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At least 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Conditional filamentation as an adaptive trait of bacteria and its ecological significance in soils

Bacteria can regulate cell morphology in response to environmental conditions, altering their physiological and metabolic characteristics to improve survival. Conditional filamentation, in which cells suspend division while continuing lateral growth, is a strategy with a range of adaptive benefits. Here, we review the causes and consequences of conditional filamentation with respect to bacterial physiology, ecology and evolution. We describe four major benefits from conditional filamentation: stress tolerance, surface colonization, gradient spanning and the facilitation of biotic interactions. Adopting a filamentous growth habit involves fitness trade-offs which are also examined. We focus on the role of conditional filamentation in soil habitats, where filamentous morphotypes are highly prevalent and where environmental heterogeneity can benefit a conditional response. Here, to illustrate the use of information presented in our review, we tested the conditions regulating filamentation by the forest soil isolate Paraburkholderia elongata 5N T . Filamentation by P. elongata was induced at elevated phosphate concentrations, and was associated with the accumulation of intracellular polyphosphate, highlighting the role of filamentation in a phosphate-solubilizing bacterium. Conditional filamentation enables bacteria to optimize their growth and metabolism in environments that are highly variable, a trait that can impact succession, symbioses, and biogeochemistry in soil environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Detection and confirmation of fentanyls in high clay‐content soil by electron ionization gas chromatography‐mass spectrometry

Abstract Detection of illicit drugs in the environment, particularly in soils, often suggests the present or past location of a clandestine production center for these substances. Thus, development of efficient methods for the analysis and detection of these chemicals is of paramount importance in the field of chemical forensics. In this work, a method involving the extraction and retrospective confirmation of fentanyl, acetylfentanyl, thiofentanyl, and acetylthiofentanyl using trichloroethoxycarbonylation chemistry in a high clay‐content soil is presented. The soil was spiked separately with each fentanyl at two concentrations (1 and 10 μg/g) and their extraction accomplished using ethyl acetate and aqueous NH 4 OH (pH ~ 11.4) with extraction recoveries ranging from ~56% to 82% for the high‐concentration (10 μg/g) samples while ranging from ~68% to 83% for the low‐concentration (1 μg/g) samples. After their extraction, residues containing each fentanyl were reacted with 2,2,2‐trichloroethoxycarbonyl chloride (Troc‐Cl) to generate two unique and predictable products from each opioid that can be used to retrospectively confirm their presence and identity using EI‐GC‐MS. The method's limit of detection (MDL/LOD) for Troc‐norfentanyl and Troc‐noracetylfentanyl were estimated to be 29.4 and 31.8 ng/mL in the organic extracts. In addition, the method's limit of quantitation for Troc‐norfentanyl and Troc‐noracetylfentanyl were determined to be 88.2 and 95.5 ng/mL, respectively. Collectively, the results presented herein strengthen the use of chloroformate chemistry as an additional chemical tool to confirm the presence of these highly toxic and lethal substances in the environment.

Valdez, Carlos A.↗
DOE OSTI2021

Spatial biases of information influence global estimates of soil respiration: how can we improve global predictions?

