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At least 1,657 records · Page 92Linked to original sources

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.

Washington↗

USGS2022

Amphibian mucus triggers a developmental transition in the frog-killing chytrid fungus

The frog-killing chytrid fungus Batrachochytrium dendrobatidis ( Bd ) is decimating amphibian populations around the world. Bd has a biphasic life cycle, alternating between motile zoospores that disperse within aquatic environments and sessile sporangia that grow within the mucus-coated skin of amphibians. Zoospores lack cell walls and swim rapidly through aquatic environments using a posterior flagellum and crawl across solid surfaces using actin structures similar to those of human cells. Bd transitions from this motile dispersal form to its reproductive form by absorbing its flagellum, rearranging its actin cytoskeleton, and rapidly building a chitin-based cell wall—a process called “encystation.” The resulting sporangium increases in volume by two or three orders of magnitude while undergoing rounds of mitosis without cytokinesis to form a large ceonocyte. The sporangium then cellurizes by dividing its cytoplasm into dozens of new zoospores. After exiting the sporangium through a discharge tube onto the amphibian skin, daughter zoospores can then reinfect the same individual or find a new host. Although encystation is critical to Bd growth, whether and how this developmental transition is triggered by external signals was previously unknown. We discovered that exposure to amphibian mucus triggers rapid and reproducible encystation within minutes. This response can be recapitulated with purified mucin, the bulk component of mucus, but not by similarly viscous methylcellulose or simple sugars. Mucin-induced encystation does not require gene expression but does require surface adhesion, calcium signaling, and modulation of the actin cytoskeleton. Mucus-induced encystation may represent a key mechanism for synchronizing Bd development with the arrival at the host.

Current Biology↗

USGS2022

Novel insights on aquatic mammal MHC evolution: Evidence from manatee DQB diversity

The low diversity in marine mammal major histocompatibility complex (MHC) appears to support the hypothesis of reduced pathogen selective pressure in aquatic systems compared to terrestrial environments. However, the lack of characterization of the aquatic and evolutionarily distant Sirenia precludes drawing more generalized conclusions. Therefore, we aimed to characterize the MHC DQB diversity of two manatee species and compare it with those reported for marine mammals. Our results identified 12 and 6 alleles in T. inunguis and T. manatus , respectively. Alleles show high rates of nonsynonymous substitutions, suggesting loci are evolving under positive selection. Among aquatic mammals, Pinnipeda DQB had smaller numbers of alleles, higher synonymous substitution rate, and a dN/dS ratio closer to 1, suggesting it may be evolving under more relaxed selection compared to fully aquatic mammals. This contradicts one of the predictions of the hypothesis that aquatic environments impose reduced pathogen pressure to mammalian immune system. These results suggest that the unique evolutionary trajectories of mammalian MHC may impose challenges in drawing ecoevolutionary conclusions from comparisons across distant vertebrate lineages.

Florida↗

USGS2025

Factors structuring macrofaunal communities of hydrocarbon seeps along the Cascadia margin

Cold seeps, fueled by hydrocarbon-based chemosynthesis, support unique benthic communities that can vary across small spatial scales influenced by local geochemistry. We examined the community structure and function of macrofauna in cold seeps along the Cascadia margin on the edge of gas hydrate stability—a dynamic environment that may fluctuate as seafloor temperatures change. These communities were assessed in relation to their sediment environment to provide baseline data for these previously uninvestigated seeps and decipher the most significant variables structuring them. Specific environmental drivers investigated include sediment organic carbon, total nitrogen, C:N ratios, stable isotopes (δ 13 C and δ 15 N), redox potential, grain size, and porefluid chemistry. Macrofaunal community composition varied across locations separating into twelve distinct clusters. Several co-located cores clustered separately, indicating high heterogeneity in these communities at small spatial scales. Significant drivers of macrofauna communities included clay and sand content, C:N, δ 15 N values, organic carbon content, and depth. Functional trait composition was influenced by similar drivers, including depth, δ 15 N values, C:N, and sand content. Our results indicate similar environmental variables structure macrofaunal community composition and function across small- and large-scale gradients, contributing to our understanding of heterogeneity in local and regional factors that shape seep macrofaunal communities. This is the first investigation of macrofauna at these recently discovered seeps and provides baseline data on the hydrate stability zone for future comparisons, advancing our knowledge of broad-scale trends in seep macrofauna ecology.

