. The focus of this study was to determine if biological samples stored on Whatman FTA Elute cards were a reasonable alternative to traditional DNA sample collection, storage, and extraction. Tissue, nasal swabs, and ocular fluid were collected from white-tailed deer ( Odocoileus virginianus ). Tissue samples and nasal swabs acted as a control to compare extraction and DNA suitability for microsatellite analysis for nasal swabs and ocular fluid extracted from FTA Elute cards. We determined that FTA Elute cards improved the extraction time and storage of samples and that nasal swabs and ocular fluid containing pigmented fluid were reasonable alternatives to traditional tissue DNA extractions.

Pennsylvania↗

USGS2021

Monitoring abundance of aggregated animals (Florida manatees) using an unmanned aerial system (UAS)

Imperfect detection is an important problem when counting wildlife, but new technologies such as unmanned aerial systems (UAS) can help overcome this obstacle. We used data collected by a UAS and a Bayesian closed capture-mark-recapture model to estimate abundance and distribution while accounting for imperfect detection of aggregated Florida manatees ( Trichechus manatus latirostris ) at thermal refuges to assess use of current and new warmwater sources in winter. Our UAS hovered for 10 min and recorded 4 K video over sites in Collier County, FL. Open-source software was used to create recapture histories for 10- and 6-min time periods. Mean estimates of probability of detection for 1-min intervals at each canal varied by survey and ranged between 0.05 and 0.92. Overall, detection probability for sites varied between 0.62 and 1.00 across surveys and length of video (6 and 10 min). Abundance varied by survey and location, and estimates indicated that distribution changed over time, with use of the novel source of warmwater increasing over time. The highest cumulative estimate occurred in the coldest winter, 2018 (N = 158, CI 141–190). Methods here reduced survey costs, increased safety and obtained rigorous abundance estimates at aggregation sites previously too difficult to monitor.

Florida↗

USGS2024

Multistage time-to-event models improve survival inference by partitioning mortality processes of tracked organisms

Advances in tagging technologies are expanding opportunities to estimate survival of fish and wildlife populations. Yet, capture and handling effects could impact survival outcomes and bias inference about natural mortality processes. We developed a multistage time-to-event model that can partition the survival process into sequential phases that reflect the tagged animal experience, including handling and release mortality, post-release recovery mortality, and subsequently, natural mortality. We demonstrate performance of multistage survival models through simulation testing and through fish and bird telemetry case studies. Models are implemented in a Bayesian framework and can accommodate left, right, and interval censorship events. Our results indicate that accurate survival estimates can be achieved with reasonable sample sizes ( n ≈ 100 + ) "> 𝑛≈100+) and that multimodel inference can inform hypotheses about the configuration and length of survival stages needed to adequately describe mortality processes for tracked specimens. While we focus on survival estimation for tagged fish and wildlife populations, multistage time-to-event models could be used to understand other phenomena of interest such as migration, reproduction, or disease events across a range of taxa including plants and insects.

Scientific Reports↗

USGS2023

Supplying ecosystem services on US rangelands

Rangelands comprise 40% of the conterminous United States and they supply essential ecosystem services to society. A scenario assessment was conducted to determine how accelerating biophysical and societal drivers may modify their future availability. Four scenarios emerged: two may maintain rural communities by sustaining the prevailing ecosystem service of beef cattle production, and two may transform rural communities through expansion of renewable energy technologies and infusion of external capital from amenity land sales. Collaborative organizations representing diverse societal sectors may most effectively identify and manage trade-offs among ecosystem service availability, and equitably prioritize food and energy security, environmental quality and cultural identity.

