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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Prediction of Distributed River Sediment Respiration Rates Using Community-Generated Data and Machine Learning

River sediment microbial respiration is a key indicator of ecosystem functioning and the biogeochemical fluxes across this critical zone link surface and subsurface waters. As such, there is tremendous interest in measuring and mapping these respiration rates. Respiration observations are expensive and labor intensive; there is limited data available to the community. An open science, collaborative initiative is collecting samples for respiration rate analysis and multi-scale metadata; this evolving data set is being used for making machine learning (ML) predictions at unsampled sites to help inform continued community engagement. However, it is a challenge to find an optimum configuration for ML models to work with this feature-rich (i.e., 100+ possible input variables) data set. Here, we present results from a two-tiered approach to managing the analysis of this complex data set: (a) a stacked ensemble of models that automatically optimizes hyperparameters and manages the training of many models and (b) feature permutation importance to detect the most important features in the models. The major elements of this workflow are modular, portable, open, and cloud-based thus making this implementation a potential template for other applications. The models developed here predict that sediment organic matter chemistry is one of the most important features for predicting sediment respiration rate. Other larger-scale, important features fall into the categories of climatic, ecological, geological, and fluvial settings. Leveraging these larger-scale features to generate data-driven estimates of river sediment respiration rates reveals spatially consistent but heterogeneous patterns across the river network of the Columbia River Basin.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1987

Expansion of space station diagnostic capability to include serological identification of viral and bacterial infections

It is necessary that an adequate microbiology capability be provided as part of the Health Maintenance Facility (HMF) to support expected microbial disease events during long periods of space flight. The applications of morphological and biochemical studies to confirm the presence of certain bacterial and fungal disease agents are currently available and under consideration. This confirmation would be greatly facilitated through employment of serological methods to aid in the identification for not only bacterial and fungal agents, but viruses as well. A number of serological approached were considered, particularly the use of Enzyme Linked Immunosorbent Assays (ELISAs), which could be utilized during space flight conditions. A solid phase, membrane supported ELISA for the detection of Bordetella pertussis was developed to show a potential model system that would meet the HMF requirements and specifications for the future space station. A second model system for the detection of Legionella pneumophilia, an expected bacterial disease agent, is currently under investigation.

Hejtmancik, Kelly E.↗
NASA NTRS1992

Gravity effects on cellulose assembly

The effect of microgravity on cellulose synthesis using the model system of Acetobacter xylinum was the subject of recent investigations using The National Aeronautics and Space Administration's Reduced Gravity Laboratory, a modified KC-135 aircraft designed to produce 20 sec of microgravity during the top of a parabolic dive. Approximately 40 parabolas were executed per mission, and a period of 2 x g was integral to the pullout phase of each parabola. Cellulose biosynthesis was initiated on agar surfaces, liquid growth medium, and buffered glucose during parabolic flight and terminated with 2.0% sodium azide or 50.0% ethanol. While careful ground and in-flight controls indicated normal, compact ribbons of microbial cellulose, data from five different flights consistently showed that during progression into the parabola regime, the cellulose ribbons became splayed. This observation suggests that some element of the parabola (the 20 sec microgravity phase, the 20 sec 2 x g phase, or a combination of both) was responsible for this effect. Presumably the cellulose I alpha crystalline polymorph normally is produced under strain, and the microgravity/hypergravity combination may relieve this stress to produce splayed ribbons. An in-flight video microscopy analysis of bacterial motions during a parabolic series demonstrated that the bacteria continue to synthesize cellulose during all phases of the parabolic series. Thus, the splaying may be a reflection of a more subtle alteration such as reduction of intermicrofibrillar hydrogen bonding. Long-term microgravity exposures during spaceflight will be necessary to fully understand the cellulose alterations from the short-term microgravity experiments.

