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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current activity. This revealed an active mobilome that shapes natural genetic diversity via differential impacts on major phyla and affects a wide range of functions, including metabolic genes involved in carbon flux and nutrient cycling. These findings and this analytic framework suggest avenues towards a better understanding of MGE diversity, activity, mobility and impacts across ecosystems.

Biological and medical sciences↗
DOE OSTI2022

Microbiome assembly in thawing permafrost and its feedbacks to climate

Abstract The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost–climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post‐thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw‐mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well‐suited to thrive in changing environmental conditions. We predict that on a short timescale and following high‐disturbance thaw (e.g., thermokarst), stochasticity dominates post‐thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower‐intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post‐thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1974

An interdisciplinary analysis of Colorado Rocky Mountain environments using ADP techniques

The author has identified the following significant results. Good ecological, classification accuracy (90-95%) can be achieved in areas of rugged relief on a regional basis for Level 1 cover types (coniferous forest, deciduous forest, grassland, cropland, bare rock and soil, and water) using computer-aided analysis techniques on ERTS/MSS data. Cost comparisons showed that a Level 1 cover type map and a table of areal estimates could be obtained for the 443,000 hectare San Juan Mt. test site for less than 0.1 cent per acre, whereas photointerpretation techniques would cost more than 0.4 cent per acre. Results of snow cover mapping have conclusively proven that the areal extent of snow in mountainous terrain can be rapidly and economically mapped by using ERTS/MSS data and computer-aided analysis techniques. A distinct relationship between elevation and time of freeze or thaw was observed, during mountain lake mapping. Basic lithologic units such as igneous, sedimentary, and unconsolidated rock materials were successfully identified. Geomorphic form, which is exhibited through spatial and textual data, can only be inferred from ERTS data. Data collection platform systems can be utilized to produce satisfactory data from extremely inaccessible locations that encounter very adverse weather conditions, as indicated by results obtained from a DCP located at 3,536 meters elevation that encountered minimum temperatures of -25.5 C and wind speeds of up to 40.9m/sec (91 mph), but which still performed very reliably.

Hoffer, R. M.↗
DOE OSTI2023

Assimilation of multiple datasets results in large differences in regional- to global-scale NEE and GPP budgets simulated by a terrestrial biosphere model

In spite of the importance of land ecosystems in offsetting carbon dioxide emissions released by anthropogenic activities into the atmosphere, the spatiotemporal dynamics of terrestrial carbon fluxes remain largely uncertain at regional to global scales. Over the past decade, data assimilation (DA) techniques have grown in importance for improving these fluxes simulated by terrestrial biosphere models (TBMs), by optimizing model parameter values while also pinpointing possible parameterization deficiencies. Although the joint assimilation of multiple data streams is expected to constrain a wider range of model processes, their actual benefits in terms of reduction in model uncertainty are still under-researched, also given the technical challenges. In this study, we investigated with a consistent DA framework and the ORCHIDEE-LMDz TBM–atmosphere model how the assimilation of different combinations of data streams may result in different regional to global carbon budgets. To do so, we performed comprehensive DA experiments where three datasets (in situ measurements of net carbon exchange and latent heat fluxes, spaceborne estimates of the normalized difference vegetation index, and atmospheric CO 2 concentration data measured at stations) were assimilated alone or simultaneously. We thus evaluated their complementarity and usefulness to constrain net and gross C land fluxes. We found that a major challenge in improving the spatial distribution of the land C sinks and sources with atmospheric CO 2 data relates to the correction of the soil carbon imbalance.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Long-term hydrological, biogeochemical, and climatological data from Walker Branch Watershed, East Tennessee, USA

In 1967, the original Walker Branch Watershed (WBW) project was established to study elemental cycling and mass balances in a relatively unimpacted watershed. Over the next 50+ years, findings from additional experimental studies and long-term observations on WBW advanced understanding of catchment hydrology, biogeochemistry, and ecology and established WBW as a seminal site for catchment science. The 97.5-ha WBW is located in East Tennessee, USA, on the U.S. Department of Energy's Oak Ridge Reservation. Vegetation on the watershed is characteristic of an eastern deciduous, second-growth forest. The watershed is divided into two subcatchments: the West Fork (38.4 ha) and the East Fork (59.1 ha). Headwater streams draining these subcatchments are fed by multiple springs, and thus flow is perennial. Stream water is high in base cations due to weathering of dolomite bedrock and nutrient concentrations are low. Long-term observations of climate, hydrology, and biogeochemistry include daily (1969–2014) and 15-min (1994–2014) stream discharge and annual runoff (1969–2014); hourly, daily, and annual rainfall (1969–2012); daily climate and soil temperature (1993–2010); and weekly stream water chemistry (1989–2013). These long-term datasets are publicly available on the WBW website (https://walkerbranch.ornl.gov/long-term-data/). While collection of these data has ceased, related long-term measurements continue through the National Ecological Observatory Network (NEON), where WBW is the core terrestrial and aquatic site in the Appalachian and Cumberland Plateau region (NEON's Domain 7) of the United States. These long-term datasets have been and will continue to be important in evaluating the influence of climatic and environmental drivers on catchment processes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A new primer set for Clade I nosZ that recovers genes from a broader range of taxa