California, Oregon, Washington↗

USGS2010

Food-web structure of seep sediment macrobenthos from the Gulf of Mexico

The slope environment of the Gulf of Mexico (GOM) supports dense communities of seep megafaunal invertebrates that rely on endosymbiotic bacteria for nutrition. Seep sediments also contain smaller macrofaunal invertebrates whose nutritional pathways are not well understood. Using stable-isotope analysis, we investigate the utilization of chemosynthetically fixed and methane-derived organic matter by macrofauna. Biological sampling was conducted in three lower-slope GOM seep environs: Green Canyon (GC852, 1428 m), Atwater Valley (AT340, 2230 m), and Alaminos Canyon (AC601, 2384 m). Infaunal delta 13 C and delta 15 N exhibited a broad range of values; most infauna appeared to be heterotrophic, although several taxa had very light delta 15 N and delta 13 C values, indicating possible reliance on chemoautotrophic symbioses. The lightest delta 13 C and delta 15 N values were observed in nematodes (delta 13 C=-54.6 + or - 0.1 per mil, delta 15 N=-6.1 + or - 0.2 per mil) and one gastropod (delta 13 C=-54.1 per mil, delta 15 N=-1.1 per mil) from Green Canyon. Mixing-model results indicated that sulfur-oxidizing Beggiatoa may be an important food source for seep infauna; the rate of utilization ranged from 60% to 100% at Green Canyon and Atwater Valley. The overall range in isotope values was similar across the three sites, suggesting that biogeochemical processes may be very similar in these geographically distinct areas.

Deep-Sea Research Part II: Topical Studies in Ocea↗

USGS2014

The geochemistry of deep-sea coral skeletons: a review of vital effects and applications for palaeoceanography

Deep-sea corals were discovered over a century ago, but it is only over recent years that focused efforts have been made to explore the history of the oceans using the geochemistry of their skeletal remains. They offer a promising archive of past oceanic environments given their global distribution, layered growth patterns, longevity and preservation as well as our ability to date them using radiometric techniques. This paper provides an overview of the current state-of-the-art in terms of geochemical approaches to using deep-sea coral skeletons to explore the history of the ocean. Deep-sea coral skeletons have a wide array of morphologies (e.g. solitary cup corals, branching colonial corals) and materials (calcite, aragonite and proteins). As such their biomineralization strategies are diverse, leading to complex geochemistry within coral skeletons. Notwithstanding these complications, progress has been made on developing methods for reconstructing the oceanographic environment in the past using trace elements and isotopic methods. Promising approaches within certain coral groups include clumped isotopes and Mg/Li for temperature reconstructions, boron isotopes and radiocarbon for carbon cycling, εNd, and radiocarbon for circulation studies and δ 15 N, P/Ca and Ba/Ca for nutrient tracer studies. Likewise there is now a range of techniques for dating deep-sea corals skeletons (e.g. U-series, radiocarbon), and determining their growth rates (e.g. radiocarbon and 210 Pb). Dating studies on historic coral populations in the Atlantic, Southern Ocean and Pacific point to climate and environmental changes being dominant controls on coral populations over millennial and orbital timescales. This paper provides a review of a range of successes and promising approaches. It also highlights areas in which further research would likely provide new insights into biomineralization, palaeoceanography and distribution of past coral populations.

Deep-Sea Research Part II: Topical Studies in Ocea↗

USGS2005

Eolian deposits in the Neoproterozoic Big Bear Group, San Bernardino Mountains, California, USA

Strata interpreted to be eolian are recognized in the Neoproterozoic Big Bear Group in the San Bernardino Mountains of southern California, USA. The strata consist of medium- to large-scale (30 cm to > 6 m) cross-stratified quartzite considered to be eolian dune deposits and interstratified thinly laminated quartzite that are problematically interpreted as either eolian translatent climbing ripple laminae, or as tidal-flat deposits. High index ripples and adhesion structures considered to be eolian are associated with the thinly laminated and cross-stratified strata. The eolian strata are in a succession that is characterized by flaser bedding, aqueous ripple marks, mudcracks, and interstratified small-scale cross-strata that are suggestive of a tidal environment containing local fluvial deposits. The eolian strata may have formed in a near-shore environment inland of a tidal flat. The Neoproterozoic Big Bear Group is unusual in the western United States and may represent a remnant of strata that were originally more widespread and part of the hypothetical Neoproterozoic supercontinent of Rodinia. The Big Bear Group perhaps is preserved only in blocks that were downdropped along Neoproterozoic extensional faults. The eolian deposits of the Big Bear Group may have been deposited during arid conditions that preceded worldwide glacial events in the late Neoproterozoic. Possibly similar pre-glacial arid events are recognized in northern Mexico, northeast Washington, Australia, and northwest Canada.

