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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

CarbStor: Development, Analysis and Modification of Carbon Storing Model Soil Communities

Soil microbial communities carry out a number of key processes including plant growth promotion, bioremediation and cycling of nutrients. Carbon cycling is among the most important of these nutrients that are metabolized and processed by the soil microbial community. Many of the carbon inputs are converted to alternative organic forms of carbon that can be used by plants or act as biomass for microbial growth. However, inorganic forms of carbon can also be produced by soil microbial communities including calcium carbonate (CaCO 3 ). Production of calcium carbonate is beneficial for the ecosystem in several ways: it can stabilize soils and improve soil health, especially denser soils with high clay content, it can act as a method of bioremediation, it can serve as an alternative carbon source for plants and it can be a way to store carbon in soil in a stable, inorganic manner for the long term. While the chemistry surrounding individual species carrying out this process is well known what is lacking is an understanding of how species interact in a community to drive carbonate production. As all microbial species in soil exist in a community setting gaining this knowledge is critical to our predicting and controlling this microbial phenotype to greatly improve soil health. The CarbStor project is focused on developing, analyzing and modifying defined microbial soil consortia that express phenotypes at both the species and community level to convert carbon into recalcitrant stable sources such as precipitated carbonate or microbial necromass. To take full advantage of the soil community for this process we will need to fill several key knowledge gaps (KG), three of which are the focus of CarbStor. KG1: Whether and to what degree microbial communities can be developed that produce precipitated carbon via microbial metabolism. KG2: What interspecies interactions drive the individual member phenotypes in defined communities that lead to carbon precipitation. KG3: How can these interactions be modified to enhance carbon sequestration beyond what native communities are capable of. We hypothesize that in a carbon sequestering community only a subset of species will express phenotypes related to carbon storage processes. We also hypothesize that these phenotypes are expressed as a result of interactions with other species in the community that are not involved in carbon storage processes and that these interactions can be harnessed to enhance community carbon sequestration.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs

The factors that influence biodiversity and productivity of hydrothermal ecosystems are not well understood. Here we investigate the relationship between fluid mixing, biodiversity, and chemosynthetic primary productivity in three co-localized hot springs (RSW, RSN, and RSE) in Yellowstone National Park that have different geochemistry. All three springs are sourced by reduced hydrothermal fluid, but RSE and RSN receive input of vapour phase gas and oxidized groundwaters, with input of both being substantially higher in RSN. Metagenomic sequencing revealed that communities in RSN were more biodiverse than those of RSE and RSW in all dimensions evaluated. Microcosm activity assays indicate that rates of dissolved inorganic carbon (DIC) uptake were also higher in RSN than in RSE and RSW. Together, these results suggest that increased mixing of reduced volcanic fluid with oxidized fluids generates additional niche space capable of supporting increasingly biodiverse communities that are more productive. These results provide insight into the factors that generate and maintain chemosynthetic biodiversity in hydrothermal systems and that influence the distribution, abundance, and diversity of microbial life in communities supported by chemosynthesis. These factors may also extend to other ecosystems not supported by photosynthesis, including the vast subterranean biosphere and biospheres beneath ice sheets and glaciers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

AquaMEND: Reconciling multiple impacts of salinization on soil carbon biogeochemistry

Soil salinization, exacerbated by climate change, poses a global threat to coastal ecosystem function and soil quality. Salinity influences carbon cycling through direct effects on microbial activity and indirect alterations to soil physicochemical properties including cation exchange, pH, and soil organic carbon availability. Current models inadequately represent these complexities, relying on linear reduction functions that overlook specific physicochemical changes induced by salinity. To address this gap, we propose an integrated model framework, AquaMEND, that combines microbial-explicit carbon decomposition and geochemical models. This model allows cation exchange and surface complexation processes to capture solute chemistry and nutrient availability in soils upon saltwater intrusion. Using response functions that capture salinity impacts on both salt-sensitive and salt-resistant microbial processes, AquaMEND simulates how the abiotic and biotic mechanisms work individually and collectively to regulate organic and inorganic pools and fluxes. Here, the parallel structure of aqueous and non-aqueous phases, together with microbial functions, result in a versatile model for solving dynamic coupling of organics, minerals and microbes under various environmental settings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing

