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At least 1,459 records · Page 81

Big data for ecologists: Highlighting the ORNL DAAC

Ecologists are increasingly confronted by questions that can be addressed only by integrating data from numerous sources, often across large geographic areas and broad time periods. The supply of ecological big data is increasing at a rapid pace as researchers are publishing their data sets and large, public science and data infrastructures (such as NEON, DataONE, LTER, & NCEAS) are producing and curating extensive volumes of complex data and metadata. While supply of, and demand for, ecological data is on the rise, many ecologists now face a new challenge in locating and synthesizing the data relevant for their particular question. Here we highlight selected popular big data products applicable to ecological research available from the NASA Distributed Active Archive Center (DAAC) located at Oak Ridge National Laboratory (ORNL).

Boyer, Alison G↗

Phylogeonomics and Ecogenomics of the Mycorrhizal Symbiosis

Mycorrhizal fungi play critical roles in host plant health, soil community structure and chemistry, and carbon and nutrient cycling, all areas of intense interest to the US Dept. of Energy (DOE) Joint Genome Institute (JGI). To this end we are building on our earlier sequencing of the Laccaria bicolor genome by partnering with INRA-Nancy and the mycorrhizal research community in the MGI to sequence and analyze 2 dozen mycorrhizal genomes of numerous known mycorrhizal orders and several ecological types (ectomycorrhizal [ECM], ericoid, orchid, and arbuscular). JGI has developed and deployed high-throughput pipelines for genomic, transcriptomic, and re-sequencing, and platforms for assembly, annotation, and analysis. In the last 2 years we have sequenced 21 genomes of mycorrhizal fungi, and resequenced 6 additional strains of L. bicolor. Most of this data is publicly available on JGI MycoCosm?s Mycorrhizal Fungi Portal (http://jgi.doe.gov/Mycorrhizal_fungi/), which provides access to both the genome data and tools with which to analyze the data. These data allow us to address long-standing issues in mycorrhizal evolution and ecology. For example, a major observation of mycorrhizal evolution is that each of the major ecological types appears to have evolved independently in multiple fungal clades. Using an ecogenomic approach we provide preliminary evidence that 2 clades (Cantharellales and Sebacinales) of a single symbiotic ecotype (orchid) utilize some common regulatory (protein tyrosine kinase) and metabolic (lipase) paths, the latter of which may be the product of HGT. Using a phylogenomic approach we provide preliminary evidence that a particular ecotype (ericoid) may have evolved more than once within a major clade (Leotiomycetes).

59 BASIC BIOLOGICAL SCIENCES↗

Decision trees for incorporating the likelihood of excessive hydrologic alteration into hydropower-ecosystem tradeoffs

Detrimental ecological impacts have often been observed or anticipated when changes in streamflow indicators exceed percent deviation thresholds believed to be ecologically critical. Yet, short pre- and post-impact flow records often make it difficult to determine whether changes exceeding tolerable thresholds are due to dam operations or natural variability. Through a hypothetical reservoir operations example, we incorporate the uncertainty of dam-induced streamflow changes into a Bayesian decision tree framework that evaluates tradeoffs between expected regrets associated with hydropower and ecology. The likelihood of over-protection (type I) and under-protection (type II) errors associated with hypothesis tests are used to compute expected hydropower and ecosystem regrets associated with dam operation decisions. We examine changes to high (annual Q5) and low flows (annual Q95) in typical years using a modified and extended nonparametric ranked-sum test that accounts for percent deviation thresholds. A multiple comparison test is then used to determine the likelihood of at least one threshold violation. An example shows that our decision-theoretic approach can lead to different dam operation recommendations than do other common methods, and highlights limitations that arise when the type I error rate is selected a priori. While we illustrate a hydropower-ecosystem tradeoff, our approach can also be applied to other multi-stakeholder reservoir and river management conflicts.