Soil respiration (Rs), the efflux of CO2 from soils to the atmosphere, is a major component of the terrestrial carbon cycle, but is poorly constrained from regional to global scales. The global soil respiration database (SRDB) is a compilation of in-situ Rs observations from around the globe that has been consistently updated with new measurements over the past decade. It is unclear whether the addition of data to new versions of the SRDB has produced better-constrained global Rs estimates. We compared two versions of the SRDB (v3.0 n=5173 and v5.0 n=10366) to determine how additional data influenced the global sum and uncertainty of Rs as predicted by a quantile regression forest model. A model parameterized using SRDBv3 yielded a global Rs sum of 88.6 Pg C yr-1, and associated uncertainty of 29.9 (mean absolute error) and 57.9 (standard deviation) Pg C yr-1, whereas parameterization using SRDBv5 yielded 96.5 Pg C yr-1 and associated uncertainty of 30.2 (mean average error) and 73.4 (standard deviation) Pg C yr-1. Empirically estimated global heterotrophic respiration (Rh) from v3 and v5 were 49.9-50.2 (mean 50.1) and 53.3-53.5 (mean 53.4) Pg C yr-1, respectively. Interestingly, SRDBv5’s inclusion of new data from underrepresented regions (e.g., Asia, Africa, South America) thus resulted in overall higher model uncertainty. The SRDBv5 is still biased towards northern latitudes and temperate zones, so we tested that an optimized global distribution of Rs measurements resulted in a global sum of 96.4 ± 21.4 Pg C yr-1 and lower model uncertainty. These results support current global estimates of Rs but highlight spatial inconsistencies that influence model parameterization and interpretation that should be addressed to improve regional- to global-scale predictions.

Stell, Emma↗
DOE OSTI2023

Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils

Abstract Peatlands are among the largest natural sources of atmospheric methane (CH 4 ) worldwide. Microbial processes play a key role in regulating CH 4 emissions from peatland ecosystems, yet the complex interplay between soil substrates and microbial communities in controlling CH 4 emissions as a function of global change remains unclear. Herein, we performed an integrated analysis of multi‐omics data sets to provide a comprehensive understanding of the molecular processes driving changes in greenhouse gas (GHG) emissions in peatland ecosystems with increasing temperature and sulfate deposition in a laboratory incubation study. We sought to first investigate how increasing temperatures (4, 21, and 35°C) impact soil microbiome–metabolome interactions; then explore the competition between methanogens and sulfate‐reducing bacteria (SRBs) with increasing sulfate concentrations at the optimum temperature for methanogenesis. Our results revealed that peat soil organic matter degradation, mediated by biotic and potentially abiotic processes, is the main driver of the increase in CO 2 production with temperature. In contrast, the decrease in CH 4 production at 35°C was linked to the absence of syntrophic communities and the potential inhibitory effect of phenols on methanogens. Elevated temperatures further induced the microbial communities to develop high growth yield and stress tolerator trait‐based strategies leading to a shift in their composition and function. On the other hand, SRBs were able to outcompete methanogens in the presence of non‐limiting sulfate concentrations at 21°C, thereby reducing CH 4 emissions. At higher sulfate concentrations, however, the prevalence of communities capable of producing sufficient low‐molecular‐weight carbon substrates for the coexistence of SRBs and methanogens was translated into elevated CH 4 emissions. The use of omics in this study enhanced our understanding of the structure and interactions among microbes with the abiotic components of the system that can be useful for mitigating GHG emissions from peatland ecosystems in the face of global change.

AminiTabrizi, Roya↗
DOE OSTI2025

Reduced Erosion Augments Soil Carbon Storage Under Cover Crops

ABSTRACT Cover crops, a promising strategy to increase soil organic carbon (SOC) storage in croplands and mitigate climate change, have typically been shown to benefit soil carbon (C) storage from increased plant C inputs. However, input‐driven C benefits may be augmented by the reduction of C outputs induced by cover crops, a process that has been tested by individual studies but has not yet been synthesized. Here we quantified the impact of cover crops on organic C loss via soil erosion (SOC erosion) and revealed the geographical variability at the global scale. We analyzed the field data from 152 paired control and cover crop treatments from 57 published studies worldwide using meta‐analysis and machine learning. The meta‐analysis results showed that cover crops widely reduced SOC erosion by an average of 68% on an annual basis, while they increased SOC stock by 14% (0–15 cm). The absolute SOC erosion reduction ranged from 0 to 18.0 Mg C −1 ha −1 year −1 and showed no correlation with the SOC stock change that varied from −8.07 to 22.6 Mg C −1 ha −1 year −1 at 0–15 cm depth, indicating the latter more likely related to plant C inputs. The magnitude of SOC erosion reduction was dominantly determined by topographic slope. The global map generated by machine learning showed the relative effectiveness of SOC erosion reduction mainly occurred in temperate regions, including central Europe, central‐east China, and Southern South America. Our results highlight that cover crop‐induced erosion reduction can augment SOC stock to provide additive C benefits, especially in sloping and temperate croplands, for mitigating climate change.

