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DOE OSTI2023

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Background: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. Results: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages ( Leviviricetes ), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. Conclusion: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Long-Term Infrasound Sensor Calibration and Characterization

Previous testing has shown that infrasound sensors deployed in the field can exhibit notable deviations from their nominal, lab-based calibrations. These variations may be due to changes in environmental conditions, long-term sensor drift, or other unresolved features. In early 2018, we installed two identical infrasound elements with five infrasound sensors at each element (Chaparral M50A, Chaparral M64LN, CEA/Martec MB2005, CEA/Seismowave MB3a, and Hyperion IFS-5113A). These sensors were accepted or under consideration for use in the International Monitoring System network of the Comprehensive Nuclear-Test-Ban Treaty. Each element had all sensors connected to a single digitizer and port to the atmosphere. We also recorded instrument enclosure air temperature and humidity and external air temperature. Using the MB2005 as the reference, we examine the relative sensor response (both magnitude and phase) as a function of time and frequency and compare it with quarterly laboratory calibrations and environmental conditions. Here, we find that the magnitude response for all sensors exhibits some variability in both the lab and field, with the amplitude variations often >5%. The field-based variations are more severe and occur on both long-term (months) and short-term (hours) timescales. Short-term variability correlates with changes in environmental conditions and is considerable (up to 25%) for the Chaparral M50A and noticeable (∼5%) for the French Alternative Energies and Atomic Energy Commission (CEA) MB3a. Long-term magnitude variability for the Chaparral M50A was up to 50% and does not clearly correlate with environmental conditions. The other sensors show some long-term magnitude offsets, but they have relatively stable responses in the conditions we examined. The MB3a also displays some frequency-dependent magnitude variability and shows a minor dependence on temperature. Phase estimates are stable and near zero for all sensors tested. These results strongly suggest sensor response and variability due to environmental conditions should be considered in future infrasound data interpretation and sensor selection and development.

Fee, David↗

NASA NTRSDate not supplied

Quantifying the Influence of Mechanistic Representation of Particle Dry Deposition on Historical Changes in Aerosol-Climate Interactions

Dry deposition removes short-lived climate forcers and their precursors from the atmosphere. The aerosol dry deposition schemes in many global climate models have been untouched for decades. Previous work hints that aerosol dry deposition is an uncertainty with respect to aerosol impacts on climate change. Here we demonstrate the impact of a more mechanistic aerosol dry deposition parameterization on the historical aerosol direct and cloud albedo effects using the NASA GISS global chemistry-climate model. We investigate two aerosol configurations – a “bulk” mass-based scheme and a modal scheme that more explicitly represents internal mixing and microphysics – of the global model. Both configurations show ~20% larger historical increases in non-dust aerosols globally with more mechanistic dry deposition. Changes to particle dry deposition, which are strongly a function of particle diameter, have a greater influence on the cloud albedo effect (up to 0.1 W m-2) when aerosols are more explicitly resolved in the modal scheme. On the other hand, impacts on the direct aerosol effect are small for both model configurations. In both aerosol configurations, the global climate effects are relatively insensitive to uncertainty in the strength of the uptake to dry deposition as suggested by (limited) measurements. In general, the low number of aerosol flux measurements and strong variability across existing observations challenge confidence in our understanding of dry depositional processes and changes with environmental conditions. Nonetheless, our work suggests that changes in dry deposition may be important for accurately estimating increases in aerosol abundances over the historical period, which is key for correct inferences about how cooling from aerosols has offset warming from greenhouse gases.

Dry deposition↗

DOE OSTI2016

Engineering microbial consortia for controllable outputs

Much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into resilient consortia, in which the division of labor is thought to lead to increased community efficiency and productivity. Here, we consider whether and how consortia can be designed to perform bioprocesses of interest beyond the metabolic flexibility limitations of a single organism. Advances in post-genomic analysis of microbial consortia and application of high-resolution global measurements now offer the promise of systems-level understanding of how microbial consortia adapt to changes in environmental variables and inputs of carbon and energy. We argue that when combined with appropriate modeling framework that predictive knowledge generates testable hypotheses and orthogonal synthetic biology tools, such understanding can dramatically improve our ability to control the fate and functioning of consortia. In this article, we articulate our collective perspective on the current and future state of microbial community engineering and control while placing specific emphasis on ecological principles that promote control over community function and emergent properties.

controllable outputs↗

DOE OSTI2025

BONCAT-Live for isolation and cultivation of active environmental bacteria

In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.