Bayesian decision-making, environmental flows, flo↗

Hydropower Role in a Power Grid with a High Proportion of Variable Renewables

The importance of hydropower increases as the power grid evolves with the higher variable renewable contribution. As conventional thermal power plants are retired, the importance of hydropower contribution increases to balance the variability of solar and wind generation. However, reservoir water resources are constrained by multiple constraints, and variability of water inflow to the reservoirs creates limitations to dam water releases for power grid needs. Coordination of multiple tools, including water resources modeling, ecological modeling, and technical and economic power grid modeling, informs dam water releases. Better representation of ecological constraints and other water use details in the suit of power grid models are required to identify the hydropower flexibility to provide multiple power grid services. Impacts of water planning and hydropower operation changes to a power grid are better understood by production cost model simulations with technical and economic data, including unserved energy, reserve failures, transmission congestion to serve load, and local marginal price increases. Similarly, PCM simulation of current and future projected power grid information, including LMP, and carbon emission rates, informs short-term water release plans and long-term investments for power plant upgrades for technical and ecological needs. Hydropower operations of several case studies are simulated to understand operation patterns, revenue, water release decisions in multiple time scales (month, day, minutes), hydropower contracts scheduling, and water variability impacts.

environmental↗

Recent Developments in the Management of Cameco Corporation's Fuel Services Division Waste - 13144

Cameco Corporation is a world leader in uranium production. Headquartered in Saskatoon, Saskatchewan our operations provide 16% of the world uranium mine production and we have approximately 435 million pounds of proven and probable uranium reserves. Cameco mining operations are located in Saskatchewan, Wyoming, Nebraska and Kazakhstan. Cameco is also a major supplier of uranium processing services required to produce fuel for the generation of clean energy. These operations are based in Blind River, Cobourg and Port Hope, Ontario and are collectively referred to as the Fuel Services Division. The Fuel Services Division produces uranium trioxide from uranium ore concentrate at the Blind River Refinery. Cameco produces uranium hexafluoride and uranium dioxide at the Port Hope Conversion Facility. Cameco operates a fuel manufacturing facility in Port Hope, Ontario and a metal fabrication facility located in Cobourg, Ontario. The company manufactures fuel bundles utilized in the Candu reactors. Cameco's Fuel Services Division produces several types of low-level radioactively contaminated wastes. Internal processing capabilities at both the Blind River Refinery and Port Hope Conversion Facility are extensive and allow for the recycling of several types of waste. Notwithstanding these capabilities there are certain wastes that are not amenable to the internal processing capabilities and must be disposed of appropriately. Disposal options for low-level radioactively contaminated wastes in Canada are limited primarily due to cost considerations. In recent years, Cameco has started to ship marginally contaminated wastes (<500 ppm uranium) to the United States for disposal in an appropriate landfill. The landfill is owned by US Ecology Incorporated and is located near Grand View, Idaho 70 miles southeast of Boise in the Owyhee Desert. The facility treats and disposes hazardous waste, non-hazardous industrial waste and low-activity radioactive material. The site's arid climate, deep groundwater and favourable geology help ensure permanent waste isolation. Combined with a state of the art multi-layer landfill liner system, the Grand View facility represents an ideal choice to minimize environmental liability. Marginally contaminated wastes from operations within the Fuel Services Division are typically loaded into PacTec IP-2 rated Intermediary Bulk Containers and then transported by road to a nearby rail siding. The Intermediary Bulk Containers are then loaded in US Ecology owned gondola rail-cars. The gondolas are then transported via Canadian Pacific and Union Pacific railroads to the US Ecology Rail Transfer facility located in Mayfield, Idaho. The Intermediary Bulk Containers are unloaded into trucks for transport to the disposal facility located approximately 32 miles away. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Environmental Stewardship at the Savannah River Site: Generations of Success - 13212