manned↗
DOE OSTI2026

Soil metagenomics umbrella narrative

Implementing accessible, authentic research experiences in introductory courses is challenging, particularly at institutions serving diverse student populations. To address this gap, we developed and deployed a Course-based Undergraduate Research Experience (CURE) focused on plant-microbe interactions in General Biology II at Northeastern Illinois University (NEIU), a minority-serving institution with a diverse student body. Students grew sugar beets (Beta vulgaris), extracted DNA from the rhizoplane, and used the Department of Energy Systems Biology Knowledgebase (KBase) for bioinformatic analysis to compare microbial relative abundance in fertilized versus unfertilized soil. Over five semesters, the CURE engaged 103 students and leveraged the intuitive KBase platform to make complex sequencing data accessible. Pre/post-course survey data revealed significant increases in student self-assessed research skills, including the ability to explain results and determine the types of data to collect. Furthermore, students reported significant gains in confidence related to experimental design and hypothesis development, alongside a strong increase in familiarity with KBase. Informal faculty feedback indicated high student engagement and appreciation for the real-world connections (e.g. food systems, agriculture, and health). This scalable, low-cost model effectively integrates data science tools into the foundational curriculum, demonstrating a potent strategy for boosting research skills and broadening participation in authentic scientific inquiry among diverse undergraduate students.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2017

Stratosphere Conditions Inactivate Bacterial Endospores from a Mars Spacecraft Assembly Facility

Every spacecraft sent to Mars is allowed to land viable microbial bioburden, including hardy endospore-forming bacteria resistant to environmental extremes. Earth's stratosphere is severely cold, dry, irradiated, and oligotrophic; it can be used as a stand-in location for predicting how stowaway microbes might respond to the Martian surface. We launched E-MIST, a high-altitude NASA balloon payload on 10 October 2015 carrying known quantities of viable Bacillus pumilus SAFR-032 (4.07?×?10(7) spores per sample), a radiation-tolerant strain collected from a spacecraft assembly facility. The payload spent 8?h at ~31?km above sea level, exposing bacterial spores to the stratosphere. We found that within 120 and 240?min, spore viability was significantly reduced by 2 and 4 orders of magnitude, respectively. By 480?min, <0.001% of spores carried to the stratosphere remained viable. Our balloon flight results predict that most terrestrial bacteria would be inactivated within the first sol on Mars if contaminated spacecraft surfaces receive direct sunlight. Unfortunately, an instrument malfunction prevented the acquisition of UV light measurements during our balloon mission. To make up for the absence of radiometer data, we calculated a stratosphere UV model and conducted ground tests with a 271.1?nm UVC light source (0.5 W/m(2)), observing a similarly rapid inactivation rate when using a lower number of contaminants (640 spores per sample). The starting concentration of spores and microconfiguration on hardware surfaces appeared to influence survivability outcomes in both experiments. With the relatively few spores that survived the stratosphere, we performed a resequencing analysis and identified three single nucleotide polymorphisms compared to unexposed controls. It is therefore plausible that bacteria enduring radiation-rich environments (e.g., Earth's upper atmosphere, interplanetary space, or the surface of Mars) may be pushed in evolutionarily consequential directions.

Planetary protection↗
DOE OSTI2023

One thousand soils for molecular understanding of belowground carbon cycling

While significant progress has been made in understanding global carbon (C) cycling, the mechanisms regulating belowground C fluxes and storage are still uncertain. New molecular technologies have the power to elucidate these processes, yet we have no widespread standardized implementation of molecular techniques. To address this gap, we introduce the Molecular Observation Network (MONet), a decadal vision from the Environmental Molecular Sciences Laboratory (EMSL), to develop a national network for understanding the molecular composition, physical structure, and hydraulic and biological properties of soil and water. These data are essential for advancing the next generation of multiscale Earth systems models. In this paper, we discuss the 1000 Soils Pilot for MONet, including a description of standardized sampling materials and protocols and a use case to highlight the utility of molecular-level and microstructural measurements for assessing the impacts of wildfire on soil. While the 1000 Soils Pilot generated a plethora of data, we focus on assessments of soil organic matter (SOM) chemistry via Fourier-transform ion cyclotron resonance-mass spectrometry and microstructural properties via X-ray computed tomography to highlight the effects of recent fire history in forested ecosystems on belowground C cycling. We observed decreases in soil respiration, microbial biomass, and potential enzyme activity in soils with high frequency burns. Additionally, the nominal oxidation state of carbon in SOM increased with burn frequency in surface soils. This results in a quantifiable shift in the molecular signature of SOM and shows that wildfire may result in oxidation of SOM and structural changes to soil pore networks that persist into deeper soils.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2005

