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At least 127 records · Page 7

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DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Peyton, Brent↗

DOE OSTI2022

KBase Narrative - Metagenome-assembled genomes from Amazonian soil microbial consortia

We report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils, in the Brazilian Eastern Amazon. Recovered MAGs constitute novel genomes with the potential to act in important ecological processes, including the degradation of carbohydrate and sulfur and nitrogen cycling.

Mandro, Jessica Adriele↗

DOE OSTI2024

KBase Narrative - van den Bergh et al

We report 14 metagenome-assembled genomes (MAGs) recovered from agricultural soils, composts, and enrichment cultures enriched therefrom, originating from the Netherlands, Belgium and Switzerland. Recovered MAGs constitute methane-cycling related organisms sequenced from isolated cultures or environmental DNA, elucidating their metabolic potential in important ecological processes like the oxidation or production of atmospheric trace gases as methane, hydrogen, and carbon monoxide.

Rocha, Gabriel Silvestre↗

DOE OSTI2023

BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event

Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Transcriptional Regulation of Drought Response in Arabidopsis and Woody Plants

Within the context of global warming, long-living plants such as perennial woody species endure adverse conditions. Among all of the abiotic stresses, drought stress is one of the most detrimental stresses that inhibit plant growth and productivity. Plants have evolved multiple mechanisms to respond to drought stress, among which transcriptional regulation is one of the key mechanisms. In this review, we summarize recent progress on the regulation of drought response by transcription factor (TF) families, which include abscisic acid (ABA)-dependent ABA-responsive element/ABRE-binding factors (ABRE/ABF), WRKY, and Nuclear Factor Y families, as well as ABA-independent AP2/ERF and NAC families, in the model plant Arabidopsis. We also review what is known in woody species, particularly Populus, due to its importance and relevance in economic and ecological processes. We discuss opportunities for a deeper understanding of drought response in woody plants with the development of high-throughput omics analyses and advanced genome editing techniques.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Ecosystem device for determining plant-microbe interactions

This disclosure provides systems, methods, and devices related to the study of ecological processes. In one aspect, a device includes a base, a substrate, and an enclosure. The substrate is in contact with a first surface of the base. The substrate and the base define a root chamber. The enclosure is in contact with a second surface of the base. The base and the enclosure define a growth chamber. The base defines a stem port connecting the root chamber and the growth chamber. The base further defines a first port in fluid communication with the root chamber and a second port in fluid communication with the root chamber. The device is operable to contain a plant, roots of the plant being in the root chamber, a stem of the plant passing through the stem port, and leaves of the plant being in the growth chamber.

Andeer, Peter↗

DOE OSTI2020

The structure of Photosystem I acclimated to far-red light illuminates an ecologically important acclimation process in photosynthesis

Phototrophic organisms are superbly adapted to different light environments but often must acclimate to challenging competition for visible light wavelengths in their niches. Some cyanobacteria overcome this challenge by expressing paralogous photosynthetic proteins and by synthesizing and incorporating ~8% chlorophyll f into their Photosystem I (PSI) complexes, enabling them to grow under far-red light (FRL). We solved the structure of FRL-acclimated PSI from the cyanobacterium Fischerella thermalis PCC 7521 by single-particle, cryo–electron microscopy to understand its structural and functional differences. Four binding sites occupied by chlorophyll f are proposed. Subtle structural changes enable FRL-adapted PSI to extend light utilization for oxygenic photosynthesis to nearly 800 nm. This structure provides a platform for understanding FRL-driven photosynthesis and illustrates the robustness of adaptive and acclimation mechanisms in nature.