Analytical Methods↗

DOE OSTI2018

What’s hot about mercury? Examining the influence of climate on mercury levels in Ontario top predator fishes

Highlights: • Fish mercury levels have recently increased in many Ontario watersheds. • Weather, climate drivers, and emissions are contributing to changes in fish mercury. • Changes in climate may be an important driver of Ontario fish mercury levels. • Higher mercury levels in walleye and largemouth bass are related to climate drivers. • Higher precipitation contributed to higher mercury levels in smallmouth bass. Mercury (Hg) levels in Ontario top predator fishes have been increasing in recent decades. These increases may be a result of many additive factors, including global climate change. Only recently has research been conducted on how climate change may impact Hg levels in freshwater fishes at large-scales. We examined the relationship between Hg trends and (1) local weather, (2) large-scale climate drivers, and (3) anthropogenic Hg emissions, in native cool water (walleye and northern pike) and warm water (smallmouth bass and largemouth bass) predatory fishes in Ontario, Canada, for historical (1970–1992) and recent (1993–2014) time periods. For each fish species studied, > 25% of Ontario's secondary watersheds shifted from historically declining to recently increasing fish Hg trends, and ≥ 50% of watersheds experienced increasing trends between 1993 and 2014. Recent fish Hg increased at up to 0.20 µg/g/decade; which were significant (p < 0.05) for walleye, northern pike and smallmouth bass. Multiple linear regressions revealed a complex interplay of local weather, large-scale climate drivers, and anthropogenic Hg emissions influencing fish Hg levels. Recent Hg levels for walleye and largemouth bass increased with changes in global climate drivers, while higher precipitation influenced smallmouth bass Hg levels the most. Walleye Hg levels increased during the positive phases of global climate drivers, reflecting the local influence of local temperatures and precipitation indirectly. Differentiating the effects of climate-related parameters and emissions is increasingly crucial to assess how changing multiple environmental stressors may impact health of wildlife and humans consuming fish.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2013

Geochemical rate processes at mineral-water interfaces: Linking molecular-scale surface properties to macroscopic observables

The project emphasis at WSU is on the understanding of the principal influences on surface chemistry, morphology, and kinetics of reactions of minerals in aqueous solutions. This emphasis, in the last project period has guided our efforts to the study of morphological relaxation in response to solution perturbations as well as to develop a methodology for creating on-demand etch pits for the purposes of generating specific step orientations on calcite surfaces. In the response of any mineral-water interface to changes in environmental conditions, dissolution and mineralization rates undergo rapid changes because the reaction rates at step edges are governed directly by these conditions. Our previous investigations of mineral dissolution have revealed that the topographic relaxation time under near equilibrium conditions can be much longer than the characteristic times of experimental investigations. The investigations described below are directed towards evaluating the effects of sample history, miscut and pretreatment on the observed dissolution behavior of our target mineral-water interface systems. In addition, we have developed a simple method for generating on-demand etch pits for the purposes of studying kinetically unstable step orientations.

Higgins, Steven R.↗

DOE OSTI2024

Vapor kinetic energy for the detection and understanding of atmospheric rivers

Poleward water vapor transport in the midlatitudes mainly occurs in meandering filaments of intense water vapor transport, spanning thousands of kilometers long and hundreds of kilometers wide and moving eastward. The water vapor filaments are known as atmospheric rivers (ARs). They can cause extreme wind gusts, intense precipitation, and flooding along densely populated coastal regions. Many recent studies about ARs focused on the statistical analyses of ARs, but a process-level understanding of ARs remains elusive. Here we show that ARs are streams of air with enhanced vapor kinetic energy (VKE) and derive a governing equation for Integrated VKE to understand what contributes to the evolution of ARs. We find that ARs grow mainly because of potential energy conversion to kinetic energy, decay largely owing to condensation and turbulence, and the eastward movement is primarily due to horizontal advection of VKE. Our VKE framework complements the integrated vapor transport framework, which is popular for identifying ARs but lacks a prognostic equation for understanding the physical processes.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2014