Nature Sustainability↗

USGS2024

Arsenic and other geogenic contaminants in global groundwater

Geogenic groundwater contaminants (GGCs) affect drinking-water availability and safety, with up to 60% of groundwater sources in some regions contaminated by more than recommended concentrations. As a result, an estimated 300–500 million people are at risk of severe health impacts and premature mortality. In this Review, we discuss the sources, occurrences and cycling of arsenic, fluoride, selenium and uranium, which are GGCs with widespread distribution and/or high toxicity. The global distribution of GGCs is controlled by basin geology and tectonics, with GGC enrichment in both orogenic systems and cratonic basement rocks. This regional distribution is broadly influenced by climate, geomorphology and hydrogeochemical evolution along groundwater flow paths. GGC distribution is locally heterogeneous and affected by in situ lithology, groundwater flow and water–rock interactions. Local biogeochemical cycling also determines GGC concentrations, as arsenic, selenium and uranium mobilizations are strongly redox-dependent. Increasing groundwater extraction and land-use changes are likely to modify GGC distribution and extent, potentially exacerbating human exposure to GGCs, but the net impact of these activities is unknown. Integration of science, policy, community involvement programmes and technological interventions is needed to manage GGC-enriched groundwater and ensure equitable access to clean water.

Nature Reviews Earth & Environment↗

USGS2026

Future water constraints on United States lithium mining under climate change

Lithium is necessary for low-carbon technologies that combat climate change, but lithium extraction is water-intensive. Changes in temperature and precipitation arising from climate change are altering water distribution, which could further strain supplies for new mines and industry, farms, and households. Here we explored how climate change, water use, and mining siting could impact lithium mining in the United States. We analyzed whether there would be sufficient water available to support the single existing and 22 proposed U.S. lithium mines at mid-century under four socioeconomic-climate scenarios and five climate models. Though dependent on socioeconomic-climate scenario, climate model, and lithium deposit type, available water supply in most subbasins would likely be unable to support new mines’ water demands, or even non-mining water demands from other sectors. Water scarcity could hinder the ability of the United States to produce enough lithium to meet domestic demand thereby necessitating higher imports.

conterminous United States↗

USGS2025

Impacts of onshore wind energy production on biodiversity

Wind is increasingly used as a renewable source of energy worldwide. However, harvesting wind energy can have negative consequences for biodiversity. In this Review, we summarize the growth of onshore wind power, its impacts on species and ecosystems, and how those impacts are assessed and mitigated. Across the construction, operation and decommissioning stages, wind facilities are associated with wildlife fatality and behavioural change as well as alteration, loss and fragmentation of terrestrial and aerial habitat. These negative consequences can be mitigated by avoiding construction of wind turbines at sensitive sites, detecting and deterring wildlife, curtailing turbines to reduce fatalities, and replacing lost habitats. Uncertainty about wildlife populations and their demographic parameters, the rate and extent of build-out of onshore wind energy, and best practices for mitigation, as well as variability in regulatory requirements by country or region, all contribute to the difficulty of predicting the consequences of this technology for biodiversity. Scenario-based modelling that incorporates population- and community-level consequences to biodiversity from varying degrees of wind energy development — including the cumulative effects of multiple facilities — is key to addressing this uncertainty.

Nature Biodiversity Reviews↗

USGS2018

An underwater observation dataset for fish classification and fishery assessment

Using Dual-Frequency Identification Sonar (DIDSON), fishery acoustic observation data was collected from the Ocqueoc River, a tributary of Lake Huron in northern Michigan, USA. Data were collected March through July 2013 and 2016 and included the identification, via technology or expert analysis, of eight fish species as they passed through the DIDSON’s field of view. A set of short DIDSON clips containing identified fish was curated. Additionally, two other datasets were created that include visualizations of the acoustic data and longer DIDSON clips. These datasets could complement future research characterizing the abundance and behavior of valued fishes such as walleye ( Sander vitreus ) or white sucker ( Catostomus commersonii ) or invasive fishes such as sea lamprey ( Petromyzon marinus ) or European carp ( Cyprinus carpio ). Given the abundance of DIDSON data and the fact that a portion of it is labeled, these data could aid in the creation of machine learning tools from DIDSON data, particularly for invasive sea lamprey which are amply represented and a destructive invader of the Laurentian Great Lakes.

