Search NASA⌕ Search

SEARCH · Search NASA

Results for “microbial scale”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function

ABSTRACT Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Scaling the Microbial Ecology of Soil Carbon (Final Report)

This work developed new techniques and discoveries in quantitative microbial ecology, focusing on soil carbon. The work advanced a new approach to stable isotope probing (SIP), adding a quantitative way to infer taxon-specific rates of growth, mortality, and associated carbon (C) fluxes in soil microbial communities, a framework that the work demonstrated can scale from individual microbial taxa to the integrated soil system. Among the “-omics” techniques in microbial ecology, those based on stable isotope probing (SIP) hold particular promise for addressing the challenge of scaling from molecules to the major biogeochemical element cycles. Because SIP measures directly the fluxes of elements into nucleic acids, it physically connects element flux to genetic information. The work explored new ways to quantify taxon-specific C-use and growth efficiency and tested hypotheses about responses of the soil microbial community to experimental warming and to latitudinal variation in temperature. This work pushed the frontier of –omics enabled techniques by demonstrating their applicability at the ecosystem scale, and by relating taxon-specific isotope assimilation to dissimilatory processes in the C cycle, thereby enabling the identification of organisms especially responsible for soil C loss, in other words, attributing ecosystem-scale element fluxes to individual microbial taxa.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Propagule Pressure in Microbial Introductions

The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the risk-release relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. The dataset filed here includes the experimemtal datafile, and a RMarkdown file that includes all the code used in in both the modeling and anaylsis.

agriculture↗
DOE OSTI2025

Using mid-infrared spectroscopy to estimate soil microbial properties at the continental scale

Understanding microbial community properties is critical to improving the predictions of biogeochemical processes for enhancing soil carbon sequestration. Here, in this observational study, mid-infrared (MIR) spectroscopy and partial least squares regression was used to predict soil microbial and chemical properties from diverse ecosystems across the continental USA. Random calibration and validation demonstrated the prediction potential for soil properties using MIR spectra, with the strongest predictions for microbial respiration, followed by microbial biomass carbon and nitrogen, ß-glucosidase activity, as well as soil chemical properties including organic carbon and total nitrogen. Microbial properties were mainly positively correlated to spectral regions associated with aliphatic C-H groups and C=O stretches of polysaccharides and negatively correlated to quartz and silicate-associated regions. We conclude that MIR spectroscopy can characterize soil microbial functions and be useful for the improvement of continental-scale soil carbon modeling and prediction programs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Biomanufacturing and Scale-Up: Pathways to Biochemicals, Biofuels, and Biomaterials

Advancing the bioeconomy requires the development of large-scale microbial bioprocesses capable of converting waste carbon streams into biofuels, biochemicals, and biomaterials at industrially relevant scales. While biomanufacturing has been successfully demonstrated at the laboratory scale for a wide range of chemicals, only a few have reached industrial-scale production. This is partly due to the inherent complexity of microbial systems, which rely on living cells with intricate metabolic pathways that are highly sensitive to environmental changes, making large-scale production difficult to optimize and predict. As a result, scaling-up bioprocesses remains a high-stakes challenge that requires deeper exploration. This involves integrating feedstock and microbial selection, upstream and downstream processes, and computational modelling, among other research efforts. Bulk and specialty chemicals derived from biological processes also face competition from fossil-based production routes, which have been refined through decades of technological advancements. While biologically derived molecules may offer more environmentally friendly production pathways than traditional chemical manufacturing, their widespread adoption depends on achieving cost parity-or superiority-relative to fossil-based methods. This emphasizes the importance of holistic research, including techno-economic analyses and life cycle assessments, to ensure both economic viability and environmental sustainability. This editorial and special issue explores state-of-the-art strategies for converting waste carbon sources into valuable products. It discusses how enzymes, single microbes (e.g., extremophiles), and microbiomes (e.g., through division of labor) can be integrated with upstream and downstream process innovations-such as consolidated bioprocessing and in situ product recovery-to improve the efficiency and scalability of biomanufacturing. The editorial further highlights the role of computational modelling in understanding, predicting, and controlling bioprocess performance across scales, and concludes by emphasizing the importance of techno-economic modelling to identify technologies that can move to market.

