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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.
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Local climatic adaptation in a widespread microorganism
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Ecosystem fluxes of hydrogen in a mid-latitude forest driven by soil microorganisms and plants
Molecular hydrogen (H 2 ) is an atmospheric trace gas with a large microbe-mediated soil sink, yet cycling of this compound throughout ecosystems is poorly understood. Measurements of the sources and sinks of H 2 in various ecosystems are sparse, resulting in large uncertainties in the global H 2 budget. Constraining the H 2 cycle is critical to understanding its role in atmospheric chemistry and climate. We measured H 2 fluxes at high frequency in a temperate mixed deciduous forest for 15 months using a tower-based flux-gradient approach to determine both the soil-atmosphere and the net ecosystem flux of H 2 . We also found that Harvard Forest is a net H 2 sink (-1.4 ± 1.1 kg H 2 ha -1 ) with soils as the dominant H 2 sink (-2.0 ± 1.0 kg H 2 ha -1 ) and aboveground canopy emissions as the dominant H 2 source (+0.6 ± 0.8 kg H 2 ha -1 ). Aboveground emissions of H 2 were an unexpected and substantial component of the ecosystem H 2 flux, reducing net ecosystem uptake by 30% of that calculated from soil uptake alone. Soil uptake was highly seasonal (July maximum, February minimum), positively correlated with soil temperature and negatively correlated with environmental variables relevant to diffusion into soils (i.e., soil moisture, snow depth, snow density). Soil microbial H 2 uptake was correlated with rhizosphere respiration rates (r = 0.8, P < 0.001), and H 2 metabolism yielded up to 2% of the energy gleaned by microbes from carbon substrate respiration. Here, we elucidate key processes controlling the biosphere–atmosphere exchange of H 2 and raise new questions regarding the role of aboveground biomass as a source of atmospheric H 2 and mechanisms linking soil H 2 and carbon cycling. Our results should be incorporated into modeling efforts to predict the response of the H 2 soil sink to changes in anthropogenic H 2 emissions and shifting soil conditions with climate and land-use change.
Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling
Abstract Numerous studies have demonstrated that fertilization with nutrients such as nitrogen, phosphorus, and potassium increases plant productivity in both natural and managed ecosystems, demonstrating that primary productivity is nutrient limited in most terrestrial ecosystems. In contrast, it has been demonstrated that heterotrophic microbial communities in soil are primarily limited by organic carbon or energy. While this concept of contrasting limitations, that is, microbial carbon and plant nutrient limitation, is based on strong evidence that we review in this paper, it is often ignored in discussions of ecosystem response to global environment changes. The plant‐centric perspective has equated plant nutrient limitations with those of whole ecosystems, thereby ignoring the important role of the heterotrophs responsible for soil decomposition in driving ecosystem carbon storage. To truly integrate carbon and nutrient cycles in ecosystem science, we must account for the fact that while plant productivity may be nutrient limited, the secondary productivity by heterotrophic communities is inherently carbon limited. Ecosystem carbon cycling integrates the independent physiological responses of its individual components, as well as tightly coupled exchanges between autotrophs and heterotrophs. To the extent that the interacting autotrophic and heterotrophic processes are controlled by organisms that are limited by nutrient versus carbon accessibility, respectively, we propose that ecosystems by definition cannot be ‘limited’ by nutrients or carbon alone. Here, we outline how models aimed at predicting non‐steady state ecosystem responses over time can benefit from dissecting ecosystems into the organismal components and their inherent limitations to better represent plant–microbe interactions in coupled carbon and nutrient models.
Isolation and Initial Characterisation of a Novel Type of Baeyer-Villiger Monooxygenase Activity From a Marine Microorganism
Abstract not provided
Global prevalence and distribution of genes and microorganisms involved in mercury methylation
Mercury methylation produces the neurotoxic, highly bioaccumulative methylmercury (MeHg). Recent identification of the methylation genes (hgcAB) provides the foundation for broadly evaluating microbial Hg-methylation potential in nature without making explicit rate measurements. We first queried hgcAB diversity and distribution in all available microbial metagenomes, encompassing most environments. The genes were found in nearly all anaerobic, but not in aerobic, environments including oxygenated layers of the open ocean. Critically, hgcAB was effectively absent in ~1500 human microbiomes, suggesting a low risk of endogenous MeHg production. New potential methylation habitats were identified, including invertebrate guts, thawing permafrost, coastal dead zones, soils, sediments, and extreme environments, suggesting multiple routes for MeHg entry into food webs. Several new taxonomic groups potentially capable of Hg-methylation emerged, including lineages having no cultured representatives. We then begin to address long-standing evolutionary questions about Hg-methylation and ancient carbon fixation mechanisms while generating a new global view of Hg-methylation potential.
