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At least 685 records · Page 38

The Role of Cyanobacteria in Stromatolite Morphogenesis, Highborn Cay Bahamas: An Integrated Field and Laboratory Simulation Study

Geomicrobiological phenomena are among the most fundamental of interactions between Earth and its biosphere. Actively growing and lithifying stromatolites at Highborne Cay Bahamas, have recently been documented and allow for detailed examination of the roles microbes play in the mineralization process. These stromatolites contain a variety of complex microbial communities with distinct distribution patterns for different microbial groups. Cyanobacteria are the primary producers in this system providing energy, directly or indirectly, for the entire stromatolite microbial community. They also play key roles in the trapping and binding of sediments. Most of these species are highly motile and can adjust their position and orientation within the sediment matrix in order to optimize their access to irradiance and nutrients. As individual species have different physical and metabolic properties, this motility generally results in segregated distributions of species, which in turn contributes to the laminated textures observed in these actively forming stromatolites. Increasingly our studies suggest that the activities and locations of various cyanobacterial species also contribute greatly to the localization of new mineral precipitation through a variety of processes. We are investigating these contributions using an integrated approach combining detailed observations of field samples with manipulative experiments using both field samples and cultures of specific organisms isolated from these stromatolites. Experiments are conducted both in standard laboratory conditions and in outdoor running seawater flumes. A variety of standard techniques; SEM (scanning electron microscopy), petrographic analyses, TEM (transmission electron microscopy), are used to compare mineralization processes in field samples with those generated in laboratory-flume simulations. Using this approach we are able to more thoroughly investigate the effects of irradiance, CaCO3 saturation, and hydrodynamic regime on cyanobacterial distribution, trapping and binding and mineral precipitation. Simulation results will be presented and compared with community and mineralization distribution patterns seen in the field samples from which these communities were isolated.

Prufert-Bebout, Leslie↗

Intrabasin Comparison of the Microbiology and Geochemistry of Produced Fluid From Hydraulically Fractured Wells in the Permian Region

The Permian Basin is the highest producing oil reservoir in the United States. Hydrocarbon extraction methods in this region are often associated with frac hits, or interwell communication events where an established well is affected by the pumping of fracture fluid into a new well. Our previous work revealed a geochemical signal indicating the presence of frac hits in the Permian Basin. We returned to this area with the goal of expanding our understanding of subsurface interactions common in this region. To do so, we collected produced water from 25 unique sites across the Permian Basin, 10 of which had previously been characterized during an active frac hit. For each sample, we measured the pH, alkalinity, geochemistry, microbial load, and microbial community composition. Permian Basin produced water is characterized by higher sulfate and lower total dissolved solids (TDS) concentrations compared to other regions. Interestingly, wells impacted by frac hits have a geochemical profile that resembles that of fracture fluid, with both lowered sulfate and lowered TDS concentrations compared to unaffected wells. Due to the year-long recovery window between sample collection periods, we anticipate that all our data will be characterized by the typical high sulfate, low TDS concentrations.

geochemistry↗

An Abundant and Diverse New Family of Electron Bifurcating Enzymes With a Non-canonical Catalytic Mechanism