California↗

USGS2021

Trade-offs in initial and long-term handling efficiency of PIT-tag and photographic identification methods

Individual identification is required for long-term investigations that examine population-level changes in survival or abundance, and mechanisms associated with these changes in wild populations. Such identification generally requires the application of a unique mark, or the documentation of characteristics distinctive to each individual animal. To minimize impacts to often declining populations, scientific and ethical concerns encourage marking strategies that minimize handling time (i.e., stress) for captured individuals. We examined the relative efficacy of passive integrated transponder (PIT)-tagging and photo-identification to identify individual Boreal toads ( Anaxyrus boreas boreas ) in field and indoor settings. We evaluated whether initial handling time was influenced by identification method (PIT-tag or photo-identification) or environment (field or indoor) and assessed the applicability of each method in long-term monitoring programs. Initial handling time was higher for PIT-tagging than photo-identification and higher in the field than in an indoor environment; however, handling time for previously PIT-tagged individuals was greatly reduced such that photo-identification led to > 5.5 times more handling time than PIT-tagging over the course of a toad's lifetime. Investigators must determine the trade-off between initial and subsequent handling times to minimize the expected (mean) cumulative handling time for an individual over the course of a study. Cumulative handling time is a function of the study design and the species’ survival and detection probabilities. We developed a Shiny Application to allow investigators to determine the identification method that minimizes handling time for their own study system.

Ecological Indicators↗

USGS2008

Allowing macroalgae growth forms to emerge: Use of an agent-based model to understand the growth and spread of macroalgae in Florida coral reefs, with emphasis on Halimeda tuna

The growth patterns of macroalgae in three-dimensional space can provide important information regarding the environments in which they live, and insights into changes that may occur when those environments change due to anthropogenic and/or natural causes. To decipher these patterns and their attendant mechanisms and influencing factors, a spatially explicit model has been developed. The model SPREAD (SPatially-explicit Reef Algae Dynamics), which incorporates the key morphogenetic characteristics of clonality and morphological plasticity, is used to investigate the influences of light, temperature, nutrients and disturbance on the growth and spatial occupancy of dominant macroalgae in the Florida Reef Tract. The model species, Halimeda and Dictyota spp., are modular organisms, with an 'individual' being made up of repeating structures. These species can also propagate asexually through clonal fragmentation. These traits lead to potentially indefinite growth and plastic morphology that can respond to environmental conditions in various ways. The growth of an individual is modeled as the iteration of discrete macroalgal modules whose dynamics are affected by the light, temperature, and nutrient regimes. Fragmentation is included as a source of asexual reproduction and/or mortality. Model outputs are the same metrics that are obtained in the field, thus allowing for easy comparison. The performance of SPREAD was tested through sensitivity analysis and comparison with independent field data from four study sites in the Florida Reef Tract. Halimeda tuna was selected for initial model comparisons because the relatively untangled growth form permits detailed characterization in the field. Differences in the growth patterns of H. tuna were observed among these reefs. SPREAD was able to closely reproduce these variations, and indicate the potential importance of light and nutrient variations in producing these patterns. ?? 2008 Elsevier B.V.

Ecological Modelling↗

USGS2009

Hierarchical demographic approaches for assessing invasion dynamics of non-indigenous species: An example using northern snakehead (Channa argus)