Huang, Wenjuan [Department of Ecology, Evolution, ↗
DOE OSTI2023

Local adaptation of switchgrass drives trait relations to yield and differential responses to climate and soil environments

Abstract Switchgrass, a potential biofuel crop, is a genetically diverse species with phenotypic plasticity enabling it to grow in a range of environments. Two primary divergent ecotypes, uplands and lowlands, exhibit trait combinations representative of acquisitive and conservative growth allocation strategies, respectively. Whether these ecotypes respond differently to various types of environmental drivers remains unclear but is crucial to understanding how switchgrass varieties will respond to climate change. We grew two upland, two lowland, and two intermediate/hybrid cultivars of switchgrass at three sites along a latitudinal gradient in the central United States. Over a 4‐year period, we measured plant functional traits and biomass yields and evaluated genotype‐by‐environment (G × E) interaction effects by analyzing switchgrass responses to soil and climate variables. We found substantial evidence of G × E interactions on biomass yield, primarily due to deviations in the response of the southern lowland cultivar Alamo, which produced more biomass in hotter and drier environments relative to other cultivars. While lowland cultivars had the highest potential for yield, their yields were more variable year‐to‐year compared to other cultivars, suggesting greater sensitivity to environmental perturbations. Models comparing soil and climate principal components as explanatory variables revealed soil properties, especially nutrients, to be most effective at predicting switchgrass biomass yield. Also, positive correlations between biomass yield and conservative plant traits, such as high stem mass and tiller height, became stronger at lower latitudes where the climate is hotter and drier, regardless of ecotype. Lowland cultivars, however, showed a greater predisposition to exhibit these conservative traits. These results suggest switchgrass trait allocation trade‐offs that prioritize aboveground biomass production are more tightly associated in hot, dry environments and that lowland cultivars may exhibit a more specialized strategy relative to other cultivars. Altogether, this research provides essential knowledge for improving the viability of switchgrass as a biofuel crop.

09 BIOMASS FUELS↗
DOE OSTI2021

Soil penetration by maize roots is negatively related to ethylene‐induced thickening

Abstract Radial expansion is a classic response of roots to a mechanical impedance that has generally been assumed to aid penetration. We analysed the response of maize nodal roots to impedance to test the hypothesis that radial expansion is not related to the ability of roots to cross a compacted soil layer. Genotypes varied in their ability to cross the compacted layer, and those with a steeper approach to the compacted layer or less radial expansion in the compacted layer were more likely to cross the layer and achieve greater depth. Root radial expansion was due to cortical cell size expansion, while cortical cell file number remained constant. Genotypes and nodal root classes that exhibited radial expansion in the compacted soil layer generally also thickened in response to exogenous ethylene in hydroponic culture, that is, radial expansion in response to ethylene was correlated with the thickening response to impedance in soil. We propose that ethylene insensitive roots, that is, those that do not thicken and can overcome impedance, have a competitive advantage under mechanically impeded conditions as they can maintain their elongation rates. We suggest that prolonged exposure to ethylene could function as a stop signal for axial root growth.