Multiagent Flight Control in Dynamic Environments with Cooperative Coevolutionary Algorithms

Dynamic environments in which objectives and environmental features change with respect to time pose a difficult problem with regards to planning optimal paths through these environments. Path planning methods are typically computationally expensive, and are often difficult to implement in real time if system objectives are changed. This computational problem is compounded when multiple agents are present in the system, as the state and action space grows exponentially with the number of agents in the system. In this work, we use cooperative coevolutionary algorithms in order to develop policies which control agent motion in a dynamic multiagent unmanned aerial system environment such that goals and perceptions change, while ensuring safety constraints are not violated. Rather than replanning new paths when the environment changes, we develop a policy which can map the new environmental features to a trajectory for the agent while ensuring safe and reliable operation, while providing 92% of the theoretically optimal performance.

Coevolution↗

NASA NTRS2014

Multiagent Flight Control in Dynamic Environments with Cooperative Coevolutionary Algorithms

Dynamic flight environments in which objectives and environmental features change with respect to time pose a difficult problem with regards to planning optimal flight paths. Path planning methods are typically computationally expensive, and are often difficult to implement in real time if system objectives are changed. This computational problem is compounded when multiple agents are present in the system, as the state and action space grows exponentially. In this work, we use cooperative coevolutionary algorithms in order to develop policies which control agent motion in a dynamic multiagent unmanned aerial system environment such that goals and perceptions change, while ensuring safety constraints are not violated. Rather than replanning new paths when the environment changes, we develop a policy which can map the new environmental features to a trajectory for the agent while ensuring safe and reliable operation, while providing 92% of the theoretically optimal performance

Experimentation↗

DOE OSTI2011

Environmental evaluation of municipal waste prevention

Highlights: > Influence of prevention on waste management systems, excluding avoided production, is relatively minor. > Influence of prevention on overall supply chain, including avoided production is very significant. > Higher relative benefits of prevention are observed in waste management systems relying mainly on landfills. - Abstract: Waste prevention has been addressed in the literature in terms of the social and behavioural aspects, but very little quantitative assessment exists of the environmental benefits. Our study evaluates the environmental consequences of waste prevention on waste management systems and on the wider society, using life-cycle thinking. The partial prevention of unsolicited mail, beverage packaging and food waste is tested for a 'High-tech' waste management system relying on high energy and material recovery and for a 'Low-tech' waste management system with less recycling and relying on landfilling. Prevention of 13% of the waste mass entering the waste management system generates a reduction of loads and savings in the waste management system for the different impacts categories; 45% net reduction for nutrient enrichment and 12% reduction for global warming potential. When expanding our system and including avoided production incurred by the prevention measures, large savings are observed (15-fold improvement for nutrient enrichment and 2-fold for global warming potential). Prevention of food waste has the highest environmental impact saving. Prevention generates relatively higher overall relative benefit for 'Low-tech' systems depending on landfilling. The paper provides clear evidence of the environmental benefits of waste prevention and has specific relevance in climate change mitigation.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Long-term measurements in a mixed-grass prairie reveal a change in soil organic carbon recalcitrance and its environmental sensitivity under warming

Soil respiration, the major pathway for ecosystem carbon (C) loss, has the potential to enter a positive feedback loop with the atmospheric CO2 due to climate warming. For reliable projections of climate-carbon feedbacks, accurate quantification of soil respiration and identification of mechanisms that control its variability are essential. Process-based models simulate soil respiration as functions of belowground C input, organic matter quality, and sensitivity to environmental conditions. However, evaluation and calibration of process-based models against the long-term in situ measurements are rare. Here, we evaluate the performance of the Terrestrial ECOsystem (TECO) model in simulating total and heterotrophic soil respiration measured during a 16-year warming experiment in a mixed-grass prairie; calibrate model parameters against these and other measurements collected during the experiment; and explore whether the mechanisms of C dynamics have changed over the years. Calibrating model parameters against observations of individual years substantially improved model performance in comparison to pre-calibration simulations, explaining 79–86% of variability in observed soil respiration. Interannual variation of the calibrated model parameters indicated increasing recalcitrance of soil C and changing environmental sensitivity of microbes. Overall, we found that (1) soil organic C became more recalcitrant in intact soil compared to root-free soil; (2) warming offset the effects of increasing C recalcitrance in intact soil and changed microbial sensitivity to moisture conditions. Furthermore, these findings indicate that soil respiration may decrease in the future due to C quality, but this decrease may be offset by warming-induced changes in C cycling mechanisms and their responses to moisture conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Microorganisms, climate change, and the Sustainable Development Goals: progress and challenges