Microorganisms utilize electron bifurcating enzymes in metabolic pathways to carry out thermodynamically unfavorable reactions. Bifurcating FeFe-hydrogenases (HydABC) reversibly oxidize NADH (E′∼−280 mV, under physiological conditions) and reduce protons to H 2 gas (E°′−414 mV) by coupling this endergonic reaction to the exergonic reduction of protons by reduced ferredoxin (Fd) (E′∼−500 mV). We show here that HydABC homologs are surprisingly ubiquitous in the microbial world and are represented by 57 phylogenetically distinct clades but only about half are FeFe-hydrogenases. The others have replaced the hydrogenase domain with another oxidoreductase domain or they contain additional subunits, both of which enable various third reactions to be reversibly coupled to NAD + and Fd reduction. We hypothesize that all of these enzymes carry out electron bifurcation and that their third substrates can include hydrogen peroxide, pyruvate, carbon monoxide, aldehydes, aryl-CoA thioesters, NADP + , cofactor F 420 , formate, and quinones, as well as many yet to be discovered. Some of the enzymes are proposed to be integral membrane-bound proton-translocating complexes. These different functionalities are associated with phylogenetically distinct clades and in many cases with specific microbial phyla. We propose that this new and abundant class of electron bifurcating enzyme be referred to as the Bfu family whose defining feature is a conserved bifurcating BfuBC core. This core contains FMN and six iron sulfur clusters and it interacts directly with ferredoxin (Fd) and NAD(H). Electrons to or from the third substrate are fed into the BfuBC core via BfuA. The other three known families of electron bifurcating enzyme (abbreviated as Nfn, EtfAB, and HdrA) contain a special FAD that bifurcates electrons to high and low potential pathways. The Bfu family are proposed to use a different electron bifurcation mechanism that involves a combination of FMN and three adjacent iron sulfur clusters, including a novel [2Fe-2S] cluster with pentacoordinate and partial non-Cys coordination. The absolute conservation of the redox cofactors of BfuBC in all members of the Bfu enzyme family indicate they have the same non-canonical mechanism to bifurcate electrons. A hypothetical catalytic mechanism is proposed as a basis for future spectroscopic analyses of Bfu family members.

59 BASIC BIOLOGICAL SCIENCES↗

Psychrophilic Biomass Producers in the Trophic Chain of the Microbial Community of Lake Untersee, Antarctica

The study of photosynthetic microorganisms from the Lake Untersee samples showed dispersed distribution of phototrophs within ~80 m water column. Lake Untersee represents a unique ecosystem that experienced complete isolation: sealed by the Anuchin Glacier for many millennia. Consequently, its biocenosis has evolved over a significant period of time without exchange or external interaction with species from other environments. The major producers of organic matter in Lake Untersee are represented by phototrophic and chemolithotrophic microorganisms. This is the traditional trophic scheme for lacustrine ecosystems on Earth. Among the phototrophs, diatoms were not found, which differentiates this lake from other known ecosystems. The dominant species among phototrophs was Chlamydomonas sp. with typical morphostructure: green chloroplasts, bright red round spot, and two polar flagella near the opening. As expected, the physiology of studied phototrophs was limited by low temperature, which defined them as obligate psychrophilic microorganisms. By the quantity estimation of methanogenesis in this lake, the litho-autotrophic production of organic matter is competitive with phototrophic production. However, pure cultures of methanogens have not yet been obtained. We discuss the primary producers of organic matter and the participation of our novel psychrophilic homoacetogen into the litho-autotrophic link of biomass production in Lake Untersee.

Pikuta, Elena V.↗

Solutions in microbiome engineering: prioritizing barriers to organism establishment

Abstract Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

59 BASIC BIOLOGICAL SCIENCES↗

The oleaginous yeast Cutaneotrichosporon oleaginosum modifies corn stover alkali lignin

The current paradigm in synthetic biology for lignin bioconversion platforms includes primarily bacteria and filamentous fungi. Yeast are notoriously understudied for their role in lignin degradation and utilization, despite their ubiquity in saprophytic microbial communities. A few publications report lignin-modifying yeasts, but investigations to date have relied on model aromatic compounds or lignin-containing substrates replete with other carbon sources. In this work, we use a suite of analytical tools to evaluate interactions between corn stover-extracted lignin and the oleaginous yeast Cutaneotrichosporon oleaginosum. Notably, 2D-NMR analysis showed a significant decrease in the H-lignin component as well as resinol (β-β) and phenylcoumaran (β-5) linkages. Using super-resolution fluorescence microscopy, we demonstrated that this yeast may uptake polymeric lignin and/or undertakes interactions at the cellular envelope. To explore mechanisms of lignin modification, transport, and aromatics catabolism, extensive secretomics and proteomics analyses were conducted. Compared to carbon-limited glucose and “No Carbon” controls, several putative laccases, quinone reductases, superoxide dismutases, and glyoxal/oxalate oxidases were upregulated in the lignin condition. Excitingly, two ferric reductases and an oxalate exchanger were only observed in the lignin condition. These results indicate that C. oleaginosum may perform extracellular quinone redox cycling to generate lignin-modifying reactive oxygen species. These findings enhance our understanding of yeast-lignin interactions and provide valuable insights for validation studies and metabolic engineering.