Models of species' demographic features are commonly used to understand population dynamics and inform management tactics. Hierarchical demographic models are ideal for the assessment of non-indigenous species because our knowledge of non-indigenous populations is usually limited, data on demographic traits often come from a species' native range, these traits vary among populations, and traits are likely to vary considerably over time as species adapt to new environments. Hierarchical models readily incorporate this spatiotemporal variation in species' demographic traits by representing demographic parameters as multi-level hierarchies. As is done for traditional non-hierarchical matrix models, sensitivity and elasticity analyses are used to evaluate the contributions of different life stages and parameters to estimates of population growth rate. We applied a hierarchical model to northern snakehead (Channa argus), a fish currently invading the eastern United States. We used a Monte Carlo approach to simulate uncertainties in the sensitivity and elasticity analyses and to project future population persistence under selected management tactics. We gathered key biological information on northern snakehead natural mortality, maturity and recruitment in its native Asian environment. We compared the model performance with and without hierarchy of parameters. Our results suggest that ignoring the hierarchy of parameters in demographic models may result in poor estimates of population size and growth and may lead to erroneous management advice. In our case, the hierarchy used multi-level distributions to simulate the heterogeneity of demographic parameters across different locations or situations. The probability that the northern snakehead population will increase and harm the native fauna is considerable. Our elasticity and prognostic analyses showed that intensive control efforts immediately prior to spawning and/or juvenile-dispersal periods would be more effective (and probably require less effort) than year-round control efforts. Our study demonstrates the importance of considering the hierarchy of parameters in estimating population growth rate and evaluating different management strategies for non-indigenous invasive species. ?? 2009 Elsevier B.V.

Ecological Modelling↗

USGS2005

Early marine life history of juvenile Pacific salmon in two regions of Puget Sound

Puget Sound could differentially represent either a simple migration corridor or an important rearing environment during the potentially critical early marine residence period for different species of Pacific salmon. Recent declines in various stocks of Puget Sound salmon could reflect degraded rearing conditions or changes in temporal-spatial utilization patterns by juvenile salmon in Puget Sound, and these patterns could vary between habitats and regions of Puget Sound in response to different environmental conditions or hatchery practices. In April-September 2001 and 2002, we evaluated spatial and temporal differences in distribution and size structure among juvenile chum, pink, coho, and chinook salmon at delta and nearshore habitats in a northern and southern region of Puget Sound, Washington. Water was consistently warmer (8-18.8??C) and less saline (0.0-27.7) in the northern (N) than in the southern region (S: 9.5-14.6??C, 13.0-30.4). Salinities were lower and water temperatures more variable in delta sites than exposed nearshore marine sites. Peak densities of juvenile salmon coincided at delta and nearshore sites within sampling regions but differed between regions. Nearshore densities were highest during April-June with pink and chum salmon generally preceding chinook and coho salmon, and peak catch rates of most species occurred in May. A second, late pulse of chinook salmon also occurred during July at northern sites. Juvenile chinook salmon were predominantly of hatchery origin in the southern region (98%), and of mixed origin in the northern region (44% marked hatchery fish) during 2002. The lengths of chinook and chum salmon in nearshore regions increased steadily through time, whereas pink and coho salmon varied inconsistently. Mean sizes of juvenile salmon were slightly but consistently smaller at delta than nearshore sites and at northern versus southern sites. Hatchery chinook salmon were slightly larger than their unmarked counterparts. Extended nearshore residence times (their seasonal duration in the catches) and significant increases in size suggested that nearshore environments may be particularly important rearing areas for juvenile chinook salmon in the northern region, and chum salmon in the southern region. Regional differences in the magnitude and timing of hatchery inputs, salinity, and water temperature likely affect the timing, nearshore use, size, and growth potential for juvenile salmon entering different regions of Puget Sound and could differentially influence subsequent marine survival. ?? 2005 Elsevier Ltd. All rights reserved.

Conference Paper↗

USGS2011

Characterizing near-surface CO2 conditions before injection - Perspectives from a CCS project in the Illinois Basin, USA