09 BIOMASS FUELS↗
DOE OSTI2026

Enabling microbial electrolysis cell scale-up via electrochemistry-, hydrodynamic-, and microbial ecology-informed framework

Microbial electrolysis cells (MECs) can produce green hydrogen while removing organic contaminants from liquid waste streams by leveraging the metabolic activity of electroactive microorganisms. Despite their potential in a sustainable, circular economy, large-scale MECs that can treat relevant volumes of wastewater have failed to deliver performance proportional to their lab-scale counterparts. The reason behind this lower performance at scale remains unclear. Here, in this study, we developed a combined electrochemistry-, hydrodynamic-, and microbial ecology-informed framework to analyze and optimize MEC performance during scale-up, enabling accurate quantification of major limitations and the identification of strategies to overcome them, ultimately facilitating equivalent performance at scale. Applying this framework to the scale-up of a zero-gap MEC from 9 cm 2 electrode area to 100 cm 2 electrode area, resulted in similar maximum current densities in a 100 cm 2 MEC (21.7 ± 1.1 A/m 2 ) compared to a 9 cm 2 system (25.1 ± 2.7 A/m 2 ), as well as equivalent hydrogen production rates of 69.3 L/L-d (100 cm 2 ) and 67.7 ± 2.4 L/L-d (9 cm 2 ). COMSOL flow dynamics simulations were used to scale up the reactor configuration without negatively affecting electrolyte velocity and distribution in the cell, minimizing the increase in internal resistances during scale-up (11.7 ± 0.5 mΩm 2 at 9 cm 2 ; 19.7 ± 1.3 mΩm 2 at 100 cm 2 ). Microbial community structures were assessed at both scales using high-throughput sequencing, highlighting the differences of populations across electrode dimensions and operational parameters. The framework presented here accelerates the development of effective strategies toward the scale-up of MECs by furthering the understanding of how electrochemical, hydrodynamic, and microbial ecology parameters change as the reactor dimension is increased. Ultimately, this approach contributes to advancing electrochemical biotechnology toward practical deployment in energy-efficient wastewater treatment systems.

Flow path↗
DOE OSTI2024

Translating macroecological models to predict microbial establishment probability in an agricultural inoculant introduction

The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Despite the importance of propagule pressure to species introductions, few tools exist in microbial ecology to predict the outcomes of agricultural microbial introductions. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the risk-release relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. Applying ecological modeling approaches like those presented here to microbial inoculants may aid their sustainable use and provide a monitoring tool for microbial inoculants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Motion Dynamics of Motile Microbes in Pore-Networks and its Implications for Reactive Transport Processes

This report outlines new methods to improve simulations of microbial transport and microbially mediated reactions in porous media. A range of experimental, modeling, and machine learning tools are introduced to make these simulations faster, more reliable, and useful for real-world applications. At the microscopic level, the study investigates how different types of bacteria move through confined spaces. A new artificial intelligence tool called DeepTrackStat, is introduced to track motions dynamics as observed in videos of particles migrating through pore networks. This tool is especially helpful for studying fast-moving microbes and requires less computing power than traditional tracking methods. At larger scales, the research looks at how microbes and chemicals interact in zones where surface water and groundwater meet. To connect the small- and large-scale findings, the study presents a neural network model called STAMNet. This tool helps scale up detailed small-scale microbial motion behaviors to predict large-scale environmental changes more efficiently. By combining lab experiments, computer models, and artificial intelligence, the research presented supports smarter environmental decision-making, especially in bioremediation of contaminated groundwater and protection of water quality.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Pilot microbial electrolysis cell closes the hydrogen loop for hydrothermal wet waste conversion to jet fuel

The global shift toward net-zero emissions necessitates resource recovery from wet waste. In this study, we demonstrate the first feasibility of combining pilot-scale microbial electrolytic cells (MECs) with hydrothermal liquefaction (HTL) for simultaneous post-hydrothermal liquefaction wastewater (PHW) treatment and efficient hydrogen (H₂) production to meet biocrude upgrading requirements. Long-term single reactor operation revealed that fixed anode potential enabled rapid startup, and low catholyte pH and high salinity were effective in suppression of cathodic methanogenesis and acetogenesis – resulting in high current density of 16.6 A m –2 and 9.3 A m –2 when feeding synthetic wastewater and PHW respectively. Additionally, the anode biofilm exhibited spatial variations in response to local environmental conditions. In conclusion, onsite parallel or serial operations of multiple MECs showed good performance using actual PHW with a record-high H 2 production rate of 0.5 L L R day –1 for MEC over 10 liters scale, and the optimal chemical oxygen demand (COD)-to-H 2 yield reached 0.127 kg-H 2 per kg-COD, supporting a self-sufficient, closed-loop upgrade to jet fuel.

