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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Endophyte mediated Populus trichocarpa water use efficiency is dependent on time of day and plant water status

Endophytes are potential partners for improving the resource use efficiency of bioenergy feedstock systems such as short rotation coppiced Populus. Endophytes isolated from members of the Salicaceae family have broad host compatibility and can improve water use efficiency (WUE) through decreases in stomatal conductance. However, the literature is inconsistent with regards to the environmental conditions and temporal patterns of these benefits. This study investigates how endophyte mediated changes in Populus trichocarpa (Torr. and Gray) ‘Nisqually-1’ stomatal conductance and WUE shift with time and scale in response to water-deficit stress. Leaf gas exchange and above-ground productivity were used to evaluate the carbon and water balances of glasshouse grown plants in response to endophyte inoculation and water-deficit. Differences in stomatal conductance between control and inoculated plants were more pronounced (39.7 % decrease, Welch’s two-sample t(14.34 dfadj) = -2.358, p-value = 0.033) under water-deficit conditions in the late morning during a period of higher light intensity. The decrease in stomatal conductance accompanied a substantial increase in intrinsic WUE (iWUE) for water-deficit inoculated plants. However, increases in iWUE did not result in improvements in aboveground productivity or shoot biomass WUE (WUEsb) for water-deficit inoculated plants. This decoupling between iWUE and aboveground productivity may be an indicator of assimilate allocation to microbial metabolism as an additional carbon sink or a shift in carbon allocation towards belowground biomass. Future work should take a whole-plant approach that accounts for diurnal patterns in incident irradiance to evaluate the impact of endophyte inoculation on host WUE and stress tolerance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A synthetic co-culture for bioproduction of ammonia from methane and air

Abstract Fixed nitrogen fertilizers feed 50% of the global population, but most fixed nitrogen production occurs using energy-intensive Haber–Bosch-based chemistry combining nitrogen (N2) from air with gaseous hydrogen (H2) from methane (CH4) at high temperatures and pressures in large-scale facilities sensitive to supply chain disruptions. This work demonstrates the biological transformation of atmospheric N2 into ammonia (NH3) using CH4 as the sole carbon and energy source in a single vessel at ambient pressure and temperature, representing a biological “room-pressure and room-temperature” route to NH3 that could ultimately be developed to support compact, remote, NH3 production facilities amenable to distributed biomanufacturing. The synthetic microbial co-culture of engineered methanotroph Methylomicrobium buryatense (now Methylotuvimicrobium buryatense) and diazotroph Azotobacter vinelandii converted three CH4 molecules to l-lactate (C3H6O3) and powered gaseous N2 conversion to NH3. The design used division of labor and mutualistic metabolism strategies to address the oxygen sensitivity of nitrogenase and maximize CH4 oxidation efficiency. Media pH and salinity were central variables supporting co-cultivation. Carbon concentration heavily influenced NH3 production. Smaller-scale NH3 production near dispersed, abundant, and renewable CH4 sources could reduce disruption risks and capitalize on untapped energy resources. One-Sentence Summary Co-culture of engineered microorganisms Methylomicrobium buryatense and Azotobacter vinelandii facilitated the use of methane gas as a sole carbon feedstock to produce ammonia in an ambient temperature, atmospheric pressure, single-vessel system.

Biotechnology & Applied Microbiology↗
DOE OSTI2024

Convergence in simulating global soil organic carbon by structurally different models after data assimilation

Abstract Current biogeochemical models produce carbon–climate feedback projections with large uncertainties, often attributed to their structural differences when simulating soil organic carbon (SOC) dynamics worldwide. However, choices of model parameter values that quantify the strength and represent properties of different soil carbon cycle processes could also contribute to model simulation uncertainties. Here, we demonstrate the critical role of using common observational data in reducing model uncertainty in estimates of global SOC storage. Two structurally different models featuring distinctive carbon pools, decomposition kinetics, and carbon transfer pathways simulate opposite global SOC distributions with their customary parameter values yet converge to similar results after being informed by the same global SOC database using a data assimilation approach. The converged spatial SOC simulations result from similar simulations in key model components such as carbon transfer efficiency, baseline decomposition rate, and environmental effects on carbon fluxes by these two models after data assimilation. Moreover, data assimilation results suggest equally effective simulations of SOC using models following either first‐order or Michaelis–Menten kinetics at the global scale. Nevertheless, a wider range of data with high‐quality control and assurance are needed to further constrain SOC dynamics simulations and reduce unconstrained parameters. New sets of data, such as microbial genomics‐function relationships, may also suggest novel structures to account for in future model development. Overall, our results highlight the importance of observational data in informing model development and constraining model predictions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Stable and high voltage and power output of CEA-MFCs internally connected in series (iCiS-MFC)

