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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Earthworms significantly enhance the temperature sensitivity of soil organic matter decomposition: Insights into future soil carbon budgeting

How and what soil fauna influence the soil organic matter (SOM) decomposition rate (Rs) and its temperature sensitivity (Q 10 ) have been largely ignored, although this is a crucial matter, especially under the scenario of global change. Further, in this study, a novel approach was adopted with a continuous changing-temperature incubation (daytime, from 7 °C to 22 °C; nighttime, from 22 °C to 7 °C) with rapid and continuous measurement, to examine the effect of soil macrofauna (specifically, earthworms) on Rs and Q 10 with three densities (no addition, low density, and high density). According to the results, the earthworms accelerated Rs. Furthermore, Rs with earthworm addition had a symmetrical pattern during daytime and nighttime cycles, which is contrary to traditional soil incubation, with only soil microbe as asymmetrical. More importantly, earthworm addition increased Q 10 markedly, ranging from 48% to 67%. Overall, the findings highlight the pivotal role of earthworms as soil macrofauna that regulating soil carbon release, and their effects should be integrated into process-based ecological models in future.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications

Agriculture is under pressure to provide food for a growing population and the feedstock required to drive the bioeconomy. Methods to breed and genetically modify plants are inadequate to keep pace. When engineering crops, traits are painstakingly introduced into plants one-at-a-time, combine unpredictably, and are continuously expressed. Synthetic biology is changing these paradigms with new genome construction tools, computer aided design (CAD), and artificial intelligence (AI). “Smart plants” contain circuits that respond to environmental change, alter morphology, or respond to threats. Further, the plant and associated microbes (fungi, bacteria, archaea) are now being viewed by genetic engineers as a holistic system. Historically, plant health has been enhanced by many natural and laboratory-evolved soil microbes marketed to enhance growth, provide nutrients, or confer pest/stress resistance. Synthetic biology has expanded the number of species that can be engineered, increased the complexity of engineered functions, controlled environmental release, and assembled stable consortia. New CAD tools will manage genetic engineering projects spanning multiple plant genomes (nucleus, chloroplast, mitochondrion) and the thousands of genomes of associated bacteria/fungi. Here, this review covers advanced genetic engineering techniques to drive the next agricultural revolution, as well as push plant engineering into new realms for manufacturing, infrastructure, sensing, and remediation.

Clauer, Phillip [Massachusetts Inst. of Technology↗
DOE OSTI2022

Drought impacts on microbial trait distribution and feedback to soil carbon cycling

Abstract Quantifying the impact of drought on microbial processes and its consequences for soil carbon cycling is hindered by the lack of underlying mechanistic understanding. Therefore, there is a need to scale up the physiological response to changing water status from individual soil microbes to collective communities across different ecosystems. Here we propose the use of a framework that incorporates trait‐based ecology to link drought‐impacted microbial processes to rates of soil carbon decomposition and stabilisation. We briefly synthesise existing knowledge on the effects of drought on microbial physiology at the individual to community scale, before integrating this understanding within a framework incorporating life‐history strategy, ecological strategy and biochemistry. This framework highlights a dynamic allocation to high yield (Y), resource acquisition (A) and stress tolerance (S) pathways as environmental conditions change. Y‐A‐S strategies represent sets of traits that tend to correlate due to physiological or evolutionary trade‐offs. This framework enables assessment of microbial processes along two key environmental gradients of water and resource availability, both of which are constrained by drought. The variable chemistry of biomass and necromass produced under different physiological strategies in response to drying–rewetting impacts organic matter decomposition and stabilisation in soils, and should also be considered when quantifying soil carbon balance. We highlight that diversion of resources away from microbial growth can alter soil organic matter chemistry and its persistence depending on the kind of microbial compounds produced. To advance such a framework, we highlight avenues of research that would enable the further identification and quantification of traits linked to Y‐A‐S strategies and the physiological outcomes at the community level under drought and rewetting, and conclude by hypothesising how ecosystem‐level changes might feedback on to the soil carbon cycle. A scalable understanding of microbial drought‐response mechanisms affecting soil carbon cycling will transform the way microbial physiology is represented in ecosystem studies. Read the free Plain Language Summary for this article on the Journal blog.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils

Abstract Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.