Science & Technology - Other Topics↗

DOE OSTI2025

Microbial Ecology of Permafrost Soils: Populations, Processes, and Perspectives

Permafrost microbial research has flourished in the past decades, due in part to improvements in sampling and molecular techniques, but also the increased focus on the permafrost greenhouse gas feedback to climate change and other ecological processes in high latitude and alpine permafrost soils. Permafrost microorganisms are adapted to these extreme environments and remain active at low temperatures and when resources are limited. They are also an important component of global elemental cycles as they regulate organic matter turnover and greenhouse gas production, particularly as permafrost thaws. Here we review the permafrost microbiology literature coupled with an exploration of its historical aspects, with a particular focus on a new understanding advanced by molecular biology techniques. We further identify knowledge gaps and ways forward to improve our understanding of microbial contributions to ecosystem biogeochemistry of permafrost-affected systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Juvenile Salmon and Their Habitats in the Columbia River Estuary: A Review and Synthesis of Knowledge Development 2000–2025

[This is a 90% discussion draft.] This is the third Synthesis Memorandum funded by the U.S. Army Corps of Engineers and developed for the Columbia Estuary Ecosystem Restoration Program (CEERP) on the topic of habitat restoration in the Columbia River Estuary (CRE) from Bonneville Dam to the river mouth. While the first two were developed by PNNL and NOAA without the benefit of stakeholder participation, for the current memo, two key activities were initiated: (1) review, by the Expert Regional Technical Group (ERTG), of status and trends monitoring and action effectiveness monitoring funded by CEERP, and (2) a workshop including representatives of the Bonneville Power Administration and the U.S. Army Corps of Engineers (the action agencies [AAs]), the National Oceanic and Atmospheric Administration (NOAA), major research agencies contributing to CEERP, and sponsors who implement CEERP restoration actions. A systematic literature review was conducted using ClarivateTM Web of ScienceTM database. The topics of interest for CRE relevant research included salmon ecology, physical processes, and wetland habitats, and therefore required the use of broad search terms. Our final search criteria included a combination of Boolean operators and an approach to combine different sets of search terms. The final search result yielded 669 records. The records were classified by groups and assigned to the relevant disciplinary expert for review. The review identified substantive advances in understanding the provision of salmon habitat functions through spatiotemporally dynamic physical and ecological processes, and the use of CRE habitats by numerous stocks of juvenile salmon. It also uncovered heretofore unincorporated historical documentation of riparian habitats across the CRE. The characterization of the structural components of floodplain habitat including plant associations and channel networks has advanced considerably, together with the understanding of seasonal changes and long-term trends. The relative influence of salmon-habitat location in the CRE as compared with temporal factors, mainly season, has been well described, which affects the prioritization of restoration. Stressors on the ecosystem and fish, and the drivers of these stressors, have been more carefully elucidated and predictive models are in various stages of development. The vision, aims, and design of restoration projects have advanced together with methods of data collection, analysis, and modeling that have seen substantial improvements. Experiments intended to inform the design of restoration projects are underway or have been completed. An important outstanding area of research that has lagged behind the advances in fundamental understanding of the ecosystem and salmon habitat functions remains the peer-reviewed documentation of the outcomes of restoration for both habitats and fish functions.

estuary↗

DOE OSTI2021

Balanced stochastic versus deterministic assembly processes benefit diverse yet uneven ecosystem functions in representative agroecosystems

Ecological assembly processes, by influencing community composition, determine ecosystem functions of microbiomes. However, debate remains on how stochastic versus deterministic assembly processes influence ecosystem functions such as carbon and nutrient cycling. Towards a better understanding, we investigated three types of agroecosystems (the upland, paddy, and flooded) that represent a gradient of stochastic versus deterministic assembly processes. Carbon and nutrient cycling multifunctionality, characterized by nine enzymes associated with soil carbon, nitrogen, phosphorous and sulfur cycling, was evaluated and then associated with microbial assembly processes and cooccurrence patterns of vital ecological groups. Our results suggest that strong deterministic processes favour microorganisms with convergent functions (as in the upland agroecosystem), while stochasticity-dominated processes lead to divergent functions (as in the flooded agroecosystem). To benefit agroecosystems services, we speculate that it is critical for a system to maintain balance between its stochastic and deterministic assembly processes (as in the paddy agroecosystem). By doing so, the system can preserve a diverse array of functional traits and also allow for particular traits to flourish. To further confirm this speculation, it is necessary to develop a systematic knowledge beyond merely characterizing general patterns towards the associations among community assembly, composition, and ecosystem functions.