Phage λ, a well-characterized temperate phage, has been recently leveraged for bacterial genome editing by selectively delivering base editors into targeted bacterial species. We extend this concept by engineering phage λ to deliver CRISPR-guided transposases, accomplishing large insertions and targeted gene disruptions. To achieve this, we engineered phage λ using homologous recombination paired with Cas13a-based counterselection for precise phage modifications. Initially, we established the utility of Cas13a in phage λ by conducting minimal recoding edits, deletions, and insertions. Subsequently, we scaled up the engineering to embed the comprehensive DNA-editing CRISPR-Cas transposase (DART) system within the phage genome, creating λ-DART phages. These modified λ-DART phages were then employed to infectEscherichia coli, generating CRISPR RNA-guided transposition events in the host genome. Applying our engineered λ-DART phages to monocultures and a mixed bacterial community comprising three genera led to efficient, precise, and specific gene knockouts and insertions in the targetedE. colicells, achieving editing efficiencies surpassing 50% of the population. This research enhances phage-mediated genome editing by enabling efficient in situ gene integrations in bacteria, offering an avenue for further application in microbial community contexts. This scalable method enables flexible microbial genome editing in situ to manipulate the function and composition of diverse ecosystems.

Science & Technology - Other Topics↗
DOE OSTI2023

Mixotrophic microbes create carbon tipping points under warming

Mixotrophs are ubiquitous and integral to microbial food webs, but their impacts on the dynamics and functioning of broader ecosystems are largely unresolved. Here, we show that mixotrophy produces a unique type of food web module that exhibits unusual ecological dynamics, with surprising consequences for carbon flux under warming. We develop a generalizable model of a mixotrophic food web module that incorporates dynamic switching between phototrophy and phagotrophy to assess ecological dynamics and total system CO 2 flux. We find that warming switches mixotrophic systems between alternative stable carbon states—including a phototrophy-dominant carbon sink state, a phagotrophy-dominant carbon source state and cycling between these two. Moreover, warming always shifts this mixotrophic system from a carbon sink state to a carbon source state, but a coordinated increase in nutrients can erase early warning signals of this transition and expand hysteresis. This suggests that mixotrophs can generate critical carbon tipping points under warming that will be more abrupt and less reversible when combined with increased nutrient levels, having widespread implications for ecosystem functioning in the face of rapid global change.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2005

BIOGEOCHEMICAL STUDIES OF PHOTOSYNTHETIC MICROBIAL MATS AND THEIR BIOTA

Photosynthetic microbial mats offer an opportunity to define holistic functionality at the millimeter scale. At the same time. their biogeochemistry contributes to environmental processes on a planetary scale. These mats are possibly direct descendents of the most ancient biological communities; communities in which oxygenic photosynthesis might have been invented. Mats provide one of the best natural systems to study how microbial populations associate to control dynamic biogeochemical gradients. These are self- sustaining, complete ecosystems in which light energy absorbed over a dial (24 hour) cycle drives the synthesis of spatially-organized, diverse biomass. Tightly-coupled microorganisms in the mat have specialized metabolisms that catalyze transformations of carbon, nitrogen, sulfur, and a host of other elements.

DesMarais, David↗
DOE OSTI2026

Heterotrophic respiration by soil microbes in a changing climate

Soil microbes strongly influence the soil organic carbon (SOC) pool, which globally stores ~2,000 PgC. Specifically, the balance between microbial heterotrophic respiration (R H ), which degrades SOC, and plant–microbe interactions that stabilize SOC determines whether terrestrial ecosystems are a net source or sink of CO 2 to the atmosphere. Here, in this Review, we evaluate how climate change alters these competing processes. R H is approximately half of total soil respiration, at ~50 PgC yr −1 , with 70% occurring in topsoils. Warming accelerates microbial metabolism, with a 10 °C temperature increase estimated to raise R H by ~50%, an effect that is particularly strong in Arctic soils. Warming also reduces soil moisture, further modulating R H , which responds nonlinearly to soil moisture, being limited by saturation and desiccation and meeting a maximum at intermediate levels. Consequently, R H is highly sensitive to future precipitation changes and drought. However, soil management strategies could enhance SOC stocks and persistence under climate change. Bacterial and fungal inoculants can promote SOC production and stabilization, while deep-rooting plants increase SOC inputs to deeper layers that experience lower R H . Agricultural practices and biochar amendments can also enhance SOC and reduce R H . Expanding field trials across regions, climates and soil types would improve empirical understanding of these responses and support better representation of R H in predictive models, enabling more accurate assessments of climate impacts on SOC storage.