Mason, Cayla N. (ORCID:0000000345983824)↗
DOE OSTI2020

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes

Despite the important roles of soil microbes, especially the most diverse rare taxa in maintaining community diversity and multifunctionality, how different climate regimes alter the stability and functions of the rare microbial biosphere remains unknown. We reciprocally transplanted field soils across a latitudinal gradient to simulate climate change and sampled the soils annually after harvesting the maize over the following 6 years (from 2005 to 2011). By sequencing microbial 16S ribosomal RNA gene amplicons, we found that changing climate regimes significantly altered the composition and dynamics of soil microbial communities. A continuous succession of the rare and abundant communities was observed. Rare microbial communities were more stable under changing climatic regimes, with lower variations in temporal dynamics, and higher stability and constancy of diversity. More nitrogen cycling genes were detected in the rare members than in the abundant members, including amoA, napA, nifH, nirK, nirS, norB and nrfA. Random forest analysis and receiver operating characteristics analysis showed that rare taxa may act as potential contributors to maize yield under changing climatics. The study indicates that the taxonomically and functionally diverse rare biosphere has the potential to increase functional redundancy and enhance the ability of soil communities to counteract environmental disturbances. With ongoing global climate change, exploring the succession process and functional changes of rare taxa may be important in elucidating the ecosystem stability and multifunctionality that are mediated by microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Tendencies of Soil Microbial NO Emissions During HI‐SCALE as Predicted by a Nitrification/Denitrification Scheme

Many atmospheric chemical processes, including the formation of secondary organic aerosol (SOA), are strongly modulated by the reactions of NO and NO 2 (NO x ). Though NO x is controlled by anthropogenic emissions near urban areas, in rural areas soil microbes can be a significant contribution to NO emission globally. The relative rates of emissions of different nitrogen-containing species (e.g., NO, N 2 O, HONO, and N 2 ) are strong functions of soil properties such as temperature, moisture content, pH, and soil carbon and nitrogen pools. However, typical large-scale biogeochemical models either express these emissions simplistically, or not at all. Here we investigate the potential impact of soil NO emissions on atmospheric chemistry and SOA formation over regional and monthly time scales, specifically the 2016 spring and summer Intensive Observational Periods (IOPs) of the Holistic Interactions of Shallow Clouds, Aerosols and Land Ecosystems (HI-SCALE) field campaign. We implement the soil NO nitrification/denitrification parameterization of Rasool et al. (2019) into the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem), supplemented by a 1-km soil moisture analysis. We then simulate both IOPs over the U.S. Great Plains, evaluating against ground stations and flight data. We show that soil NO emissions can account for a large fraction of total NO x and locally increase O 3 concentrations by up to 25%, while alleviating negative biases of gases and aerosols toward observations. Soil moisture and temperature changes between IOP1 and IOP2 lead to overall differences in emissions, but with large regional variability due to heterogeneous surface characteristics.

Atmoshpheric Chemistry↗
DOE OSTI2023

Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants

Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13 C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Here, our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Time as a microbial resource

Microbes need resources for energy and cellular building material. They also need access to clement conditions with liquid water and a cellular damage rate that is lower than repair. When deprived of resources and clement conditions, microbes often enter some form of dormancy (e.g., by ceasing cell division, slowing metabolic rate, or forming an endospore) until they can grow again. For example, at night, phototrophs wait for the sun to return. In winter, soil microbes wait for warmer temperatures. Microbes that cause diseases like tuberculosis can stay dormant for years, waiting for the cessation of antibiotic or immune system bombardment. But what about longer timescales? Unlike multicellular life, microbes survive in an extremely broad range of conditions and can access an amazing variety of resources to maintain cellular functions in the absence of cell division. This means that they have the potential to be dormant for much longer than a few months or years. There is no theoretical reason microbes cannot survive on maintenance energy for hundreds or thousands of years, or longer, with little to no cell proliferation. Here, given this lack of theoretical constraints on the length of microbial dormancy intervals, two questions arise, (i) is there evidence for the existence of organisms experiencing very long dormancies? And (ii) what could be the advantages of such long wait times?