The forthcoming UN summit marks the halfway point to 2030 and presents an important milestone in global efforts to address various challenges, including those related to climate change and environmental preservation. The UN SDGs include several related to microorganisms and climate change. Importantly, microbiology research is key to understanding and mitigating climate change, and in maintaining the health of terrestrial and aquatic ecosystems (SDGs 13, 14 and 15).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

DARHT : Enduring Lessons from a Technical Project in a National Laboratory Context [Slides]

The Dual-Axis Radiographic Hydrodynamic Test (DARHT) facility at Los Alamos National Laboratory (LANL) is the world’s first flash x-ray facility able to take multiple high-resolution radiographs of the interior features of fast-moving dense objects during a single experiment. DARHT’s radiography and complimentary diagnostics makes it an important diagnostic tool in support of the US Department of Energy’s (DOE)/National Nuclear Security Administration (NNSA)’s stewardship of the US nuclear deterrent. The project to construct DARHT ran from 1988 through 2003. Initial Operating Capability along a single axis began in 1999. A technical issue delayed Critical Decision 4 for the full dual-axis capability until 2008. DARHT was characterized by several directed changes resulting from an environmental impact study, changes to the global security context resulting from the end of underground nuclear testing, and rapid evolution of applicable technology. Conventional building and lab-space construction were part of the project, but the project was dominated by Special Facility Equipment that, together with the mission to support the nuclear weapons program, required the project to be completed by national laboratories. Although the project pre-dated implementation of DOE Order 413.3, several important lessons for national laboratory projects remain applicable today and will be discussed here, including projects appropriate for the national laboratory environment, scope stability, risk acceptance and mitigation, communication, and collaboration. Finally, considerations for DOE contractor project managers are offered based upon the DARHT experience.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2014

The Effect of Diel Temperature and Light Cycles on the Growth of Nannochloropsis oculata in a Photobioreactor Matrix

A matrix of photobioreactors integrated with metabolic sensors was used to examine the combined impact of light and temperature variations on the growth and physiology of the biofuel candidate microalgal species Nannochloropsis oculata. The experiments were performed with algal cultures maintained at a constant 20 °C versus a °15 C to 25 °C diel temperature cycle, where light intensity also followed a diel cycle with a maximum irradiance of 1920 mmol photons m -2 s -1 . No differences in algal growth (Chlorophyll a) were found between the two environmental regimes; however, the metabolic processes responded differently throughout the day to the change in environmental conditions. The variable temperature treatment resulted in greater damage to photosystem II due to the combined effect of strong light and high temperature. Cellular functions responded differently to conditions before midday as opposed to the afternoon, leading to strong hysteresis in dissolved oxygen concentration, quantum yield of photosystem II and net photosynthesis. Overnight metabolism performed differently, probably as a result of the temperature impact on respiration. Our photobioreactor matrix has produced novel insights into the physiological response of Nannochloropsis oculata to simulated environmental conditions. This information can be used to predict the effectiveness of deploying Nannochloropsis oculata in similar field conditions for commercial biofuel production.