09 BIOMASS FUELS↗

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↗

Small Molecule Interactions with Membranes (CRADA No. TC02321 Final Report)

This was a collaborative effort between Lawrence Livermore National Security, LLC (LLNS) as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Procter & Gamble (P&G) to develop and use a multiscale simulation method to explore and evaluate the nature of industrially relevant compounds in the presence of models that represent microbial membranes.

59 BASIC BIOLOGICAL SCIENCES↗

Definition of exobiology experiments for future Mars missions

During the past year we have concentrated on two objectives. The first objective is ongoing and is to define the experimental parameters that are necessary to conduct autonomously a mineralogical analysis of the Martian surface in situ using differential thermal analysis coupled with gas chromatography (DTA/GC). The rationale in support of this objective is that proper interpretation of the mineralogical data from the DTA/GC can be used to better describe the present and past environments of Mars, leading to a better assessment of the probability of life evolving on Mars. To meet these objectives we have analyzed a number of samples collected from nature using the DTA/GC. One of the more significant findings was that in samples of desert varnish we detected magnetite and maghemite that may serve as potential biomarkers applicable to DTA/GC analyses of Martian surface material during landed missions. The second objective follows from the first and is to better understand microbe-environment interactions by determining the response of microbes to changes in their environment, including extreme desiccation and solar UV-radiation. The rationale behind this is to develop hypotheses regarding what may have happened to life that may have arose on Mars, and microbial life that may get to the surface of Mars via spacecraft, or meteors from Earth. To accomplish this objective we have exposed microbes, collected from NaCl and gypsum-halite crystals, to the space environment aboard the ESA-German Biopan facility for 15 days. The most significant finding was that these microbes survived the exposure better than others.

Mancinelli, Rocco L.↗

Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces

Background: To disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such “fungal highways” may be driven both by mycelial physical properties and by interactions between bacteria and fungi. However, we still do not have a way to disentangle the biotic and abiotic elements. Results: We designed and 3D printed two devices establishing stable liquid films that support bacteria dispersal in the absence of biotic interactions. The thickness of the liquid film determined the presence of hydraulic flow capable of transporting non-motile cells. In the absence of flow, only motile cells can disperse in the presence of an energy source. Non-motile cells could not disperse autonomously without flow but dispersed as “hitchhikers” when co-inoculated with motile cells. Conclusions: The 3D printed devices can be used as an abiotic control to study bacterial dispersal on hydrated surfaces, such as plant roots and fungal hyphae networks in the soil. By teasing apart the abiotic and biotic dimensions, these 3D printed devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments.

3D printing↗

Biochemical Process Modeling and Simulation (BPMS)

The Biochemical Process Modeling and Simulation project aims to reduce the cost and time of research by applying theory, modeling, and simulation to the most relevant bottlenecks in the biochemical process. We use molecular modeling, quantum mechanics, metabolic modeling, fluid dynamics, and reaction-diffusion methods in close collaboration with pretreatment, hydrolysis, upgrading, and TEA. The project's outcomes are increased yields and efficiency of the biochemical process, added value to products, and reduced price of fuels by specifically targeting catalytic efficiency, reactor design, enzyme efficiency, and microbial design. We work closely with experimental projects to identify problems and iterate with experiments to find and refine solutions. By working with experimentalists, we decide on problems that can be solved with simulation that could otherwise not be solved or would take too long with experiment alone to reach BETO's targets. Over the years, we have produced solutions that have resulted in determining the most likely fatty-acid derivative for passive transport out of bacteria that upgrade biomass, and we have also designed enzyme mutations for enhanced lignin upgrading. Metabolic models have been developed to tune the activity of 2,3 butanediol production for the 2030 target. A computational method to deliver understanding of how complex omics data can be interpreted in the metabolic pathways of organisms used in the Agile Biofoundry. We have found methods to overcome specific barriers and continue to develop those methods. Our reactor studies have guided the design of both the microbes and reactors for aerobic and micro-aerobic production at all scales and have been instrumental in improving the accuracy of techno-economic analysis models. This project is essential in the process of selecting the final processes for 2030 SAF production targets. More specifically, recently, we have: 1) Predicted the strength of the basic structural interactions in commodity plastics to provide guidance for plastics upcycling strategies. 2) Developed computational tool to improve the characterization of lignin-derived compounds 3) Developed new methodologies to enable Machine Learning-based Directed Evolution for protein engineering. 4) Developed Machine Learning methods to predict protein promiscuity and mutations to further improve microbial and enzymatic driven processes and demonstrated the utility of ML approaches to engineering proteins from sparse experimental datasets. 5) Developed new methods to enable high-fidelity simulation of aerobic fermentation at industrial scale and resolving mismatch of time scales through subcycling/operator splitting 7) Identified the difficulty in preventing local high-oxygen conditions in industrial bubble columns, which leads to less-desirable acetoin production, suggesting future research directions in alternative reactor configurations (e.g loop reactors, shallow-channel reactors).