Self‐Healing of Concrete Cracks by Ceramsite‐Loaded Microorganisms
Protective carrier is essential for the self‐healing of concrete cracks by microbially induced CaCO 3 precipitation, owing to the harsh conditions in concrete. In this paper, porous ceramsite particles are used as microbial carrier. Heat treatment and NaOH soaking are first employed to improve the loading content of the ceramsite. The viability of bacterial spores is assessed by urea decomposition measurements. Then, the self‐healing efficiency of concrete cracks by spores is evaluated by a series of tests including compressive strength regain, water uptake, and visual inspection of cracks. Results indicate that heat treatment can improve the loading content of ceramsite while not leading to a reduction of concrete strength by the ceramsite addition. The optimal heating temperature is 750°C. Ceramsite particles act as a shelter and protect spores from high‐pH environment in concrete. When nutrients and spores are incorporated in ceramsite particles at the same time, nutrients are well accessible to the cells. The regain ratio of the compressive strength increases over 20%, and the water absorption ratio decreases about 30% compared with the control. The healing ratio of cracks reaches 86%, and the maximum crack width healed is near 0.3 mm.
Discovery of Microorganisms and Enzymes Involved in High-Solids Decomposition of Rice Straw Using Metagenomic Analyses
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Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms
Growth rate has long been considered one of the most valuable phenotypes that can be measured in cells. Aside from being highly accessible and informative in laboratory cultures, maximal growth rate is often a prime determinant of cellular fitness, and predicting phenotypes that underlie fitness is key to both understanding and manipulating life. Despite this, current methods for predicting microbial fitness typically focus on yields [e.g., predictions of biomass yield using GEnomescale metabolic Models (GEMs)] or notably require many empirical kinetic constants or substrate uptake rates, which render these methods ineffective in cases where fitness derives most directly from growth rate. Here we present a new method for predicting cellular growth rate, termed SUMEX, which does not require any empirical variables apart from a metabolic network (i.e., a GEM) and the growth medium. SUMEX is calculated by maximizing the SUM of molar EXchange fluxes (hence SUMEX) in a genome-scale metabolic model. SUMEX successfully predicts relative microbial growth rates across species, environments, and genetic conditions, outperforming traditional cellular objectives (most notably, the convention assuming biomass maximization). The success of SUMEX suggests that the ability of a cell to catabolize substrates and produce a strong proton gradient enables fast cell growth. Easily applicable heuristics for predicting growth rate, such as what we demonstrate with SUMEX, may contribute to numerous medical and biotechnological goals, ranging from the engineering of faster-growing industrial strains, modeling of mixed ecological communities, and the inhibition of cancer growth.
Microorganisms Associated with Hydrocarbon Contaminated Sites and Reservoirs for Microbially Enhanced Oil Recovery (MEOR)
Russian partner Institutes tested a number of strains from their collection and/or selected at oilfield contamination/ extraction sites to determine their ability to create aggregates that could plug oil well reservoirs to enhance oil recovey. Among these tested, five facultative anaerobic organisms that performed the best in the Russian Institutes' trials were shipped to Argonne and evaluated at Argonne for their ability to produce aggregates that plug pores in oil reservoirs formations. Results were provided to the Industrial Partner who is interested in receiving the strains for further testing.
Systems-Level Description of Metabolic and Regulatory Pathways for a Hydrogen-Producing Model Microorganism
We sought to improve our understanding of the metabolic and regulatory networks that control hydrogen (H 2 ) production in the hyperthermophilic marine archaeon Pyrococcus furiosus (Pf), a model microbial H 2 producer. We used an approach based on genomic and transcriptomic analyses of stress response along with genetic and biochemical characterization of identified pathways to further define control checkpoints in H 2 production that will be valuable in future metabolic engineering efforts.
