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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Microbial diversity drives carbon use efficiency in a model soil

Abstract Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Temporal changes in global soil respiration since 1987

As the second-largest terrestrial carbon (C) flux, soil respiration (R S ) has been stimulated by climate warming. However, the magnitude and dynamics of such stimulations of soil respiration are highly uncertain at the global scale, undermining our confidence in future climate projections. Here, we present an analysis of global R S observations from 1987–2016. R S increased (P < 0.001) at a rate of 27.66 g C m -2 yr -2 (equivalent to 0.161 Pg C yr -2 ) in 1987–1999 globally but became unchanged in 2000–2016, which were related to complex temporal variations of temperature anomalies and soil C stocks. However, global heterotrophic respiration (R h ) derived from microbial decomposition of soil C increased in 1987–2016 (P < 0.001), suggesting accumulated soil C losses. Given the warmest years on records after 2015, our modeling analysis shows a possible resuscitation of global R S rise. This study of naturally occurring shifts in R S over recent decades has provided invaluable insights for designing more effective policies addressing future climate challenges.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Hi-C metagenome sequencing reveals soil phage–host interactions

Abstract Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi–C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lytic infections result in more host death and inversely influence host abundance. This study provides empirical evidence of phage-mediated bacterial population dynamics in soil by directly capturing specific phage-host interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Composition and metabolism of microbial communities in soil pores

Delineation of microbial habitats within the soil matrix and characterization of their environments and metabolic processes are crucial to understand soil functioning, yet their experimental identification remains persistently limited. We combined single- and triple-energy X-ray computed microtomography with pore specific allocation of 13 C labeled glucose and subsequent stable isotope probing to demonstrate how long-term disparities in vegetation history modify spatial distribution patterns of soil pore and particulate organic matter drivers of microbial habitats, and to probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) and small (4-10 µm Ø) soil pores in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C. We propose a microbial habitat classification concept based on biogeochemical mechanisms and localization of soil processes and also suggests interventions to mitigate the environmental consequences of agricultural management.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition

Soil organic matter (SOM) decomposition by microorganisms is a major uncertainty in predicting terrestrial carbon–atmosphere feedbacks, partly because we lack understanding of the microbial diversity involved in depolymerizing different carbon pools across environmental gradients. We address this gap using a continental-scale dataset pairing shotgun metagenomes with high-resolution SOM chemistry, assembling 0.76 Tbp of prokaryotic MAGs (828 genomes) and identifying 66,727 SOM molecules from 47 standardized U.S. soil cores selected using respiration rates from 106 soils. Integrating these datasets reveals widespread microbial potential for depolymerizing chemically-recalcitrant SOM previously considered stable. We uncover complementary metabolic specialization between genera affiliated with two abundant bacterial orders, Rhizobiales and Chthoniobacterales, and an archaeal order, Nitrososphaerales. This metabolic partitioning is consistent across soil depths and activity levels, suggesting coordinated decomposition of complex SOM through distinct but complementary biochemical strategies. The metabolic potential for depolymerization of chemically-recalcitrant compounds is supported by the abundance of these molecules across the soils, as indicated by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), and by flux balance analysis of metabolic models. Our results show that a substantial portion of ostensibly stable SOM remains vulnerable to microbial decomposition, a mechanism not captured in current Earth System Models.

Song, Young C. [Pacific Northwest National Laborat↗
DOE OSTI2022

A soil-inspired dynamically responsive chemical system for microbial modulation

Interactions between the microbiota and their colonized environments mediate critical pathways from biogeochemical cycles to homeostasis in human health. Here, in this study, we report a soil-inspired chemical system that consists of nanostructured minerals, starch granules and liquid metals. Fabricated via a bottom-up synthesis, the soil-inspired chemical system can enable chemical redistribution and modulation of microbial communities. We characterize the composite, confirming its structural similarity to the soil, with three-dimensional X-ray fluorescence and ptychographic tomography and electron microscopy imaging. We also demonstrate that post-synthetic modifications formed by laser irradiation led to chemical heterogeneities from the atomic to the macroscopic level. The soil-inspired material possesses chemical, optical and mechanical responsiveness to yield write-erase functions in electrical performance. The composite can also enhance microbial culture/biofilm growth and biofuel production in vitro. Finally, we show that the soil-inspired system enriches gut bacteria diversity, rectifies tetracycline-induced gut microbiome dysbiosis and ameliorates dextran sulfate sodium-induced rodent colitis symptoms within in vivo rodent models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A global database of soil microbial phospholipid fatty acids and enzyme activities

Abstract Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.