09 BIOMASS FUELS↗

DOE OSTI2022

Chronological changes in soil biogeochemical properties of the glacier foreland of Midtre Lovénbreen, Svalbard, attributed to soil-forming factors

We report that Glacier forelands provide an excellent opportunity to investigate vegetation succession and soil development along the chronosequence; however, there are few studies on soil biogeochemical changes from environmental factors, aside from time. This study aimed to investigate soil development and biogeochemical changes in the glacier foreland of Midtre Lovenbreen, Svalbard, by considering various factors, including time. Eighteen vegetation and soil variables were measured at 38 different sampling sites of varying soil age, depth, and glacio-fluvial activity. Soil organic matter (SOM) was quantitatively measured, and the compositional changes in SOM were determined following size-density fractionation. In the topsoil, the soil organic carbon (SOC) and total nitrogen (N) content was found to increase along the soil chronosequence and were highly correlated with vegetation-associated variables. These findings suggest that plant-derived material was the main driver of the light fraction of SOM accumulation in the topsoil. The heavy fractions of SOM were composed of microbially transformed organic compounds, eventually contributing to SOM stabilization within short 90-yr deglaciation under harsh climatic conditions. In addition to time, the soil vertical profiles showed that other environmental parameters, also affected the soil biogeochemical properties. The high total phosphorous (P) content and electrical conductivity in the topsoil were attributed to unweathered subglacial materials and a considerable amount of inorganic ions from subglacial meltwater. The high P and magnesium content in the subsoil were attributed to parent materials, while the high sodium and potassium content in the surface soil were a result of sea-salt deposition. Glacio-fluvial runoff hampered ecosystem development by inhibiting vegetation development and SOM accumulation. This study emphasizes the importance of considering various soil-forming factors, including parent/subglacial materials, aeolian deposition, and glacio-fluvial runoff, as well as soil age, to obtain a comprehensive understanding of the ecosystem development in glacier forelands.

glacio-fluvial runoff↗

DOE OSTI2016

TYPE Ia SUPERNOVAE: CAN CORIOLIS FORCE BREAK THE SYMMETRY OF THE GRAVITATIONAL CONFINED DETONATION EXPLOSION MECHANISM?

Currently the number of models aimed at explaining the phenomena of type Ia supernovae is high and distinguishing between them is a must. In this work we explore the influence of rotation on the evolution of the nuclear flame that drives the explosion in the so-called gravitational confined detonation models. Assuming that the flame starts in a pointlike region slightly above the center of the white dwarf (WD) and adding a moderate amount of angular velocity to the star we follow the evolution of the deflagration using a smoothed particle hydrodynamics code. We find that the results are very dependent on the angle between the rotational axis and the line connecting the initial bubble of burned material with the center of the WD at the moment of ignition. The impact of rotation is larger for angles close to 90° because the Coriolis force on a floating element of fluid is maximum and its principal effect is to break the symmetry of the deflagration. Such symmetry breaking weakens the convergence of the nuclear flame at the antipodes of the initial ignition volume, changing the environmental conditions around the convergence region with respect to non-rotating models. These changes seem to disfavor the emergence of a detonation in the compressed volume at the antipodes and may compromise the viability of the so-called gravitational confined detonation mechanism.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

The herbaceous landlord: integrating the effects of symbiont consortia within a single host

Plants are typically infected by a consortium of internal fungal associates, including endophytes in their leaves, as well as arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) in their roots. It is logical that these organisms will interact with each other and the abiotic environment in addition to their host, but there has been little work to date examining the interactions of multiple symbionts within single plant hosts, or how the relationships among symbionts and their host change across environmental conditions. We examined the grass Agrostis capillaris in the context of a climate manipulation experiment in prairies in the Pacific Northwest, USA. Each plant was tested for presence of foliar endophytes in the genus Epichloë, and we measured percent root length colonized (PRLC) by AMF and DSE. We hypothesized that the symbionts in our system would be in competition for host resources, that the outcome of that competition could be driven by the benefit to the host, and that the host plants would be able to allocate carbon to the symbionts in such a way as to maximize fitness benefit within a particular environmental context. We found a correlation between DSE and AMF PRLC across climatic conditions; we also found a fitness cost to increasing DSE colonization, which was negated by presence of Epichloë endophytes. These results suggest that selective pressure on the host is likely to favor host/symbiont relationships that structure the community of symbionts in the most beneficial way possible for the host, not necessarily favoring the individual symbiont that is most beneficial to the host in isolation. These results highlight the need for a more integrative, systems approach to the study of host/symbiont consortia.

54 ENVIRONMENTAL SCIENCES↗