Approximately sixty years ago, the Savannah River Site (SRS) was built to produce nuclear materials. SRS production operations impacted air, soil, groundwater, ecology, and the local environment. Throughout its history, SRS has addressed these contamination issues directly and has maintained a commitment to environmental stewardship. The Site boasts many environmental firsts. Notably, SRS was the first major Department of Energy (DOE) facility to perform a baseline ecological assessment. This pioneering effort, by Ruth Patrick and the Philadelphia Academy of Sciences, was performed during SRS planning and construction in the early 1950's. This unique early generation of work set the stage for subsequent efforts. Since that time, the scientists and engineers at SRS pro-actively identified environmental problems and developed and implemented effective and efficient environmental management and remediation solutions. This second generation, spanning the 1980's through the 2000's, is exemplified by numerous large and small cleanup actions to address metals and radionuclides, solvents and hydrocarbons, facility and area decommissioning, and ecological restoration. Recently, a third generation of environmental management was initiated as part of Enterprise SRS. This initiative to 'Develop and Deploy Next Generation Cleanup Technologies' formalizes and organizes the major technology matching, development, and implementation processes associated with historical SRS cleanup success as a resource to support future environmental management missions throughout DOE. The four elements of the current, third generation, effort relate to: 1) transition from active to passive cleanup, 2) in situ decommissioning of large nuclear facilities, 3) new long term monitoring paradigms, and 4) a major case study related to support for recovery and restoration of the Japanese Fukushima-Daiichi nuclear power plant and surrounding environment. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Pastures to Prairies to Pools: An Update on Natural Resource Damages Settlement Projects at the Fernald Preserve - 13198

The DOE Office of Legacy Management oversees implementation and monitoring of two ecological restoration projects at the Fernald Preserve, Fernald, Ohio, that are funded through a CERCLA natural resource damage settlement. Planning and implementation of on-property ecological restoration projects is one component of compensation for natural resource injury. The Paddys Run Tributary Project involves creation of vernal pool wetland habitat with adjacent forest restoration. The Triangle Area Project is a mesic tall-grass prairie establishment, similar to other efforts at the Fernald Preserve. The goal of the Fernald Natural Resource Trustees is to establish habitat for Ambystomatid salamander species, as well as grassland birds. Field implementation of these projects was completed in May 2012. Herbaceous cover and woody vegetation survival was determined in August and September 2012. Results show successful establishment of native vegetation. Additional monitoring will be needed to determine whether project goals have been met. As with the rest of the Fernald Preserve, ecological restoration has helped turn a DOE liability into a community asset. (authors)

54 ENVIRONMENTAL SCIENCES↗

Natural Resource Damages Settlement Projects at the Fernald Preserve - 12316

This paper describes the development and implementation of two ecological restoration projects at the Fernald Preserve that are funded through a CERCLA natural resource damage settlement. The Paddys Run Tributary Project involves creation of vernal pool wetland habitat with adjacent forest restoration. The Triangle Area Project is a mesic tall-grass prairie establishment, similar to other efforts at the Fernald Preserve. The goal of the Fernald Natural Resource Trustees is to establish habitat for Ambystomatid salamander species, as well as grassland birds. Planning and implementation of on-property ecological restoration projects is one component of compensation for natural resource injury. As with the rest of the Fernald Preserve, ecological restoration has helped turn a DOE liability into a community asset. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Integrated Disposal Facility Performance Assessment: Modeling Consistency to Support Regulatory Decision Making at Hanford - 17398

Under DOE Order 435.1, 'Radioactive Waste Management', Washington River Protection Solutions, LLC and INTERA, Inc are currently preparing a performance assessment for the Hanford Integrated Disposal Facility, a near-surface low-activity waste disposal facility located on the Hanford Site in southeast Washington State. The disposal facility is expected to receive vitrified low-activity waste produced at the Hanford Waste Treatment and Immobilization Plant, as well as other secondary solid wastes generated during the treatment process. The performance assessment performs the analyses that will be relied upon to receive the Disposal Authorization Statement, establish waste acceptance criteria, modify the RCRA permit for the facility and make a waste-incidental-to-reprocessing determination for the vitrified tank waste. In January 2006 in the case State of Washington v. Bodman (Civil No. 2:03-cv-05018-AAM), DOE, the Washington State Department of Ecology (Ecology) and the State of Washington Attorney General's office reached a settlement agreement in Ecology's claim regarding off-site waste shipments to Hanford and the adequacy of modeling in the environmental impact statement. In response to the agreement, the DOE Office of Environmental Management set a policy to establish a consistent use of commercially available and public domain software for a vadose zone and groundwater model platform to support regulatory decisions at Hanford. In October 2012, the Associate Principal Deputy Assistant Secretary for Environmental Management released a memorandum to the manager of the Richland Operation Office directing how future environmental modeling activities to support regulatory decision making on the Hanford Site would be undertaken to be consistent with the 2006 settlement agreement. The preparation of the performance assessment must meet DOE Order 435.1 requirements and the additional direction provided by DOE. This paper will identify the approach taken to comply with the requirements in the 2012 memorandum. The paper will describe how environmental modeling performed for the 2017 Integrated Disposal Facility Performance Assessment was planned in a phased approach and how the current modeling is tied to the analyses that supported the decisions made in the environmental impact statement published in 2012. Additionally, the selection and qualification of the software selected to perform modeling activities for the performance assessment will be described. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Direct Feed Low Activity Waste Integrated Permitting - 16642