Denitrification is an important global N cycle process. The gene encoding NosZ that converts nitrous oxide (N 2 O) to N 2 has been widely used as a biomarker to study denitrifying communities. However, conventional PCR primers target a limited range of the genetically diverse Clade I nosZ, and the amplicons are too long for sequencing on current NGS platforms. To address these issues, here we developed a new PCR primer set that amplifies a 355-bp region of Clade I nosZ and captures broader taxonomic coverage than conventional primers in in silico tests. When compared with the widely used nosZF_nosZR_Rich_2003 set using the same soil samples and the same sequencing depth, the new set retrieved genes from four times more unique species, with consistently higher general diversity-based metrics. The new primer set performed well with different sequencing platforms (Ion Torrent and Illumina), and among a wide variety of soils from polar to tropical, desert to agricultural, and surface to a very low biomass subsoil, with significant differences in denitrifying community diversity and composition. This new primer set for Clade I together with the primers recently reported for Clade II by Chee-Sanford et al. provides a more comprehensive assessment of denitrifier gene hosts, their ecological patterns, and the degree of novelty in retrieved gene sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada: For Calendar Year 2020 (Rev. 2)

This report serves as the combined annual report for post-closure activities in compliance with the requirements listed in Resource Conservation and Recovery Act (RCRA) Permit Number NEV HW0101 associated with the following closed corrective action units (CAUs): 1) CAU 90, Area 2 Bitcutter Containment; 2) CAU 91, Area 3 U-3fi Injection Well; 3) CAU 92, Area 6 Decon Pond Facility; 4) CAU 110, Area 3 WMD U-3ax/bl Crater; 5) CAU 111, Area 5 WMD Retired Mixed Waste Pits; 6) CAU 112, Area 23 Hazardous Waste Trenches The locations of the sites are shown in Figure ES-1. This report covers calendar year 2020. The post-closure requirements for these sites are described in RCRA Permit NEV HW0101 and are summarized in each CAU-specific section of this report. The results of the inspections, a summary of maintenance activities, and an evaluation of monitoring data are presented in this report. Site inspections are conducted annually at CAUs 90, 91, and 112; semiannually at CAUs 92 and 110; and quarterly at CAU 111. Additional inspections are conducted at CAUs 92 and 111 if precipitation occurs in excess of 1.0 inch in a 24-hour period. Inspections include an evaluation of the condition of the units, including covers, fences, signs, gates, and locks. At CAUs 110 and 111, soil moisture monitoring and subsidence surveys are conducted in addition to the visual inspections. At CAU 110, the site fence, gate, lock, and use restriction signs are evaluated. At CAU 111, an ecological survey, direct radiation monitoring, air monitoring, radon flux monitoring, and groundwater monitoring are also conducted. This report will address all monitoring item notes above except groundwater monitoring. Groundwater monitoring is documented in the Nevada National Security Site Data Report: Groundwater Monitoring Program Area 5 Radioactive Waste Management Site. All required inspections, maintenance, and monitoring were conducted in accordance with the post-closure requirements of the permit. Revision 6 of RCRA Permit NEV HW0101 was issued effective December 10, 2015, and remained in effect until December 10, 2020. At the time of this report submittal, the new RCRA permit application was in review.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Microbial Ecology of the Plant Rhizosphere (PlantMicrobe)

The growth of bioenergy crops has the potential to help fulfill the nation’s demand for energy. However, growing these crops on arable lands may lead to socioeconomic concerns. One proposed solution is to grow biofuel crops in nutrient poor soils that aren’t well suited for food-crop growth. Therefore, in order to understand the impact of nutrient poor environments on plants, there is a need to investigate model plants and their rhizospheres in these environments using high throughput molecular analyses. Here the rhizosphere can be defined as the zone around underground portion of the plant that is influenced by the plant’s roots, and can include chemical, biological, and physical influences.