Lunar and Planetary Science XXXVI, Part 22

The Lunar and Planetary Science XXXVI, Part 22 is presented. The topics include: 1) Pressure Histories from Thin and Thick Shock-induced Melt Veins in Meteorites; 2) Nano-structured Minerals as Signature of Microbial Activity; 3) The Insoluble Carbonaceous Material of CM Chondrites as Possible Source of Discrete Organics During the Asteroidal Aqueous Phase; 4) Discovery of Abundant Presolar Silicates in Subgroups of Antarctic Micrometeorites; 5) Characteristics of a Seismometer for the LUNAR-A Penetrator; 6) Heating Experiments of the HaH 262 Eucrite and Implication for the Metamorphic History of Highly Metamorphosed Eucrites; 7) Measurements of Ejecta Velocity Distribution by a High-Speed Video Camera; 8) Petrological Comparison of Mongolian Jalanash Ureilite and Twelve Antarctic Ureilites; 9) Metallographic Cooling Rate of IVA Irons Revisited; 10) Inhomogeneous Temperature Distribution in Chondrules in Shock-Wave Heating Model; 11) Subsurface Weathering of Rocks and Soils at Gusev Crater; 12) Extinct Radioactivities in the Early Solar System and the Mean Age of the Galaxy; 13) Correlation of Rock Spectra with Quantitative Morphologic Indices: Evidence for a Single Rock Type at the Mars Pathfinder Landing Site; 14) Silicon Isotopic Ratios of Presolar Grains from Supernovae; 15) Current Status and Readiness on In-Situ Exploration of Asteroid Surface by MINERVA Rover in Hayabusa Mission; 16) Long Formation Period of Single CAI: Combination of O and Mg Isotope Distribution; 17) Supra-Canonical Initial 26Al/27Al Indicate a 105 Year Residence Time for CAIs in the Solar Proto-Planetary Disk; 18) Evolution of Mercury's Obliquity; 19) First Results from the Huygens Surface Science Package; 20) Polyhedral Serpentine Grains in CM Chondrites; 21) Mountainous Units in the Martian Gusev Highland Region: Volcanic, Tectonic, or Impact Related? 22) Petrography of Lunar Meteorite MET 01210, A New Basaltic Regolith Breccia; 23) Earth-Moon Impacts at ~300 Ma and ~500 Ma Ago; 24) Chemical and Isotopic Analyses of Apollo 16 Glasses: An Integrated Approach; 25) Measuring the Surfaces on Mars; 26) Melting in Martian Snowbanks; 27) The Effect of Ni on Fe-FeS Phase Relations: Implications for the Chemistry of the Martian Core; 28) Shorelines in the Western United States as Analogs for Hypothesized Shoreline Features on Mars; 29) Al and Ti Isotopic Ratios of Presolar SiC Grains of Type Z; 30) Physicochemical Conditions of Clinopyroxene Crystallization in the Parental Bodies of Ordinary Chondrites; 31) Metamorphosed CM and CI Carbonaceous Chondrites Could be from the Breakup of the Same Earth-crossing Asteroid; 32) Aqueous Alteration and Hydrogen Generation on Parent Bodies of Unequilibrated Ordinary Chondrites: Thermodynamic Modeling for the Semarkona Composition; and 33) Preliminary Analysis of Relative Abundances of Hydrothermal Alteration Products in the C1-N10, Y6-N19, and Yax-1_863.51 Impact Melt Samples, Chicxulub Structure, Mexico