Vanhees, Dorien J.↗
DOE OSTI2023

Leaves as bottlenecks: The contribution of tree leaves to hydraulic resistance within the soil–plant–atmosphere continuum

Within vascular plants, the partitioning of hydraulic resistance along the soil-to-leaf continuum affects transpiration and its response to environmental conditions. In trees, the fractional contribution of leaf hydraulic resistance (R leaf ) to total soil-to-leaf hydraulic resistance (R total ), or fR leaf (= R leaf /R total ), is thought to be large, but this has not been tested comprehensively. Here, we compiled a multi-biome dataset of fR leaf using new and previously published measurements of pressure differences within trees in situ. Across 80 samples, fR leaf averaged 0.51 (95% confidence interval [CI] = 0.46-0.57) and it declined with tree height. We also used the allometric relationship between field-based measurements of soil-to-leaf hydraulic conductance and laboratory-based measurements of leaf hydraulic conductance to compute the average fR leaf for 19 tree samples, which was 0.40 (95% CI = 0.29-0.56). The in-situ technique produces a more accurate descriptor of fR leaf because it accounts for dynamic leaf hydraulic conductance. Both approaches demonstrate the outsized role of leaves in controlling tree hydrodynamics. A larger fR leaf may play a role in protecting stems from loss of hydraulic conductance. Thus, the decline in fR leaf with tree height would contribute to greater drought vulnerability in taller trees and potentially to their observed disproportionate drought mortality.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

In situ diversity of metabolism and carbon use efficiency among soil bacteria

The central carbon (C) metabolic network harvests energy to power the cell and feed biosynthesis for growth. In pure cultures, bacteria use some but not all of the network’s major pathways, such as glycolysis and pentose phosphate and Entner-Doudoroff pathways. However, how these pathways are used in microorganisms in intact soil communities is unknown. Here, we analyzed the incorporation of 13 C from glucose isotopomers into phospholipid fatty acids. We showed that groups of Gram-positive and Gram-negative bacteria in an intact agricultural soil used different pathways to metabolize glucose. They also differed in C use efficiency (CUE), the efficiency with which a substrate is used for biosynthesis. Our results provide experimental evidence for diversity among microbes in the organization of their central carbon metabolic network and CUE under in situ conditions. These results have important implications for our understanding of how community composition affects soil C cycling and organic matter formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Soil carbon formation is promoted by saturation deficit and existing mineral-associated carbon, not by microbial carbon-use efficiency

Mineral-associated organic carbon (MAOC) is the largest terrestrial pool of organic carbon, yet controls on its formation remain unresolved. Existing MAOC is thought to preclude additional C storage on minerals, but this perspective is difficult to reconcile with observations that MAOC stacks in multilayers, suggesting that existing MAOC could promote greater C retention. Here, in a manipulative experiment using 118 soils from 15 agricultural sites across the United States, we show that MAOC formation is promoted by both existing MAOC and its counterpart—MAOC saturation deficit. The positive effect of existing MAOC on the formation of new MAOC persists after accounting for soil physicochemical properties that covary with MAOC. In contrast with current theory, we found that MAOC formation was not clearly influenced by microbial carbon-use efficiency (CUE). Our findings demonstrate that existing MAOC and saturation deficit, not microbial CUE, are key to determining new MAOC formation in agricultural soils.

King, Alison E. [Colorado State Univ., Fort Collin↗
DOE OSTI2024

Metatranscriptomes of California grassland soil microbial communities in response to rewetting

When very dry soil is rewet, rapid stimulation of microbial activity has important implications for ecosystem biogeochemistry, yet associated changes in microbial transcription are poorly known. Here, we present metatranscriptomes of California annual grassland soil microbial communities, collected over 1 week from soils rewet after a summer drought—providing a time series of short-term transcriptional response during rewetting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil

The addition of glucose to soil has long been used to study the metabolic activity of microbes in soil; however, the response of the microbial ecophysiology remains poorly characterized. To address this, we sequenced the metagenomes and metatranscriptomes of glucose-amended soil microbial communities in a laboratory incubation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Optical coherence tomography imaging of plant root growth in soil