Jansson, Janet K. [Pacific Northwest National Labo↗
DOE OSTI2022

Effects of fine-root senescence upon soil communities and nutrient flux into soil pools (Final Report)

Fine roots represent an important flux of carbon into terrestrial soils. Much of this flux occurs through the exudation of polysaccharides and other carbon compounds during the lifetime of fine-roots, but little is known about their contributions to flux as roots senesce, die and decompose. This project was designed 1) to test approaches for inducing senescence in fine roots and 2) assess the effects of the treatments on fine roots and the associated rhizosphere community. We implemented two fine-root treatments, a steam girdling approach and full severing of fine root modules from the tree, and we contrasted them with a control where roots were handled but not girdled. Fine roots and their associated community subjected to each of these three treatments were subsequently analyzed for changes in physical structure, nutrient content, community structure and gene function. Both girdling manipulations resulted in tissue disruption in fine roots and changes in the soil community relative to controls. In particular, microbial diversity for most taxa declined in girdled treatments whereas fungal diversity increased. We also observed changes in overall plant and fungal gene expression associated with treatment with plant gene expression declining over time in girdled roots with a simultaneous increase in fungal gene expression in these same treatments. Finally, in girdled fine root modules, we observed changes in gene function associated with senescence and plant stress in pine-associated genes while at the same time observing upregulation of genes associated with growth and proliferation in fungi. In conclusion, we were able to successfully girdle fine-roots in a field setting and resolve plant-level and community level changes in response to these girdling treatments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Long-Term Persistence of Three Microbial Wildfire Biomarkers in Forest Soils

Long-term monitoring of microbial communities in the rhizosphere of post-fire forests is currently one of the key knowledge gaps. Knowing the time scale of the effects is indispensable to aiding post-fire recovery in vulnerable woodlands, including holm oak forests, that are subjected to a Mediterranean climate, as is the case with forests that are found in protected areas such as the Sierra Nevada National and Natural Park in southeastern Spain. We took rhizosphere soil samples from burned and unburned holm oak trees approximately 3, 6, and 9 years after the 2005 fire that devastated almost 3500 ha in southeastern Spain. We observed that the prokaryotic communities are recovering but have not yet reached the conditions observed in the unburned forest. A common denominator between this fire and other fires is the long-term persistence of three ecosystem recovery biomarkers—specifically, higher proportions of the genera Arthrobacter, Blastococcus, and Massilia in soil microbial communities after a forest fire. These pyrophilous microbes possess remarkable resilience against adverse conditions, exhibiting traits such as xerotolerance, nitrogen mineralization, degradation of aromatic compounds, and copiotrophy in favorable conditions. Furthermore, these biomarkers thrive in alkaline environments, which persist over the long term following forest fires. The relative abundance of these biomarkers showed a decreasing trend over time, but they were still far from the values of the control condition. In conclusion, a decade does not seem to be enough for the complete recovery of the prokaryotic communities in this Mediterranean ecosystem.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Metagenome-assembled genomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021)

The pathways of carbon transport and loss through and from soils—soil organic matter (SOM) depolymerization to dissolved organic carbon and mineralization to carbon dioxide (CO2)—are fundamentally driven by microbial activity, which is strongly regulated by environmental conditions. As part of LBNL (Lawrence Berkeley National Laboratory) TES (Terrestrial Ecosystem Science) Belowground Biogeochemistry Science Focus Area (SFA), we have established a novel whole-soil long-term warming experiment at the University of California (UC) Blodgett Forest Research Station (Sierra Nevada) in 2014, where we study the role of biogeochemical, microbial and geochemical process interactions in SOM decomposition and stabilization.Here, we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from soil depth profiles collected from 2014 to 2021 from three paired control and warming plots. We collected soil samples across a range of depth profiles (spanning surface to 90 cm deep) from three paired control and warming plots from a temperate mixed forest in Northern California. Each paired plot had been subjected to experimental warming since June 2014 to simulate a predicted climate change scenario for northern California. 101 soil metagenomes were sequenced at JGI (Joint Genome Institute) and UCSF (University of California San Francisco) Center for Advanced Technology and can be found under the JGI (Joint Genome Institute) GOLD (Genomes Online Database) Sequencing project Gs0151586 and NCBI (National Center for Biotechnology Information) Projects PRJNA1225762 and PRJEB39497. Metagenomes were assembled using JGI (Joint Genome Institute) Metagenome Workflow (10.1128/mSystems.00804-20). For each metagenome, the assembled contigs were binned into genomes using 3 binning algorithms (cocacola, metabat, and maxbin) and the resulting bins were consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>50%) and contamination (<25%), and dereplicated at 99% ANI (average nucleotide identity) using dRep (https://github.com/MrOlm/drep).The dataset includes a zip file of 2321 MAG (Metagenome Assembled Genome) fasta files, the accession numbers for the underlying metagenomes, and a csv file with MAG (Metagenome Assembled Genome) quality metrics and taxonomic classification (GTDB -Genome Taxonomy Database-RS220). This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type. A sample metadata file (samples.csv) that contains site information has also been included.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Optimizing Cryo-Focused Pyrolysis GC/MS for Tracing Soil Organic Matter Across Diverse Ecosystems