Source record↗
NASA NTRS2013

Ocean Biological Pump Sensitivities and Implications for Climate Change Impacts

The ocean is one of the principal reservoirs of CO2, a greenhouse gas, and therefore plays a crucial role in regulating Earth's climate. Currently, the ocean sequesters about a third of anthropogenic CO2 emissions, mitigating the human impact on climate. At the same time, the deeper ocean represents the largest carbon pool in the Earth System and processes that describe the transfer of carbon from the surface of the ocean to depth are intimately linked to the effectiveness of carbon sequestration.The ocean biological pump (OBP), which involves several biogeochemical processes, is a major pathway for transfer of carbon from the surface mixed layer into the ocean interior. About 75 of the carbon vertical gradient is due to the carbon pump with only 25 attributed to the solubility pump. However, the relative importance and role of the two pumps is poorly constrained. OBP is further divided to the organic carbon pump (soft tissue pump) and the carbonate pump, with the former exporting about 10 times more carbon than the latter through processes like remineralization.Major uncertainties about OBP, and hence in the carbon uptake and sequestration, stem from uncertainties in processes involved in OBP such as particulate organicinorganic carbon sinkingsettling, remineralization, microbial degradation of DOC and uptakegrowth rate changes of the ocean biology. The deep ocean is a major sink of atmospheric CO2 in scales of hundreds to thousands of years, but how the export efficiency (i.e. the fraction of total carbon fixation at the surface that is transported at depth) is affected by climate change remains largely undetermined. These processes affect the ocean chemistry (alkalinity, pH, DIC, particulate and dissolved organic carbon) as well as the ecology (biodiversity, functional groups and their interactions) in the ocean. It is important to have a rigorous, quantitative understanding of the uncertainties involved in the observational measurements, the models and the projections of future changes.

particulates↗
NASA NTRS2002

Planetary Evolution and Microbe-Environment Interactions

During the three-year period of this Cooperative Agreement my laboratory conducted physiological and ecological studies regarding the abiotic/biotic relationship in microbial ecosystems. The overall objective of the research performed in the three years of this cooperative agreement is to determine how living systems respond to environmental stress. To accomplish this objective microbes were subjected to a variety of different environmental stresses including decreases in water activity, changes in radiation flux, and nutrient limitation. This research addressees two subsets of the astrobiology questions including: If life arose on early Mars what would have become of it once Mars lost most of its atmosphere and water? and if Earth organisms traveled to Mars what would become of them. To help answer this question we used microbes as model systems not only because they were the first living systems to arise, but also because they are the most likely to be able to withstand a broad range of environmental factors. To meet this objective we conducted laboratory and field work.

Mancinelli, Rocco L.↗
DOE OSTI2025

Integrating catalytic fractionation and microbial funneling to produce 2-pyrone-4,6-dicarboxylic acid and ethanol

Replacing biorefinery designs that use stepwise fractionation, depolymerization, and conversion processes with designed tandem process steps can greatly reduce a biorefinery's operating costs and environmental impact. Reductive Catalytic Fractionation (RCF) is a highly efficient lignin-first approach that combines biomass fractionation and lignin depolymerization to generate a hydrogenolysis oil and pulp. The oil is composed of a complex mixture of phenolic monomers, dimers, and oligomers. Intergrating this chemical deconstruction process with microbial funneling of phenolics can simplify the product mixture and make high-value products. We applied RCF to poplar biomass in a biomass-to-bioproduct processing chain in which the phenolics were funneled to 2-pyrone-4,6-dicarboxylic acid (PDC) by an engineered strain of Novosphingobium aromaticivorans DSM12444. The pulp was enzymatically digested and the glucose and xylose was funneled to ethanol by an engineered strain of Saccharomyces cerevisiae GLBRCY945. By combining biomass fractionation and lignin depolymerization we removed a costly processing step that directly translated into a 29% reduction in the minimum selling price of PDC. This work combines experimentation with process modeling of an integrated biorefinery design to show how utilizing tandem process steps can significantly reduce operating expenses and environmental impact of upgrading lignocellulosic biomass to a portfolio of high value products.

Sener, Canan [Great Lakes Bioenergy Research Cente↗
NASA NTRS2023

Robotic and Crewed Mars Missions Increasing the Demand for Planetary Protection Technology Needs