Liu, Wenjing↗

DOE OSTI2021

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient

Significance Increasing evidence suggests that evolutionary processes frequently shape ecological patterns; however, most microbiome studies thus far have focused on only the ecological responses of these communities. By using parallel field experiments and focusing in on a model soil bacterium, we showed that bacterial “species” are differentially adapted to local climates, leading to changes in their composition. Furthermore, we detected strain-level evolution, providing direct evidence that both ecological and evolutionary processes operate on annual timescales. The consideration of eco-evolutionary dynamics may therefore be important to understand the response of soil microbiomes to future environmental change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Parallel Battery: The Framework and Process for an Intelligent and Ecological Battery System and Related Services

The concept, framework, process methodology and applications of parallel battery were proposed from both virtual and real aspects.The parallel battery was an application of ACP-based parallel intelligence in battery and related energy system areas.The real battery system was running with its equivalent, and the artificial battery system was in a virtual space, in a parallel and interactive manner.The artificial battery system contained the descriptive, predictive, and prescriptive functions on the real battery and related energy systems.There was a closed-loop workflow between the real battery system and the artificial battery system, which iteratively optimizes the battery and related energy systems, leading to a new paradigm of intelligent and ecological parallel battery system management.

ACP approach↗

DOE OSTI2020

Risk to Ecological Resources on Burial Waste Sites on the Hanford Site, Washington - 20248

The US and other nations have a large nuclear and chemical waste remediation task remaining from World War II, the Cold War, and industrial activities. The US Department of Energy (DOE) has the largest task in the U.S., with Hanford (Washington State) being the most contaminated site, with the longest and most costly cleanup program projected to extend to the end of the century. One of the greatest remediation problems at Hanford are the burial waste facilities, some of which are inside the 200 Areas on the Central Plateau, while others are outside the 200 Areas. These areas are associated with waste sites, pipes, and contaminated trenches, posing technical cleanup challenges to meet DoE's remediation goals, including protection of human health and the environment commensurate with Tri- Party Agreement and current regulatory requirements. In this paper we select one of the legacy waste sites (the BC Cribs and Trenches) as a case study to explore how risk to ecological resources varies during and as a consequence of remediation on sites primarily considered legacy waste sites. We used the risk methodology developed by the Consortium for Risk Evaluation with Stakeholder Participation (CRESP) during the Hanford Site-wide Risk Review. The CRESP methodology included evaluating the risk to receptors, including human health, the Columbia River, groundwater, and ecological and cultural resources. The risk evaluation process for ecological receptors included defining the boundaries of each evaluation unit (EU) to be remediated, definition of a suitable buffer area that might be affected, and consideration of the known resource value based on field work. This information, coupled with known remediation options or strategies, allowed us to develop a risk rating for ecological resources. Site risks were evaluated on a scale of 'not discernible' to 'very high' risk. Consideration of the risks at the buried waste sites was complicated by uncertainties in remediation methods and the degree of restoration that would occur as part of the remediation process. We use the BC Cribs and Trenches as a case study to explore why the risks are low currently but increase during remediation. The current 'not discernible to low' risk rating is due to the lack of high quality ecological resources on the BC Cribs and Trenches EU, except for edge areas (with some state-listed species). During remediation the risks increase to 'medium', mainly due to high quality resources on adjacent buffer lands, which could be disrupted during active remediation. Medium and high quality resources on the edge of the site are continuous with higher quality native shrub-steppe habitat on the buffer. Ecological resources on some of the areas surrounding the 200 East and West Areas are some of the highest quality shrub-steppe areas on the Hanford Site, and risk to these resources could be prevented by planning before and during remediation to minimize disruption. For example, lay down areas for the BC Cribs and Trenches can be minimized by careful planning. Heavy truck and other vehicular traffic can be minimized. Spread of the noxious weeds now on some of the site can be prevented, and the spread of invasive species into the site (particularly near undisturbed shrub-steppe habitat) can be reduced. Further, the areas around and between the 200 East and West Areas have been largely undisturbed and can serve as a source of seeds and propagules for any revegetation that occurs as part of the remediation process. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