Science & Technology - Other Topics↗
DOE OSTI2026

The Q 10 of in situ microbial soil respiration varies with mean annual temperature, precipitation, pH, and plant cover: a meta-analysis and spatial prediction of Q 10

The temperature sensitivity of soil microbial respiration, commonly quantified using the Q 10 coefficient, is a key parameter in carbon cycle models. Uncovering how environmental factors affect in situ Q 10 values can therefore provide critical insight into potential shifts in global carbon stocks under climate change. We collected data from previously published field experiments that measured soil microbial respiration across a range of temperatures. We hypothesized that the Q 10 coefficient of in situ soil microbial respiration would vary based on environmental factors including mean annual temperature (MAT), mean annual precipitation (MAP), plant cover type, pH, soil C:N, and latitude. Linear regression revealed that Q 10 correlates negatively with MAT and MAP and positively with pH and absolute latitude. Additionally, average Q 10 varied significantly across different plant cover types; it was highest in mountain grasslands and lowest in tropical moist forests. Variation in microbial Q 10 across environmental factors may arise from underlying mechanisms such as enzyme kinetics, substrate availability and complexity, and microbial adaptation. To capture patterns in Q 10 more comprehensively, we developed a multiple linear regression model of Q 10 based on the most individually significant environmental drivers and applied it to public datasets to generate a global map of predicted Q 10 . Q 10 was higher in high-latitude and high-altitude regions, where large permafrost carbon stores are vulnerable to thawing and decomposition. We also compared fits between the Q 10 equation and a model produced from macromolecular rate theory (MMRT). We found that the MMRT model had the superior fit and may be better suited to model temperature sensitivity of complex biological reactions. Overall, our results emphasize that relationships between microbial Q 10 and environmental variables should be accounted for in climate models. Incorporating these variations in the Q 10 parameter, rather than using a fixed value, will help predict whether CO 2 emissions will be buffered or exacerbated by soil microbial respiration under climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Soil nitrogen concentration mediates the relationship between leguminous trees and neighbor diversity in tropical forests

Legumes provide an essential service to ecosystems by capturing nitrogen from the atmosphere and delivering it to the soil, where it may then be available to other plants. However, this facilitation by legumes has not been widely studied in global tropical forests. Demographic data from 11 large forest plots (16–60 ha) ranging from 5.25° S to 29.25° N latitude show that within forests, leguminous trees have a larger effect on neighbor diversity than non-legumes. Where soil nitrogen is high, most legume species have higher neighbor diversity than non-legumes. Where soil nitrogen is low, most legumes have lower neighbor diversity than non-legumes. No facilitation effect on neighbor basal area was observed in either high or low soil N conditions. The legume–soil nitrogen positive feedback that promotes tree diversity has both theoretical implications for understanding species coexistence in diverse forests, and practical implications for the utilization of legumes in forest restoration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Spatial controls of methane uptake in upland soils across climatic and geological regions in Greenland

Abstract In the Arctic, the spatiotemporal variation of net methane uptake in upland soils depends on unresolved interactive controls between edaphic and microbial factors not yet included in current models, underpinning the uncertainty of upscaling the Arctic methane budget. Here we show that upland soils in Greenland are consistent methane sinks (−1.83 ± 0.19 nmol methane g −1 dw d −1 ) across a N-S (64–83 °N) pedoclimatic transect. We demonstrate that methane oxidizers abundance, soil pH, and available soil copper are important controls on the spatial variation in methane oxidation. We revised a soil biogeochemical model with a high-resolution land classification and meteorological data for Greenland and tested it against our methane uptake measurements. The model simulated well the magnitudes of observed methane uptake but not the spatial variation across all sites. This work provides novel insights into the controls of methane uptake, which are critical for the accuracy of methane budgets.