Complex interactions between roots and soil provide the nutrients and physical support required for robust plant growth. Yet, visualizing the root-soil interface is challenged by soil’s opaque scattering characteristics. In this paper, we describe methods for using optical coherence tomography (OCT) to provide non-destructive 3D and cross-sectional root imaging not available with traditional bright field microscopy. OCT is regularly used for bioimaging, especially in ophthalmology where it can detect retinal abnormalities. Prior use of OCT in plant biology has focused on surface defects of above ground tissues, predominantly in food crops. Our results show OCT is also viable for detailed, in situ study of living plant roots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Community Geothermal: Soil Conductivity, Borehole Design, Energy Models, and Load Data for a Residential System Development - Hinesburg, VT

This dataset contains materials from the Coalition for Community-Supported Affordable Geothermal Energy Systems (C2SAGES) project, which evaluated the techno-economic feasibility of a community geothermal system for a residential development in Hinesburg, VT. The dataset includes detailed soil conductivity test reports, energy models, borehole design reports, hourly energy loads for heating, cooling, and hot water, and design layouts. EnergyPlus was used to model building energy loads, and Modelica software was applied for geothermal loop sizing based on these loads and soil conductivity results. Python scripts for network design further refined the models. Key files include PDF reports on borehole design (with projections for 1-year, 15-year, and 30-year systems), soil conductivity test results, EnergyPlus modeling outputs, and 2D/3D design drawings in PDF, DWG, and DXF formats. Python notebooks for network design and OnePipe model files are also provided, with Modelica required for viewing certain files. Outputs and modeling data are in various formats including CSV, JPG, HTML, and IDF, with units and data clearly labeled to support understanding of system design and performance for the proposed geothermal solution.

15 GEOTHERMAL ENERGY↗
DOE OSTI2020

Calibrated soil moisture data from Manaus, Brazil, August 2018 - December 2019

This dataset contains calibrated soil moisture and rainfall data for ecohydrological studies in the Central Amazon (2.6099 ºS, 60.2093 ºW) taken at 30-min intervals. Soil moisture data was collected at depths of 0.025-, 0.05-, 0.15-, 0.30-, 0.50-,0.8-, 1.6-, 2.4-, 3.2-, 4.8-, 6.4-, 8.8-, and 14.20 m. Inconsistent data was removed during the QA/QC process. Further information including data collection methods are available in the associated publication, Negron-Juarez et al. 2020. Measurement and characterization of soil moisture dynamics in a Central Amazonian tropical forest (to be submitted).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Soil Water Content (m3 m-3) located in the Dominican Republic , February 2013 - December 2016

Daily data that has been processed to monthly. Data represents near-surface soil moisture (depth of 0-10 cm) at a latitude of 17.90 N, and longitude -71.67 E. Data was downloaded from the PBO soil moisture data network and is publicly available. Data from this site is referenced as Dominican Republic (2) in Table 1 and Figure 4 of Solander et al., 2020, The pan-tropical soil moisture response to El Nino, Hydrol. Earth Syst. Sci., in press.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Soil Water Content (m3 m-3) from the Dominican Republic, February 2013 - August 2017.

Daily data that has been processed to monthly. Data represents near-surface soil moisture (depth of 0-10 cm) at a latitude of 19.76 N, and longitude -70.57 E. Data was downloaded from the PBO soil moisture data network and is publicly available. Data from this site is referenced as Dominican Republic (1) in Table 1 and Figure 4 of Solander et al., 2020, The pan-tropical soil moisture response to El Nino, Hydrol. Earth Syst. Sci., in press.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Soil Water Content (m3 m-3) from Australia, June 2011 - December 2016

Hourly data processed to monthly. Data collected from Cosmic Neutron Probes at variable depth averaging 38 cm that was interpolated to near-surface (0-10 cm). Site located at latitude -14.16 deg N, longitude 131.39 deg E. Data was downloaded from the The COsmic-ray Soil Moisture Observing System (COSMOS) soil moisture data network and is publicly available. Data from this site located at, referenced as Australia (2) in Table 1 and Figure 4 of Solander et al., 2020, The pan-tropical soil moisture response to El Nino, Hydrol. Earth Syst. Sci., in press.

54 ENVIRONMENTAL SCIENCES↗