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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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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Microbial Evolution Drives Adaptation of Substrate Degradation on Decadal to Centennial Time Scales Relevant to Global Change

ABSTRACT Understanding microbial adaptation is crucial for predicting how soil carbon dynamics and global biogeochemical cycles will respond to climate change. This study employs the DEMENT model of microbial decomposition, along with empirical mutation and dispersal rates, to explore the roles of mutation and dispersal in the adaptation of soil microbial populations to shifts in litter chemistry, changes that are anticipated with climate‐driven vegetation dynamics. Following a change in litter chemistry, mutation generally allows for a higher rate of litter decomposition than dispersal, especially when dispersal predominantly introduces genotypes already present in the population. These findings challenge the common idea that mutation rates are too low to affect ecosystem processes on ecological timescales. These results demonstrate that evolutionary processes, such as mutation, can help maintain ecosystem functioning as the climate changes.

Abs, Elsa↗
DOE OSTI2024

Biogeochemical consequences of microbial evolution under drought (Final technical report)

As the climate changes, droughts may become more severe. Scientists are uncertain about how drought will affect the natural world, particularly the bacteria, fungi, and other microbes that live in soils and control the Earth’s flows of carbon and nutrients. Researchers at the University of California, Irvine, and Lawrence Berkeley National Laboratory teamed up to study how microbes at the soil surface change with drought and what that means for the carbon cycle. Since 2007, the researchers have used shelters with retractable roofs to prevent nearly half of normal rainfall from reaching grass and shrub landscapes, and their soil microbiomes, in Southern California.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

The diversity and evolution of microbial dissimilatory phosphite oxidation

Significance Geochemical models of the phosphorus (P) cycle uniquely ignore microbial redox transformations. Yet phosphite is a reduced P source that has been detected in several environments at concentrations that suggest a contemporary P redox cycle. Microbial dissimilatory phosphite oxidation (DPO) converts soluble phosphite into phosphate, and a false notion of rarity has limited our understanding of its diversity and environmental distribution. Here we demonstrate that DPO is an ancient energy metabolism hosted by taxonomically diverse, autotrophic bacteria that exist globally throughout anoxic environments. DPO microorganisms are therefore likely to have provided bioavailable phosphate and fixed carbon to anoxic ecosystems throughout Earth’s history and continue to do so in contemporary environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Genetic Basis of Chromate Adaptation and the Role of the Pre-existing Genetic Divergence during an Experimental Evolution Study with Desulfovibrio vulgaris Populations

Hexavalent chromium [Cr(VI)] is a common environmental pollutant. However, little is known about the genetic basis of microbial evolution under Cr(VI) stress and the influence of the prior evolution histories on the subsequent evolution under Cr(VI) stress. In this study, Desulfovibrio vulgaris Hildenborough (DvH), a model sulfate-reducing bacterium, was experimentally evolved for 600 generations. By evolving the replicate populations of three genetically diverse DvH clones, including ancestor (AN, without prior experimental evolution history), non-stress-evolved EC3-10, and salt stress-evolved ES9-11, the contributions of adaptation, chance, and pre-existing genetic divergence to the evolution under Cr(VI) stress were able to be dissected. Significantly decreased lag phases under Cr(VI) stress were observed in most evolved populations, while increased Cr(VI) reduction rates were primarily observed in populations evolved from EC3-10 and ES9-11. The pre-existing genetic divergence in the starting clones showed strong influences on the changes in lag phases, growth rates, and Cr(VI) reduction rates. Additionally, the genomic mutation spectra in populations evolved from different starting clones were significantly different. A total of 14 newly mutated genes obtained mutations in at least two evolved populations, suggesting their importance in Cr(VI) adaptation. An in-frame deletion mutation of one of these genes, the chromate transporter gene DVU0426, demonstrated that it played an important role in Cr(VI) tolerance. Overall, our study identified potential key functional genes for Cr(VI) tolerance and demonstrated the important role of pre-existing genetic divergence in evolution under Cr(VI) stress conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Microbial Community Structure and Functional Potential Along a Hypersaline Gradient

© 2018 Kimbrel, Ballor, Wu, David, Hazen, Simmons, Singer and Jansson. Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants.

Kimbrel, Jeffrey A.↗
DOE OSTI2021

Gulf of Mexico blue hole harbors high levels of novel microbial lineages

Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole’s rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40–75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80–110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Three-Dimensional Free Gas Flow Focuses Basin-Wide Microbial Methane to Concentrated Methane Hydrate Reservoirs in Geological System

Here, we present a systematic model that links the generation, migration, phase partitioning, and accumulation of methane into a closed loop as the sediment is deposited from the seafloor and buried through the base of hydrate stability zone (BHSZ). In our model, methane is generated by biodegradation of organic carbon in muds. Hydrate does not form and methane is not trapped until a coarse-grained layer is deposited, because the small pores prevent hydrate formation in muds. Instead, methane diffuses into sands/silts where methane solidifies into hydrate. As hydrate-bearing sands/silts pass through the BHSZ during sediment burial, methane hydrate dissociates, and releases free gas. The released and the newly generated free gas below the BHSZ concentrates into a vertical/dipping zone with low capillary entry pressure and high permeability and flows upward driven its buoyancy. When free gas reaches the hydrate stability zone (HSZ), capillary forces drive free gas to flow laterally, preferentially enter sands/silts, feed hydrate growth, and elevate hydrate saturation. With three-dimensional focused free gas flow, microbial methane that is generated from a much larger fetch area of the entire basin, both above and below the BHSZ, is concentrated into coarse-grained layers at structural closures for hydrate formation. Our model illustrates how geological evolution, microbial methane generation, and gas flow by buoyancy couple to generate concentrated hydrate deposits in geological system. These insights can be used to explore for high-concentration methane hydrate and are important for understanding the methane budget and carbon cycle under the seafloor.