The Midwest Geological Sequestration Consortium is conducting a large-scale carbon capture and storage (CCS) project in Decatur, Illinois, USA to demonstrate the ability of a deep saline formation to store one million tonnes of carbon dioxide (CO 2 ) from an ethanol facility. Beginning in early 2011, CO 2 will be injected at a rate of 1,000 tonnes/day for three years into the Mount Simon Sandstone at a depth of approximately 2,100 meters. An extensive Monitoring, Verification, and Accounting (MVA) program has been undertaken for the Illinois Basin Decatur Project (IBDP) and is focused on the 0.65 km2 project site. Goals include establishing baseline conditions to evaluate potential impacts from CO 2 injection, demonstrating that project activities are protective of human health and the environment, and providing an accurate accounting of stored CO 2 . MVA efforts are being conducted pre-, during, and post- CO 2 injection. Soil and net CO 2 flux monitoring has been conducted for more than one year to characterize near-surface CO 2 conditions. More than 2,200 soil CO 2 flux measurements have been manually collected from a network of 118 soil rings since June 2009. Three ring types have been evaluated to determine which type may be the most effective in detecting potential CO 2 leakage. Bare soil, shallow-depth rings were driven 8 cm into the ground and were prepared to minimize surface vegetation in and near the rings. Bare soil, deep-depth rings were prepared similarly, but were driven 46 cm. Natural-vegetation, shallow-depth rings were driven 8 cm and are most representative of typical vegetation conditions. Bare-soil, shallow-depth rings had the smallest observed mean flux (1.78 μmol m −2 s −1 ) versus natural-vegetation, shallow-depth rings (3.38 μmol m −2 s −1 ). Current data suggest bare ring types would be more sensitive to small CO 2 leak signatures than natural ring types because of higher signal to noise ratios. An eddy covariance (EC) system has been in use since June 2009. Baseline data from EC monitoring is being used to characterize pre-injection conditions, and may then be used to detect changes in net exchange CO 2 fluxes (Fc) that could be the result of CO 2 leakage into the near-surface environment during or following injection. When injection at IBDP begins, soil and net CO 2 monitoring efforts will have established a baseline of near-surface conditions that will be important to help demonstrate the effectiveness of storage activities.

Illinois↗

USGS2016

Soil amplification with a strong impedance contrast: Boston, Massachusetts

In this study, we evaluate the effect of strong sediment/bedrock impedance contrasts on soil amplification in Boston, Massachusetts, for typical sites along the Charles and Mystic Rivers. These sites can be characterized by artificial fill overlying marine sediments overlying glacial till and bedrock, where the depth to bedrock ranges from 20 to 80 m. The marine sediments generally consist of organic silts, sand, and Boston Blue Clay. We chose these sites because they represent typical foundation conditions in the city of Boston, and the soil conditions are similar to other high impedance contrast environments. The sediment/bedrock interface in this region results in an impedance ratio on the order of ten, which in turn results in a significant amplification of the ground motion. Using stratigraphic information derived from numerous boreholes across the region paired with geologic and geomorphologic constraints, we develop a depth-to-bedrock model for the greater Boston region. Using shear-wave velocity profiles from 30 locations, we develop average velocity profiles for sites mapped as artificial fill, glaciofluvial deposits, and bedrock. By pairing the depth-to-bedrock model with the surficial geology and the average shear-wave velocity profiles, we can predict soil amplification in Boston. We compare linear and equivalent-linear site response predictions for a soil layer of varying thickness over bedrock, and assess the effects of varying the bedrock shear-wave velocity (V Sb ) and quality factor (Q). In a moderate seismicity region like Boston, many earthquakes will result in ground motions that can be modeled with linear site response methods. We also assess the effect of bedrock depth on soil amplification for a generic soil profile in artificial fill, using both linear and equivalent-linear site response models. Finally, we assess the accuracy of the model results by comparing the predicted (linear site response) and observed site response at the Northeastern University (NEU) vertical seismometer array during the 2011 M 5.8 Mineral, Virginia, earthquake. Site response at the NEU vertical array results in amplification on the order of 10 times at a period between 0.7-0.8 s. The results from this study provide evidence that the mean short-period and mean intermediate-period amplification used in design codes (i.e., from the F a and F v site coefficients) may underpredict soil amplification in strong impedance contrast environments such as Boston.

Massachusetts↗

USGS2008

Wetlands as principal zones of methylmercury production in southern Louisiana and the Gulf of Mexico region

It is widely recognized that wetlands, especially those rich in organic matter and receiving appreciable atmospheric mercury (Hg) inputs, are important sites of methylmercury (MeHg) production. Extensive wetlands in the southeastern United States have many ecosystem attributes ideal for promoting high MeHg production rates; however, relatively few mercury cycling studies have been conducted in these environments. We conducted a landscape scale study examining Hg cycling in coastal Louisiana (USA) including four field trips conducted between August 2003 and May 2005. Sites were chosen to represent different ecosystem types, including: a large shallow eutrophic estuarine lake (Lake Pontchartrain), three rivers draining into the lake, a cypress-tupelo dominated freshwater swamp, and six emergent marshes ranging from a freshwater marsh dominated by Panicum hemitomon to a Spartina alterniflora dominated salt marsh close to the Gulf of Mexico. We measured MeHg and total Hg (THg) concentrations, and ancillary chemical characteristics, in whole and filtered surface water, and filtered porewater. Overall, MeHg concentrations were greatest in surface water of freshwater wetlands and lowest in the profundal (non-vegetated) regions of the lake and river mainstems. Concentrations of THg and MeHg in filtered surface water were positively correlated with the highly reactive, aromatic (hydrophobic organic acid) fraction of dissolved organic carbon (DOC). These results suggest that DOC plays an important role in promoting the mobility, transport and bioavailability of inorganic Hg in these environments. Further, elevated porewater concentrations in marine and brackish wetlands suggest coastal wetlands along the Gulf Coast are key sites for MeHg production and may be a principal source of MeHg to foodwebs in the Gulf of Mexico. Examining the relationships among MeHg, THg, and DOC across these multiple landscape types is a first step in evaluating possible links between key zones for Hg(II)-methylation and the bioaccumulation of mercury in the biota inhabiting the Gulf of Mexico region