Planetary protection (PP) policy seeks to avoid harmful contamination by limiting biological and relevant organic contamination from spacecraft as well as preventing adverse changes to Earth’s biosphere when extraterrestial samples are brought back to Earth. The PP policy at NASA was updated in 2021 (NPR 8715.24) and 2022 (NASA-STD-8719.27) to enable missions by expanding the decades old prescriptive requirements to allow for an option of adopting performance-based requirements that are objectivesdriven, risk-informed and case-assured. In parallel, the final PP knowledge gap workshop was completed representing the international consensus on the key areas to be considered in developing crew PP policy. These knowledge gaps focused on key technology development areas in 1) microbial and human health monitoring, 2) technical and operations needed for contamination control and 3) natural transport of contamination on Mars. As robotic missions start to implement performance-based approaches and research and technology efforts commence to inform crew policy the demand for data quality driven verification and validation in relevant space environments. Examples of the types of testing that is envisioned includes test as you fly validation and verification of decontamination systems in a relevant on-orbit and Mars environment, developing lethality curves of terrestrial organisms to further our understanding of the biocidal impacts of Mars and the space environment, and particle transport model validation and verification. Thus, the PP discipline has identified the need for groundbased space environments to perform preliminary testing as validation and verification of flight systems and to advance the technology readiness level prior to further testing on-orbit or lunar environments to prepare for Mars.

J. Nick Benardini↗
NASA NTRSDate not supplied

Robotic and Crewed Mars Missions Increasing the Demand for Planetary Protection Technology Needs

Planetary protection (PP) policy seeks to avoid harmful contamination by limiting biological and relevant organic contamination from spacecraft as well as preventing adverse changes to Earth’s biosphere when extraterrestrial samples are brought back to Earth. The PP policy at NASA was updated in 2021 (NPR 8715.24) and 2022 (NASA-STD-8719.27) to enable missions by expanding the decades old prescriptive requirements to allow for an option of adopting performance-based requirements that are objectives-driven, risk-informed and case-assured. In parallel, the final PP knowledge gap workshop was completed representing the international consensus on the key areas to be considered in developing crew PP policy. These knowledge gaps focused on key technology development areas in 1) microbial and human health monitoring, 2) technical and operations needed for contamination control and 3) natural transport of contamination on Mars. As robotic missions start to implement performance-based approaches and research and technology efforts commence to inform crew policy the demand for data quality driven verification and validation in relevant space environments. Examples of the types of testing that is envisioned includes test as you fly validation and verification of decontamination systems in a relevant on-orbit and Mars environment, developing lethality curves of terrestrial organisms to further our understanding of the biocidal impacts of Mars and the space environment, and particle transport model validation and verification. Thus, the PP discipline has identified the need for ground-based space environments to perform preliminary testing as validation and verification of flight systems and to advance the technology readiness level prior to further testing on-orbit or lunar environments to prepare for Mars.

J Nick Benardini↗
DOE OSTI2024

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Spatiotemporal Dynamics of the Relative Abundance of Soil Nutrient‐Degrading Enzyme‐Encoding Genes Across Continental US Ecoregions

Understanding the spatiotemporal patterns in the relative abundance of soil extracellular enzyme‐encoding genes is critical for predicting microbial responses to environmental change and their potential role in nutrient cycling. Yet, integrating novel metagenomic observations with spatiotemporal environmental gradients to infer regional patterns and future trajectories has remained unclear. To address this gap, we applied a machine learning (ML) approach, integrating soil metagenomic data with environmental variables—soil properties, topography, vegetation, and climate—to predict the relative abundance of enzyme‐encoding genes for soil carbon (C), nitrogen (N), and phosphorus (P) across surface soils of the continental United States. We assessed potential responses under future emission scenarios (SSP2‐4.5 and SSP5‐8.5) by comparing a baseline (1985–2014) to a future period (2071–2100). The ML model explained 57%–63% of baseline variation. Precipitation was identified as the most influential factor for the relative abundance of C‐ and N‐degrading enzyme‐encoding genes, while slope length, representing horizontal distance that water can travel downslope, was the primary driver for P‐degrading enzyme‐encoding genes abundance. Projections revealed spatially heterogeneous shifts across continental US ecoregions: the relative abundance of C‐ and N‐degrading enzyme‐encoding genes decreased in wetter ecoregions and increased in drier ecoregions under future climate, while P‐degrading enzyme‐encoding genes abundance decreased significantly in semiarid and Mediterranean ecoregions. This study demonstrates the utility of metagenomic data for mapping soil genetic potential and predicting its regional response to environmental change, to inform ecosystem management strategies.