58 GEOSCIENCES↗
DOE OSTI2020

Deep Learning Prediction of Interspecies Interactions from Self-organized Spatiotemporal Patterns of Co-evolving Organisms

Microorganisms colonizing natural habits such as soils co-evolve to form specific spatial patterns through interspecies interactions. These self-organized patterns are a key ecological phenotype, which provides critical information on their interaction mechanisms. However, conventional network inference techniques that analyze species population data in bulk have yet to be extended to account for such spatial heterogeneity. Here we proposed supervised deep learning as a new network inference tool for predicting interspecies interactions from spatiotemporal patterns of microbial evolution. Due to lack of biological imaging data that can be used for training deep learning networks, we used in silico data generated from high-fidelity agent-based models to determine model structure and parameters. Even though networks were trained under simple configurations where interaction coefficients are assumed to be spatially invariant, we demonstrated that the resulting model can be utilized to successfully predict spatial variation of interactions in more complex domains (i.e., configured with a context-dependent mixture of interaction coefficients) as well as in simple domains without further training. In the further test against real biological data obtained through imaging experiments of a binary consortium (Pseudomonas fluorescens and a mutant of Escherichia coli), our model also predicted the dramatic shifts in interactions of the two organisms across different environmental contexts. Through various successful demonstrations in this work, the combined use of the agent-based model and machine learning algorithm provides a means to use new type of data - microscopic images - for extracting microbial interactions, therefore presenting itself as a useful tool for the analysis of more complex microbial community interactions.

Lee, Joon-Yong↗
DOE OSTI2020

Type IV-like pili facilitate transformation in naturally competent archaea

Naturally competent organisms are capable of DNA uptake directly from the environment through the process of transformation. Despite the importance of transformation to microbial evolution, DNA uptake remains poorly characterized outside the bacterial domain. Here, we identify the pilus as a necessary component of the transformation machinery in archaea. We describe two naturally competent organisms: Methanococcus maripaludis and Methanoculleus thermophilus. In M. maripaludis, replicative vectors were transferred with an average efficiency of 2.4 x 10 3 transformants μg -1 DNA. In M. thermophilus, integrative vectors were transferred with an average efficiency of 2.7 x 10 3 transformants μg -1 DNA. Additionally, natural transformation of M. thermophilus could be used to introduce chromosomal mutations. To our knowledge, this is the first demonstration of a method to introduce targeted mutations in a member of the order Methanomicrobiales. For both organisms, mutants lacking structural components of the type IV-like pilus filament were defective for DNA uptake, demonstrating the importance of pili for natural transformation. Interestingly, competence could be induced in a non-competent strain of M. maripaludis by expressing pilin genes from a replicative vector. Furthermore, these results expand the known natural competence pili to include examples from the archaeal domain and highlight the importance of pili for DNA uptake in diverse microbial organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genome‐enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats

Summary As a young bacteriologist just launching my career during the early days of the ‘microbial revolution’ in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross‐disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize ‘wild’ bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited ‘How we did it’ perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene‐ and genome‐enabled surveys, and application of genome‐guided, cultivation‐independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population’s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population’s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microbial ecology of acidic, biogenic gypsum: community structure and distribution of extremophiles on freshly formed and relict sulfate deposits in a hydrogen sulfide-rich cave

Sulfate minerals are abundant on the Martian surface, and many of these evaporite deposits are thought to have precipitated from acidic fluids. On Earth, gypsum (CaSO 4 •2H 2 O) and other sulfates sometimes form under acidic conditions, so exploring the extremophilic life that occurs in these mineral environments can help evaluate the astrobiological potential of acid sulfate depositional settings. Here, we characterized the microbial communities associated with acidic gypsum deposits in a sulfuric acid cave, where sulfate precipitation is driven by sulfide-oxidizing bacteria and archaea. We used 16S rRNA gene sequencing and cell counts to characterize gypsum-associated microorganisms in freshly formed and relict deposits throughout the cave, to test how microbial community composition and abundance would vary with distance from the sulfidic water table and with the concentration of H 2 S(g) and other gases in the cave atmosphere. We found that actively forming gypsum in the lower cave levels was colonized by low-diversity communities that have few cells compared to other environments in the cave. The most abundant taxa were Acidithiobacillus, Metallibacterium, Mycobacteria, and three different Thermoplasmatales-group archaea, which occupied distinct niches based on proximity to sulfidic streams and the concentration of gases in the cave air. By contrast, deposits in older cave levels had more diverse communities that were distinct from those associated with freshly formed gypsum and likely represent a community reliant on different energy resources. These findings show that acidic sulfate deposits serve as habitats for extremophilic microorganisms and broaden our knowledge of the life associated with terrestrial sulfates.

58 GEOSCIENCES↗
DOE OSTI2025

Effects of soluble electron shuttles on microbial iron reduction and methanogenesis

In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and −0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.

Anaerobic Redox Reactions↗
DOE OSTI2025

BONCAT-Live for isolation and cultivation of active environmental bacteria

In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.

Analytical Methods↗