Scientific Data↗

USGS2016

A portable trap with electric lead catches up to 75% of an invasive fish species

A novel system combining a trap and pulsed direct current electricity was able to catch up to 75% of tagged invasive sea lamprey Petromyzon marinus in free-flowing streams. Non-target mortality was rare and impacts to non-target migration were minimal; likely because pulsed direct current only needed to be activated at night (7 hours of each day). The system was completely portable and the annual cost of the trapping system was low ($4,800 U.S. dollars). Use of the technology is poised to substantially advance integrated control of sea lamprey, which threaten a fishery valued at 7 billion U.S. dollars annually, and help restore sea lamprey populations in Europe where they are native, but imperiled. The system may be broadly applicable to controlling invasive fishes and restoring valued fishes worldwide, thus having far reaching effects on ecosystems and societies.

Scientific Reports↗

USGS2017

Local geology controlled the feasibility of vitrifying Iron Age buildings

During European prehistory, hilltop enclosures made from polydisperse particle-and-block stone walling were exposed to temperatures sufficient to partially melt the constituent stonework, leading to the preservation of glassy walls called ‘vitrified forts’. During vitrification, the granular wall rocks partially melt, sinter viscously and densify, reducing inter-particle porosity. This process is strongly dependent on the solidus temperature, the particle sizes, the temperature-dependence of the viscosity of the evolving liquid phase, as well as the distribution and longevity of heat. Examination of the sintering behaviour of 45 European examples reveals that it is the raw building material that governs the vitrification efficiency. As Iron Age forts were commonly constructed from local stone, we conclude that local geology directly influenced the degree to which buildings were vitrified in the Iron Age. Additionally, we find that vitrification is accompanied by a bulk material strengthening of the aggregates of small sizes, and a partial weakening of larger blocks. We discuss these findings in the context of the debate surrounding the motive of the wall-builders. We conclude that if wall stability by bulk strengthening was the desired effect, then vitrification represents an Iron Age technology that failed to be effective in regions of refractory local geology.

Scientific Reports↗

USGS2021

Introduction: Metallurgical slags - Environmental liability or valuable resource?

Slags are important by-products generated by ferrous and non-ferrous pyrometallurgical operations, with hundreds of millions of tonnes generated globally each year. Depending on the chemical and mineralogical compositions of slags, they may be disposed of as waste, which can then weather and release contaminants into the environment with the potential to impact the ecosystem and humans. Alternately, slags can find use as raw materials with numerous applications in civil engineering or environmental technologies. Furthermore, residual metals, either those targeted for extraction or those that co-occur in the ore or furnace feed and partition into the slag, can be recovered for value. With the ultimate goal of a sustainable environment and a circular economy, the research on slags that is presented in this book will lead us to a better understanding of the environmental consequences of slag disposed of as waste and motivate us to find value in it.

Book chapter↗

USGS1998

Re-evaluation and extension of the scope of elements in US Geological Survey Standard Reference Water Samples

More than 100 US Geological Survey (USGS) Standard Reference Water Samples (SRWSs) were analyzed for numerous trace constituents, including Al, As, B, Ba, Be, Bi, Br, Cd, Cr, Co, Cu, I, Fe, Pb, Li, Mn, Mo, Ni, Rb, Sb, Se, Sr, Te, Tl, U, V, Zn and major elements (Ca, Mg, Na, SiO2, SO4, Cl) by inductively coupled plasma mass spectrometry and inductively coupled plasma atomic emission spectrometry. In addition, 15 USGS SRWSs and National Institute of Standards and Technology (NIST) standard reference material (SRM) 1641b were analyzed for mercury using cold vapor atomic fluorescence spectrometry. Also USGS SRWS Hg-7 was analyzed using isotope dilution-inductively coupled plasma mass spectrometry. The results were compared with the reported certified values of the following standard reference materials: NIST SRM 1643a, 1643b, 1643c and 1643d and National Research Council of Canada Riverine Water Reference Materials for Trace Metals SLRS-1, SLRS-2 and SLRS-3. New concentration values for trace and major elements in the SRWSs, traceable to the certified standards, are reported. Additional concentration values are reported for elements that were neither previously published for the SRWSs nor traceable to the certified reference materials. Robust statistical procedures were used that were insensitive to outliers. These data can be used for quality assurance/quality control purposes in analytical laboratories.