An overall Hanford permitting strategy for the U. S. Department of Energy (DOE) Office of River Protection (ORP) is being developed to support the Direct Feed Low- Activity Waste (DFLAW) Program. The strategy identifies new permits and modifications of existing permits, as well as major regulatory approvals to support the startup and operation of nuclear systems necessary to feed low activity tank waste, pretreat the waste, operate the Waste Treatment and Immobilization Plant (WTP) Low Activity Waste (LAW) facility to treat tank waste, and dispose of waste streams. Types of permits include hazardous waste, toxic air, and radiological air licenses. Four different Contractors manage operations at Tank Farms, WTP, Utilities/Infrastructure, and Waste Disposal. Due to this complexity and the number of interfaces required, the need to have a strategic overview of all permits was evident. Approximately 25 permits and 4 major regulatory approvals are identified to implement DFLAW. The strategy will help guide integrated planning, scheduling and sequencing of permits and regulatory approvals to support DOE ORP's overall schedule for construction, commissioning and operation of DFLAW. Development of the strategy included extensive collaboration and coordination of an Integrated Permitting Team with staff and management representation from DOE, CH2M Hill Plateau Remediation Contractor (CHPRC), Washington River Protection Solutions LLC (WRPS), and Bechtel National Inc. (BNI). Information sessions and briefings have been conducted with the Washington State Department of Ecology (Ecology) and Washington State Department of Health (DOH) in the development of this overall strategy. Additionally, interface meetings are held with Ecology and DOH on specific projects early in the design phase to validate the permitting approach, identify key issues and information, and discuss requirements and assumptions. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Evaluating the influence of life‐history characteristics on genetic structure: a comparison of small mammals inhabiting complex agricultural landscapes

Abstract Conversion of formerly continuous native habitats into highly fragmented landscapes can lead to numerous negative demographic and genetic impacts on native taxa that ultimately reduce population viability. In response to concerns over biodiversity loss, numerous investigators have proposed that traits such as body size and ecological specialization influence the sensitivity of species to habitat fragmentation. In this study, we examined how differences in body size and ecological specialization of two rodents (eastern chipmunk; Tamias striatus and white‐footed mouse; Peromyscus leucopus ) impact their genetic connectivity within the highly fragmented landscape of the Upper Wabash River Basin ( UWB ), Indiana, and evaluated whether landscape configuration and complexity influenced patterns of genetic structure similarly between these two species. The more specialized chipmunk exhibited dramatically more genetic structure across the UWB than white‐footed mice, with genetic differentiation being correlated with geographic distance, configuration of intervening habitats, and complexity of forested habitats within sampling sites. In contrast, the generalist white‐footed mouse resembled a panmictic population across the UWB , and no landscape factors were found to influence gene flow. Despite the extensive previous work in abundance and occupancy within the UWB , no landscape factor that influenced occupancy or abundance was correlated with genetic differentiation in either species. The difference in predictors of occupancy, abundance, and gene flow suggests that species‐specific responses to fragmentation are scale dependent.