The voltage output of a single MFC is normally less than 0.8 V, often less than 0.3 V at maximum power output, which greatly limits the application of MFCs. When MFCs are scaled up, however, increasing reactor size has typically resulted in decreased power density. In this study, we developed a novel MFC configuration that contains multiple cloth electrode assemblies in which the MFCs were internally connected in series (iCiS-MFC). The iCiS-MFC, equivalent to 3 CEA-MFCs, produced a high voltage output over 1.8 V and a maximum power density of 3.5 W m -2 using carbon cloth cathodes containing activated carbon as the catalyst. This power density is 6% higher than that reported for a similar smaller CEA-MFC, indicating that power can be maintained during scale-up with a greater than 33-fold increase in total cathode surface area and greater than 20-fold increase in reactor volume. High stability was also demonstrated based on the performance of the iCiS-MFC over a period of one year of operation. The high power and stability is likely due, in part, to a more efficient means of current collection through the internal series connection, which also avoids the use of expensive current collectors. These results clearly demonstrate the great potential of this MFC design for further scaling-up.

25 ENERGY STORAGE↗
DOE OSTI2026

Biohydrogen Generation from Un-Pretreated Spent Coffee Grounds with Clostridium Thermocellum

Coffee is among the world's most widely consumed beverages, generating 18 million wet tonnes of waste spent coffee grounds annually. Disposal of SCGs is complicated by their high moisture content, their recalcitrant chemical composition, and the presence of caffeine and other bioactive compounds. Dark fermentation is a promising technology for conversion of waste cellulosic biomass into renewable hydrogen, carbon dioxide, and volatile fatty acids. Typical SCGs have high moisture content, are pre-milled to fine particle sizes, and contain 8%-19% cellulose and up to 40% hemicellulose, making them an attractive feedstock for dark fermentation. In this study, we investigate biohydrogen production from unpretreated SCGs using Clostridium thermocellum strain KJC19-9, a cellulolytic bacterium engineered to co-utilize xylose, specifically examining the inhibitory effects of residual caffeine and high solids loadings on microbial growth and hydrogen production efficiency. While SCGs were initially resistant to both cell growth and biohydrogen production, a strategy to co-ferment with low concentrations of cellobiose dramatically enhanced process performance, reducing lag phase duration and enabling cellulosome production for efficient cellulose hydrolysis. This co-substrate approach generated up to 944 mL hydrogen per L reaction from 50 g/L of spent coffee grounds over 120 h (1.34 mol H2/mol carbohydrate), validating SCGs as a promising dark fermentation feedstock and underscoring the value of mixed substrate approaches in consolidated bioprocessing.

08 HYDROGEN↗
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗
DOE OSTI2023

Diversifying and perennializing plants in agroecosystems alters retention of new C and N from crop residues