BIOMASS FUELS↗

Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH 4 + :NO 2 - , where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH 4 + :NO 2 - ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH 4 + :NO 2 - ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89–202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169–200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0–89, compared to 85.49 ± 0.01% from day 89–169, and 83.04 ± 0.01% from day 169–200). When the ratio was slightly increased to 1:1.17–1:1.2 (day 202–253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH 4 + :NO 2 - ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

59 BASIC BIOLOGICAL SCIENCES↗

Rhizogrids and 3D molecular root imaging workflow

Rhizogrid guided molecular root imaging workflow enables investigating root rhizosphere interactions in a near native environment. Non-invasive root images are captured, and three-dimensional root images are reconstructed using x-ray computed tomography technique. Root and rhizosphere samples are then harvested and processed for root-rhizosphere metabolite and microbial profiling.

Handakumbura, Pubudu↗

Constructing Regulatory Networks to Compare Axenic and Interspecies Microbial Gene Transcription

In this preliminary study, we constructed gene regulatory networks (GRNs) from transcriptional expression data of axenic and interspecies microbial cultures with the goal of predicting how cocultivation affected greenhouse gas respiration by these species. The specific strains of Methylotuvimicrobium alkaliphilum 20Z, a methylotroph, and Cyanobacterium stanieri HL-69, a phototroph, were chosen for their viability in industrial bioprocessing. We ranked directed interactions between gene pairs based on the ability of the input gene to predict the expression of a target gene relative to their transcriptomes. While we were able to identify topological differences between conditions, our initial findings require validation through experimental analysis and further modeling. We aimed to develop a systematic thresholding approach to optimize the accuracy of our networks. We filtered out trial networks separately from top gene interactions of the scored rankings. Parameters of unfiltered and filtered networks were used to test and develop thresholding approaches. Knee point detection of edge weight distributions was explored as an approach for separating significant interactions from insignificant interactions in unfiltered networks. While knee detection failed to produce analogous networks for broad cross-condition comparisons, the results informed us about the proportions of significant edges present in unfiltered networks. We also calculated the average mean degree for nodes in a selection of trial networks to find a thresholding value characteristic to all groups. While we did not reach a definitive conclusion, we gained insight into the coregulatory structures of our groups and made critical evaluations of systematic methods for filtering networks. We recommend an iterative process for the inference of GRNs, where the most significant results from preliminary explorations are used to improve the efficiency with which regulatory motifs are chosen for experimental characterization. Experimental results can then inform the framework of adjusted models to improve broad interpretations of GRNs.

59 BASIC BIOLOGICAL SCIENCES↗

Log-normal model for microbial survival in heat sterilization

An analytical model is developed for the survival times of organisms in heat sterilization in which the probability of inactivation as a function of exposure time is log-normally distributed. Experimental data is examined relative to this model and it is concluded that the model is valid except during the initial period of heating when an additional interaction between the organisms and their surrounding medium appears to be present. At long heating times, the log-normal model appears more accurate for extrapolating to low survival probabilities than the usual logarithmic survivor curves and is generally more conservative.