59 BASIC BIOLOGICAL SCIENCES↗

Predicting ecosystem metaphenome from community metagenome: A grand challenge for environmental biology

Abstract Elucidating how an organism's characteristics emerge from its DNA sequence has been one of the great triumphs of biology. This triumph has cumulated in sophisticated computational models that successfully predict how an organism's detailed phenotype emerges from its specific genotype. Inspired by that effort's vision and empowered by its methodologies, a grand challenge is described here that aims to predict the biotic characteristics of an ecosystem, its metaphenome, from nucleic acid sequences of all the species in its community, its metagenome. Meeting this challenge would integrate rapidly advancing abilities of environmental nucleic acids (eDNA and eRNA) to identify organisms, their ecological interactions, and their evolutionary relationships with advances in mechanistic models of complex ecosystems. Addressing the challenge would help integrate ecology and evolutionary biology into a more unified and successfully predictive science that can better help describe and manage ecosystems and the services they provide to humanity.

59 BASIC BIOLOGICAL SCIENCES↗

A tale of two towers: comparing NEON and AmeriFlux data streams at Bartlett Experimental Forest

Long-term ecological data are essential for detecting impacts of climate change and other global change factors, and for making informed predictions about future change. However, long-term measurements are rarely replicated at the site level, which raises questions about their representativeness. We used a multiscale approach to evaluate the agreement of parallel observations from AmeriFlux and NEON (National Ecological Observatory Network) towers at Bartlett Experimental Forest, New Hampshire, USA. The two towers are separated by a horizontal distance of 93 m. Here, we focused our analysis on standard meteorological variables; fluxes of CO 2 , sensible heat, and latent heat measured by eddy covariance; and phenology derived from PhenoCam imagery. Results suggest excellent agreement between AmeriFlux and NEON in meteorology and phenology, and good agreement in fluxes at the half-hourly scale. However, large disagreements in CO 2 and latent heat fluxes occurred at the annual scale, with implications especially for the forest carbon balance. The AmeriFlux tower measurements indicate a site that is close to carbon-neutral (-8 ± 65 g C m -2 y -1 , mean ± 1 SD), whereas the NEON tower measurements indicate a forest that is a carbon sink (-137 ± 10 g C m -2 y -1 ). Causes of this disagreement may include measurement height (26 m vs. 35 m), which resulted in different flux footprints being measured by the two towers, and differences in the flux measurement systems. Our results suggest the need for caution when attempting to merge long-term flux data from two different measurement platforms, and when using measurements from any one measurement platform to inform decision-making on issues related to carbon accounting or natural climate solutions.

Carbon cycle↗

How to improve scaling from traits to ecosystem processes

Scaling approaches in ecology assume that traits are the main attributes by which organisms influence ecosystem functioning. However, several recent empirical papers have found only weak links between traits and ecosystem functioning, questioning the usefulness of trait-based ecology (TBE). Here, we argue that these studies often suffer from one or more widespread misconceptions. Specifically, these studies often (i) conflict with the conceptual foundations of TBE, (ii) lack theory- or hypothesis-driven selection and use of traits, (iii) tend to ignore intraspecific variation, and (iv) use experimental or study designs that are not well suited to make strong tests of TBE assumptions. Addressing these aspects could significantly improve our ability to scale from traits to ecosystem functioning.

54 ENVIRONMENTAL SCIENCES↗

Moving beyond the van Krevelen diagram: A new stoichiometric approach for compound classification in organisms

van Krevelen diagrams (O:C vs H:C ratios of elemental formulas) have been widely used in studies to obtain an estimation of the main compound categories present in environmental samples. However, the limits defining a specific compound category based solely on O:C and H:C ratios of elemental formulas have never been accurately listed or proposed to classify metabolites in biological samples. Furthermore, while O:C vs. H:C ratios of elemental formulas can provide an overview of the compound categories, such classification is inefficient because of the large overlap among different compound categories along both axes. We propose a more accurate compound classification for biological samples analyzed by high-resolution mass spectrometry-based on an assessment of the C:H:O:N:P stoichiometric ratios of over 130,000 elemental formulas of compounds classified in 6 main categories: lipids, peptides, amino-sugars, carbohydrates, nucleotides and phytochemical compounds (oxy-aromatic compounds). Our multidimensional stoichiometric compound classification (MSCC) constraints showed a highly accurate categorization of elemental formulas to the main compound categories in biological samples with over 98% of accuracy representing a substantial improvement over any classification based on the classic van Krevelen diagram. This method represents a significant step forward in environmental research, especially ecological stoichiometry and eco-metabolomics studies, by providing a novel and robust tool to further our understanding the ecosystem structure and function through the chemical characterization of different biological samples.