Environmental Sciences & Ecology↗
DOE OSTI2025

Uptake of polystyrene nanospheres by wheat and Arabidopsis roots in agar, hydroponics, and soil

Plant uptake of micro- and nanoplastics can lead to contamination of food with plastic particles and subsequent human consumption of plastics. There is evidence that plant roots can take up micro and nanoplastics; however, most of this evidence stems from experiments conducted with plants grown in hydroponics or agar systems where uptake of nanoparticles by roots is more favorable than when plants were grown in soil. Here, we discern the root uptake and accumulation of polystyrene nanospheres in plants grown in different growth media: agar, hydroponics, and soil. In addition, we tested the impacts of nanospheres on plant biomass and plant stress. Wheat and Arabidopsis thaliana were grown in agar, hydroponics, and soil media and exposed to polystyrene nanospheres. Three different nanospheres were used (40 nm and 200 nm carboxylate-modified and 200 nm amino-modified polystyrene) and uniformly mixed into the growth media. Plants were grown for 7 to 10 days and the roots were then examined for the presence of nanospheres by confocal laser scanning microscopy and scanning electron microscopy. Plant stress was evaluated by measuring reactive oxygen species (ROS). We observed the 40 nm nanospheres inside the plant roots, but the 200 nm nanospheres only adhered to the root cap cells showing no uptake into the roots. Furthermore, confocal images indicated that root uptake of nanospheres was favored in hydroponic solutions as compared to agar and soil media. Plant biomass was generally not affected by the nanospheres, except for hydroponically grown Arabidopsis thaliana, where biomass was significantly reduced. Small sized (40 nm) and positively charged (200 nm amino-modified) nanospheres showed higher ROS accumulation in plants than negatively charged 200 nm carboxylate-modified nanospheres. In conclusion, this study provides evidence that polystyrene nanospheres can be taken up into the interior of plant roots and cause plant stress, but these impacts are less pronounced in media where the plastic particles are less mobile, like in agar and soil media as compared to hydroponic systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Grassland-to-cropland conversion increased soil, nutrient, and carbon losses in the US Midwest between 2008 and 2016

After decades of declining cropland area, the United States (US) experienced a reversal in land use/land cover change in recent years, with substantial grassland conversion to cropland in the US Midwest. Although previous studies estimated soil carbon (C) loss due to cropland expansion, other important environmental indicators, such as soil erosion and nutrient loss, remain largely unquantified. In this study, we simulated the environmental impacts from the conversion of grassland to corn and soybeans for 12 US Midwestern states using the EPIC (Environmental Policy Integrated Climate) model. Between 2008 and 2016, over 2 Mha of grassland were converted to crop production in these states, with much less cropland concomitantly abandoned or retired from production. The net grassland-cropland conversion increased annual soil erosion by 7.9%, nitrogen (N) loss by 3.7%, and soil organic carbon loss by 5.6% relative to that of existing cropland, despite an associated increase in cropland area of only 2.5%. Notably, the above estimates represent the scenario of converting unmanaged grassland to tilled corn and soybeans, and impacts varied depending upon crop type and tillage regime. Corn and soybeans are dominant biofuel feedstocks, yet the grassland conversion and subsequent environmental impacts simulated in this study are likely not attributable solely to biofuel-driven land use change since other factors also contribute to corn and soybean prices and land use decisions. Nevertheless, our results suggest grassland conversion in the Upper Midwest has resulted in substantial degradation of soil quality, with implications for air and water quality as well. Additional conservation measures are likely necessary to counterbalance the impacts, particularly in areas with high rates of grassland conversion (e.g. the Dakotas, southern Iowa).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Accumulation of trace elements in soil and fauna within a site historically contaminated with coal combustion residues

Legacy contaminants tied to energy production are a worldwide concern. Coal combustion residues (CCRs) contain high concentrations of potentially toxic trace elements such as arsenic (As), mercury (Hg), and selenium (Se), which can persist for decades after initial contamination. Coal combustion residue disposal methods, including aquatic settling basins and landfills, can facilitate environmental exposure through intentional and accidental releases. Wildlife exposed to CCRs can experience numerous deleterious effects, such as on development, reproduction, and survival. In the current study, we quantified and compared concentrations of As, Hg, Se, and strontium (Sr) within soils and target fauna (three vertebrate and three invertebrate taxa) from a CCR-contaminated site and a reference site within the U.S. Department of Energy’s Savannah River Site, South Carolina, United States. Our objectives were to (1) compare current concentrations of tested elements in soil and resident fauna to levels from our reference site, (2) assess natural attenuation of elements in soils by comparing current concentrations to historic levels, and (3) evaluate the biomagnification potential of the elements measured via body burden and trophic position correlations among fauna. Here, element concentrations were higher in contaminated soils than reference soils; however, concentrations in 2022 were unchanged from concentrations measured in 2003, suggesting no natural attenuation of tested elements. Additionally, target fauna had elevated As, Se, and Sr levels in comparison to reference samples. A positive correlation was observed in southern toads between Sr concentrations and trophic position, as assessed by nitrogen stable isotope ratios, suggesting potential for biomagnification of Sr within our study system. Collectively, our results demonstrate that legacy contaminants are still present and bioaccumulate in a diversity of taxa in a CCR-contaminated site that has not received effluents in more than 50 years, suggesting monitoring programs in CCR-contaminated sites should be maintained long term in the absence of remediation.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2021