The effects of Fe-oxidizing microorganisms on post-biostimulation permeability reduction and oxidative processes at the Rifle IFRC site
Fe oxidation and biomineral formation is important in aquifers because the highly-reactive oxides can control the mobility of nutrients (e.g. phosphate, C) and metals (e.g. arsenic, uranium). Mineral formation also has the potential to affect hydrology, depending on the volume and distribution in pore spaces. In this exploratory study, we sought to understand how microbial Fe-oxidizers and their biominerals affect, and are affected by groundwater flow. As part of work at the Rifle aquifer in Colorado, we initially hypothesized that Fe-oxidizers were contributing to aquifer clogging problems associated with enhanced bioremediation. To demonstrate the presence of Fe-oxidizers in the Rifle aquifer, we enriched FeOM from groundwater samples, and isolated two novel chemolithotrophic, microaerophilic Fe-oxidizing Betaproteobacteria, Hydrogenophaga sp. P101 and Curvibacter sp. CD03. To image cells and biominerals in the context of pores, we developed a “micro-aquifer,” a sand-filled flow-through culture chamber that allows for imaging of sediment pore space with multiphoton confocal microscopy. Fe oxide biofilms formed on sand grains, demonstrating that FeOM produce Fe oxide sand coatings. Fe coatings are common on aquifer sands, and tend to sequester contaminants; however, it has never previously been shown that microbes are responsible for their formation. In contrast to our original hypothesis, the biominerals did not clog the mini-aquifer. Instead, Fe biofilm distribution was dynamic: they grew as coatings, then periodically sloughed off sand grains, with some flocs later caught in pore throats. This has implications for physical hydrology, including pore scale architecture, and element transport. The sloughing of coatings likely prevents the biominerals from clogging wells and aquifers, at least initially. Although attached biomineral coatings sequester Fe-associated elements (e.g. P, As, C, U), when biominerals detach, these elements are transported as particles through the aquifer. Our work shows that microbial mineralization impacts in aquifers are dynamic, and that the fate and transport of biomineral-associated elements depend not only on geochemical conditions, but also physical pore-scale processes.
Investigations into the metabolic diversity of microorganisms as part of microbial diversity
DOE funds supported a key portion of the MBL Microbial Diversity (Woods Hole) program across 6 complete summers. The initial 4 years of the funded period were overseen by two co-Directors, Daniel Buckley (Cornell) and Steve Zinder (Cornell), who then completed their term. The final 2 summers were overseen by 2 new co-Directors, Jared R. Leadbetter (Caltech) and Dianne Newman (Caltech). The 6 funded summer iterations of the course included the incorporation of new themes such as single cell approaches applied to natural microbial communities (cell separation and sorting, genome amplification from single cells, and the use of Nano-SIMS to examine assimilation of carbon and nitrogen from isotopically labeled substrates into single cells), genetics and genomics on bacteria freshly isolated during the course of the programs, quantitative systems biology, and modern quantitative light microscopy.
Synthetic Design of Microorganisms for Lignin Fuel
Despite the proof-of-the-concept for lignin bioconversion at the time when the project was first funded, the conversion efficiency and titer were extremely low for bioconversion of lignin into lipid. The low conversion efficiency is due the inherent recalcitrance of lignin and limited understanding of lignin chemistry. In nature, lignin is a complex aromatic heteropolymer composed of phenylpropane units cross-linked via a variety of chemically stable bonds, which makes it particularly difficult for microbial degradation. In addition to the recalcitrance, lignin as a biorefinery waste is also highly heterogeneous in terms of chemical linkage abundance, functional group distribution, molecular weight and uniformity. In order to achieve better lignin bioconversion, it is critical to understand how lignin chemistry impacts the conversion performance. Throughout the project, we have clearly found that ‘not all lignin are created equal’, in particular, for the lignin out of different biochemical conversion processes. In addition, we have clearly shown that lignin chemistry defines its functionality and processiblity for bioconversion. In particular, the S/G/H ratio, functional groups, chemical linkages and molecular weight defines the reactivity of lignin during bioconversion. Throughout the project, we have advanced the understanding for the impact of lignin chemistry on reactivity, developed a series of lignin 3 fractionation technologies to improve lignin processibility, and ultimately advanced biorefinery design holistically for simultaneous optimization of carbohydrate release and lignin reactivity. In addition to lignin reactivity, another important consideration for lignin bioconversion is the available microbial strains for bioconversion. Natural biomass utilization systems evolved mechanisms for lignin degradation, often with at least three sequential steps: lignin depolymerization into aromatic compounds, subsequent degradation of aromatic compounds into common intermediates like acetyl-CoA, and eventually the conversion of central metabolites into target bioproducts like lipid and PHA. Extensive work has gone into understanding the mechanisms of lignin depolymerization in model systems such as white rot fungi and termites. Despite interest, no fungus-based commercial process for lignin depolymerization has been developed, due in large part to the practical challenges of fungal genetic manipulations. In addition to white rot fungi, a few members of the Actinobacteria, α-Proteobacteria, and γ-Proteobacteria (including Rhodococcus putida) have lignin degradation activity in vitro. However, most of lignindegrading bacteria has very low lignin conversion efficiency, in particular, for lignin depolymerization. The project focused on addressing the issue with systems biology-guided microbial design to improve lignin bioconversion. The project first established that laccase enzyme can synergize with bacteria to promote lignin depolymerization, and further utilized synthetic biology approach to designed functional modules for lignin depolymerization, aromatic compound utilization, and bioproduct accumulation. The integration of biorefinery design, synthetic biology, and fermentation optimization eventually allowed us to achieve the target yield of 10g/L lipid production from lignin-containing biorefinery waste. In this summary, we hereby briefly review the major discoveries from the project with reference to different sections of this report.