Compound Classification, Ecological Stoichiometry,↗

The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings

Many organisms benefit from being pre-adapted to niches shaped by human activity, and have successfully invaded man-made habitats. One such species is the dry rot fungus Serpula lacrymans, which has a wide distribution in buildings in temperate and boreal regions, where it decomposes coniferous construction wood. Comparative genomic analyses and growth experiments using this species and its wild relatives revealed that S. lacrymans evolved a very effective brown rot decay compared to its wild relatives, enabling an extremely rapid decay in buildings under suitable conditions. Adaptations in intracellular transport machineries promoting hyphal growth, and nutrient and water transport may explain why it is has become a successful invader of timber in houses. Further, we demonstrate that S. lacrymans has poor combative ability in our experimental setup, compared to other brown rot fungi. In sheltered indoor conditions, the dry rot fungus may have limited encounters with other wood decay fungi compared to its wild relatives. Overall, our analyses indicate that the dry rot fungus is an ecological specialist with poor combative ability against other fungi.

fungal biology↗

Constraints and variation in food web link-species space

Predicting food web structure in future climates is a pressing goal of ecology. These predictions may be impossible without a solid understanding of the factors that structure current food webs. Here, the most fundamental aspect of food web structure—the relationship between the number of links and species—is still poorly understood. Some species interactions may be physically or physiologically ‘forbidden'—like consumption by non-consumer species—with possible consequences for food web structure. We show that accounting for these ‘forbidden interactions' constrains the feasible link-species space, in tight agreement with empirical data. Rather than following one particular scaling relationship, food webs are distributed throughout this space according to shared biotic and abiotic features. Our study provides new insights into the long-standing question of which factors determine this fundamental aspect of food web structure.

59 BASIC BIOLOGICAL SCIENCES↗

Guidelines and considerations for designing field experiments simulating precipitation extremes in forest ecosystems

1. Precipitation regimes are changing in response to climate change, yet understanding of how forest ecosystems respond to extreme droughts and pluvials remains incomplete. As future precipitation extremes will likely fall outside the range of historical variability, precipitation manipulation experiments (PMEs) are critical to advancing knowledge about potential ecosystem responses. However, few PMEs have been conducted in forests compared to short-statured ecosystems, and forest PMEs have unique design requirements and constraints. Moreover, past forest PMEs have lacked coordination, limiting cross-site comparisons. Here, we review and synthesize approaches, challenges, and opportunities for conducting PMEs in forests, with the goal of guiding design decisions, while maximizing the potential for coordination. 2. We reviewed 63 forest PMEs at 70 sites world-wide. Workshops, meetings, and communications with experimentalists were used to generate and build consensus around approaches for addressing the key challenges and enhancing coordination. 3. Past forest PMEs employed a variety of study designs related to treatment level, replication, plot and infrastructure characteristics, and measurement approaches.Important considerations for establishing new forest PMEs include: selecting appropriate treatment levels to reach ecological thresholds; balancing cost, logistical complexity, and effectiveness in infrastructure design; and preventing unintended water subsidies. Response variables in forest PMEs were organized into three broad tiers reflecting increasing complexity and resource intensiveness, with the first tier representing a recommended core set of common measurements. 4. Differences in site conditions combined with unique research questions of experimentalists necessitate careful adaptation of guidelines for forest PMEs to balance local objectives with coordination among experiments. We advocate adoption of a common framework for coordinating forest PME design to enhance cross-site comparability and advance fundamental knowledge about the response and sensitivity of diverse forest ecosystems to precipitation extremes.

Climate Extremes, drought, ecological thresholds, ↗