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Community for Data Integration 2014 annual report

The U.S. Geological Survey (USGS) researches Earth science to help address complex issues affecting society and the environment. In 2006, the USGS held the first Scientific Information Management Workshop to bring together staff from across the organization to discuss the data and information management issues affecting the integration and delivery of Earth science research and investigate the use of “communities of practice” as mechanisms to share expertise about these issues. Out of this effort emerged the Council for Data Integration, which was conceived as an official organizational function that would help guide data integration activities and formalize communities of practice into working groups; however, by 2009 it became evident that many members of the Council for Data Integration had an interest in developing data integration solutions and sharing expertise in a less formal, grassroots manner, which transformed the Council into a Community for Data Integration (CDI). As of 2014, the CDI represents a dynamic community of practice focused on advancing science data and information management and integration capabilities across the USGS and the CDI community. The CDI fosters an environment for collaboration and sharing by bringing together expertise from external partners and representatives across the USGS who are involved in research, data management, and information technology. Membership is voluntary and open to USGS employees and other individuals and organizations willing to contribute to the community (if interested, contact cdi@usgs.gov). The purpose of the CDI is to do the following: • advance understanding of Earth systems through enhanced use of data and information including associated tools and techniques, • provide a forum for people doing work with data integration to come together to share ideas and learn new skills and techniques, and • grow overall USGS capabilities with data and information by increasing visibility of the work of many people throughout the USGS and the CDI community. To achieve these goals, the CDI operates within four applied areas: monthly forums, annual workshop/webinar series, working groups, and projects. The monthly forums, also known as the Opportunity/Challenge of the Month, provide an open dialogue to share and learn about data integration efforts or to present problems that invite the community to offer solutions, advice, and support. Since 2010, the CDI has also sponsored annual workshops/webinar series to encourage the exchange of ideas, sharing of activities, presentations of current projects, and networking among members. Stemming from common interests, the working groups are focused on efforts to address data management and technical challenges including the development of standards and tools, improving interoperability and information infrastructure, and data preservation within USGS and its partners. The growing support for the activities of the working groups led to the CDI’s first formal request for proposals (RFP) process in 2013 to fund projects that produced tangible products. As of 2014, the CDI continues to hold an annual RFP that creates data management tools and practices, collaboration tools, and training in support of data integration and delivery.

Open-File Report↗

Pliocene-Pleistocene coastal events and history along the western margin of Australia

Coastal deposits along the western coastal margin of Australia, a region of relative tectonic stability, record Plio-Pleistocene events and processes affecting the inner shelf and adjacent hinterland. Tectonic deformation of these deposits is more apparent in the Carnarvon Basin, and rather less so in the Perth Basin. The most complete record comes from the Perth Basin, where units of Pliocene and Pleistocene ages are well represented. In the Perth Basin, the predominantly siliciclastic Yoganup Formation, Ascot Formation and Bassendean Sand represent a complex of shoreline, inner shelf and regressive-dune facies equivalents, the deposition of which began at an undetermined stage of the Pliocene, through to the Early Pleistocene. The deposition of this sequence closed with a major regression and significant faunal extinction. Bioclastic carbonates characterize the Middle and Late Pleistocene of the Perth and Carnarvon basins. Fossil assemblages include a distinct subtropical element, unknown from the Ascot Formation and suggesting a strengthening of the Leeuwin Current. The estuarine arcoid bivalve Anadara trapezia characterizes assemblages of Oxygen Isotope Stages 5 and 7 in the Perth and Carnarvon basins, where it is now extinct. Deposits of Substage 5e (Perth Basin) also record a southerly expansion of warm-water corals and other fauna consistent with shelf temperatures warmer than present. New uranium-series ages on corals from marine sequences of the Tantabiddi Member, of the Bundera Calcarenite of the western Cape Range are consistent with the ‘double peak’ hypothesis for levels of Substage 5e but the evidence remains less than conclusive. Initial uranium-series dates from the Bibra and Dampier formations of Shark Bay indicate that both derive from the Late Pleistocene. These numerical ages contradict previous interpretations of relative ages obtained from field studies. The age relationship of the units requires further investigation.