08 HYDROGEN↗
DOE OSTI2023

Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites

Secondary metabolites are not essential for the growth of microorganisms, but they play a critical role in how microbes interact with their surroundings. In addition to this important ecological role, secondary metabolites also have a variety of agricultural, medicinal, and industrial uses, and thus the examination of secondary metabolism of plants and microbes is a growing scientific field. While the chemical production of certain secondary metabolites is possible, industrial-scale microbial production is a green and economically attractive alternative. This is even more true, given the advances in bioengineering that allow us to alter the workings of microbes in order to increase their production of compounds of interest. This type of engineering requires detailed knowledge of the “chassis” organism’s metabolism. Since the resources and the catalytic capacity of enzymes in microbes is finite, it is important to examine the tradeoffs between various bioprocesses in an engineered system and alter its working in a manner that minimally perturbs the robustness of the system while allowing for the maximum production of a product of interest. The in silico multi-objective analysis of metabolism using genome-scale models is an ideal method for such examinations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow

Subsurface microbial community distribution patterns are influenced by biogeochemical and groundwater fluxes and may inform hydraulic connections along groundwater-flow paths. This study examined the regional-scale microbial community of the Death Valley Regional Flow System and evaluated whether subsurface communities can be used to identify groundwater-flow paths between recharge and discharge areas. Samples were collected from 36 sites in three groundwater basins: Pahute Mesa–Oasis Valley (PMOV), Ash Meadows (AM), and Alkali Flat–Furnace Creek Ranch (AFFCR). Microbial diversity within and between communities varied by location, and communities were separated into two overall groups that affiliated with the AM and PMOV/AFFCR basins. Network analysis revealed patterns between clusters of common microbes that represented groundwaters with similar geochemical conditions and largely corroborated hydraulic connections between recharge and discharge areas. Null model analyses identified deterministic and stochastic ecological processes contributing to microbial community assemblages. Most communities were more different than expected and governed by dispersal limitation, geochemical differences, or undominating processes. However, certain communities from sites located within or near the Nevada National Security Site were more similar than expected and dominated by homogeneous dispersal or selection. Overall, the (dis)similarities between the microbial communities of DVRFS recharge and discharge areas supported previously documented hydraulic connections between: (1) Spring Mountains and Ash Meadows; (2) Frenchman and Yucca Flat and Amargosa Desert; and (3) Amargosa Desert and Death Valley. However, only a portion of the flow path between Pahute Mesa and Oasis Valley could be supported by microbial community analyses, likely due to well-associated artifacts in samples from the two Oasis Valley sites. This study demonstrates the utility of combining microbial data with hydrologic, geologic, and water-chemistry information to comprehensively characterize groundwater systems, highlighting both strengths and limitations of this approach.

54 ENVIRONMENTAL 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 OSTI2024

Data for Scale-up of Microbial Lipid and Bioethanol Production from Oilcane

Microbial oils are a sustainable biomass-derived substitute for liquid fuels and vegetable oils. Oilcane, an engineered sugarcane with superior feedstock characteristics for biodiesel production, is a promising candidate for bioconversion. This study describes the processing of oilcane stems into juice and hydrothermally pretreated lignocellulosic hydrolysate and their valorization to ethanol and microbial oil using Saccharomyces cerevisiae and engineered Rhodosporidium toruloides strains, respectively. A bioethanol titer of 106 g/L was obtained from S. cerevisiae grown on oilcane juice in a 3 L fermenter, and a lipid titer of 8.8 g/L was obtained from R. toruloides grown on oilcane hydrolysate in a 75 L fermenter. Oil was extracted from the R. toruloides cells using supercritical CO2, and the observed fatty acid profile was consistent with previous studies on this strain. These results demonstrate the feasibility of pilot-scale lipid production from oilcane hydrolysate as part of an integrated bioconversion strategy.