Analyst↗

USGS2004

Resolving global versus local/regional Pu sources in the environment using sector ICP-MS

Sector inductively coupled plasma mass spectrometry is a versatile method for the determination of plutonium activities and isotopic compositions in samples containing this element at fallout levels. Typical detection limits for 239+240Pu are 0.1, 0.02 and 0.002 Bq kg -1Pu for samples sizes of 0.5 g, 3 g, and 50 g of soil, respectively. The application of sector ICP-MS-based Pu determinations is demonstrated in studies in sediment chronology, soil Pu inventory and depth distribution, and the provenance of global fallout versus local or regional Pu sources. A sediment core collected from Sloans Lake (Denver, Colorado, USA) exhibits very similar 137Cs and 239+240Pu activity profiles; 240Pu/239Pu atom ratios indicate possible small influences from the Nevada Test Site and/or the Rocky Flats Environmental Technology Site. An undisturbed soil profile from Lockett Meadow (Flagstaff, Arizona, USA) exhibits an exponential decrease in 239+240Pu activity versus depth; 240Pu/239Pu in the top 3 cm is slightly lower than the global fallout range of 0.180 ?? 0.014 due to possible regional influence of Nevada Test Site fallout. The 239??240Pu inventory at Lockett Meadow is 56 ?? 4 Bq m-2, consistent with Northern Hemisphere mid-latitude fallout. Archived NdF3 sources, prepared from Polish soils, demonstrate that substantial 239+240Pu from the 1986 Chernobyl disaster has been deposited in north eastern regions of Poland; compared to global fallout, Chernobyl Pu exhibits higher abundances of 240Pu and 241Pu. The ratios 240Pu/239pu and 241Pu/239Pu co-vary and range from 0.186-0.348 and 0.0029-0.0412, respectively, in forest soils (241Pu/239Pu = 0.2407??[240Pu/239Pu] - 0.0413; r2 = 0.9924). ?? The Royal Society of Chemistry 2004.

Journal of Analytical Atomic Spectrometry↗

USGS2006

Persistent organic pollutants in Alaskan ringed seal ( Phoca hispida ) and walrus ( Odobenus rosmarus ) blubber

Since 1987, the Alaska Marine Mammal Tissue Archival Project (AMMTAP) has collected tissues from 18 marine mammal species. Specimens are archived in the National Institute of Standards and Technology's National Biomonitoring Specimen Bank (NIST-NBSB). AMMTAP has collected blubber, liver and/or kidney specimens from a number of ringed seals ( Phoca hispida ) from the areas near Nome and Barrow, Alaska and walruses ( Odobenus rosmarus ) from several locations in the Bering Sea. Thirty-three ringed seal and 15 walrus blubber samples from the NIST-NBSB were analyzed for persistent organic pollutants (POPs). The compounds determined included PCBs (28 congeners or congener groups), DDT and related compounds, hexachlorobenzene (HCB), hexachlorocyclohexane isomers (HCHs), chlordanes, dieldrin, and mirex. POP concentrations in ringed seal blubber were significantly higher in Barrow than in Nome when statistically accounting for the interaction of age and gender; HCB, however, was not statistically different between the two locations. Unlike males, POP concentrations and age were not significantly correlated in females probably as a result of lactational loss. POP concentrations in walrus blubber were lower than in ringed seal blubber for ΣPCBs, chlordanes, and HCHs, but higher for dieldrin and mirex. POP concentrations in ringed seals and walrus from Alaska provide further evidence that the western Arctic tends to have lower or similar POP concentrations compared to the eastern Canadian Arctic.

Alaska↗