Engineered Microorganisms for Enhanced Rare Earth Element Bio-mining and Separations (Final Technical Report)
Rare earth elements (REE) are critical ingredients of sustainable energy technologies, but their extraction from ore and separation from one another pose formidable challenges. To solve the challenge of REE supply, we used advanced genomics, high-throughput screening with synthetic REE minerals, and synthetic biology to engineer two sets of exotic microbes to (1) extract REE from ores, spent cracking catalysts, coal ash and electronic waste with high efficiency and selectivity, and (2) to purify REE into single element batches, all under benign conditions without the need of harsh solvents and high temperatures. This work integrated our expertise in systems and synthetic biology (Buz Barstow); rare-earth geochemistry (Esteban Gazel) and mineral synthesis (Megan Holycross); and microsystems engineering (Mingming Wu) by first elucidating the set of rules that predict an organism’s phenotype and then applying them to solve this critical problem in sustainable energy. These new technologies could help to revitalize the US rare earth industry and provide a new source of these critical elements for future energy technologies. We have already had some big success in tech transfer. Two of our team members (postdoctoral fellow Alexa Schmitz and graduate student Sean Medin) were able to study the supply chain for REE in the United States, and identify an opportunity to commercialize our REE mineral-dissolution technology. Alexa and Sean recently founded REEgen, Inc., an REE biomining company. Dr. Schmitz was recently awarded a fellowship from the Activate Foundation to support the first two years of REEgen. Cornell showed its support for this technology and company, and Dr. Schmitz was awarded the Rising Women Innovator’s award. These two awards unlocked support from Cornell’s Praxis Incubator.
Enigmatic life underneath us: genomic analysis of deep subsurface microorganisms
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Genomic reconstruction to resolve the functional potential of microorganisms from deep-sea hydrothermal vent sediments
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Microbial Iron Cycling in Acidic Geothermal Springs of Yellowstone National Park: Integrating Molecular Surveys, Geochemical Processes, and Isolation of Novel Fe-Active Microorganisms
Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats inYellowstone National Park. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 88°C and pH 2.4 to 3.6. All iron oxide mats exhibited high diversity of crenarchaeal sequences from the Sulfolobales, Thermoproteales, and Desulfurococcales. The predominant Sulfolobales sequences were highly similar to Metallosphaera yellowstonensis str. MK1, previously isolated from one of these sites. Other groups of archaea were consistently associated with different types of iron oxide mats, including undescribed members of the phyla Thaumarchaeota and Euryarchaeota. Bacterial sequences were dominated by relatives of Hydrogenobaculum spp. above 65–70°C, but increased in diversity below 60°C. Cultivation of relevant iron-oxidizing and iron-reducing microbial isolates included Sulfolobus str. MK3, Sulfobacillus str. MK2, Acidicaldus str. MK6, and a new candidate genus in the Sulfolobales referred to as Sulfolobales str. MK5. Strains MK3 and MK5 are capable of oxidizing ferrous iron autotrophically, while strain MK2 oxidizes iron mixotrophically. Similar rates of iron oxidation were measured for M. yellowstonensis str. MK1 and Sulfolobales str. MK5. Biomineralized phases of ferric iron varied among cultures and field sites, and included ferric oxyhydroxides, K-jarosite, goethite, hematite, and scorodite depending on geochemical conditions. Strains MK5 and MK6 are capable of reducing ferric iron under anaerobic conditions with complex carbon sources. The combination of geochemical and molecular data as well as physiological observations of isolates suggests that the community structure of acidic Fe mats is linked with Fe cycling across temperatures ranging from 53 to 88°C.