Bioproducts↗
DOE OSTI2023

CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics

Abstract. Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes and that can integrate genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions. The model couples a lattice Boltzmann implementation of Navier–Stokes (flow) and advection–diffusion-reaction (mass conservation) equations. Reaction formulations can include both kinetic rate expressions and flux balance analysis, thereby integrating reactive transport modeling and systems biology. We also show that the use of surrogate models such as neural network representations of in silico cell models can speed up computations significantly, facilitating applications to complex environmental systems. Parallelization enables simulations that resolve heterogeneity at multiple scales, and a cellular automaton module provides additional capabilities to simulate biofilm dynamics. The code thus constitutes a platform suitable for a range of environmental, engineering and – potentially – medical applications, in particular ones that involve the simulation of microbial dynamics.

58 GEOSCIENCES↗
DOE OSTI2024

Quantitative principles of microbial metabolism shared across scales

Metabolism is the complex network of chemical reactions occurring within every cell and organism, maintaining life, mediating ecosystem processes and affecting Earth’s climate. Experiments and models of microbial metabolism often focus on one specific scale, overlooking the connectivity between molecules, cells and ecosystems. Here we highlight quantitative metabolic principles that exhibit commonalities across scales, which we argue could help to achieve an integrated perspective on microbial life. Mass, electron and energy balance provide quantitative constraints on their flow within metabolic networks, organisms and ecosystems, shaping how each responds to its environment. The mechanisms underlying these flows, such as enzyme–substrate interactions, often involve encounter and handling stages that are represented by equations similar to those for cells and resources, or predators and prey. Here we propose that these formal similarities reflect shared principles and discuss how their investigation through experiments and models may contribute to a common language for studying microbial metabolism across scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Scaling-up up-flow microbial electrolysis cells with a compact electrode configuration for continuous hydrogen production

Maintaining high current densities is a key challenge in scaling-up microbial electrolysis cell (MEC) reactors. In this study, a novel 10 L MEC reactor with a total electrode surface area > 1 m 2 was designed and evaluated to maximize the current density and H 2 recovery. Performances of the reactor suggest that the longitudinal structure with parallel vertical orientation of the electrodes encouraged high fluid mixing and the sheet metal electrode frames provided distributed electrical connection. Results also demonstrated that the electrode pairs located next to reactor walls decreased current density, as did separating the electrodes with separators. High volumetric H 2 production rate of 5.9 L/L/d was achieved at a volumetric current density of 970 A/m 3 (34 A/m 2 ). Furthermore, the observed current densities of the large reactor were accurately predicted based on the internal resistance analysis of small scale MECs (0.15 L), demonstrating the scalability of the single chamber MEC design.

08 HYDROGEN↗
DOE OSTI2022

Effects of Microbial-Mineral Interactions on Organic Carbon Stabilization in a Ponderosa Pine Root Zone: A Micro-Scale Approach

Soil microbial communities affect the formation of micro-scale mineral-associated organic matter (MAOM) where complex processes, including adhesion, aggregate formation, microbial mineral weathering and soil organic matter stabilization occur in a narrow zone of large biogeochemical gradients. Here we designed a field study to examine carbon stabilization mechanisms by using in-growth mesh bags containing biotite that were placed in a ponderosa pine root zone for 6 months and compared to the surrounding bulk soil. We sought to determine the composition of the microbial community in the mesh bags compared to the surrounding soils, analyze the direct interactions between microbes and biotite, and finally identify the nature of the newly formed MAOM within the mesh-bags. Our results revealed that minerals in the mesh bags were colonized by a microbial community that produced organic matter in situ. The 16S rRNA gene sequencing and ITS2 region characterization showed phylogenetic similarity between the mesh bag and bulk soil archaea/bacteria and fungi microbiomes, with significant differences in alpha- and beta-diversity and species abundances. Organic matter pools in the mesh bags, analyzed by Fourier transform ion cyclotron resonance mass spectrometry, contained protein- (peptides) and lipid-like compounds while the bulk soil OM was comprised of lignin-like and carboxyl-rich alicyclic molecules. These results support that the newly formed biotite associated organic compounds have a microbial signature in the mesh bags. High-resolution electron microscopy documented strongly adhered organic compounds to biotite surfaces, formation of microaggregates, elemental uptake at the microbe (organic matter)-mineral interface, and distortion of biotite layers. Overall, this study shows the direct and indirect involvement of soil microbial communities from the root zone of ponderosa pine in the formation of MAOM, soil organic carbon stabilization, microaggregation, and mineral weathering at micro- and nano-scales.

58 GEOSCIENCES↗