A defined medium based on R2A for cultivation and exometabolite profiling of soil bacteria

SummaryExometabolomics is an approach to assess how microorganisms alter their environments through the depletion and secretion of chemical compounds. Comparisons of inoculated with uninoculated media can be used to provide direct biochemical observations on depleted and secreted metabolites which can be used to predict resource competition, cross-feeding and secondary metabolite production in microbial isolates and communities. This approach is most powerful when used with defined media that enable tracking of all depleted metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through LC-MS/MS. Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse bacteria but is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 53 phylogenetically diverse soil bacterial isolates and all of its metabolites were trackable through LC–MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for cultivating and characterizing diverse microbial isolates and communities.Originality-Significance StatementWe build a defined medium based on the metabolite composition of R2A medium and soil, elemental stoichiometry requirements, and knowledge of metabolite usage by different bacteria. The newly formulated defined medium was evaluated on its ability to support the growth of soil isolates and its application for metabolite utilization profiling. We found that of 53 phylogenetically diverse soil bacterial isolates grew on the defined medium and all of its metabolites were trackable through LC–MS/MS analysis. This demonstrates the viability and utility of the constructed defined medium for cultivating and characterizing diverse microbial isolates and communities.

de Raad, Markus↗
DOE OSTI2020

Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil

Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 108 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Metagenomic stable isotope probing reveals bacteriophage participation in soil carbon cycling

Soil viruses are important components of the carbon (C) cycle, yet we still know little about viral ecology in soils. We added diverse 13 C-labelled carbon sources to soil and we used metagenomic-SIP to detect 13 C assimilation by viruses and their putative bacterial hosts. These data allowed us to link a 13 C-labelled bacteriophage to its 13 C-labelled Streptomyces putative host, and we used qPCR to track the dynamics of the putative host and phage in response to C inputs. Following C addition, putative host numbers increased rapidly for 3 days, and then more gradually, reaching maximal abundance on Day 6. Viral abundance and virus:host ratio increased dramatically over 6 days, and remained high thereafter (8.42 ± 2.94). From Days 6 to 30, virus:host ratio remained high, while putative host numbers declined more than 50%. Putative host populations were 13 C-labelled on Days 3–30, while 13 C-labelling of phage was detected on Days 14 and 30. This dynamic suggests rapid growth and 13 C-labelling of the host fueled by new C inputs, followed by extensive host mortality driven by phage lysis. Furthermore, these findings indicate that the viral shunt promotes microbial turnover in soil following new C inputs, thereby altering microbial community dynamics, and facilitating soil organic matter production.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Mycorrhizal effects on crop yield and soil ecosystem functions in a long‐term tillage and fertilization experiment

Summary It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long‐term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no‐tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no‐till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low‐input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.

Peng, Zhenling↗
DOE OSTI2026

Modelling belowground plant acclimation to low soil nitrogen – a heuristic optimality-based approach

Increased root growth to access greater soil mineral nitrogen resources and increased root exudation to stimulate microbial mineralization of soil organic nitrogen are widely observed plant acclimations to nitrogen limitation. However, their quantitative contribution to plant growth and ecosystem productivity remains largely elusive. Here, we present a novel optimality-based eco-evolutionary model in which plants dynamically regulate carbon partitioning between root growth and exudation to maximize their aboveground growth. Our simulations indicated that the availability of soil mineral and organic nitrogen as well as plant nitrogen demand and nitrogen uptake capacity shape optimal carbon partitioning between root growth and exudation. The simulated carbon allocation patterns aligned with empirical studies on belowground plant responses to varying soil nitrogen resources. Our eco-evolutionary approach represents a paradigmatic change in modelling plant nitrogen foraging, which is essential to generate hypotheses on optimal plant acclimation in future soil environments characterized by more erratic nitrogen availability.

Chakrawal, Arjun (ORCID:0000000345724347)↗