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Effects of physical, chemical, and biological ageing on the mineralization of pine wood biochar by a Streptomyces isolate

If biochar is to be used for carbon (C) management, we must understand how weathering or ageing affects biochar C mineralization. Here, we incubated aged and unaged eastern white pine wood biochar produced at 350 and 550°C with a Streptomyces isolate, a putative biochar-decomposing microbe. Ageing was accelerated via three different processes, namely, (a) physical ageing–subjecting biochar to alternating freeze-thaw and wet-dry cycles, (b) chemical ageing–treating biochar with concentrated hydrogen peroxide and (c) biological ageing–incubating biochar in the presence of nutrients and microorganisms. Elemental composition and surface chemistry (Fourier Transform Infrared spectroscopy) of biochar samples were compared before and after ageing. Biochar C mineralization between ageing treatments was significantly different in the case of 350°C biochar ( p value = 0.03). Among the 350°C biochars, physical ageing resulted in the greatest increase (by 103%) in biochar C mineralization ( p value = 0.05). However, in the case of 550°C biochar, ageing did not result in a significant change in biochar C mineralization ( p value = 0.40). Biochar C mineralization was positively correlated with an increase in O/C ratio post-ageing ( r s = 0.86, p value = 0.01). In the case of 350°C biochar, surface oxidation during ageing enhanced biochar degradation by the isolate. For 550°C biochar, however, ageing did not significantly increase biochar C mineralization, likely due to high condensed aromatic C content and lower surface oxidation during ageing. The results from our study suggest that low temperature aged biochar is more susceptible to biological degradation by soil microbes. These findings have implications for the use of biochar for long term C storage in soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Bacterial and fungal composition and exometabolites control the development and persistence of soil water repellency

Soil water repellency (SWR), the reduced affinity of soil for water, is a phenomenon that affects soils globally. With worsening climate change, SWR is expected to increase emphasizing the need to understand the mechanisms driving SWR development and persistence. The importance of the soil microbes in SWR has been postulated for decades, but limited research has been conducted into whole-community interactions and the role of community metabolic activity. To address this gap in knowledge, we investigated the direct effect of microbial community composition, activity, and diversity, as well as their associated metabolites on the development and persistence of SWR by inoculating microcosms containing model soils with 15 different microbial communities and quantified respiration and SWR over time. Six communities that consistently produced either a hydrophobic or hydrophilic phenotype were characterized using metagenomics and metabolomics to determine the impact of microbial and metabolite composition and diversity on SWR. We identified several bacterial genera with significant changes in abundance between SWR phenotypes including Nocardiopsis and Kocuria in hydrophilic and Streptomyces and Cutibacterium in hydrophobic. We discovered that hydrophilic communities were more positively connected when compared to hydrophobic communities, which could be due to an increase in defense mechanism genes. Additionally, we identified specific metabolites associated with hydrophilic and hydrophobic phenotypes including an increase in the osmolyte ectoine in hydrophilic and an increase in plant-derived decomposition products in hydrophobic communities. Finally, our research suggests that fungi, previously thought to cause hydrophobicity, may actually contribute to hydrophilicity through their preferential consumption of hydrophobic compounds.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Uptake of individual and mixed per- and polyfluoroalkyl substances (PFAS) by soybean and their effects on functional genes related to nitrification, denitrification, and nitrogen fixation