The cycling of organic matter in terrestrial soils and sediments is central to a range of biogeochemical processes that regulate nutrient cycling, crop productivity, trace gas emissions, and contaminant transport. Pyrolysis-gas chromatography/mass spectrometry (py-GC/MS) is a powerful tool for characterizing bulk soil organic matter (SOM) at the molecular level. In this study, we used a cryo-focused py-GC/MS system to analyze soil samples from seven diverse ecosystems: vernal pool, prairie pothole, temperate forest, tropical forest, tundra, wildfire-affected boreal forest, and grassland. We addressed a key bottleneck in molecular-level SOM characterization by developing an automated data analysis pipeline to optimize py-GC/MS and complementary evolved gas analysis/mass spectrometry (EGA/MS) methods, incorporating advanced tools for peak deconvolution, developing a custom compound class library, and implementing fragmentation spectrum-based molecular networking for the first time. This improved workflow was applied to soil samples from all seven ecosystems, including multiple depths and density fractions. Our findings demonstrate that ecosystem type plays a dominant role in shaping compositional differences in SOM. We also identified trends in the source of SOM compounds (e.g., microbial vs plantderived) across soil depth and density fractions, which are critical for understanding persistence and turnover of SOM. Our molecular networking analysis indicated that although many compounds are widespread across ecosystems, others are restricted to specific environments, such as wetlands. This underscores the utility of molecular-level data in elucidating the complexity of SOM composition and the environmental drivers that shape it. Such molecular-level insights can deepen our knowledge of biogeochemical SOM cycles.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1984

Mechanisms of nitrogen retention in forest ecosystems - A field experiment

Intensive forest management led to elevated losses of nitrogen from a recently harvested loblolly pine plantation in North Carolina. Measurements of nitrogen-15 retention in the field demonstrated that microbial uptake of nitrogen during the decomposition of residual organic material was the most important process retaining nitrogen. Management practices that remove this material cause increased losses of nitrogen to aquatic ecosystems and the atmosphere.

Vitousek, P. M.↗
NASA NTRS1994

Subsurface Intertidal Microbes: A Cryptic Source Of Organic Carbon For Beach Ecosystems

Some freshwater, marine or hotspring beaches have no visible source of primary production, yet beneath the surface is an interstitial photosynthetic microbial community. To assess the significance of this source of organic carbon, we measured in situ carbon fixation rates in an intertidal marine beach through a diurnal cycle. Gross fixation for a transect (99 x 1 m) perpendicular to the shore was approx. 4041 mg C fixed/ day, or approx. 41 mg C fixed/ sq m day. In contrast, an adjacent well-established cyanobacterial (Lyngbya) mat was approx. 12 x as productive (approx. 490 mg C fixed/sq m day). Thus, subsurface sand mats may be an overlooked, yet important, endogenous source of organic carbon for intertidal ecosystems, as well as a sink in the global carbon cycle.

Rothschild, Lynn J.↗
DOE OSTI2020

Investigating drivers of microbial activity and respiration in a forested bog

Northern peatlands store nearly one-third of terrestrial carbon (C) stocks while covering only 3% of the global landmass; nevertheless, the drivers of C cycling in these often-waterlogged ecosystems are different from those that control C dynamics in upland forested soils. To explore how multiple abiotic and biotic characteristics of bogs interact to shape microbial activity in a northern, forested bog, we added a labile C tracer ( 13 C-labeled starch) to in situ peat mesocosms and correlated heterotrophic respiration with natural variation in several microbial predictor variables, such as enzyme activity and microbial biomass, as well as with a suite of abiotic variables and proximity to vascular plants aboveground. We found that peat moisture content was positively correlated with respiration and microbial activity, even when moisture levels exceeded total saturation, suggesting that access to organic matter substrates in drier environments may be limiting for microbial activity. Proximity to black spruce trees decreased total and labile heterotrophic respiration. This negative relationship may reflect the influence of tree evapotranspiration and peat shading effects; i.e., microbial activity may decline as peat dries and cools near trees. Here, we isolated the response of heterotrophic respiration to explore the variation in, and interactions among, multiple abiotic and biotic drivers that influence microbial activity. This approach allowed us to reveal the relative influence of individual drivers on C respiration in these globally important C sinks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Rooting for function: community‐level fine‐root traits relate to many ecosystem functions