Quaternary Science Reviews↗

Bottled water, spas, and early years of water chemistry

Although hot springs have been used and enjoyed for thousands of years, it was not until the late 1700s that they changed the course of world civilization by being the motivation for development of the science of chemistry. The pioneers of chemistry such as Priestley, Cavendish, Lavoisier, and Henry were working to identify and generate gases, in part, to determine their role in carbonated beverages. In the 18th century, spas in America were developed to follow the traditional activities of popular European spas. However, they were to become a dominant political and economic force in American history on three major points: (1) By far the most important was to provide a place for the leaders of individual colonies to meet and discuss the need for separation from England and the necessity for the Revolutionary War; (2) the westward expansion of the United States was facilitated by the presence of hot springs in many locations that provided the economic justification for railroads and settlement; and (3) the desire for the preservation of hot springs led to the establishment of the National Park Service. Although mineral springs have maintained their therapeutic credibility in many parts of the world, they have not done so in the United States. We suggest that the American decline was prompted by: (1) the establishment of The Johns Hopkins School of Medicine in 1893; (2) enactment of the Pure Food and Drug Act of 1907; and (3) the remarkable achievement of providing safe water supplies for American cities by the end of the 1920s. The current expanding market for bottled water is based in part on bottled water being an alternative beverage Ito alcohol and sweetened drinks and the inconsistent palatability and perceived health hazards of some tap waters.

Groundwater↗

Influence of propagule flotation longevity and light availability on establishment of introduced mangrove species in Hawai'i

Although no mangrove species are native to the Hawaiian Archipelago, both Rbizopbora mangle and Bruguiera sexangula were introduced and have become naturalized. Rbizopbora mangle has spread to almost every major Hawaiian island, but B. sexangula has established only on O'ahu, where it was intentionally introduced. To examine the possibility that differences in propagule characteristics maintain these patterns of distribution, we first reviewed the literature on surface currents around the Hawaiian Islands, which suggest that propagules ought to disperse frequently from one island to another within 60. days. We then tested the ability of propagules of the two species to float for periods of up to 63 days and to establish under two light intensities. On average, R. mangle propagules floated for longer periods than those of B. sexangula , but at least some propagules of both species floated for a full 60 days and then rooted and grew for 4 months under relatively dense shade. A large percentage (???83%) of R. mangle propagules would be expected to float beyond 60 days, and approximately 10% of B. sexangula propagules also would have remained afloat. Therefore, it seems likely that factors other than flotation ability are responsible for the failure of B. sexangula to become established on other Hawaiian islands.

Hawaii↗

Geomorphic expression of rapid Holocene silicic magma reservoir growth beneath Laguna del Maule, Chile

Large rhyolitic volcanoes pose a hazard, yet the processes and signals foretelling an eruption are obscure. Satellite geodesy has revealed surface inflation signaling unrest within magma reservoirs underlying a few rhyolitic volcanoes. Although seismic, electrical, and potential field methods may illuminate the current configuration and state of these reservoirs, they cannot fully address the processes by which they grow and evolve on geologic time scales. We combine measurement of a deformed paleoshore surface, isotopic dating of volcanism and surface exposure, and modeling to determine the rate of growth of a rhyolite-producing magma reservoir. The numerical approach builds on a magma intrusion model developed to explain the current, decade-long, surface inflation at >20 cm/year. Assuming that the observed 62-m uplift reflects several non-eruptive intrusions of magma, each similar to the unrest over the past decade, we find that ~13 km 3 of magma recharged the reservoir at a depth of ~7 km during the Holocene, accompanied by the eruption of ~9 km 3 of rhyolite. The long-term rate of magma input is consistent with reservoir freezing and pluton formation. Yet, the unique set of observations considered here implies that large reservoirs can be incubated and grow at shallow depth via episodic high-flux magma injections. These replenishment episodes likely drive rapid inflation, destabilize cooling systems, propel rhyolitic eruptions, and thus should be carefully monitored.