Here in this study, we set up a soil-microbe-soybean system spiked with PFOA, PFOS, or a PFAS mixture of eight PFAS and investigated the distribution of PFAS in the system and impacts on the abundance and expression level of genes involved in the nitrogen (N) cycle. When soybean was exposed to the PFAS mixtures, synergistic uptake by shoots was detected. PFAS exhibited remarkable impacts on abundance of nitrification and denitrification genes in both bulk soil and rhizosphere as well as expression of N fixation gene in soybean nodules. The abundance of nitrification genes AOA and AOB amoA and denitrification gene nirK was significantly reduced (p < 0.05) in almost all treatments in bulk soil, except PFOA at 10 μg/kg. The abundance of other functional genes, such as nirS and norZ was affected differently depending on PFAS concentrations and sample location, either bulk soil or the rhizosphere. Interestingly, the N fixation gene nifH in soybean nodules was overexpressed by a PFAS mixture at 100 μg/kg. Hence, this work provided in-depth knowledge regarding the distribution of PFAS and their impacts on the N cycle for the studied system. Results from this study provide insights on assessing risks posed by individual or mixed PFAS to soybean.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Coupling plant litter quantity to a novel metric for litter quality explains C storage changes in a thawing permafrost peatland

Abstract Permafrost thaw is a major potential feedback source to climate change as it can drive the increased release of greenhouse gases carbon dioxide (CO 2 ) and methane (CH 4 ). This carbon release from the decomposition of thawing soil organic material can be mitigated by increased net primary productivity (NPP) caused by warming, increasing atmospheric CO 2 , and plant community transition. However, the net effect on C storage also depends on how these plant community changes alter plant litter quantity, quality, and decomposition rates. Predicting decomposition rates based on litter quality remains challenging, but a promising new way forward is to incorporate measures of the energetic favorability to soil microbes of plant biomass decomposition. We asked how the variation in one such measure, the nominal oxidation state of carbon (NOSC), interacts with changing quantities of plant material inputs to influence the net C balance of a thawing permafrost peatland. We found: (1) Plant productivity (NPP) increased post‐thaw, but instead of contributing to increased standing biomass, it increased plant biomass turnover via increased litter inputs to soil; (2) Plant litter thermodynamic favorability (NOSC) and decomposition rate both increased post‐thaw, despite limited changes in bulk C:N ratios; (3) these increases caused the higher NPP to cycle more rapidly through both plants and soil, contributing to higher CO 2 and CH 4 fluxes from decomposition. Thus, the increased C‐storage expected from higher productivity was limited and the high global warming potential of CH 4 contributed a net positive warming effect. Although post‐thaw peatlands are currently C sinks due to high NPP offsetting high CO 2 release, this status is very sensitive to the plant community's litter input rate and quality. Integration of novel bioavailability metrics based on litter chemistry, including NOSC, into studies of ecosystem dynamics, is needed to improve the understanding of controls on arctic C stocks under continued ecosystem transition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria

Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (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 soil bacteria but also 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 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested 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 growing and characterizing diverse microbial isolates and communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The GREEN ‘omics of Nutrient Feedbacks to Soil Warming

The GREEN ‘omics of Nutrient Feedbacks in Soil project advanced the DOE Biological and Environmental Research (BER) mission by developing and applying isotope-enabled ’omics tools to understand how soil microbes regulate carbon and nutrient cycling. Guided by the Growth Rate, growth Efficiency, and stoichiometry of Essential Nutrients (GREEN ’omics) framework, the project aimed to build a predictive, systems-level understanding of microbial traits that control ecosystem biogeochemistry. In a collaboration among Northern Arizona University (lead), West Virginia University, Lawrence Livermore National Laboratory, and Pacific Northwest National Laboratory, we combined quantitative stable isotope probing (qSIP), Chip-SIP, NanoSIMS, and genome-resolved metagenomics across long-term experiments in Arctic, boreal, temperate, and tropical ecosystems. The project produced three key outcomes: 1) We showed that community-weighted temperature sensitivities of bacterial growth (Q10) can predict ecosystem-scale soil respiration responses across diverse soils. 2) We provided the first in situ evidence for density-dependent population dynamics in soil bacteria and demonstrated that nutrient additions intensify competition, concentrating carbon use into fewer taxa. 3) We improved and extended isotope-enabled ’omics methods by quantifying qSIP measurement error to guide experimental design and coupling SIP with genome-resolved metagenomics to reveal cross-kingdom interactions among bacteria, fungi, and viruses. Together, these results show that a small number of microbial traits and taxa exert disproportionate control over soil carbon and nutrient cycling, providing critical data and methods to improve representation of microbial processes in Earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Life history strategies of soil bacterial communities across global terrestrial biomes