Humans are driving biodiversity change, which also alters community functional traits. However, how changes in the functional traits of the community alter ecosystem functions—especially belowground—remains an important gap in our understanding of the consequences of biodiversity change. We test hypotheses for how the root traits of the root economics space (composed of the collaboration and conservation gradients) are associated with proxies for ecosystem functioning across grassland and forest ecosystems in both observational and experimental datasets from 810 plant communities. First, we assessed whether community-weighted means of the root economics space traits adhered to the same trade-offs as species-level root traits. Then, we examined the relationships between community-weighted mean root traits and aboveground biomass production, root standing biomass, soil fauna biomass, soil microbial biomass, decomposition of standard and plot-specific material, ammonification, nitrification, phosphatase activity, and drought resistance. We found evidence for a community collaboration gradient but not for a community conservation gradient. Yet, links between community root traits and ecosystem functions were more common than we expected, especially for aboveground biomass, microbial biomass, and decomposition. These findings suggest that changes in species composition, which alter root trait means, will in turn affect critical ecosystem functions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Disturbance triggers non-linear microbe–environment feedbacks

Abstract. Conceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting–drying transitions. Our refined framework includes relationships between cumulative properties of a microbial community (e.g., microbial membership, community assembly properties, and biogeochemical rates), environmental features (e.g., organic matter thermodynamics), and emergent ecosystem function. Our primary aim was to evaluate the hypothesized relationships that comprise the conceptual framework and contrast outcomes from the whole and putatively active bacterial and archaeal communities. Throughout the system we found threshold-like responses to the duration of desiccation. Membership of the putatively active community – but not the whole bacterial and archaeal community – responded due to enhanced deterministic selection (an emergent community property). Concurrently, the thermodynamic properties of organic matter (OM) became less favorable for oxidation (an environmental component), and respiration decreased (a microbial process). While these responses were step functions of desiccation, we found that in deterministically assembled active communities, respiration was lower and thermodynamic properties of OM were less favorable. Placing the results in context of our conceptual framework points to previously unrecognized internal feedbacks that are initiated by disturbance and mediated by thermodynamics and that cause the impacts of disturbance to be dependent on the history of disturbance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Microbial processing of plant remains is co-limited by multiple nutrients in global grasslands

Microbial processing of aggregate-unprotected organic matter inputs is key for soil fertility, long-term ecosystem carbon and nutrient sequestration and sustainable agriculture. In this work, we investigated the effects of adding multiple nutrients (nitrogen, phosphorus and potassium plus nine essential macro- and micro-nutrients) on decomposition and biochemical transformation of standard plant materials buried in 21 grasslands from four continents. Addition of multiple nutrients weakly but consistently increased decomposition and biochemical transformation of plant remains during the peak-season, concurrent with changes in microbial exoenzymatic activity. Higher mean annual precipitation and lower mean annual temperature were the main climatic drivers of higher decomposition rates, while biochemical transformation of plant remains was negatively related to temperature of the wettest quarter. Nutrients enhanced decomposition most at cool, high rainfall sites, indicating that in a warmer and drier future fertilized grassland soils will have an even more limited potential for microbial processing of plant remains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions

The dynamic structures of microbial communities emerge from the complex network of interactions between their constituent microorganisms. Quantitative measurements of these interactions are important for understanding and engineering ecosystem structure. Here, we present the development and application of the BioMe plate, a redesigned microplate device in which pairs of wells are separated by porous membranes. BioMe facilitates the measurement of dynamic microbial interactions and integrates easily with standard laboratory equipment. We first applied BioMe to recapitulate recently characterized, natural symbiotic interactions between bacteria isolated from the Drosophila melanogaster gut microbiome. Specifically, the BioMe plate allowed us to observe the benefit provided by two Lactobacillus strains to an Acetobacter strain. We next explored the use of BioMe to gain quantitative insight into the engineered obligate syntrophic interaction between a pair of Escherichia coli amino acid auxotrophs. We integrated experimental observations with a mechanistic computational model to quantify key parameters associated with this syntrophic interaction, including metabolite secretion and diffusion rates. This model also allowed us to explain the slow growth observed for auxotrophs growing in adjacent wells by demonstrating that, under the relevant range of parameters, local exchange between auxotrophs is essential for efficient growth. The BioMe plate provides a scalable and flexible approach for the study of dynamic microbial interactions.

3D printed device↗