Laguna del Maule↗

Pharmaceuticals and personal care products (PPCPs) are ecological disrupting compounds (EcoDC)

Pharmaceuticals and personal care products (PPCPs) are ubiquitous in freshwater ecosystems worldwide and are recognized as contaminants of concern. Currently, contaminants of concern are classified for their persistence, bioaccumulation, and toxicity (PBT criteria). PPCPs are not classified as persistent organic pollutants (POPs), although some PPCPs share characteristics similar to POPs. For example, PPCPs are known to be pseudopersistent due to constant discharge into the environment, often at low concentrations. At commonly reported environmental concentrations, PPCPs are rarely toxic, but the ability of these compounds to disrupt ecological processes and functions in freshwater ecosystems is often overlooked. Herein we briefly summarize recent studies highlighting the potential ecological effects of PPCPs, including effects on key ecological processes (e.g. primary productivity and community respiration), and we propose that appropriate screening for harmful effects of PPCPs in surface waters should be expanded to include Ecologically Disrupting Compounds (EcoDC) in addition to the established PBT criteria.

Elementa: Science of the Anthropocene↗

Radargrammetry on three planets

Synthetic Aperture Radar (SAR) can provide useful images in situations where passive optical imaging cannot, either because the microwaves used can penetrate atmospheric clouds, because active imaging can "see in the dark," or both. We have participated in the NASA Magellan mission to Venus in the 1990s and the current NASA-ESA Cassini-Huygens mission to Saturn and Titan, which have used SAR to see through the clouds of Venus and Titan, respectively, and have developed software and techniques for the production of digital topographic models (DTMs) from radar stereopairs. We are currently preparing for similar radargrammetric analysis of data from the Mini-RF instrument to be carried to the Moon on both the ISRO Chandrayaan-1 and NASA Lunar Reconnaissance Orbiter (LRO) missions later in 2008. These instruments are intended to image the permanently shadowed areas at the lunar poles and even see below the surface to detect possible water ice deposits. In this paper, we describe our approach to radargrammetric topographic mapping, based on the use of the USGS ISIS software system to ingest and prepare data, and the commercial stereoanalysis software SOCET SET (® BAE Systems), augmented with custom sensor models we have implemented, for DTM production and editing. We describe the commonalities and differences between the various data sets, and some of the lessons learned, both radargrammetric and geoscientific.

The International Archives of the Photogrammetry, ↗

Persistent and novel threats to the biodiversity of Kazakhstan’s steppes and semi-deserts

Temperate grasslands have suffered disproportionally from conversion to cropland, degradation and fragmentation. A large proportion of the world’s remaining near-natural grassland is situated in Kazakhstan. We aimed to assess current and emerging threats to steppe and semi-desert biodiversity in Kazakhstan and evaluate conservation research priorities. We conducted a horizon-scanning exercise among conservationists from academia and practice. We first compiled a list of 45 potential threats. These were then ranked by the survey participants according to their perceived severity, the need for research on them, and their novelty. The highest-ranked threats were related to changes in land use (leading to habitat loss and deterioration), direct persecution of wildlife, and rapid infrastructure development due to economic and population growth. Research needs were identified largely in the same areas, and the mean scores of threat severity and research need were highly correlated. Novel threats comprised habitat loss by photovoltaic and wind power stations, climate change and changes in agriculture such as the introduction of biofuels. However, novelty was not correlated with threat severity or research priority, suggesting that the most severe threats are the established ones. Important goals towards more effective steppe and semi-desert conservation in Kazakhstan include more cross-sector collaboration (e.g. by involving stakeholders in conservation and agriculture), greater allocation of funds to under-staffed areas (e.g. protected area management), better representativeness and complementarity in the protected area system and enhanced data collection for wildlife monitoring and threat assessments (including the use of citizen-science databases).

Biodiversity and Conservation↗

Salt marsh ecosystem restructuring enhances elevation resilience and carbon storage during accelerating relative sea-level rise