SURVIVAL↗

Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture

Trichoderma fungi support sustainable agriculture by suppressing plant diseases and improving crop performance. However, emerging pathogenicity of Trichoderma warrants further ecological and genetic characterization. Here we used machine learning to correlate genomic data from 37 Trichoderma strains with over 140 phenotypic traits, spanning metabolic versatility, biotic interactions, stress tolerance and reproductive strategies. We determined Trichoderma to be an ancient, genetically cohesive and physiologically diverse genus with spores capable of germination in water and dispersal via air and water droplets. Metabolic preferences indicate universal adaptation to mycoparasitism and to niches like arboreal microbial mats, alongside broader saprotrophic versatility. Our analyses are consistent with character displacement among close relatives and convergent evolution in distant lineages, with both processes shaping ecological plasticity and traits including dispersal modes, terrestrialization or endophytism. Our findings reveal that while some Trichoderma species show traits of biosafety concern, its vast ecophysiological diversity enables the development of safe, targeted bioeffectors.

Steindorff, Andrei S. [USDOE Joint Genome Institut↗

Remote sensing of wetland biomass and productivity for global biosystem research

The study of ecosystem function and the contributions of particular ecosystems to global elemental cycling will require data collection from orbital platforms. Presently used ground sampling techniques are not adequate for large area vegetation assessments. The research was directed toward an understanding of the relationship between spectral radiance and plant canopy biomass. Changes in the architecture of the canopy alters the observed spectral radiance patterns. The green components of a plant canopy interacts most strongly with incident radiation and usually reflect edaphic conditions as they relate to plant vigor. Plant biomass serves as an excellent integrator of the environmental factors encountered by the plant and can be used as an indicator for predicting soil redox, nutrient status, microbial activity, etc. The use was examined of TM spectral data to discriminate biomass classes and, in turn, to relate the biomass classes to the chemical status of the soil. Several preliminary studies have indicated that solar angle can be used to improve biomass predictions. This important observation also suggests that latitudinal extrapolation of the biomass predicting models will be possible if selected characteristics of the incident radiation are known.

Hardisky, M. A.↗

Human Factors and Habitability Challenges for Mars Missions

As NASA is planning to send humans deeper into space than ever before, adequate crew health and performance will be critical for mission success. Within the NASA Human Research Program (HRP), the Space Human Factors and Habitability (SHFH) team is responsible for characterizing the risks associated with human capabilities and limitations with respect to long-duration spaceflight, and for providing mitigations (e.g., guidelines, technologies, and tools) to promote safe, reliable and productive missions. SHFH research includes three domains: Advanced Environmental Health (AEH), Advanced Food Technology (AFT), and Space Human Factors Engineering (SHFE). The AEH portfolio focuses on understanding the risk of microbial contamination of the spacecraft and on the development of standards for exposure to potential toxins such as chemicals, bacteria, fungus, and lunar/Martian dust. The two risks that the environmental health project focuses on are adverse health effects due to changes in host-microbe interactions, and risks associated with exposure to dust in planetary surface habitats. This portfolio also proposes countermeasures to these risks by making recommendations that relate to requirements for environmental quality, foods, and crew health on spacecraft and space missions. The AFT portfolio focuses on reducing the mass, volume, and waste of the entire integrated food system to be used in exploration missions, and investigating processing methods to extend the shelf life of food items up to five years, while assuring that exploration crews will have nutritious and palatable foods. The portfolio also delivers improvements in both the food itself and the technologies for storing and preparing it. SHFE sponsors research to establish human factors and habitability standards and guidelines in five risk areas, and provides improved design concepts for advanced crew interfaces and habitability systems. These risk areas include: Incompatible vehicle/habitat design, inadequate human-computer interaction, inadequate critical task design, inadequate human-automation/robotic interaction, and performance errors due to training deficiencies. To address the identified research gaps within each risk, SHFH's research plan includes studies in the laboratory, in analogs, and on International Space Station (ISS). In addition to establishing and maintaining the risk-based research portfolio, SHFH is also implementing a qualitative approach to determine how we at NASA evaluate human performance. Via interviews with experts, such as trainers, flight controllers, and flight surgeons, we are collecting the metrics by which they assess human performance, evidence of performance issues, and potential or actual consequences. The Human Performance Data Project will determine what human performance data have been collected in the past at NASA, and what data should be collected in the future in order to complete our knowledgebase and reduce risks related to human factors and habitability.

Whitmore, Mihriban↗