Environmental Pollution↗

USGS2017

Highlighting the complexities of a groundwater pilot study during an avian influenza outbreak: Methods, lessons learned, and select contaminant results

The highly pathogenic avian influenza (H5N2) outbreak in the Midwestern United States (US) in 2015 was historic due to the number of birds and poultry operations impacted and the corresponding economic loss to the poultry industry and was the largest animal health emergency in US history. The U.S. Geological Survey (USGS), with the assistance of several state and federal agencies, aided the response to the outbreak by developing a study to determine the extent of virus transport in the environment. The study goals were to: develop the appropriate sampling methods and protocols for measuring avian influenza virus (AIV) in groundwater, provide the first baseline data on AIV and outbreak- and poultry-related contaminant occurrence and movement into groundwater, and document climatological factors that may have affected both survival and transport of AIV to groundwater during the months of the 2015 outbreak. While site selection was expedient, there were often delays in sample response times due to both relationship building between agencies, groups, and producers and logistical time constraints. This study's design and sampling process highlights the unpredictable nature of disease outbreaks and the corresponding difficulty in environmental sampling of such events. The lessons learned, including field protocols and approaches, can be used to improve future research on AIV in the environment.

Iowa↗

USGS2017

Shallow water benthic imaging and substrate characterization using recreational-grade sidescan-sonar

In recent years, lightweight, inexpensive, vessel-mounted ‘recreational grade’ sonar systems have rapidly grown in popularity among aquatic scientists, for swath imaging of benthic substrates. To promote an ongoing ‘democratization’ of acoustical imaging of shallow water environments, methods to carry out geometric and radiometric correction and georectification of sonar echograms are presented, based on simplified models for sonar-target geometry and acoustic backscattering and attenuation in shallow water. Procedures are described for automated removal of the acoustic shadows, identification of bed-water interface for situations when the water is too turbid or turbulent for reliable depth echosounding, and for automated bed substrate classification based on singlebeam full-waveform analysis. These methods are encoded in an open-source and freely-available software package, which should further facilitate use of recreational-grade sidescan sonar, in a fully automated and objective manner. The sequential correction, mapping, and analysis steps are demonstrated using a data set from a shallow freshwater environment.

Environmental Modelling and Software↗

USGS2007

Petrology and tectonics of Phanerozoic continent formation: From island arcs to accretion and continental arc magmatism