Salt marshes respond to sea-level rise through a series of complex and dynamic bio-physical feedbacks. In this study, we found that sea-level rise triggered salt marsh habitat restructuring, with the associated vegetation changes enhancing salt marsh elevation resilience. A continuous record of marsh elevation relative to sea level that includes reconstruction of high-resolution, sub-decadal, marsh elevation over the past century, coupled with a lower-resolution 1500-year record, revealed that relative sea-level rose 1.5 ± 0.4 m, following local glacial isostatic adjustment (1.2 mm/yr). As sea-level rise has rapidly accelerated, the high marsh zone dropped 11 cm within the tidal frame since 1932, leading to greater inundation and a shift to flood- and salt-tolerant low marsh species. Once the marsh platform fell to the elevation favored by low-marsh Spartina alterniflora , the elevation stabilized relative to sea level. Currently low marsh accretion keeps pace with sea-level rise, while present day high marsh zones that have not transitioned to low marsh have a vertical accretion deficit. Greater biomass productivity, and an expanding subsurface accommodation space favorable for salt marsh organic matter preservation, provide a positive feed-back between sea-level rise and marsh platform elevation. Carbon storage was 46 ± 28 g C/m 2 /yr from 550 to 1800 CE, increasing to 129 ± 50 g C/m 2 /yr in the last decade. Enhanced carbon storage is controlled by vertical accretion rates, rather than soil carbon density, and is a direct response to anthropogenic eustatic sea-level rise, ultimately providing a negative feedback on climate warming.

Massachusetts↗

Modern pollen data from North America and Greenland for multi-scale paleoenvironmental applications

The modern pollen network in North America and Greenland is presented as a database for use in quantitative calibration studies and paleoenvironmental reconstructions. The georeferenced database includes 4634 samples from all regions of the continent and 134 pollen taxa that range from ubiquitous to regionally diagnostic taxa. Climate data and vegetation characteristics were assigned to every site. Automated and manual procedures were used to verify the accuracy of geographic coordinates and identify duplicate records among datasets, incomplete pollen sums, and other potential errors. Data are currently available for almost all of North America, with variable density. Pollen taxonomic diversity, as measured by the Shannon-Weiner coefficient, varies as a function of location, as some vegetation regions are dominated by one or two major pollen producers, while other regions have a more even composition of pollen taxa. Squared-chord distances computed between samples show that most modern pollen samples find analogues within their own vegetation zone. Both temperature and precipitation inferred from best analogues are highly correlated with observed values but temperature exhibits the strongest relation. Maps of the contemporary distribution of several pollen types in relation to the range of the plant taxon illustrate the correspondence between plant and pollen ranges. ?? 2005 Elsevier Ltd. All rights reserved.

Quaternary Science Reviews↗

Transient simulations of nitrogen load for a coastal aquifer and embayment, Cape Cod, MA

A time-varying, multispecies, modular, three-dimensional transport model (MT3DMS) was developed to simulate groundwater transport of nitrogen from increasing sources on land to the shore of Nauset Marsh, a coastal embayment of the Cape Cod National Seashore. Simulated time-dependent nitrogen loads at the coast can be used to correlate with current observed coastal eutrophic effects, to predict current and ultimate effects of development, and to predict loads resulting from source remediation. A time-varying nitrogen load, corrected for subsurface loss, was applied to the land subsurface in the transport model based on five land-use coverages documenting increasing development from 1951 to 1999. Simulated nitrogen loads to Nauset Marsh increased from 230 kg/yr before 1930 to 4390 kg/yr in 2001 to 7130 kg/yr in 2100, assuming future nitrogen sources constant at the 1999 land-use rate. The simulated nitrogen load per area of embayment was 5 times greater for Salt Pond, a eutrophic landward extension of Nauset Marsh, than for other Nauset Marsh areas. Sensitivity analysis indicated that load results were little affected by changes in vertical discretization and annual recharge but much affected by the nitrogen loss rate assumed for a kettle lake downgradient from a landfill.

Environmental Science & Technology↗

An estimation of carrying capacity for sea otters along the California coast

Carrying capacity (K) for the California sea otter ( Enhydra lutris nereis ) was estimated as a product of the density of sea otters at equilibrium within a portion of their existing range and the total area of available habitat. Equilibrium densities were determined using the number of sea otters observed during spring surveys in 1994, 1995, and 1996 in each of three habitat types where sea otters currently exist. Potential sea otter habitat was defined as from the California coastline to the 40-m isobath and classified as rocky, sandy, or mixed habitat according to the amount of kelp and rocky substrate in the area. The amount of habitat available to sea otters in California was estimated using a Geographic Information Systems (GIS) program. The estimated mean number of sea otters that could be supported by the marine environment to a depth of 40 m in California was 15,941 (95% CI 13,538–18,577). The GIS-based approach incorporated detailed bathymetric contours, produced repeatable and accurate estimates, and served as an innovative method of measuring sea otter habitat. We believe the approach described in this paper represents the best available information on how a sea otter population at equilibrium would be distributed along the California coast.