Microbial Evolution Drives Adaptation of Substrate Degradation on Decadal to Centennial Time Scales Relevant to Global Change

ABSTRACT Understanding microbial adaptation is crucial for predicting how soil carbon dynamics and global biogeochemical cycles will respond to climate change. This study employs the DEMENT model of microbial decomposition, along with empirical mutation and dispersal rates, to explore the roles of mutation and dispersal in the adaptation of soil microbial populations to shifts in litter chemistry, changes that are anticipated with climate‐driven vegetation dynamics. Following a change in litter chemistry, mutation generally allows for a higher rate of litter decomposition than dispersal, especially when dispersal predominantly introduces genotypes already present in the population. These findings challenge the common idea that mutation rates are too low to affect ecosystem processes on ecological timescales. These results demonstrate that evolutionary processes, such as mutation, can help maintain ecosystem functioning as the climate changes.

Abs, Elsa↗

DOE OSTI2024

Using Diel Solute Signals to Assess Ecohydrological Processing in Lotic Systems

Lotic systems are a prominent ecohydrological interface within which complex, coupled interactions occur between ecological, hydrological, and geochemical processes. This chapter reviews the ecological processes driving diel signals in oxygen as well as major nutrients and other trace elements. It discusses how diel signals can be used to evaluate functioning and interactions within stream ecosystems. The chapter considers potential future research directions and outstanding questions still to be addressed by or about diel solute signals and associated processes. High-resolution sensor-based time series and associated tools and conceptual advances are being integrated into environmental management. Quantitative tools to disentangle diel biogeochemically-driven signals from other sources of variability in continuous time series are growing. Theoretical models of diel process dynamics are helping to spur hypothesis generation and new ways of approaching diel signals in lotic systems.

Kurz, Marie↗

DOE OSTI2020

Carbon budget of the Harvard Forest Long-Term Ecological Research site: pattern, process, and response to global change

How, where, and why carbon (C) moves into and out of an ecosystem through time are long-standing questions in biogeochemistry. Here, we bring together hundreds of thousands of C-cycle observations at the Harvard Forest in central Massachusetts, USA, a mid-latitude landscape dominated by 80–120-yr-old closed-canopy forests. These data answered four questions: (1) where and how much C is presently stored in dominant forest types; (2) what are current rates of C accrual and loss; (3) what biotic and abiotic factors contribute to variability in these rates; and (4) how has climate change affected the forest’s C cycle? Harvard Forest is an active C sink resulting from forest regrowth following land abandonment. Soil and tree biomass comprise nearly equal portions of existing C stocks. Net primary production (NPP) averaged 680–750 g C·m –2 ·yr –1 ; belowground NPP contributed 38–47% of the total, but with large uncertainty. Mineral soil C measured in the same inventory plots in 1992 and 2013 was too heterogeneous to detect change in soil-C pools; however, radiocarbon data suggest a small but persistent sink of 10–30 g C·m –2 ·yr –1 . Net ecosystem production (NEP) in hardwood stands averaged ~300 g C·m –2 ·yr –1 . NEP in hemlock-dominated forests averaged ~450 g C·m –2 ·yr –1 until infestation by the hemlock woolly adelgid turned these stands into a net C source. Since 2000, NPP has increased by 26%. For the period 1992–2015, NEP increased 93%. The increase in mean annual temperature and growing season length alone accounted for ~30% of the increase in productivity. Interannual variations in GPP and NEP were also correlated with increases in red oak biomass, forest leaf area, and canopy-scale light-use efficiency. Compared to long-term global change experiments at the Harvard Forest, the C sink in regrowing biomass equaled or exceeded C cycle modifications imposed by soil warming, N saturation, and hemlock removal. Furthermore, the results of this synthesis and comparison to simulation models suggest that forests across the region are likely to accrue C for decades to come but may be disrupted if the frequency or severity of biotic and abiotic disturbances increases.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors

Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors.

16S rRNA↗