Mesozoic continental arcs in the North American Cordillera were examined here to establish a baseline model for Phanerozoic continent formation. We combine new trace-element data on lower crustal xenoliths from the Mesozoic Sierra Nevada Batholith with an extensive grid-based geochemical map of the Peninsular Ranges Batholith, the southern equivalent of the Sierras. Collectively, these observations give a three-dimensional view of the crust, which permits the petrogenesis and tectonics of Phanerozoic crust formation to be linked in space and time. Subduction of the Farallon plate beneath North America during the Triassic to early Cretaceous was characterized by trench retreat and slab rollback because old and cold oceanic lithosphere was being subducted. This generated an extensional subduction zone, which created fringing island arcs just off the Paleozoic continental margin. However, as the age of the Farallon plate at the time of subduction decreased, the extensional environment waned, allowing the fringing island arc to accrete onto the continental margin. With continued subduction, a continental arc was born and a progressively more compressional environment developed as the age of subducting slab continued to young. Refinement into a felsic crust occurred after accretion, that is, during the continental arc stage, wherein a thickened crustal and lithospheric column permitted a longer differentiation column. New basaltic arc magmas underplate and intrude the accreted terrane, suture, and former continental margin. Interaction of these basaltic magmas with pre-existing crust and lithospheric mantle created garnet pyroxenitic mafic cumulates by fractional crystallization at depth as well as gabbroic and garnet pyroxenitic restites at shallower levels by melting of pre-existing lower crust. The complementary felsic plutons formed by these deep-seated differentiation processes rose into the upper crust, stitching together the accreted terrane, suture and former continental margin. The mafic cumulates and restites, owing to their high densities, eventually foundered into the mantle, leaving behind a more felsic crust. Our grid-based sampling allows us to estimate an unbiased average upper crustal composition for the Peninsular Ranges Batholith. Major and trace-element compositions are very similar to global continental crust averaged over space and time, but in detail, the Peninsular Ranges are slightly lower in compatible to mildly incompatible elements, MgO, Mg#, V, Sc, Co, and Cr. The compositional similarities suggest a strong arc component in global continental crust, but the slight discrepancies suggest that additional crust formation processes are also important in continent formation as a whole. Finally, the delaminated Sierran garnet pyroxenites have some of the lowest U/Pb ratios ever measured for silicate rocks. Such material, if recycled and stored in the deep mantle, would generate a reservoir with very unradiogenic Pb, providing one solution to the global Pb isotope paradox.

Earth and Planetary Science Letters↗

USGS2018

Sulfur cycle in the Valles Caldera volcanic complex, New Mexico – Letter 1: Sulfate sources in aqueous system, and implications for S isotope record in Gale Crater on Mars

Initial in situ sulfur (S) isotope measurements of the Martian bedrock in Gale Crater have revealed an unexpectedly wide range of δ 34 S values (−47 to +28%). Generally, it is unclear what processes could have contributed to these large isotope fractionations. Therefore, we studied S sources and aqueous SO 2− 4 cycling in the Valles Caldera volcanic complex, New Mexico to better understand S isotope fractionations related to S degassing, hydrothermal activity, and low-temperature processes in aqueous environment. Overall, our study demonstrates that volcanic systems show large spatial heterogeneity in δ 34 S. Magmatic S sources are obvious in steam-dominated H 2 S degassing and precipitation of secondary minerals from hydrothermal fluids with low δ 34 S values of +0.9 ±3%. Locally, however, hydrothermal processes have resulted in more negative δ 34 S values in sulfide minerals (−18 to −4%) and more positive δ 34 S values in sulfate minerals (−1 to +3%). Major aqueous SO 2− 4 sources are oxidation of H 2 S from modern hydrothermal gas emission, and oxidation and dissolution of sulfide and sulfate minerals present in the hydrothermally altered bedrock and crater-lake sediments. The δ 34 S of aqueous SO 2− 4 in surface water and groundwater varies widely (−8 to +5%) and is similar to major S endmembers that undergo oxidation and/or dissolution by active hydrological system. Minor SO 2− 4 contributions with more positive δ 34 S values (+9 to +14%) come from deeply circulating geothermal fluids and negligible amounts from atmospheric deposition (+5 to +7% in snow). Elevated SO 2− 4 contents are mainly associated with modern and past H 2 S emissions and oxidations near the surface. On regional scale, however, most of the intracaldera bedrock is S-depleted, thus the SO 2− 4 contents are usually low in the surface aquatic system and younger sedimentary lake deposits formed at times of negligible near surface hydrothermal activity. In general, magmatic-hydrothermal processes apparently cause the largest δ 34 S variation in S-bearing minerals on volcanic terrains. Therefore, we infer that the measured wide range of δ 34 S values in the Gale sediments by the Curiosity rover on Mars can be explained by S isotope composition of magmatic-hydrothermal sulfide and sulfate minerals that were present in the initial igneous/volcanic rocks prior to crater formation. Later aqueous processes involved oxidation and dissolution of S minerals initially present in these rocks and led to subsequent formation of diagenetic fluids and alteration products enriched in SO 2− 4 with relatively large δ 34 S variation. Additionally, physical erosion, transport and deposition of detrital hydrothermal S minerals from igneous/volcanic rocks might be in part responsible for the measured wide range of δ 34 S in Gale Crater. These unique S isotope results, measured in situ on another planet for the first time, imply the importance of magmatic-hydrothermal fluids in S transport on early Mars and their subsequent alteration in low-temperature aqueous environments.

New Mexico↗