California↗

Recent population trends of mountain goats in the Olympic Mountains, Washington

Mountain goats ( Oreamnos americanus ) were introduced in Washington's Olympic Mountains during the 1920s. The population subsequently increased in numbers and expanded in range, leading to concerns by the 1970s over the potential effects of non-native mountain goats on high-elevation plant communities in Olympic National Park. The National Park Service (NPS) transplanted mountain goats from the Olympic Mountains to other ranges between 1981 and 1989 as a means to manage overabundant populations, and began monitoring population trends of mountain goats in 1983. We estimated population abundance of mountain goats during 18–25 July 2011, the sixth survey of the time series, to assess current population status and responses of the population to past management. We surveyed 39 sample units, comprising 39% of the 59,615-ha survey area. We estimated a population of 344 ± 72 (90% confidence interval [CI]) mountain goats in the survey area. Retrospective analysis of the 2004 survey, accounting for differences in survey area boundaries and methods of estimating aerial detection biases, indicated that the population increased at an average annual rate of 4.9% since the last survey. That is the first population growth observed since the cessation of population control measures in 1990. We postulate that differences in population trends observed in western, eastern, and southern sections of the survey zone reflected, in part, a variable influence of climate change across the precipitation gradient in the Olympic Mountains.

Washington↗

Holocene relative sea-level change along the tectonically active Chilean coast

We present a comprehensive relative sea-level (RSL) database for north, central, and south-central Chile (18.5°S – 43.6°S) using a consistent, systematic, and internationally comparable approach. Despite its latitudinal extent, this coastline has received little rigorous or systematic attention and details of its RSL history remain largely unexplored. To address this knowledge gap, we re-evaluate the geological context and age of previously published sea-level indicators, providing 78 index points and 84 marine or terrestrial limiting points spanning from 11 ka to the present day. Many data points were originally collected for research in other fields and have not previously been examined for the information they provide on sea-level change. Additionally, we describe new sea-level data from four sites located between the Gulf of Arauco and Valdivia. By compiling RSL histories for 11 different regions, we summarise current knowledge of Chilean RSL. These histories indicate mid Holocene sea levels above present in all regions, but at highly contrasting elevations from ∼30 m to <5 m. We compare the spatiotemporal distribution of sea-level data points with a suite of glacial isostatic adjustment models and place first-order constraints on the influence of tectonic processes over 10 3 –10 4 year timescales. While seven regions indicate uplift rates <1 m ka −1 , the remaining regions may experience substantially higher rates. In addition to enabling discussion of the factors driving sea-level change, our compilation provides a resource to assist attempts to understand the distribution of archaeological, palaeoclimatic, and palaeoseismic evidence in the coastal zone and highlights directions for future sea-level research in Chile.

Quaternary Science Reviews↗

The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice

The Coalition for Conservation Genetics (CCG) brings together four eminent organizations with the shared goal of improving the integration of genetic information into conservation policy and practice. We provide a historical context of conservation genetics as a field and reflect on current barriers to conserving genetic diversity, highlighting the need for collaboration across traditional divides, international partnerships, and coordinated advocacy. We then introduce the CCG and illustrate through examples how a coalition approach can leverage complementary expertise and improve the organizational impact at multiple levels. The CCG has proven particularly successful at implementing large synthesis-type projects, training early-career scientists, and advising policy makers. Achievements to date highlight the potential for the CCG to make effective contributions to practical conservation policy and management that no one “parent” organization could achieve on its own. Finally, we reflect on the lessons learned through forming the CCG, and our vision for the future.