Abstract Managing soils to retain new plant inputs is key to moving toward a sustainable and regenerative agriculture. Management practices, like diversifying and perennializing agroecosystems, may affect the decomposer organisms that regulate how new residue is converted to persistent soil organic matter. Here we tested whether 12 years of diversifying/perennializing plants in agroecosystems through extended rotations or grassland restoration would decrease losses of new plant residue inputs and, thus, increase retention of carbon (C) and nitrogen (N) in soil. We tracked dual‐labeled ( 13 C and 15 N), isotopically enriched wheat ( Triticum aestivum ) residue in situ for 2 years as it decomposed in three agroecosystems: maize–soybean (CS) rotation, maize–soybean–wheat plus red clover and cereal rye cover crops (CSW2), and spring fallow management with regeneration of natural grassland species (seven to 10 species; SF). We measured losses of wheat residue (C wheat and N wheat ) in leached soil solution and greenhouse gas fluxes, as well as how much was recovered in microbial biomass and bulk soil at 5‐cm increments down to 20 cm. CSW2 and SF both had unique, significant effects on residue decomposition and retention dynamics that were clear only when using nuanced metrics that able to tease apart subtle differences. For example, SF retained a greater portion of C wheat in 0–5 cm surface soils (155%, p = 0.035) and narrowed the C wheat to N wheat ratio ( p < 0.030) compared to CS. CSW2 increased an index of carbon‐retention efficiency, C wheat retained in the mesocosm divided by total measured, from 0.18 to 0.27 (49%, p = 0.001), compared to CS. Overall, we found that diversifying and extending the duration of living plants in agroecosystems can lead to greater retention of new residue inputs in subtle ways that require further investigation to fully understand.

McDaniel, Marshall D.↗
DOE OSTI2024

Integration of genome-scale metabolic model with biorefinery process model reveals market-competitive carbon-negative sustainable aviation fuel utilizing microbial cell mass lipids and biogenic CO 2

Producing scalable, economically viable, low-carbon biofuels or biochemicals hinges on more efficient bioconversion processes. While microbial conversion can offer robust solutions, the native microbial growth process often redirects a large fraction of carbon to CO 2 and cell mass. By integrating genome-scale metabolic models with techno-economic and life cycle assessment models, this study analyzes the effects of converting cell mass lipids to hydrocarbon fuels, and CO 2 to methanol on the facility’s costs and life-cycle carbon footprint. Results show that upgrading microbial lipids or both microbial lipids and CO 2 using renewable hydrogen produces carbon-negative bisabolene. Additionally, on-site electrolytic hydrogen production offers a supply of pure oxygen to use in place of air for bioconversion and fuel combustion in the boiler. To reach cost parity with conventional jet fuel, renewable hydrogen needs to be produced at less than $\$2.2$ to $\$3.1$/kg, with a bisabolene yield of 80% of the theoretical yield, along with cell mass and CO 2 yields of 22 wt% and 54 wt%, respectively. The economic combination of cell mass, CO 2 , and bisabolene yields demonstrated in this study provides practical insights for prioritizing research, selecting suitable hosts, and determining necessary engineered production levels.

09 BIOMASS FUELS↗
DOE OSTI2026

Microbial valorization of lignin to malic acid by Aspergillus niger

Lignin is the largest renewable source of aromatic carbon, yet its heterogeneity and recalcitrance limit its use in higher-value bioconversion processes. In this study, Aspergillus niger was engineered to enable the bioconversion of lignin-derived aromatics and base-catalyzed depolymerized (BCD) lignin streams into malic acid, a value-added C4 dicarboxylic acid with broad industrial relevance. Overexpression of the C4 dicarboxylate transporter C4T318 from Aspergillus oryzae enhanced malic acid secretion, while medium optimization under buffered conditions further improved the production. The engineered strain efficiently assimilated representative lignin-derived aromatics, including 4-hydroxybenzoic acid and p-coumaric acid, producing up to 3.9 g/L malic acid. Conversion of BCD lignin liquors from poplar and sorghum demonstrated effective utilization of heterogeneous aromatic mixtures, generating up to 0.82 g/L malic acid. This work demonstrates direct fungal conversion of real lignin streams into malic acid and establishes A. niger as a promising platform for sustainable lignin valorization.