The life history strategies of soil microbes determine their metabolic potential and their response to environmental changes. Yet these strategies remain poorly understood. Here we use shotgun metagenomes from terrestrial biomes to characterize overarching covariations of the genomic traits that capture dominant life history strategies in bacterial communities. The emerging patterns show a triangle of life history strategies shaped by two trait dimensions, supporting previous theoretical and isolate-based studies. The first dimension ranges from streamlined genomes with simple metabolisms to larger genomes and expanded metabolic capacities. As metabolic capacities expand, bacterial communities increasingly differentiate along a second dimension that reflects a trade-off between increasing capacities for environmental responsiveness or for nutrient recycling. Random forest analyses show that soil pH, C:N ratio and precipitation patterns together drive the dominant life history strategy of soil bacterial communities and their biogeographic distribution. Finally, our findings provide a trait-based framework to compare life history strategies of soil bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Warming and disturbance alter soil microbiome diversity and function in a northern forest ecotone

ABSTRACT The response to global change by soil microbes is set to affect important ecosystem processes. These impacts could be most immediate in transitional zones, such as the temperate-boreal forest ecotone, yet previous work in these forests has primarily focused on specific subsets of microbial taxa. Here, we examined how bacterial and fungal communities respond to simulated above- and below-ground warming under realistic field conditions in closed and open canopy treatments in Minnesota, USA. Our results show that warming and canopy disturbance shifted bacterial and fungal community structure as dominant bacterial and fungal groups differed in the direction and intensity of their responses. Ectomycorrhizal and saprotrophic fungal communities with greater connectivity (higher prevalence of strongly interconnected taxa based on pairwise co-occurrence relationships) were more resistant to compositional change. Warming effects on soil enzymes involved in the hydrolytic and oxidative liberation of carbon from plant cell walls and nutrients from organic matter were most strongly linked to fungal community responses, although community structure–function relationships differed between fungal guilds. Collectively, these findings indicate that warming and disturbance will influence the composition and function of microbial communities in the temperate-boreal ecotone, and fungal responses are particularly important to understand for predicting future ecosystem functioning.

Microbiology↗
DOE OSTI2023

Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest

Drought impacts on microbial activity can alter soil carbon fate and lead to the loss of stored carbon to the atmosphere as CO 2 and volatile organic compounds (VOCs). Here we examined drought impacts on carbon allocation by soil microbes in the Biosphere 2 artificial tropical rainforest by tracking 13 C from position-specific 13 C-pyruvate into CO 2 and VOCs in parallel with multi-omics. During drought, efflux of 13 C-enriched acetate, acetone and C 4 H 6 O 2 (diacetyl) increased. These changes represent increased production and buildup of intermediate metabolites driven by decreased carbon cycling efficiency. Simultaneously, 13 C-CO 2 efflux decreased, driven by a decrease in microbial activity. However, the microbial carbon allocation to energy gain relative to biosynthesis was unchanged, signifying maintained energy demand for biosynthesis of VOCs and other drought-stress-induced pathways. Overall, while carbon loss to the atmosphere via CO 2 decreased during drought, carbon loss via efflux of VOCs increased, indicating microbially induced shifts in soil carbon fate.

59 BASIC BIOLOGICAL SCIENCES↗