Conservation Science and Practice↗

The influence of large woody debris on post-wildfire debris flow sediment storage

Debris flows transport large quantities of water and granular material, such as sediment and wood, and this mixture can have devastating impacts on life and infrastructure. The proportion of large woody debris (LWD) incorporated into debris flows can be enhanced in forested areas recently burned by wildfire, because wood recruitment into channels accelerates in burned forests. In this study, we explored how LWD transported in post-wildfire debris flows acts to retain sediment within small headwater channels. We found that the largest amount of debris flow sediment is stored in channel reaches with a ratio of LWD length to channel width between 0.25 and 1. Moreover, the largest debris flow deposits forced by LWD were found in low-angle channel reaches. We examined two models for debris flow volume estimation: (1) the current volume prediction model used in U.S. Geological Survey debris flow hazard assessments, and (2) a regional model developed to predict the sediment yield associated with debris-laden flows. We found that the regional model better matched the magnitude of the observed sediment at the terminal fan, suggesting the utility of regionally calibrated parameters for debris flow volume prediction. However, large wood created sediment storage upstream of the terminal fan, and this volume was of the same magnitude as the total volume at the terminal fans. Finally, we demonstrate a method for estimating debris flow velocity based on estimates of the critical velocity required to break wood, which can be used in future field studies to estimate minimum debris flow velocity values.

New Mexico↗

Routine screening of harmful microorganisms in beach sands: implications to public health

Beaches worldwide provide recreational opportunities to hundreds of millions of people and serve as important components of coastal economies. Beach water is often monitored for microbiological quality to detect the presence of indicators of human sewage contamination so as to prevent public health outbreaks associated with water contact. However, growing evidence suggests that beach sand can harbor microbes harmful to human health, often in concentrations greater than the beach water. Currently, there are no standards for monitoring, sampling, analyzing, or managing beach sand quality. In addition to indicator microbes, growing evidence has identified pathogenic bacteria, viruses, and fungi in a variety of beach sands worldwide. The public health threat associated with these populations through direct and indirect contact is unknown because so little research has been conducted relating to health outcomes associated with sand quality. In this manuscript, we present the consensus findings of a workshop of experts convened in Lisbon, Portugal to discuss the current state of knowledge on beach sand microbiological quality and to develop suggestions for standardizing the evaluation of sand at coastal beaches. The expert group at the “Microareias 2012” workshop recommends that 1) beach sand should be screened for a variety of pathogens harmful to human health, and sand monitoring should then be initiated alongside regular water monitoring; 2) sampling and analysis protocols should be standardized to allow proper comparisons among beach locations; and 3) further studies are needed to estimate human health risk with exposure to contaminated beach sand. Much of the manuscript is focused on research specific to Portugal, but similar results have been found elsewhere, and the findings have worldwide implications.

Science of the Total Environment↗

Cyanobacteria and aquatic ecosystem dynamics across 28,000 years of environmental changes in subtropical North America

Ecological pressures on aquatic ecosystems have increased over recent centuries due to human activities and climate change. However, contextualizing ecosystem deterioration is often challenging due to limited knowledge of environmental changes over millennial timescales. Subtropical Carolina bays in North Carolina, USA, have remained unglaciated, preserving paleolimnological records that extend back to the last glacial period. Here, we analyzed a sediment core from the ecologically rich Lake Waccamaw spanning more than 28,000 years for aquatic proxies of nutrients, photosynthetic pigments, cyanotoxins, carbon isotopes, and terrestrial proxies of pollen and charcoal. The study explored paleolimnological changes in the aquatic environment connected to land changes and climate during the late Quaternary in the southeastern Atlantic Coastal Plain. Results reveal that while current levels of colonial cyanobacteria are high, past levels of cyanobacteria, other primary producers, and cyanotoxins were higher under natural climate variability. Abrupt ecosystem responses to increasing trophic conditions during Interstadial 3 (27.8–26.4 cal ka BP) and the early Holocene (11.4–7 cal ka BP) were marked by increases in primary producer abundance, deciduous vegetation expansion, and fire activity. Cyanobacteria remained dominant throughout the record, with colonial forms prevailing during the Holocene. Increases in pigment concentrations aligned with Quercus and were primarily driven by hydroclimatic variability and nutrient stoichiometry. Transitions between Pinus and Quercus pollen matched stadials and interstadials in the δ 18 Ο record from the North Greenland Ice Core Project (NGRIP). This study highlights the value of multi-proxy millennial-scale paleolimnological records for understanding aquatic ecosystem responses to climate conditions during the late Pleistocene.

North Carolina↗