09 BIOMASS FUELS↗
DOE OSTI2024

Heating effects on pyrogenic organic matter mass loss and temperature in a sand matrix in a lab setting from 2022

This dataset contains data associated with the preprint “A laboratory method for simulating the effects of subsequent fires on pyrogenic organic matter at different exposure depths in a sand matrix” (https://doi.org/10.1101/2024.07.30.605814), which has been accepted for publication in the International Journal of Wildland Fire. The dataset was generated to investigate the effects of subsequent fires on preexisting pyrogenic organic matter (PyOM) at different soil depths. Specifically, we designed a laboratory method to simulate soil heating from above, applying realistic heat flux profiles (High, Low, Control) derived from jack pine (Pinus banksiana Lamb.) log burns. Using a cone calorimeter, these profiles were applied to buried jack pine PyOM (produced at 350°C) in a sand matrix pyrocosm to examine PyOM mass loss at different depths (surface, 1 cm, 5 cm). Each treatment (e.g., High heat flux at 1 cm depth) was applied once to five replicates in a pyrocosm.The dataset includes mass loss fraction of PyOM and time-series temperature profiles (measured with type K thermocouples). Additionally, calibration datasets for high and low heat flux profiles are provided, including programmed heat flux profile data and three sets of calibration results. All datasets are in .csv format and were analyzed in R using code found at https://github.com/MengmengLuo/Reburning-pyrogenic-organic-matter-A-laboratory-method-for-dosing-dynamic-heat-fluxes-from-above. This dataset supports research on PyOM transformations during subsequent fires, and methodological advancements in simulating soil heating. It can be used to explore fire-induced PyOM alterations across different fire intensities and soil depths.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Key Environmental and Ecological Variables of Wetland CH 4 and CO 2 Fluxes Change With Warming

Wetlands are important ecosystems for the global carbon cycle, impacting regional and global methane (CH 4 ) and carbon dioxide (CO 2 ) budgets. This study examines how environmental and ecological variables impact wetland CH 4 flux and net ecosystem exchange of CO 2 (NEE) across 17 sites globally. We also quantified the importance of variables for each wetland type and site at monthly scale under normal and warm temperatures using dominance analysis. We identified soil and air temperature (TS, TA, respectively) as key variables influencing wetland CH4, and latent heat (LE) and shortwave radiation (SW) for NEE under normal and warm conditions. However, the importance of some variables shifted with warming. For predicting the variability of wetland CH4 flux under warming, gross primary productivity (GPP) and LE, replacing wind direction (WD), were dominant variables for tropical swamps, while NEE was important for high-latitude fens and bogs under warm temperatures. For wetland NEE, the role of TA and TS decreased across all wetland types with warming, while vapor pressure deficit (VPD) became more important for mid and high-latitude wetlands. Our results reveal the complex responses of wetland carbon flux to environmental and ecological variables with warming and provide new insights into improving wetland models by incorporating additional variables and accounting for the changing roles of variables in carbon flux under warming.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Melanization slows the rapid movement of fungal necromass carbon and nitrogen into both bacterial and fungal decomposer communities and soils

Microbial necromass contributes significantly to both soil carbon (C) persistence and ecosystem nitrogen (N) availability, but quantitative estimates of C and N movement from necromass into soils and decomposer communities are lacking. Additionally, while melanin is known to slow fungal necromass decomposition, how it influences microbial C and N acquisition as well as elemental release into soils remains unclear. Here, we tracked decomposition of isotopically labeled low and high melanin fungal necromass and measured 13 C and 15 N accumulation in surrounding soils and microbial communities over 77 d in a temperate forest in Minnesota, USA. Mass loss was significantly higher from low melanin necromass, corresponding with greater 13 C and 15 N soil inputs. A taxonomically and functionally diverse array of bacteria and fungi was enriched in 13 C and/or 15 N at all sampling points, with enrichment being consistently higher on low melanin necromass and earlier in decomposition. Similar patterns of preferential C and N enrichment of many bacterial and fungal genera early in decomposition suggest that both microbial groups co-contribute to the rapid assimilation of resource-rich soil organic matter inputs. While overall richness of taxa enriched in C was higher than in N for both bacteria and fungi, there was a significant positive relationship between C and N in co-enriched taxa. Collectively, our results demonstrate that melanization acts as a key ecological trait mediating not only fungal necromass decomposition rate but also necromass C and N release and that both elements are rapidly co-utilized by diverse bacterial and fungal decomposers in natural settings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Carbon cycling across ecosystem succession in a north temperate forest: Controls and management implications