Aromatic bioconversion↗
DOE OSTI2026

Divergent carbon use efficiency-growth rate tradeoff in popular biological growth models

Carbon use efficiency (CUE) is an important trait emerging from processes regulating biological growth. CUE can be computed either based on the growth of structural biomass or total biomass divided by substrate uptake rate. Nonequilibrium thermodynamics and observations suggest that, for an exponentially growing population of cells, structural biomass CUE should first increase, then peak, and finally decrease with specific growth rate; meanwhile, total biomass CUE increases asymptotically with specific growth rate. We compared predictions from six popular models that are often used for plant and microbial growth in existing ecosystem models. We found that, for an exponentially growing population of biological cells, (1) the source-driven Pirt and Compromise models predict that structural biomass CUE increase asymptotically with growth rate; (2) the apparent sink-driven modified Droop model predicts that structural biomass CUE decreases with growth rate; and (3) the sink-driven variable internal storage model and two dynamic energy budget models predict that structural biomass CUE first increases, then peaks, and finally decreases with growth rate. Moreover, the modified Droop model predicts that total biomass CUE is constant with growth rate, while all other five models predict that total biomass CUE increases with growth rate asymptotically. For non-exponential biological growth, we show that there is no static relationship between total biomass CUE or structural biomass CUE with respect to either growth rate or temperature. Therefore, we contend that biological growth models should explicitly represent interactions between substrate acquisition, substate transformation, and maintenance respiration to better capture observed CUE dynamics, and the sink-driven model should be preferred for general ecosystem biogeochemistry modeling.

Tang, Jinyun [Lawrence Berkeley National Laborator↗
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

Environmental matrix and moisture are key determinants of microbial phenotypes expressed in a reduced complexity soil-analog

Soil moisture and porosity regulate microbial metabolism by influencing factors such as redox conditions, substrate availability, and soil connectivity. However, the inherent biological, chemical, and physical heterogeneity of soil complicates laboratory investigations into microbial phenotypes that mediate community metabolism. This difficulty arises from challenges in accurately representing the soil environment and in establishing a tractable microbial community that limits confounding variables. To address these challenges in our investigation of community metabolism, we use a reduced-complexity microbial consortium grown in a soil analog using a glass-bead matrix amended with chitin. Long-read and short-read metagenomes, metatranscriptomes, metaproteomes, and metabolomes were analyzed to test the effects of soil structure and moisture on chitin degradation. Our soil structure analog system greatly altered microbial expression profiles compared to the liquid-only incubations, emphasizing the importance of incorporating environmental parameters, like pores and surfaces, for understanding microbial phenotypes relevant to soil ecosystems. These changes were mainly driven by differences in overall expression of chitin-degrading Streptomyces species and stress-tolerant Ensifer. Our findings suggest that the success of Ensifer in a structured environment is likely related to its ability to repurpose carbon via the glyoxylate shunt while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits like motility, stress resistance, and biofilm formation that underlie the degradation of chitin across our treatments and inform how they may ultimately alter carbon use efficiency. Together our results demonstrate that community functions like decomposition are sensitive to environmental conditions and more complex than the multi-enzyme pathways involved in depolymerization.

Rodriguez-Ramos, Josue A↗
DOE OSTI2021

Consequences of Altered Root Nutrient Uptake for Soil Carbon Stabilization (Final Report)

Objectives: The primary objectives of this project are to improve our understanding of tropical forest belowground processes, and to increase representation of this biome in ecosystem-scale and global C cycle models. Belowground dynamics present a major source of uncertainty inhibiting our ability to predict C cycle responses to climate change. Representation of tropical forests in these models is particularly lacking, even though these ecosystems hold >25% of terrestrial C stocks. While the majority of humid tropical forests exist on relatively infertile soils (i.e. poor in rock-derived nutrients), enormous gradients in soil nutrient availability exist at landscape-scales due to shifts in geology and soil order. Soil fertility is likely to greatly influence how tropical soil C storage will respond to the declines in precipitation predicted for the tropics. In particular, root dynamics vary across soil fertility gradients, with roots representing the major input of C to subsurface soils. Root characteristics related to soil fertility include biomass, turnover, C exudates, tissue chemistry, and nutrient uptake rates, with each of these likely sensitive to changes in moisture. The proposed project will fully integrate field research with an existing ecosystem model to assess potential effects of drying on belowground tropical C dynamics across a range of soil fertilities. Project Description:. This project will identify key linkages among soil fertility, root nutrient uptake, root dynamics, and soil C storage. The hypothesized framework for understanding these linkages is: Tropical rainforest roots in relatively fertile soils have lesser root biomass, faster turnover, fewer exudates, and improved root tissue quality relative to infertile sites, all resulting from increased root nutrient uptake. Ultimately, these root characteristics in fertile soils promote proportionally greater long-term soil C storage in organo-mineral associations. Specifically, lower root exudates and improved root tissue quality in fertile soils reduce microbial respiration of extant soil C (i.e. “priming) and increase microbial C use efficiency, leading to sorption of protein-rich microbial and plant organic matter on soil mineral surfaces. However, the larger pools of mineral-associated C in fertile tropical soils are more vulnerable to decreased rainfall than smaller C pools in infertile soils, in part because of the lesser root biomass, faster turnover, and softer, more labile root tissues. Also, the shallower lateral rooting structures typical in fertile soils experience greater desiccation and death than deeper roots in infertile sites, with little short-term adaptation to drying.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Imaginary admittance and charge transfer resistance correlate to the physiological status of Shewanella oneidensis cultures in real time