extracellular enzyme-encoding genes↗
DOE OSTI2024

Microbial Reduction of Geogenic and Synthetic Goethite and Hematite

The microbial reduction of Fe(III) is a major component of Fe cycling in terrestrial and aquatic environments and is affected by the Fe(III) mineralogy of the system. The majority of the research examining the bioreduction of Fe(III) oxides by Fe(III)-reducing bacteria (IRB) has focused on the reduction of poorly crystalline Fe(III) phases, primarily ferrihydrite; however, crystalline Fe(III) oxides like goethite (α-FeOOH) and hematite (α-Fe 2 O 3 ) comprise the majority of Fe(III) oxides in soils. This study examined the bioreduction of goethite and hematite of geogenic and synthetic origin by Shewanella putrefaciens CN2, a well-studied model IRB, in laboratory incubations. Overall, the rate and extent of Fe(II) production were greater for goethite than for hematite, and for geogenic Fe(III) oxides relative to their synthetic analogs. Although there was substantial production of Fe(II) (i.e., >5 mM Fe(II)) in many of the systems, X-ray diffraction analysis of the solids at the end of the incubation did not indicate the formation of any Fe(II)-bearing secondary minerals (e.g., magnetite, siderite, green rust, etc.). The results of this study demonstrate the variability in the extent of bioreduction of geogenic goethite and hematite, and furthermore, that synthetic goethite and hematite may not be good analogs for the biogeochemical behavior of Fe(III) oxides in aquatic and terrestrial environments.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

Technical Challenges of Drilling on Mars

In the last year, NASA's Mars science advisory committee (MEPAG: Mars Exploration Payload Advisory Group) has formally recommended that deep drilling be undertaken as a priority investigation to meet astrobiology and geology goals. This proposed new dimension in Mars exploration has come about for several reasons. Firstly, geophysical models of the martian subsurface environment indicate that we may well find liquid water (in the form of brines) under ground-ice at depths of several kilometers near the equator. On Earth we invariably find life forms associated with any environmental niche that supports liquid water. New data from the Mars Global Surveyor have shown that the most recent volcanism on Mars is very young so we cannot rule out contemporary volcanism -- in which case subsurface temperatures consistent with having water in its liquid phase may be found at relatively shallow depths. Secondly, in recent decades we have learned to our surprise that the Earth's subsurface (microbial) biosphere extends to depths of many kilometers and this discovery provides the basis for planning to explore the martian subsurface in search of ancient or even extant microbial life forms. We know (from Viking measurements) that all the biogenic elements (C, H, O, N, P, S) are available on Mars. What we therefore hope to learn is whether or not the evolution of life is inevitable given the necessary ingredients and, by implication, whether the Universe may be teeming with life. The feasibility of drilling deep into the surface of Mars has been the subject of increasing attention within NASA (and more recently among some of its international partners) for several years and this led to a broad-based feasibility study carried out by the Los Alamos National Laboratory and, subsequently, to the development of several hardware prototypes. This paper is intended to provide a general survey of that activity.

Briggs, Geoffrey↗
DOE OSTI2024

Characterization of lignin-degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid

Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) dehydrogenase, which acts on the substrate CHMS. We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations, we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme's mechanism. These findings are expected to help guide efforts in protein and metabolic engineering to enhance PDC yields in biological routes to polymer feedstock synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1997

Whiting events: biogenic origin due to the photosynthetic activity of cyanobacterial picoplankton

An annual whiting event occurs each year in late May to early June in Fayetteville Green Lake, New York. The initiation of this event correlates with exponential growth of the Synechococcus population within the lake. Synechococcus is the dominant (by approximately 4 orders of magnitude) autotrophic organism owing to the oligotrophic condition of the lake. The delta 13C values of the dissolved inorganic C range seasonally from -9.5% in winter to -6.2% in summer due to photosynthetic activity. Calcite precipitates principally in the microenvironment surrounding Synechococcus because of a photosynthetically driven alkalization process and the availability of the cells as nucleation sites. This calcite has a heavier delta 13C value (>4%) than does the dissolved inorganic C of the lake water owing to the cells' preferential uptake of 12C. A conceptual model suggests that photosynthetic activity and cell surface chemistry, together with the substantial surface area that arises from the great abundance of micron-sized cells, allow Synechococcus to dominate the annual whiting events in Fayetteville Green Lake.

NASA Center ARC↗