Despite decades of progress, much remains unknown about successional trajectories of carbon (C) cycling in north temperate forests. Drivers and mechanisms of these changes, including the role of different types of disturbances, are particularly elusive. To address this gap, we synthesized decades of data from experimental chronosequences and long-term monitoring at a well-studied, regionally representative field site in northern Michigan, USA. Our study provides a comprehensive assessment of changes in above- and belowground ecosystem components over two centuries of succession, links temporal dynamics in C pools and fluxes with underlying drivers, and offers several conceptual insights to the field of forest ecology. Our first advance shows how temporal dynamics in some ecosystem components are consistent across severe disturbances that reset succession and partial disturbances that slightly modify it: both of these disturbance types increase soil N availability, alter fungal community composition, and alter growth and competitive interactions between short-lived pioneer and longer-lived tree taxa. Further, these changes in turn affect soil C stocks, respiratory emissions, and other belowground processes. Second, we show that some other ecosystem components have effects on C cycling that are not consistent over the course of succession. For example, canopy structure does not influence C uptake early in succession but becomes important as stands develop, and the importance of individual structural properties changes over the course of two centuries of stand development. Third, we show that in recent decades, climate change is masking or overriding the influence of community composition on C uptake, while respiratory emissions are sensitive to both climatic and compositional change. In synthesis, we emphasize that time is not a driver of C cycling; it is a dimension within which ecosystem drivers such as canopy structure, tree and microbial community composition change. Changes in those drivers, not in forest age, are what control forest C trajectories, and those changes can happen quickly or slowly, through natural processes or deliberate intervention. Stemming from this view and a whole-ecosystem perspective on forest succession, we offer management applications from this work and assess its broader relevance to understanding long-term change in other north temperate forest ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Differential Trends in Iron Concentrations of Boreal Streams Linked to Catchment Characteristics

Increasing iron (Fe) concentrations have been reported for freshwaters across northern Europe over the last decades. This increase, together with elevated concentrations of dissolved organic carbon (DOC), leads to browning of freshwaters, which affects aquatic organisms, ecosystem functioning, biogeochemical cycles, and brings challenges to drinking water production. However, how such increasing trends in stream Fe concentrations reflect the contribution of different catchment sources remains poorly resolved. Here, we explored how catchment characteristics, that is, mires and coniferous soils, regulate spatial and temporal patterns of Fe in a boreal stream network. For this, we determined Fe speciation in riparian and mire soils, and studied temporal Fe dynamics in soil-water and stream-water over a span of 18 years. Positive Fe trends were found in the solution of the riparian soil, while no long-term trend was observed in the mire. These differences were reflected in stream-water, where three headwater streams dominated by coniferous cover also displayed positive Fe trends, whereas the mire dominated stream showed no trend. Surprisingly, the majority of higher order streams showed declining Fe trends, despite long-term increases in DOC. In addition, we found that an extreme drought event led to a prolonged release of Fe and DOC from the riparian soils, that could have long-term effects on stream Fe concentrations. Our results show that riparian forest soils can be major contributors to ongoing increases in freshwater Fe concentrations and that drought can further promote the release of Fe from organic soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Microtomographic Measurements of Total Air‐Water Interfacial Areas for Soils

Abstract Synchrotron X‐ray microtomography (XMT) was used to measure total air‐water interfacial areas (A aw ) as a function of water saturation (S w ) for several soils that comprise a range of physical and geochemical properties. Measurements were also conducted for glass beads and quartz sands for comparison. Apparent near‐linearA aw ‐S w relationships are observed for the three sands and the three sandy soils. In contrast, the measured interfacial areas for two soils that contain greater proportions of silt and clay are strongly nonlinear functions of water saturation. The greater degree of nonlinearity observed for these two soils is due to their much greater particle‐size distributions (i.e., uniformity coefficients) and their concomitant greater range in pore sizes. Interfacial areas determined with the thermodynamic method were used to benchmark the XMT measurements. XMT‐measured interfacial areas compare well to the thermodynamic‐determined values for the sands and sandy soils. In contrast, the XMT‐measured interfacial areas for the two soils with larger particle‐size distributions are not fully congruent with the thermodynamic‐determined values. Both of these soils have large fractions of pore space comprising nominal pore diameters smaller than the resolution of the XMT imaging. These results suggest that air‐water interfacial area may not always be fully characterized by standard XMT for soils with large particle‐size distributions.

Environmental Sciences & Ecology↗
DOE OSTI2022

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

59 BASIC BIOLOGICAL SCIENCES↗