Monitoring microbial activity is essential for industrial and environmental applications to proceed efficiently. To minimize time and labor-intensive monitoring, a new paradigm is required for in-situ, real time analysis. Since bioconversion of organics is accomplished by microorganisms through the oxidation of feedstocks linked to the reduction of electron acceptors, microorganisms can be viewed as electrochemical catalysts. In this respect, cell membranes have an electrical potential, which is analogous to a conventional capacitor and linked dynamically to cellular activity. Here, in this study, we demonstrate the use of electrochemical impedance spectrometry (EIS) and cyclic voltammetry (CV) for monitoring microbial metabolic activity in real time, in-situ. The effect of organic electron donors as a function of concentration to the physiological status of strains of Shewanella oneidensis was determined. In this study, the pyomelanin overproducer (S. oneidensis ΔhmgA) and the pyomelanin deficient mutant (S. oneidensis ΔmelA) were chosen due to different surface electrochemical characteristics along with differences in oxygen utilization efficiency. CV, relative admittance, phase shift and permittivity changed with growth status and correlated with electron flow from organic carbon sources and terminal electron acceptor availability. This work offers a novel and inexpensive approach to real time monitoring with the advantage of abundant data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Gene Amplification, Laboratory Evolution, and Biosensor Screening Reveal MucK as a Terephthalic Acid Transporter in Acinetobacter baylyi ADP1

Microbial terephthalic acid (TPA) catabolic pathways are conserved among the few bacteria known to turnover this xenobiotic aromatic compound. However, to date there are few reported cases in which this pathway has been successfully expressed in heterologous hosts to impart efficient utilization of TPA as a sole carbon source. In this work, we aimed to engineer TPA conversion in Acinetobacter baylyi ADP1 via the heterologous expression of catabolic and transporter genes from a native TPA-utilizing bacterium. Specifically, we obtained ADP1-derived strains capable of growing on TPA as the sole carbon source using chromosomal insertion and targeted amplification of the tph catabolic operon from Comamonas sp. E6. Adaptive laboratory evolution was then used to improve growth on this substrate. TPA consumption rates of the evolved strains, which retained multiple copies of the tph genes, were ~0.2 g/L/h (or ~1 g TPA/g cells/h), similar to that of Comamonas sp. E6 and almost 2-fold higher than that of Rhodococcus jostii RHA1, another native TPA-utilizing strain. To evaluate TPA transport in the evolved ADP1 strains, we engineered a TPA biosensor consisting of the transcription factor TphR and a fluorescent reporter. In combination with whole-genome sequencing, the TPA biosensor revealed that transport of TPA was not mediated by the heterologous proteins from Comamonas sp. E6. Instead, the endogenous ADP1 muconate transporter MucK, a member of the major facilitator superfamily, was responsible for TPA transport in several evolved strains in which MucK variants were found to enhance TPA uptake. Furthermore, the IclR-type transcriptional regulator DcaS was identified as a repressor of mucK expression. Overall, this work presents an unexpected function of a native protein identified through gene amplification, adaptive laboratory evolution, and a combination of screening methods. This study also provides a TPA biosensor for application in ADP1 and identifies transporter variants for use in metabolic engineering applications focused on plastic upcycling of polyesters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Microbial necromass in cropland soils: A global meta-analysis of management effects

Microbial necromass is a large and persistent component of soil organic carbon (SOC), especially under croplands. The effects of cropland management on microbial necromass accumulation and its contribution to SOC have been measured in individual studies but have not yet been summarized on the global scale. For this study, we conducted a meta-analysis of 481-paired measurements from cropland soils to examine the management effects on microbial necromass and identify the optimal conditions for its accumulation. Nitrogen fertilization increased total microbial necromass C by 12%, cover crops by 14%, no or reduced tillage (NT/RT) by 20%, manure by 21%, and straw amendment by 21%. Microbial necromass accumulation was independent of biochar addition. NT/RT and straw amendment increased fungal necromass and its contribution to SOC more than bacterial necromass. Manure increased bacterial necromass higher than fungal, leading to decreased ratio of fungal-to-bacterial necromass. Greater microbial necromass increases after straw amendments were common under semi-arid and in cool climates in soils with pH <8, and were proportional to the amount of straw input. In contrast, NT/RT increased microbial necromass mainly under warm and humid climates. Manure application increased microbial necromass irrespective of soil properties and climate. Management effects were especially strong when applied during medium (3–10 years) to long (10+ years) periods to soils with larger initial SOC contents, but were absent in sandy soils. Close positive links between microbial biomass, necromass and SOC indicate the important role of stabilized microbial products for C accrual. Microbial necromass contribution to SOC increment (accumulation efficiency) under NT/RT, cover crops, manure and straw amendment ranged from 45% to 52%, which was 9%–16% larger than under N fertilization. In summary, long-term cropland management increases SOC by enhancing microbial necromass accumulation, and optimizing microbial necromass accumulation and its contribution to SOC sequestration requires site-specific management.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Integrating Chemical Catalysis and Biological Conversion of Carbon Intermediates for Deriving Value-Added Products from Carbon Dioxide

Carbon dioxide valorization represents an appealing approach to reducing greenhouse gases in the atmosphere. While electrocatalysis is an effective tool to reduce CO 2 into small carbon compounds, it becomes increasingly challenging to efficiently produce compounds with more carbon atoms. In contrast, while biological systems struggle to utilize CO 2 , they can readily upcycle other small carbon compounds. This project explores the use of a two-stage process that electrocatalytically converts CO 2 into methanol, formate, or acetate which is subsequently utilized by Methylotuvimicrobium alcaliphilum 20Z to produce medium chain length polyhydroxyalkanoate. A techno-economic analysis and life cycle assessment evaluates the commercial viability of the process as well as its carbon emissions. We show here an enhanced CO 2 -to-methanol electroconversion step coupled with the use of a microbial culture adapted to the process conditions to be the optimal configuration for economic potential.

09 BIOMASS FUELS↗
DOE OSTI2024

Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities

Ensuring the efficient engineering of microbially induced calcium carbonate precipitation (MICP) is crucial for a variety of environmental and civil engineering applications, such as soil stabilization and carbon sequestration. Addressing this need, we present a comprehensive multi-scale workflow that begins with the isolation of calcium carbonate-producing microbes from soil samples, followed by metagenomic sequencing and metabolic reconstruction. We then characterize microbial growth phenotypes under diverse nutrient conditions, compare observed growth with metabolic model predictions, and apply the Consistent Reproduction of Phenotype (CROP) algorithm to refine these models. Furthermore, we analyze metabolite consumption and production, and develop a consumer-resource model that is calibrated using time-series measurements of growth rates, pH levels, and calcium carbonate precipitation. The primary benefit of our approach lies in its ability to predict and control MICP outcomes, facilitated by a Bayesian methodology that incorporates priors on initial conditions and parameters. This allows us to compute posteriors by integrating experimental data, and to solve a risk optimization problem under uncertainty to identify nutrient conditions that maximize calcium carbonate production. In contrast to non-Bayesian methods, which fail to quantify uncertainty accurately, our approach provides a more reliable pathway to optimizing nutrient conditions, enhancing the likelihood of achieving desired MICP outcomes. This positions our method as a superior alternative in the quest to improve MICP through engineered microbial consortia.

54 ENVIRONMENTAL SCIENCES↗